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
C1orf70	339453	broad.mit.edu	37	1	1471947	1471947	+	Intron	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:1471947delG	uc009vkf.2	-							NM_001114748	NP_001108220			hypothetical protein LOC339453							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;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;1.74e-36)|OV - Ovarian serous cystadenocarcinoma(86;2.06e-22)|GBM - Glioblastoma multiforme(42;4.66e-06)|Colorectal(212;0.000159)|COAD - Colon adenocarcinoma(227;0.000193)|Kidney(185;0.0023)|BRCA - Breast invasive adenocarcinoma(365;0.00465)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0342)|Lung(427;0.199)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	1527371	1527371	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:1527371delA								SSU72 (17109 upstream) : MIB2 (23513 downstream)																																			---	---	---	---
CALML6	163688	broad.mit.edu	37	1	1843597	1843597	+	5'Flank	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:1843597delT	uc001aih.1	+							NM_138705	NP_619650			calmodulin-like 6							cytoplasm|nucleus	calcium ion 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;1.94e-37)|OV - Ovarian serous cystadenocarcinoma(86;2.83e-23)|GBM - Glioblastoma multiforme(42;3.23e-08)|Colorectal(212;3.98e-05)|COAD - Colon adenocarcinoma(227;0.000193)|Kidney(185;0.00229)|BRCA - Breast invasive adenocarcinoma(365;0.00437)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.034)|Lung(427;0.199)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	1867290	1867290	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:1867290delT								TMEM52 (16550 upstream) : KIAA1751 (17462 downstream)																																			---	---	---	---
PRKCZ	5590	broad.mit.edu	37	1	2099323	2099325	+	Intron	DEL	CCT	-	-	rs71578363		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:2099323_2099325delCCT	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_5'Flank	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)														---	---	---	---
PLCH2	9651	broad.mit.edu	37	1	2411479	2411479	+	Intron	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:2411479delG	uc001aji.1	+						PLCH2_uc010nyz.1_5'Flank|PLCH2_uc009vle.1_5'Flank|PLCH2_uc001ajj.1_5'Flank|PLCH2_uc001ajk.1_5'Flank	NM_014638	NP_055453			phospholipase C, eta 2						intracellular signal transduction|lipid catabolic process	cytoplasm|plasma membrane	calcium ion binding|phosphatidylinositol phospholipase C activity|signal transducer activity			central_nervous_system(3)|ovary(1)|skin(1)	5	all_cancers(77;0.000161)|all_epithelial(69;5.98e-05)|all_lung(157;0.016)|Lung NSC(156;0.0376)|Ovarian(185;0.0634)	all_epithelial(116;7.32e-16)|all_lung(118;1.15e-06)|Lung NSC(185;6.26e-05)|Renal(390;0.00571)|Breast(487;0.00832)|Hepatocellular(190;0.0268)|Myeloproliferative disorder(586;0.028)|Ovarian(437;0.127)|Medulloblastoma(700;0.151)|Lung SC(97;0.217)		Epithelial(90;1.44e-37)|OV - Ovarian serous cystadenocarcinoma(86;6.78e-23)|GBM - Glioblastoma multiforme(42;2.8e-08)|Colorectal(212;4.19e-05)|COAD - Colon adenocarcinoma(227;0.000195)|Kidney(185;0.00034)|BRCA - Breast invasive adenocarcinoma(365;0.00443)|KIRC - Kidney renal clear cell carcinoma(229;0.00548)|STAD - Stomach adenocarcinoma(132;0.00644)|Lung(427;0.2)														---	---	---	---
PRDM16	63976	broad.mit.edu	37	1	3040178	3040179	+	Intron	INS	-	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:3040178_3040179insG	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	3249118	3249118	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:3249118delT	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								---	---	---	---
Unknown	0	broad.mit.edu	37	1	3723042	3723043	+	IGR	DEL	AG	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:3723042_3723043delAG								LRRC47 (9974 upstream) : KIAA0562 (5602 downstream)																																			---	---	---	---
DFFB	1677	broad.mit.edu	37	1	3794719	3794721	+	Intron	DEL	TTT	-	-	rs112553640		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:3794719_3794721delTTT	uc001alc.2	+						DFFB_uc001ale.2_Intron|DFFB_uc009vlp.2_Intron|DFFB_uc001alb.2_Intron|DFFB_uc010nzn.1_Intron|DFFB_uc009vlq.2_Intron|DFFB_uc009vlr.2_Intron|DFFB_uc001ald.2_Intron	NM_004402	NP_004393			DNA fragmentation factor, 40 kD, beta						apoptotic chromosome condensation|DNA fragmentation involved in apoptotic nuclear change|intracellular signal transduction	cytosol|nucleoplasm	deoxyribonuclease activity|enzyme binding				0	all_cancers(77;0.0395)|Ovarian(185;0.0634)|all_lung(157;0.222)|Lung NSC(156;0.227)	all_cancers(23;2.05e-30)|all_epithelial(116;6.22e-21)|all_lung(118;2.65e-08)|Lung NSC(185;6.25e-06)|Breast(487;0.000659)|Renal(390;0.00121)|all_neural(13;0.0019)|Hepatocellular(190;0.00705)|Colorectal(325;0.0113)|all_hematologic(16;0.0194)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0308)|Lung SC(97;0.0548)|Medulloblastoma(700;0.211)		Epithelial(90;1.18e-39)|OV - Ovarian serous cystadenocarcinoma(86;7.28e-23)|GBM - Glioblastoma multiforme(42;2.95e-17)|Colorectal(212;1.23e-05)|COAD - Colon adenocarcinoma(227;5.94e-05)|Kidney(185;0.000371)|BRCA - Breast invasive adenocarcinoma(365;0.00038)|KIRC - Kidney renal clear cell carcinoma(229;0.00571)|STAD - Stomach adenocarcinoma(132;0.00645)|Lung(427;0.124)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	4001279	4001280	+	Intron	DEL	AG	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:4001279_4001280delAG	uc001ali.1	+											Homo sapiens cDNA FLJ42718 fis, clone BRAMY3010411.																														---	---	---	---
Unknown	0	broad.mit.edu	37	1	4129947	4129947	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:4129947delT								LOC100133612 (296070 upstream) : LOC284661 (342164 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	4889803	4889803	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:4889803delT								AJAP1 (45953 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	5180925	5180926	+	IGR	INS	-	CATC	CATC	rs145060254	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:5180925_5180926insCATC								AJAP1 (337075 upstream) : NPHP4 (741944 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	5735366	5735367	+	IGR	INS	-	AT	AT	rs147029402		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:5735366_5735367insAT								AJAP1 (891516 upstream) : NPHP4 (187503 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	5861051	5861051	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:5861051delA								None (None upstream) : NPHP4 (61819 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	5913037	5913037	+	IGR	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:5913037delG								None (None upstream) : NPHP4 (9833 downstream)																																			---	---	---	---
KCNAB2	8514	broad.mit.edu	37	1	6053050	6053050	+	Intron	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:6053050delC	uc009vlv.1	+						NPHP4_uc001alq.1_5'Flank|NPHP4_uc001als.1_5'Flank|NPHP4_uc009vlt.1_5'Flank|NPHP4_uc001alt.1_5'Flank	NM_003636	NP_003627			potassium voltage-gated channel, shaker-related							cytoplasm|integral to membrane|juxtaparanode region of axon	oxidoreductase activity|potassium channel regulator activity|voltage-gated potassium channel activity				0	Ovarian(185;0.0634)	all_cancers(23;5.85e-39)|all_epithelial(116;4.88e-22)|all_lung(118;4.21e-08)|Lung NSC(185;9.77e-07)|all_hematologic(16;2.78e-06)|all_neural(13;3.18e-06)|Acute lymphoblastic leukemia(12;0.000272)|Breast(487;0.000496)|Renal(390;0.0007)|Colorectal(325;0.00106)|Glioma(11;0.00203)|Hepatocellular(190;0.00308)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0393)|Medulloblastoma(700;0.211)		Epithelial(90;6.9e-37)|GBM - Glioblastoma multiforme(13;8.8e-31)|OV - Ovarian serous cystadenocarcinoma(86;1.45e-19)|Colorectal(212;2.46e-07)|COAD - Colon adenocarcinoma(227;2.07e-05)|Kidney(185;7.88e-05)|KIRC - Kidney renal clear cell carcinoma(229;0.00131)|BRCA - Breast invasive adenocarcinoma(365;0.00133)|STAD - Stomach adenocarcinoma(132;0.00391)|READ - Rectum adenocarcinoma(331;0.0649)														---	---	---	---
KCNAB2	8514	broad.mit.edu	37	1	6066678	6066678	+	Intron	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:6066678delC	uc009vlv.1	+							NM_003636	NP_003627			potassium voltage-gated channel, shaker-related							cytoplasm|integral to membrane|juxtaparanode region of axon	oxidoreductase activity|potassium channel regulator activity|voltage-gated potassium channel activity				0	Ovarian(185;0.0634)	all_cancers(23;5.85e-39)|all_epithelial(116;4.88e-22)|all_lung(118;4.21e-08)|Lung NSC(185;9.77e-07)|all_hematologic(16;2.78e-06)|all_neural(13;3.18e-06)|Acute lymphoblastic leukemia(12;0.000272)|Breast(487;0.000496)|Renal(390;0.0007)|Colorectal(325;0.00106)|Glioma(11;0.00203)|Hepatocellular(190;0.00308)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0393)|Medulloblastoma(700;0.211)		Epithelial(90;6.9e-37)|GBM - Glioblastoma multiforme(13;8.8e-31)|OV - Ovarian serous cystadenocarcinoma(86;1.45e-19)|Colorectal(212;2.46e-07)|COAD - Colon adenocarcinoma(227;2.07e-05)|Kidney(185;7.88e-05)|KIRC - Kidney renal clear cell carcinoma(229;0.00131)|BRCA - Breast invasive adenocarcinoma(365;0.00133)|STAD - Stomach adenocarcinoma(132;0.00391)|READ - Rectum adenocarcinoma(331;0.0649)														---	---	---	---
KCNAB2	8514	broad.mit.edu	37	1	6099339	6099339	+	Intron	DEL	A	-	-	rs1295088	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:6099339delA	uc009vlv.1	+						KCNAB2_uc001alv.1_Intron|KCNAB2_uc001alw.1_Intron|KCNAB2_uc001alx.1_Intron|KCNAB2_uc001alu.2_Intron	NM_003636	NP_003627			potassium voltage-gated channel, shaker-related							cytoplasm|integral to membrane|juxtaparanode region of axon	oxidoreductase activity|potassium channel regulator activity|voltage-gated potassium channel activity				0	Ovarian(185;0.0634)	all_cancers(23;5.85e-39)|all_epithelial(116;4.88e-22)|all_lung(118;4.21e-08)|Lung NSC(185;9.77e-07)|all_hematologic(16;2.78e-06)|all_neural(13;3.18e-06)|Acute lymphoblastic leukemia(12;0.000272)|Breast(487;0.000496)|Renal(390;0.0007)|Colorectal(325;0.00106)|Glioma(11;0.00203)|Hepatocellular(190;0.00308)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0393)|Medulloblastoma(700;0.211)		Epithelial(90;6.9e-37)|GBM - Glioblastoma multiforme(13;8.8e-31)|OV - Ovarian serous cystadenocarcinoma(86;1.45e-19)|Colorectal(212;2.46e-07)|COAD - Colon adenocarcinoma(227;2.07e-05)|Kidney(185;7.88e-05)|KIRC - Kidney renal clear cell carcinoma(229;0.00131)|BRCA - Breast invasive adenocarcinoma(365;0.00133)|STAD - Stomach adenocarcinoma(132;0.00391)|READ - Rectum adenocarcinoma(331;0.0649)														---	---	---	---
CAMTA1	23261	broad.mit.edu	37	1	7058038	7058038	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:7058038delT	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	7237536	7237537	+	Intron	INS	-	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:7237536_7237537insA	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	7558252	7558253	+	Intron	DEL	GT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:7558252_7558253delGT	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	7605727	7605727	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:7605727delT	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)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	8065713	8065714	+	IGR	DEL	TT	-	-	rs71567341		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-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	8222715	8222715	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:8222715delT								ERRFI1 (136322 upstream) : SLC45A1 (161675 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	8236492	8236493	+	IGR	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:8236492_8236493delAA								ERRFI1 (150099 upstream) : SLC45A1 (147897 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	8266829	8266830	+	IGR	INS	-	A	A	rs146340196	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:8266829_8266830insA								ERRFI1 (180436 upstream) : SLC45A1 (117560 downstream)																																			---	---	---	---
ENO1	2023	broad.mit.edu	37	1	8933289	8933290	+	Intron	INS	-	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:8933289_8933290insG	uc001apj.1	-						ENO1_uc001api.1_5'Flank|ENO1_uc001apk.1_Intron|ENO1_uc001apl.1_Intron|ENO1_uc009vmi.1_Intron|ENO1_uc009vmj.1_Intron|ENO1_uc009vmk.1_Intron|ENO1_uc009vml.1_Intron|ENO1_uc009vmm.1_Intron	NM_001428	NP_001419			enolase 1						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	9142940	9142944	+	Intron	DEL	AAAAA	-	-	rs142987088		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:9142940_9142944delAAAAA	uc010oab.1	-							NM_003039	NP_003030			solute carrier family 2 (facilitated						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	9421604	9421604	+	Intron	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:9421604delC	uc010oae.1	+						SPSB1_uc001apv.2_Intron	NM_025106	NP_079382			splA/ryanodine receptor domain and 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)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	9521716	9521716	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:9521716delA								SPSB1 (92128 upstream) : SLC25A33 (77812 downstream)																																			---	---	---	---
SLC25A33	84275	broad.mit.edu	37	1	9624316	9624316	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:9624316delT	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)														---	---	---	---
CLSTN1	22883	broad.mit.edu	37	1	9860403	9860403	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:9860403delA	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)														---	---	---	---
UBE4B	10277	broad.mit.edu	37	1	10134404	10134406	+	Intron	DEL	TTT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:10134404_10134406delTTT	uc001aqs.3	+						UBE4B_uc001aqr.3_Intron|UBE4B_uc010oai.1_Intron|UBE4B_uc010oaj.1_Intron	NM_001105562	NP_001099032			ubiquitination factor E4B isoform 1						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	10313704	10313704	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:10313704delA	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)														---	---	---	---
CASZ1	54897	broad.mit.edu	37	1	10757648	10757648	+	Intron	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:10757648delC	uc001aro.2	-						CASZ1_uc001arp.1_Intron	NM_001079843	NP_001073312			castor homolog 1, zinc finger isoform a						regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	DNA binding|zinc ion binding			skin(1)	1	Ovarian(185;0.203)|all_lung(157;0.204)	Lung NSC(185;4.96e-06)|all_lung(284;1.22e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00212)|Hepatocellular(190;0.00913)|Ovarian(437;0.0229)|Myeloproliferative disorder(586;0.0255)	STAD - Stomach adenocarcinoma(5;0.0224)	UCEC - Uterine corpus endometrioid carcinoma (279;0.0265)|Colorectal(212;3.54e-08)|COAD - Colon adenocarcinoma(227;9.56e-06)|BRCA - Breast invasive adenocarcinoma(304;0.000219)|Kidney(185;0.00142)|KIRC - Kidney renal clear cell carcinoma(229;0.00381)|READ - Rectum adenocarcinoma(331;0.0419)|STAD - Stomach adenocarcinoma(132;0.0623)														---	---	---	---
EXOSC10	5394	broad.mit.edu	37	1	11150817	11150817	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:11150817delT	uc001asa.2	-						EXOSC10_uc001asb.2_Intron|EXOSC10_uc009vmy.1_Intron	NM_001001998	NP_001001998			exosome component 10 isoform 1						CUT catabolic process|histone mRNA catabolic process|maturation of 5.8S rRNA|nuclear polyadenylation-dependent rRNA catabolic process|nuclear retention of unspliced pre-mRNA at the site of transcription|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay	cytoplasm|nuclear exosome (RNase complex)|nucleolus|transcriptionally active chromatin	3'-5' exonuclease activity|exoribonuclease activity|identical protein binding|nucleotide binding|protein serine/threonine kinase activity|RNA binding			upper_aerodigestive_tract(1)	1	Ovarian(185;0.249)	Lung NSC(185;1.74e-05)|all_lung(284;2.05e-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)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;4.18e-07)|COAD - Colon adenocarcinoma(227;8.33e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000315)|Kidney(185;0.000832)|KIRC - Kidney renal clear cell carcinoma(229;0.00269)|READ - Rectum adenocarcinoma(331;0.0526)|STAD - Stomach adenocarcinoma(313;0.202)														---	---	---	---
MTOR	2475	broad.mit.edu	37	1	11175117	11175117	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:11175117delA	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																		---	---	---	---
Unknown	0	broad.mit.edu	37	1	11490496	11490496	+	IGR	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:11490496delC								UBIAD1 (142006 upstream) : PTCHD2 (48799 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	11660044	11660045	+	IGR	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:11660044_11660045delTT								PTCHD2 (62405 upstream) : FBXO2 (48405 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	11678352	11678353	+	IGR	DEL	AC	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:11678352_11678353delAC								PTCHD2 (80713 upstream) : FBXO2 (30097 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	11790371	11790372	+	IGR	INS	-	CA	CA	rs148305842	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:11790371_11790372insCA								C1orf187 (10035 upstream) : AGTRAP (5770 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	11818396	11818396	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:11818396delA								AGTRAP (7569 upstream) : MTHFR (27391 downstream)																																			---	---	---	---
PLOD1	5351	broad.mit.edu	37	1	12014544	12014544	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:12014544delA	uc001atm.2	+						PLOD1_uc010obb.1_Intron	NM_000302	NP_000293			lysyl hydroxylase 1 precursor						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)													---	---	---	---
TNFRSF8	943	broad.mit.edu	37	1	12133650	12133650	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:12133650delT	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)														---	---	---	---
TNFRSF8	943	broad.mit.edu	37	1	12142824	12142825	+	Intron	INS	-	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:12142824_12142825insA	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)														---	---	---	---
VPS13D	55187	broad.mit.edu	37	1	12381710	12381710	+	Intron	DEL	G	-	-	rs76134606	byFrequency;by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:12381710delG	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)														---	---	---	---
VPS13D	55187	broad.mit.edu	37	1	12493315	12493317	+	Intron	DEL	AAA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:12493315_12493317delAAA	uc001atv.2	+						VPS13D_uc001atw.2_Intron|VPS13D_uc001atx.2_Intron|VPS13D_uc009vnl.2_Intron|VPS13D_uc010obd.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)														---	---	---	---
VPS13D	55187	broad.mit.edu	37	1	12537850	12537850	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:12537850delT	uc001atv.2	+						VPS13D_uc001atw.2_Intron|VPS13D_uc001atx.2_Intron|VPS13D_uc009vnl.2_Intron|VPS13D_uc010obd.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	12615096	12615096	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:12615096delT								VPS13D (43000 upstream) : DHRS3 (12844 downstream)																																			---	---	---	---
AADACL4	343066	broad.mit.edu	37	1	12702835	12702835	+	5'Flank	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:12702835delA	uc001auf.2	+							NM_001013630	NP_001013652			arylacetamide deacetylase-like 4							integral to membrane	carboxylesterase activity				0	Ovarian(185;0.249)	Renal(390;0.000469)|Lung NSC(185;0.000937)|all_lung(284;0.00122)|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;6.81e-07)|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;0.0384)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	12765382	12765382	+	IGR	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:12765382delC								AADACL4 (38286 upstream) : AADACL3 (10736 downstream)																																			---	---	---	---
LOC440563	440563	broad.mit.edu	37	1	13184079	13184080	+	5'Flank	INS	-	T	T	rs146762683	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:13184079_13184080insT	uc010obg.1	-							NM_001136561	NP_001130033			heterogeneous nuclear ribonucleoprotein C-like							ribonucleoprotein complex	nucleic acid binding|nucleotide binding				0																		---	---	---	---
PRAMEF17	391004	broad.mit.edu	37	1	13719052	13719052	+	3'UTR	DEL	T	-	-	rs141370897	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-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	13929225	13929225	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:13929225delT	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	13997888	13997891	+	IGR	DEL	AAAA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:13997888_13997891delAAAA								PDPN (53438 upstream) : PRDM2 (28844 downstream)																																			---	---	---	---
PRDM2	7799	broad.mit.edu	37	1	14101323	14101323	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:14101323delT	uc001avi.2	+						PRDM2_uc001avg.2_Intron|PRDM2_uc001avh.2_Intron|PRDM2_uc001avj.2_Intron|PRDM2_uc009vod.1_Intron|PRDM2_uc001avk.2_Intron|PRDM2_uc009voe.2_Intron|PRDM2_uc009vof.2_Intron	NM_012231	NP_036363			retinoblastoma protein-binding zinc finger							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)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	14395001	14395001	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:14395001delA								PRDM2 (243429 upstream) : KAZ (530212 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	14665584	14665601	+	IGR	DEL	AGAGAGAGACAGAGACTG	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:14665584_14665601delAGAGAGAGACAGAGACTG								PRDM2 (514012 upstream) : KAZ (259612 downstream)																																			---	---	---	---
KAZ	23254	broad.mit.edu	37	1	15005781	15005781	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:15005781delT	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	15041458	15041458	+	Intron	DEL	T	-	-	rs78168211		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:15041458delT	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	15084653	15084654	+	Intron	INS	-	CCTT	CCTT	rs151056074	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:15084653_15084654insCCTT	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	15374639	15374639	+	Intron	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:15374639delC	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																		---	---	---	---
FHAD1	114827	broad.mit.edu	37	1	15681173	15681173	+	Intron	DEL	A	-	-	rs34552889		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:15681173delA	uc001awb.2	+						FHAD1_uc001awd.1_Intron|FHAD1_uc010obl.1_Intron|FHAD1_uc001awe.1_Intron	NM_052929	NP_443161			forkhead-associated (FHA) phosphopeptide binding											skin(1)	1																		---	---	---	---
DNAJC16	23341	broad.mit.edu	37	1	15863352	15863352	+	Intron	DEL	T	-	-	rs112015425		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:15863352delT	uc001aws.2	+						DNAJC16_uc001awr.1_Intron|DNAJC16_uc001awt.2_Intron	NM_015291	NP_056106			DnaJ (Hsp40) homolog, subfamily C, member 16						cell redox homeostasis|protein folding	integral to membrane	heat shock protein binding|unfolded protein binding			urinary_tract(1)|lung(1)|kidney(1)	3		Colorectal(325;0.00108)|Renal(390;0.00145)|Breast(348;0.00173)|all_lung(284;0.00459)|Lung NSC(340;0.00499)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0798)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;9.18e-07)|COAD - Colon adenocarcinoma(227;4.5e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000133)|KIRC - Kidney renal clear cell carcinoma(229;0.00262)|STAD - Stomach adenocarcinoma(313;0.00774)|READ - Rectum adenocarcinoma(331;0.0657)														---	---	---	---
SPEN	23013	broad.mit.edu	37	1	16214216	16214217	+	Intron	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:16214216_16214217delAA	uc001axk.1	+						SPEN_uc010obp.1_Intron	NM_015001	NP_055816			spen homolog, transcriptional regulator						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)														---	---	---	---
EPHA2	1969	broad.mit.edu	37	1	16464093	16464093	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:16464093delA	uc001aya.1	-						EPHA2_uc010oca.1_Intron	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)													---	---	---	---
SPATA21	374955	broad.mit.edu	37	1	16740510	16740511	+	Intron	INS	-	T	T	rs140009046	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:16740510_16740511insT	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)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	16837358	16837358	+	IGR	DEL	T	-	-	rs75961085		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:16837358delT								CROCCL2 (18162 upstream) : NBPF1 (53054 downstream)																																			---	---	---	---
CROCC	9696	broad.mit.edu	37	1	17205586	17205586	+	Intron	DEL	A	-	-	rs67126650		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-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	17229819	17229820	+	Intron	INS	-	A	A	rs147278844		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:17229819_17229820insA	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	17234271	17234272	+	Intron	INS	-	A	A	rs144504920		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:17234271_17234272insA	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-4200-01A-01D-1126-08	TCGA-BR-4200-11A-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	17262557	17262558	+	Intron	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:17262557_17262558delTT	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)														---	---	---	---
ATP13A2	23400	broad.mit.edu	37	1	17322723	17322723	+	Intron	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:17322723delC	uc001baa.2	-						ATP13A2_uc001bab.2_Intron|ATP13A2_uc001bac.2_Intron|ATP13A2_uc009vpa.1_Intron|ATP13A2_uc001bad.1_Intron	NM_022089	NP_071372			ATPase type 13A2 isoform 1						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)														---	---	---	---
PADI4	23569	broad.mit.edu	37	1	17680744	17680744	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:17680744delA	uc001baj.2	+							NM_012387	NP_036519			peptidyl arginine deiminase, type IV						chromatin modification|peptidyl-citrulline biosynthetic process from peptidyl-arginine|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	calcium ion binding|protein-arginine deiminase activity			ovary(1)|skin(1)	2		Colorectal(325;3.46e-05)|Breast(348;0.000162)|all_lung(284;0.000338)|Lung NSC(340;0.00042)|Renal(390;0.000518)|Ovarian(437;0.00409)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00537)|BRCA - Breast invasive adenocarcinoma(304;8.54e-06)|COAD - Colon adenocarcinoma(227;1.33e-05)|Kidney(64;0.000223)|KIRC - Kidney renal clear cell carcinoma(64;0.00313)|STAD - Stomach adenocarcinoma(196;0.00707)|READ - Rectum adenocarcinoma(331;0.0689)|Lung(427;0.199)	L-Citrulline(DB00155)													---	---	---	---
ARHGEF10L	55160	broad.mit.edu	37	1	17864561	17864561	+	5'Flank	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:17864561delA	uc001ban.2	+						ARHGEF10L_uc009vpe.1_5'Flank	NM_018125	NP_060595			Rho guanine nucleotide exchange factor (GEF)						regulation of Rho protein signal transduction	cytoplasm	Rho guanyl-nucleotide exchange factor activity			large_intestine(1)|ovary(1)|pancreas(1)	3		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;0.00598)|COAD - Colon adenocarcinoma(227;1.62e-05)|BRCA - Breast invasive adenocarcinoma(304;1.68e-05)|Kidney(64;0.000269)|KIRC - Kidney renal clear cell carcinoma(64;0.00361)|STAD - Stomach adenocarcinoma(196;0.00656)|READ - Rectum adenocarcinoma(331;0.0718)|Lung(427;0.204)														---	---	---	---
ARHGEF10L	55160	broad.mit.edu	37	1	17913941	17913943	+	Intron	DEL	CTT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:17913941_17913943delCTT	uc001ban.2	+						ARHGEF10L_uc009vpe.1_Intron|ARHGEF10L_uc001bao.2_Intron|ARHGEF10L_uc001bap.2_Intron|ARHGEF10L_uc010ocr.1_5'Flank	NM_018125	NP_060595			Rho guanine nucleotide exchange factor (GEF)						regulation of Rho protein signal transduction	cytoplasm	Rho guanyl-nucleotide exchange factor activity			large_intestine(1)|ovary(1)|pancreas(1)	3		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;0.00598)|COAD - Colon adenocarcinoma(227;1.62e-05)|BRCA - Breast invasive adenocarcinoma(304;1.68e-05)|Kidney(64;0.000269)|KIRC - Kidney renal clear cell carcinoma(64;0.00361)|STAD - Stomach adenocarcinoma(196;0.00656)|READ - Rectum adenocarcinoma(331;0.0718)|Lung(427;0.204)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	18245826	18245826	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:18245826delT								ACTL8 (92270 upstream) : IGSF21 (188414 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	18376102	18376106	+	IGR	DEL	GTAGT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:18376102_18376106delGTAGT								ACTL8 (222546 upstream) : IGSF21 (58134 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	18427886	18427886	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:18427886delT								ACTL8 (274330 upstream) : IGSF21 (6354 downstream)																																			---	---	---	---
IGSF21	84966	broad.mit.edu	37	1	18680904	18680904	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:18680904delA	uc001bau.1	+							NM_032880	NP_116269			immunoglobin superfamily, member 21 precursor							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)														---	---	---	---
IGSF21	84966	broad.mit.edu	37	1	18685830	18685831	+	Intron	INS	-	AAAA	AAAA	rs72178016		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:18685830_18685831insAAAA	uc001bau.1	+						IGSF21_uc001bav.1_5'Flank	NM_032880	NP_116269			immunoglobin superfamily, member 21 precursor							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)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	18803060	18803060	+	IGR	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:18803060delC								IGSF21 (98084 upstream) : KLHDC7A (4364 downstream)																																			---	---	---	---
PAX7	5081	broad.mit.edu	37	1	19053866	19053867	+	Intron	DEL	AC	-	-	rs113079809		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:19053866_19053867delAC	uc001bay.2	+						PAX7_uc001baz.2_Intron|PAX7_uc010oct.1_Intron	NM_002584	NP_002575			paired box 7 isoform 1						anti-apoptosis	nucleus	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity		PAX7/FOXO1(197)	soft_tissue(197)|lung(3)|prostate(1)|ovary(1)|breast(1)	203		Colorectal(325;3.46e-05)|all_lung(284;0.000439)|Renal(390;0.000518)|Lung NSC(340;0.000543)|Breast(348;0.00093)|Ovarian(437;0.00768)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00609)|BRCA - Breast invasive adenocarcinoma(304;4.71e-05)|Kidney(64;0.000279)|KIRC - Kidney renal clear cell carcinoma(64;0.00371)|STAD - Stomach adenocarcinoma(196;0.00658)|READ - Rectum adenocarcinoma(331;0.0576)				T	FOXO1A	alveolar rhabdomyosarcoma								---	---	---	---
IFFO2	126917	broad.mit.edu	37	1	19231800	19231800	+	3'UTR	DEL	G	-	-	rs28478026	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:19231800delG	uc001bbd.2	-	9					ALDH4A1_uc001bbb.2_5'Flank|ALDH4A1_uc001bbc.2_5'Flank	NM_001136265	NP_001129737			intermediate filament family orphan 2												0																		---	---	---	---
UBR4	23352	broad.mit.edu	37	1	19474752	19474752	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:19474752delA	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	19514156	19514156	+	Intron	DEL	A	-	-	rs144801649		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-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)														---	---	---	---
KIAA0090	23065	broad.mit.edu	37	1	19568019	19568019	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:19568019delT	uc001bbo.2	-						KIAA0090_uc001bbp.2_Intron|KIAA0090_uc001bbq.2_Intron|KIAA0090_uc001bbr.2_Intron	NM_015047	NP_055862			hypothetical protein LOC23065 precursor							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)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	19606422	19606422	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:19606422delT								AKR7L (5854 upstream) : AKR7A3 (2635 downstream)																																			---	---	---	---
AKR7A3	22977	broad.mit.edu	37	1	19610328	19610329	+	Intron	DEL	AA	-	-	rs11581031		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:19610328_19610329delAA	uc001bbv.1	-							NM_012067	NP_036199			aldo-keto reductase family 7, member A3						cellular aldehyde metabolic process	cytosol	aldo-keto reductase (NADP) activity|electron carrier activity				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;0.00459)|BRCA - Breast invasive adenocarcinoma(304;1.78e-05)|Kidney(64;0.00016)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|GBM - Glioblastoma multiforme(114;0.00276)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	20269190	20269190	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:20269190delA								PLA2G2E (19080 upstream) : PLA2G2A (32735 downstream)																																			---	---	---	---
CAMK2N1	55450	broad.mit.edu	37	1	20809350	20809351	+	3'UTR	DEL	GT	-	-	rs71714511		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:20809350_20809351delGT	uc001bdh.2	-	2					CAMK2N1_uc001bdg.2_RNA	NM_018584	NP_061054			calcium/calmodulin-dependent protein kinase II							cell junction|postsynaptic density|postsynaptic membrane|synaptosome					0		Colorectal(325;3.46e-05)|Renal(390;0.000147)|all_lung(284;0.000247)|Lung NSC(340;0.000285)|Breast(348;0.0013)|Ovarian(437;0.00327)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|COAD - Colon adenocarcinoma(152;1.11e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000132)|Kidney(64;0.00016)|GBM - Glioblastoma multiforme(114;0.00116)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.195)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	20873435	20873435	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:20873435delT								MUL1 (38761 upstream) : FAM43B (5497 downstream)																																			---	---	---	---
KIF17	57576	broad.mit.edu	37	1	21016831	21016831	+	Intron	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:21016831delG	uc001bdr.3	-						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	21082898	21082898	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:21082898delA	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	21188467	21188467	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:21188467delA	uc001bec.2	-						EIF4G3_uc010odi.1_Intron|EIF4G3_uc010odj.1_Intron|EIF4G3_uc009vpz.2_Intron|EIF4G3_uc001bed.2_Intron|EIF4G3_uc001bef.2_Intron|EIF4G3_uc001bee.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	21198325	21198325	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:21198325delT	uc001bec.2	-						EIF4G3_uc010odi.1_Intron|EIF4G3_uc010odj.1_Intron|EIF4G3_uc009vpz.2_Intron|EIF4G3_uc001bed.2_Intron|EIF4G3_uc001bef.2_Intron|EIF4G3_uc001bee.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	21209419	21209419	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:21209419delA	uc001bec.2	-						EIF4G3_uc010odi.1_Intron|EIF4G3_uc010odj.1_Intron|EIF4G3_uc009vpz.2_Intron|EIF4G3_uc001bed.2_Intron|EIF4G3_uc001bef.2_Intron|EIF4G3_uc001bee.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	21242940	21242940	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:21242940delA	uc001bec.2	-						EIF4G3_uc010odi.1_Intron|EIF4G3_uc010odj.1_Intron|EIF4G3_uc009vpz.2_Intron|EIF4G3_uc001bed.2_Intron|EIF4G3_uc001bef.2_Intron|EIF4G3_uc001bee.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	21257358	21257358	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:21257358delT	uc001bec.2	-						EIF4G3_uc010odi.1_Intron|EIF4G3_uc010odj.1_Intron|EIF4G3_uc009vpz.2_Intron|EIF4G3_uc001bed.2_Intron|EIF4G3_uc001bef.2_Intron|EIF4G3_uc001bee.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	21299378	21299380	+	Intron	DEL	AAA	-	-	rs76449388		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:21299378_21299380delAAA	uc001bec.2	-						EIF4G3_uc010odi.1_Intron|EIF4G3_uc010odj.1_Intron|EIF4G3_uc009vpz.2_Intron|EIF4G3_uc001bed.2_Intron|EIF4G3_uc001bef.2_Intron|EIF4G3_uc001bee.2_Intron|EIF4G3_uc001beg.2_Intron|EIF4G3_uc010odk.1_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	21427213	21427214	+	Intron	INS	-	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:21427213_21427214insA	uc001bec.2	-						EIF4G3_uc001bed.2_Intron|EIF4G3_uc001bef.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)														---	---	---	---
ECE1	1889	broad.mit.edu	37	1	21553520	21553520	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:21553520delT	uc001bek.2	-						ECE1_uc001bem.2_Intron|ECE1_uc001bej.2_Intron|ECE1_uc001bei.2_Intron|ECE1_uc010odl.1_Intron	NM_001397	NP_001388			endothelin converting enzyme 1 isoform 1						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)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	21751553	21751554	+	Intron	DEL	GA	-	-	rs144443608	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:21751553_21751554delGA	uc001bep.1	-											Homo sapiens cDNA FLJ25572 fis, clone JTH05111.																														---	---	---	---
RAP1GAP	5909	broad.mit.edu	37	1	21926260	21926260	+	Intron	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:21926260delC	uc001bex.2	-						RAP1GAP_uc001bev.2_Intron|RAP1GAP_uc001bew.2_Intron|RAP1GAP_uc001bey.2_Intron	NM_002885	NP_002876			RAP1 GTPase activating protein isoform c						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	21963328	21963329	+	Intron	INS	-	GAA	GAA			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:21963328_21963329insGAA	uc001bex.2	-						RAP1GAP_uc001bew.2_Intron|RAP1GAP_uc001bey.2_Intron	NM_002885	NP_002876			RAP1 GTPase activating protein isoform c						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)														---	---	---	---
USP48	84196	broad.mit.edu	37	1	22027858	22027859	+	Intron	INS	-	A	A	rs35780642		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:22027858_22027859insA	uc001bfb.2	-						USP48_uc001bfa.2_Intron|USP48_uc010odq.1_Intron|USP48_uc009vqc.2_Intron|USP48_uc001bfc.2_Intron|USP48_uc001bfd.1_Intron	NM_032236	NP_115612			ubiquitin specific protease 48 isoform a						ubiquitin-dependent protein catabolic process	mitochondrion|nucleus	cysteine-type peptidase activity|ubiquitin thiolesterase activity			ovary(1)|lung(1)	2		Colorectal(325;3.46e-05)|all_lung(284;4.29e-05)|Lung NSC(340;4.66e-05)|Renal(390;0.000219)|Breast(348;0.00222)|Ovarian(437;0.00308)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0182)|OV - Ovarian serous cystadenocarcinoma(117;4.74e-26)|COAD - Colon adenocarcinoma(152;1.3e-05)|GBM - Glioblastoma multiforme(114;1.86e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000614)|STAD - Stomach adenocarcinoma(196;0.00644)|KIRC - Kidney renal clear cell carcinoma(1967;0.00711)|Lung(427;0.0327)|READ - Rectum adenocarcinoma(331;0.0657)|LUSC - Lung squamous cell carcinoma(448;0.0753)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	22132912	22132912	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:22132912delT								USP48 (23224 upstream) : LDLRAD2 (5846 downstream)																																			---	---	---	---
HSPG2	3339	broad.mit.edu	37	1	22163939	22163943	+	Intron	DEL	TTTTT	-	-	rs71569852		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:22163939_22163943delTTTTT	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)													---	---	---	---
HSPG2	3339	broad.mit.edu	37	1	22254085	22254085	+	Intron	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:22254085delC	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)													---	---	---	---
CDC42	998	broad.mit.edu	37	1	22385621	22385622	+	Intron	INS	-	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:22385621_22385622insT	uc001bfq.2	+						CDC42_uc009vqg.1_Intron|CDC42_uc001bfp.2_Intron|CDC42_uc001bfr.2_Intron|CDC42_uc010odr.1_Intron|CDC42_uc010ods.1_Intron|CDC42_uc009vqh.2_Intron	NM_001039802	NP_001034891			cell division cycle 42 isoform 1						actin cytoskeleton organization|axon guidance|blood coagulation|epidermal growth factor receptor signaling pathway|establishment or maintenance of cell polarity|macrophage differentiation|muscle cell differentiation|negative regulation of epidermal growth factor receptor signaling pathway|negative regulation of protein complex assembly|positive regulation of muscle cell differentiation|positive regulation of pseudopodium assembly|regulation of filopodium assembly|regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction|T cell costimulation	cytosol|filopodium|plasma membrane	GTP binding|GTPase activity|protein binding|thioesterase binding			haematopoietic_and_lymphoid_tissue(1)	1		Colorectal(325;3.46e-05)|all_lung(284;5.94e-05)|Lung NSC(340;6.55e-05)|Renal(390;0.000219)|Breast(348;0.00222)|Ovarian(437;0.00308)|Myeloproliferative disorder(586;0.0255)|Prostate(1639;0.0792)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0452)|OV - Ovarian serous cystadenocarcinoma(117;7.32e-26)|Colorectal(126;1.35e-07)|COAD - Colon adenocarcinoma(152;7.73e-06)|GBM - Glioblastoma multiforme(114;8.62e-06)|BRCA - Breast invasive adenocarcinoma(304;0.000649)|STAD - Stomach adenocarcinoma(196;0.00644)|KIRC - Kidney renal clear cell carcinoma(1967;0.00767)|READ - Rectum adenocarcinoma(331;0.0419)|Lung(427;0.207)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	22591868	22591873	+	IGR	DEL	GTGTGC	-	-	rs148406788	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:22591868_22591873delGTGTGC								WNT4 (121483 upstream) : ZBTB40 (186471 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	22619724	22619724	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:22619724delA								WNT4 (149339 upstream) : ZBTB40 (158620 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	22663392	22663395	+	IGR	DEL	ATCC	-	-	rs150691282		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:22663392_22663395delATCC								WNT4 (193007 upstream) : ZBTB40 (114949 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	22746218	22746218	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:22746218delA								WNT4 (275833 upstream) : ZBTB40 (32126 downstream)																																			---	---	---	---
EPHA8	2046	broad.mit.edu	37	1	22913275	22913276	+	Intron	INS	-	GGT	GGT	rs72180983		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:22913275_22913276insGGT	uc001bfx.1	+						EPHA8_uc001bfw.2_Intron	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)														---	---	---	---
EPHB2	2048	broad.mit.edu	37	1	23042831	23042831	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:23042831delT	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				---	---	---	---
EPHB2	2048	broad.mit.edu	37	1	23109271	23109271	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:23109271delA	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				---	---	---	---
EPHB2	2048	broad.mit.edu	37	1	23154573	23154573	+	Intron	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:23154573delG	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				---	---	---	---
LUZP1	7798	broad.mit.edu	37	1	23428527	23428527	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:23428527delT	uc001bgk.2	-						LUZP1_uc010odv.1_Intron|LUZP1_uc001bgl.2_Intron|LUZP1_uc001bgm.1_Intron	NM_033631	NP_361013			leucine zipper protein 1							nucleus					0		Colorectal(325;3.46e-05)|Lung NSC(340;4.15e-05)|all_lung(284;6.64e-05)|Renal(390;0.000219)|Ovarian(437;0.00373)|Breast(348;0.00815)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|OV - Ovarian serous cystadenocarcinoma(117;4.88e-27)|Colorectal(126;8.36e-08)|COAD - Colon adenocarcinoma(152;4.31e-06)|GBM - Glioblastoma multiforme(114;8.64e-05)|BRCA - Breast invasive adenocarcinoma(304;0.00112)|KIRC - Kidney renal clear cell carcinoma(1967;0.00176)|STAD - Stomach adenocarcinoma(196;0.0146)|READ - Rectum adenocarcinoma(331;0.0686)|Lung(427;0.0967)|LUSC - Lung squamous cell carcinoma(448;0.199)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	24102387	24102387	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:24102387delT	uc001bhp.1	-						C1orf128_uc001bhq.2_5'Flank|C1orf128_uc010oeb.1_5'Flank					Human gene from PAC 886K2, chromosome 1.																														---	---	---	---
HMGCL	3155	broad.mit.edu	37	1	24167643	24167643	+	5'Flank	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:24167643delA	uc001bic.2	-							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	24184564	24184564	+	Intron	DEL	T	-	-	rs71794603		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:24184564delT	uc001bie.2	-						FUCA1_uc009vqt.1_Intron	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	24247638	24247638	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:24247638delT								CNR2 (7821 upstream) : PNRC2 (38663 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	24379369	24379370	+	IGR	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:24379369_24379370delAA								PNRC2 (89422 upstream) : MYOM3 (3162 downstream)																																			---	---	---	---
MYOM3	127294	broad.mit.edu	37	1	24401567	24401571	+	Intron	DEL	AAAAG	-	-	rs113201863		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:24401567_24401571delAAAAG	uc001bin.3	-						MYOM3_uc001bim.3_Intron|MYOM3_uc001bio.2_Intron	NM_152372	NP_689585			myomesin family, member 3											skin(2)|ovary(1)	3		Colorectal(325;3.55e-05)|Renal(390;0.000703)|Lung NSC(340;0.001)|all_lung(284;0.0014)|Ovarian(437;0.00351)|Breast(348;0.0126)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|OV - Ovarian serous cystadenocarcinoma(117;5.31e-24)|Colorectal(126;7.52e-08)|COAD - Colon adenocarcinoma(152;4.01e-06)|GBM - Glioblastoma multiforme(114;4.36e-06)|BRCA - Breast invasive adenocarcinoma(304;0.00108)|KIRC - Kidney renal clear cell carcinoma(1967;0.00404)|STAD - Stomach adenocarcinoma(196;0.00966)|READ - Rectum adenocarcinoma(331;0.0678)|Lung(427;0.153)														---	---	---	---
IL22RA1	58985	broad.mit.edu	37	1	24453804	24453806	+	Intron	DEL	TTT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:24453804_24453806delTTT	uc001biq.1	-						IL22RA1_uc010oeg.1_Intron|IL22RA1_uc009vrb.1_Intron|IL22RA1_uc010oeh.1_Intron	NM_021258	NP_067081			interleukin 22 receptor, alpha 1 precursor							integral to membrane	interferon receptor activity			skin(1)	1		Colorectal(325;3.46e-05)|Renal(390;0.0007)|Lung NSC(340;0.000992)|all_lung(284;0.00138)|Ovarian(437;0.00348)|Breast(348;0.0126)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|OV - Ovarian serous cystadenocarcinoma(117;3.84e-24)|Colorectal(126;6.43e-08)|COAD - Colon adenocarcinoma(152;3.51e-06)|GBM - Glioblastoma multiforme(114;5.06e-05)|BRCA - Breast invasive adenocarcinoma(304;0.00104)|KIRC - Kidney renal clear cell carcinoma(1967;0.00371)|STAD - Stomach adenocarcinoma(196;0.00911)|READ - Rectum adenocarcinoma(331;0.0655)|Lung(427;0.148)														---	---	---	---
IL28RA	163702	broad.mit.edu	37	1	24493209	24493210	+	Intron	DEL	TT	-	-	rs111879080		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:24493209_24493210delTT	uc001bis.2	-						IL28RA_uc001bir.2_Intron|IL28RA_uc001bit.2_Intron|IL28RA_uc001biu.2_Intron|IL28RA_uc001biv.2_Intron	NM_170743	NP_734464			interleukin 28 receptor, alpha isoform 1						cytokine-mediated signaling pathway|negative regulation of cell proliferation|regulation of defense response to virus by host	interleukin-28 receptor complex	protein binding|receptor activity				0		Colorectal(325;3.46e-05)|Renal(390;0.0007)|Lung NSC(340;0.00117)|all_lung(284;0.00151)|Ovarian(437;0.00348)|Breast(348;0.0126)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|OV - Ovarian serous cystadenocarcinoma(117;3.21e-24)|Colorectal(126;6.61e-08)|COAD - Colon adenocarcinoma(152;3.56e-06)|GBM - Glioblastoma multiforme(114;0.000132)|BRCA - Breast invasive adenocarcinoma(304;0.00104)|KIRC - Kidney renal clear cell carcinoma(1967;0.00374)|STAD - Stomach adenocarcinoma(196;0.00918)|READ - Rectum adenocarcinoma(331;0.0656)|Lung(427;0.0853)|LUSC - Lung squamous cell carcinoma(448;0.185)														---	---	---	---
NIPAL3	57185	broad.mit.edu	37	1	24765039	24765039	+	Intron	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:24765039delG	uc001bjh.2	+						NIPAL3_uc010oek.1_Intron|NIPAL3_uc001bjg.2_Intron|NIPAL3_uc009vrc.2_Intron	NM_020448	NP_065181			NIPA-like domain containing 3							integral to membrane					0																		---	---	---	---
Unknown	0	broad.mit.edu	37	1	25175749	25175749	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:25175749delT								CLIC4 (4934 upstream) : RUNX3 (50254 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	25380738	25380738	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:25380738delA								RUNX3 (89126 upstream) : SYF2 (168029 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	25396561	25396561	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:25396561delT								RUNX3 (104949 upstream) : SYF2 (152206 downstream)																																			---	---	---	---
C1orf63	57035	broad.mit.edu	37	1	25573523	25573523	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:25573523delA	uc001bjw.2	-							NM_020317	NP_064713			hypothetical protein LOC57035											pancreas(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;7.9e-27)|Colorectal(126;8.83e-09)|COAD - Colon adenocarcinoma(152;6.43e-07)|STAD - Stomach adenocarcinoma(196;0.000333)|BRCA - Breast invasive adenocarcinoma(304;0.000443)|KIRC - Kidney renal clear cell carcinoma(1967;0.000716)|GBM - Glioblastoma multiforme(114;0.000932)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.199)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	25595006	25595006	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:25595006delA								C1orf63 (21021 upstream) : RHD (3975 downstream)																																			---	---	---	---
TMEM50A	23585	broad.mit.edu	37	1	25677497	25677497	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:25677497delA	uc001bke.2	+						TMEM50A_uc010oeq.1_Intron|TMEM50A_uc009vrr.2_Intron|TMEM50A_uc009vrs.2_Intron	NM_014313	NP_055128			small membrane protein 1							endoplasmic reticulum|integral to 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;0.0422)|OV - Ovarian serous cystadenocarcinoma(117;3.47e-27)|Colorectal(126;1.1e-08)|COAD - Colon adenocarcinoma(152;7.48e-07)|STAD - Stomach adenocarcinoma(196;0.00035)|BRCA - Breast invasive adenocarcinoma(304;0.00047)|KIRC - Kidney renal clear cell carcinoma(1967;0.000755)|GBM - Glioblastoma multiforme(114;0.00106)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.204)														---	---	---	---
TMEM57	55219	broad.mit.edu	37	1	25805451	25805452	+	Intron	INS	-	A	A	rs35109971	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:25805451_25805452insA	uc001bkk.2	+						TMEM57_uc009vru.2_Intron|TMEM57_uc009vrv.2_Intron	NM_018202	NP_060672			transmembrane protein 57							axon|integral to membrane|neuron projection terminus|nuclear membrane|synapse part					0		Colorectal(325;0.000147)|Renal(390;0.00211)|Lung NSC(340;0.00715)|all_lung(284;0.00989)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.051)|Breast(348;0.0675)|all_neural(195;0.201)		UCEC - Uterine corpus endometrioid carcinoma (279;0.042)|OV - Ovarian serous cystadenocarcinoma(117;1.85e-26)|Colorectal(126;2.99e-08)|COAD - Colon adenocarcinoma(152;1.7e-06)|KIRC - Kidney renal clear cell carcinoma(1967;0.000751)|STAD - Stomach adenocarcinoma(196;0.000766)|BRCA - Breast invasive adenocarcinoma(304;0.000986)|GBM - Glioblastoma multiforme(114;0.0191)|READ - Rectum adenocarcinoma(331;0.0649)														---	---	---	---
MAN1C1	57134	broad.mit.edu	37	1	26005498	26005499	+	Intron	DEL	GA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:26005498_26005499delGA	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)														---	---	---	---
RPS6KA1	6195	broad.mit.edu	37	1	26870974	26870974	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:26870974delT	uc001bmr.1	+						RPS6KA1_uc010ofe.1_Intron|RPS6KA1_uc010off.1_Intron|RPS6KA1_uc001bms.1_5'Flank|RPS6KA1_uc009vsl.1_5'Flank	NM_002953	NP_002944			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|caspase inhibitor activity|magnesium ion binding|protein binding|protein serine/threonine kinase activity			lung(1)	1		all_cancers(24;2.49e-24)|Colorectal(325;3.46e-05)|all_lung(284;4.76e-05)|Lung NSC(340;5.83e-05)|Renal(390;0.0007)|Ovarian(437;0.00473)|Breast(348;0.00571)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|Epithelial(14;1.12e-50)|OV - Ovarian serous cystadenocarcinoma(117;2.89e-29)|Colorectal(126;1.4e-08)|COAD - Colon adenocarcinoma(152;9.31e-07)|BRCA - Breast invasive adenocarcinoma(304;0.000537)|KIRC - Kidney renal clear cell carcinoma(1967;0.000759)|STAD - Stomach adenocarcinoma(196;0.00151)|GBM - Glioblastoma multiforme(114;0.0361)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.161)|LUSC - Lung squamous cell carcinoma(448;0.234)														---	---	---	---
ARID1A	8289	broad.mit.edu	37	1	27089873	27089873	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:27089873delA	uc001bmv.1	+						ARID1A_uc001bmt.1_Intron|ARID1A_uc001bmu.1_Intron|ARID1A_uc001bmw.1_Intron	NM_006015	NP_006006			AT rich interactive domain 1A isoform a						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								---	---	---	---
Unknown	0	broad.mit.edu	37	1	27147986	27147987	+	IGR	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:27147986_27147987delTT								PIGV (23100 upstream) : ZDHHC18 (5214 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	27378976	27378976	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:27378976delA								FAM46B (39643 upstream) : SLC9A1 (46325 downstream)																																			---	---	---	---
WDTC1	23038	broad.mit.edu	37	1	27580006	27580007	+	Intron	DEL	TT	-	-	rs78873971		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:27580006_27580007delTT	uc009vst.2	+						WDTC1_uc001bno.2_Intron	NM_015023	NP_055838			WD and tetratricopeptide repeats 1								protein binding			ovary(1)|central_nervous_system(1)	2		all_cancers(24;3.12e-19)|all_epithelial(13;4.18e-18)|Colorectal(325;0.000147)|all_lung(284;0.000366)|Lung NSC(340;0.000548)|Renal(390;0.00211)|Breast(348;0.00257)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0707)|all_neural(195;0.0966)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0443)|OV - Ovarian serous cystadenocarcinoma(117;1.09e-27)|Colorectal(126;8.83e-09)|COAD - Colon adenocarcinoma(152;1.02e-06)|BRCA - Breast invasive adenocarcinoma(304;0.000544)|KIRC - Kidney renal clear cell carcinoma(1967;0.00201)|STAD - Stomach adenocarcinoma(196;0.00321)|READ - Rectum adenocarcinoma(331;0.0476)														---	---	---	---
SYTL1	84958	broad.mit.edu	37	1	27680355	27680356	+	3'UTR	DEL	CT	-	-	rs10335		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:27680355_27680356delCT	uc001bnw.1	+	15					SYTL1_uc001bnv.1_3'UTR|SYTL1_uc009vsu.1_3'UTR|SYTL1_uc009vsv.1_3'UTR	NM_032872	NP_116261			synaptotagmin-like 1						exocytosis|intracellular protein transport	extrinsic to plasma membrane|melanosome|soluble fraction	neurexin binding|Rab GTPase binding			ovary(1)	1		Colorectal(325;0.000147)|all_lung(284;0.000366)|Lung NSC(340;0.000548)|Renal(390;0.00211)|Breast(348;0.0115)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0908)|all_neural(195;0.0966)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0416)|OV - Ovarian serous cystadenocarcinoma(117;1.5e-28)|Colorectal(126;1.24e-08)|COAD - Colon adenocarcinoma(152;1.7e-06)|BRCA - Breast invasive adenocarcinoma(304;0.0013)|KIRC - Kidney renal clear cell carcinoma(1967;0.00158)|STAD - Stomach adenocarcinoma(196;0.00303)|READ - Rectum adenocarcinoma(331;0.0419)														---	---	---	---
STX12	23673	broad.mit.edu	37	1	28125231	28125231	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:28125231delA	uc001bou.3	+							NM_177424	NP_803173			syntaxin 12						cholesterol efflux|intracellular protein transport|protein stabilization|vesicle-mediated transport	Golgi apparatus|integral to membrane|membrane raft|phagocytic vesicle	SNAP receptor activity			breast(1)|central_nervous_system(1)	2		Colorectal(325;3.46e-05)|all_lung(284;9.43e-05)|Lung NSC(340;0.000185)|Renal(390;0.00121)|Breast(348;0.0021)|Ovarian(437;0.00503)|all_neural(195;0.0208)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0434)|OV - Ovarian serous cystadenocarcinoma(117;3.96e-24)|Colorectal(126;3.46e-08)|COAD - Colon adenocarcinoma(152;1.83e-06)|BRCA - Breast invasive adenocarcinoma(304;0.00258)|KIRC - Kidney renal clear cell carcinoma(1967;0.00302)|STAD - Stomach adenocarcinoma(196;0.00311)|READ - Rectum adenocarcinoma(331;0.0649)														---	---	---	---
C1orf38	9473	broad.mit.edu	37	1	28208354	28208354	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:28208354delA	uc001bpc.3	+						C1orf38_uc001boz.2_Intron|C1orf38_uc001bpa.2_Intron|C1orf38_uc010ofn.1_Intron|C1orf38_uc010ofo.1_Intron	NM_001105556	NP_001099026			basement membrane-induced gene isoform 3						cell adhesion|inflammatory response					ovary(1)	1		Colorectal(325;3.46e-05)|all_lung(284;0.000129)|Lung NSC(340;0.000259)|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;0.0416)|OV - Ovarian serous cystadenocarcinoma(117;2.52e-24)|Colorectal(126;2.96e-08)|COAD - Colon adenocarcinoma(152;1.7e-06)|BRCA - Breast invasive adenocarcinoma(304;0.00244)|KIRC - Kidney renal clear cell carcinoma(1967;0.0027)|STAD - Stomach adenocarcinoma(196;0.00303)|READ - Rectum adenocarcinoma(331;0.0649)														---	---	---	---
EYA3	2140	broad.mit.edu	37	1	28346386	28346386	+	Intron	DEL	T	-	-	rs113647455		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:28346386delT	uc001bpi.1	-						EYA3_uc010ofs.1_Intron|EYA3_uc010oft.1_Intron|EYA3_uc001bpj.2_Intron|EYA3_uc001bpk.1_Intron|EYA3_uc010ofu.1_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)														---	---	---	---
EYA3	2140	broad.mit.edu	37	1	28382507	28382508	+	Intron	DEL	TT	-	-	rs35066303		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:28382507_28382508delTT	uc001bpi.1	-						EYA3_uc010ofs.1_Intron|EYA3_uc010oft.1_Intron|EYA3_uc001bpj.2_Intron|EYA3_uc001bpk.1_Intron|EYA3_uc010ofu.1_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	28504249	28504249	+	5'Flank	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:28504249delT	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)														---	---	---	---
DNAJC8	22826	broad.mit.edu	37	1	28543154	28543154	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:28543154delA	uc001bpn.2	-						DNAJC8_uc001bpo.2_Intron	NM_014280	NP_055095			DnaJ (Hsp40) homolog, subfamily C, member 8						nuclear mRNA splicing, via spliceosome|protein folding	nucleoplasm	heat shock protein binding|unfolded protein binding				0		Colorectal(325;3.46e-05)|Lung NSC(340;4.08e-05)|all_lung(284;4.29e-05)|Renal(390;0.00121)|Breast(348;0.00345)|Ovarian(437;0.0105)|all_neural(195;0.0208)|Myeloproliferative disorder(586;0.0255)		OV - Ovarian serous cystadenocarcinoma(117;2.81e-22)|Colorectal(126;2.99e-08)|COAD - Colon adenocarcinoma(152;1.7e-06)|KIRC - Kidney renal clear cell carcinoma(1967;0.00275)|BRCA - Breast invasive adenocarcinoma(304;0.0059)|STAD - Stomach adenocarcinoma(196;0.00671)|READ - Rectum adenocarcinoma(331;0.0649)														---	---	---	---
ATPIF1	93974	broad.mit.edu	37	1	28564029	28564029	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-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)														---	---	---	---
SESN2	83667	broad.mit.edu	37	1	28595177	28595177	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:28595177delA	uc001bps.2	+							NM_031459	NP_113647			sestrin 2						cell cycle arrest	cytoplasm|nucleus				skin(3)|ovary(2)|pancreas(1)|lung(1)	7		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;2.98e-22)|Colorectal(126;3.04e-08)|COAD - Colon adenocarcinoma(152;1.7e-06)|KIRC - Kidney renal clear cell carcinoma(1967;0.00279)|STAD - Stomach adenocarcinoma(196;0.00303)|BRCA - Breast invasive adenocarcinoma(304;0.00595)|READ - Rectum adenocarcinoma(331;0.0649)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	28612105	28612105	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:28612105delT								SESN2 (3104 upstream) : MED18 (43408 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	28618053	28618056	+	IGR	DEL	AAAA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:28618053_28618056delAAAA								SESN2 (9052 upstream) : MED18 (37457 downstream)																																			---	---	---	---
PHACTR4	65979	broad.mit.edu	37	1	28697435	28697435	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:28697435delA	uc001bpw.2	+						PHACTR4_uc001bpu.2_Intron|PHACTR4_uc001bpv.1_Intron|PHACTR4_uc001bpx.2_Intron	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)														---	---	---	---
PHACTR4	65979	broad.mit.edu	37	1	28769963	28769963	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:28769963delT	uc001bpw.2	+						PHACTR4_uc001bpu.2_Intron|PHACTR4_uc001bpv.1_Intron|PHACTR4_uc001bpx.2_Intron|PHACTR4_uc001bpy.2_Intron	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)														---	---	---	---
PHACTR4	65979	broad.mit.edu	37	1	28804214	28804214	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:28804214delT	uc001bpw.2	+						PHACTR4_uc001bpv.1_Intron|PHACTR4_uc001bpx.2_Intron|PHACTR4_uc001bpy.2_Intron	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)														---	---	---	---
RCC1	1104	broad.mit.edu	37	1	28849160	28849160	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:28849160delA	uc001bqg.1	+						SNHG3-RCC1_uc001bqa.1_Intron|SNHG3-RCC1_uc001bqb.1_Intron|SNHG3-RCC1_uc001bqc.1_Intron|RCC1_uc001bqe.1_Intron|RCC1_uc001bqf.1_Intron	NM_001269	NP_001260			regulator of chromosome condensation 1 isoform						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)														---	---	---	---
OPRD1	4985	broad.mit.edu	37	1	29176006	29176007	+	Intron	DEL	AC	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:29176006_29176007delAC	uc001brf.1	+							NM_000911	NP_000902			opioid receptor, delta 1						immune response|protein import into nucleus, translocation	integral to plasma membrane	delta-opioid receptor activity|protein binding			ovary(1)|central_nervous_system(1)	2		Colorectal(325;3.46e-05)|Lung NSC(340;0.000947)|all_lung(284;0.00131)|Renal(390;0.00758)|Breast(348;0.00765)|all_neural(195;0.0199)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0563)|Medulloblastoma(700;0.123)		Colorectal(126;1.29e-07)|COAD - Colon adenocarcinoma(152;7.51e-06)|STAD - Stomach adenocarcinoma(196;0.00306)|BRCA - Breast invasive adenocarcinoma(304;0.0241)|READ - Rectum adenocarcinoma(331;0.0649)|KIRC - Kidney renal clear cell carcinoma(1967;0.147)	Butorphanol(DB00611)|Codeine(DB00318)|Fentanyl(DB00813)|Hydrocodone(DB00956)|Hydromorphone(DB00327)|Loperamide(DB00836)|Morphine(DB00295)|Nalbuphine(DB00844)|Naloxone(DB01183)|Naltrexone(DB00704)|Oxycodone(DB00497)|Pimozide(DB01100)|Propoxyphene(DB00647)													---	---	---	---
EPB41	2035	broad.mit.edu	37	1	29286514	29286516	+	Intron	DEL	TTT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:29286514_29286516delTTT	uc001brl.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	NM_004437	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)														---	---	---	---
EPB41	2035	broad.mit.edu	37	1	29320677	29320677	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:29320677delT	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)														---	---	---	---
EPB41	2035	broad.mit.edu	37	1	29347174	29347175	+	Intron	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:29347174_29347175delTT	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)														---	---	---	---
MECR	51102	broad.mit.edu	37	1	29546018	29546019	+	Intron	DEL	AA	-	-	rs113214340		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:29546018_29546019delAA	uc001brq.1	-						MECR_uc001brp.1_Intron|MECR_uc001brr.1_Intron|MECR_uc001brs.1_Intron|MECR_uc001brt.1_Intron|MECR_uc010ofz.1_Intron	NM_016011	NP_057095			trans-2-enoyl-CoA reductase, mitochondrial						fatty acid biosynthetic process	mitochondrion	trans-2-enoyl-CoA reductase (NADPH) activity|zinc ion binding			ovary(1)	1		Colorectal(325;0.000389)|Breast(348;0.00765)|Lung NSC(340;0.0081)|all_lung(284;0.00914)|all_neural(195;0.0199)|Ovarian(437;0.0228)|Myeloproliferative disorder(586;0.0255)|Medulloblastoma(700;0.123)		Colorectal(126;3.39e-07)|COAD - Colon adenocarcinoma(152;2.04e-05)|STAD - Stomach adenocarcinoma(196;0.0195)|BRCA - Breast invasive adenocarcinoma(304;0.053)|READ - Rectum adenocarcinoma(331;0.0649)|KIRC - Kidney renal clear cell carcinoma(1967;0.137)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	30047209	30047209	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:30047209delA								PTPRU (393894 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	30976427	30976427	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:30976427delA								None (None upstream) : MATN1 (207699 downstream)																																			---	---	---	---
ZCCHC17	51538	broad.mit.edu	37	1	31791791	31791792	+	Intron	INS	-	A	A	rs56053258		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-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)														---	---	---	---
ZCCHC17	51538	broad.mit.edu	37	1	31820866	31820867	+	Intron	DEL	CT	-	-	rs3049349		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:31820866_31820867delCT	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	31948727	31948727	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:31948727delT								SERINC2 (41203 upstream) : LOC284551 (35309 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	32319394	32319395	+	IGR	DEL	TC	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:32319394_32319395delTC								SPOCD1 (37814 upstream) : PTP4A2 (54398 downstream)																																			---	---	---	---
PTP4A2	8073	broad.mit.edu	37	1	32375887	32375888	+	Intron	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:32375887_32375888delTT	uc001bty.1	-						PTP4A2_uc010ogs.1_Intron|PTP4A2_uc001btz.1_Intron	NM_080391	NP_536316			protein tyrosine phosphatase type IVA, member 2							early endosome|plasma membrane	prenylated protein tyrosine phosphatase activity|protein binding|protein tyrosine/serine/threonine phosphatase activity				0		Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0606)|all_neural(195;0.0837)|Breast(348;0.174)																---	---	---	---
Unknown	0	broad.mit.edu	37	1	32452203	32452203	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:32452203delA								PTP4A2 (48215 upstream) : KHDRBS1 (27288 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	32459067	32459068	+	IGR	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:32459067_32459068delAA								PTP4A2 (55079 upstream) : KHDRBS1 (20423 downstream)																																			---	---	---	---
KPNA6	23633	broad.mit.edu	37	1	32584234	32584234	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:32584234delA	uc001bug.2	+						KPNA6_uc001buh.2_Intron|KPNA6_uc010ogx.1_Intron	NM_012316	NP_036448			karyopherin alpha 6						NLS-bearing substrate import into nucleus	cytoplasm|nuclear pore	protein binding				0		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0837)|Ovarian(437;0.101)|Breast(348;0.174)																---	---	---	---
ZBTB8A	653121	broad.mit.edu	37	1	33020589	33020589	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:33020589delA	uc001bvn.2	+						ZBTB8A_uc001bvk.2_Intron|ZBTB8A_uc001bvm.2_Intron	NM_001040441	NP_001035531			zinc finger and BTB domain containing 8A						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0																		---	---	---	---
RBBP4	5928	broad.mit.edu	37	1	33135036	33135036	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:33135036delT	uc001bvr.2	+						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)																---	---	---	---
SYNC	81493	broad.mit.edu	37	1	33146114	33146114	+	3'UTR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:33146114delT	uc001bvt.2	-	5					SYNC_uc010ohl.1_3'UTR|RBBP4_uc001bvr.2_3'UTR|RBBP4_uc001bvs.2_3'UTR|RBBP4_uc010ohj.1_3'UTR|RBBP4_uc010ohk.1_3'UTR	NM_030786	NP_110413			syncoilin, intermediate filament 1 isoform 1							intermediate filament|perinuclear region of cytoplasm	structural molecule activity			ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	1	33191388	33191389	+	IGR	INS	-	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:33191388_33191389insC								SYNC (23027 upstream) : KIAA1522 (16123 downstream)																																			---	---	---	---
FNDC5	252995	broad.mit.edu	37	1	33330043	33330047	+	Intron	DEL	TTTTT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:33330043_33330047delTTTTT	uc001bwf.1	-						FNDC5_uc001bwe.2_Intron	NM_153756	NP_715637			fibronectin type III domain containing 5							integral to membrane|peroxisomal membrane				ovary(1)	1		Myeloproliferative disorder(586;0.0393)|all_neural(195;0.186)																---	---	---	---
RNF19B	127544	broad.mit.edu	37	1	33415573	33415573	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:33415573delT	uc010oho.1	-						RNF19B_uc001bwm.3_Intron|RNF19B_uc010ohp.1_Intron	NM_153341	NP_699172			ring finger protein 19B isoform a							integral to membrane	ligase activity|protein binding|zinc ion binding				0		Myeloproliferative disorder(586;0.0393)|all_neural(195;0.186)																---	---	---	---
AK2	204	broad.mit.edu	37	1	33475993	33475994	+	3'UTR	INS	-	C	C	rs113029003		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:33475993_33475994insC	uc001bwo.1	-	7					uc001bwn.2_Intron|AK2_uc010ohq.1_3'UTR|AK2_uc009vud.1_3'UTR	NM_013411	NP_037543			adenylate kinase 2 isoform b						nucleobase, nucleoside and nucleotide interconversion	mitochondrial intermembrane space	adenylate kinase activity|ATP binding				0		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0837)																---	---	---	---
TRIM62	55223	broad.mit.edu	37	1	33620400	33620401	+	Intron	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:33620400_33620401delAA	uc001bxb.2	-							NM_018207	NP_060677			tripartite motif-containing 62							intracellular	zinc ion binding				0		Myeloproliferative disorder(586;0.0393)																---	---	---	---
ZNF362	149076	broad.mit.edu	37	1	33745854	33745854	+	Frame_Shift_Del	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-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)																---	---	---	---
C1orf94	84970	broad.mit.edu	37	1	34679455	34679455	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:34679455delA	uc001bxs.3	+						C1orf94_uc001bxt.2_Intron	NM_032884	NP_116273			hypothetical protein LOC84970 isoform b								protein binding				0		Myeloproliferative disorder(586;0.0393)																---	---	---	---
Unknown	0	broad.mit.edu	37	1	34757943	34757943	+	IGR	DEL	T	-	-	rs67024924		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:34757943delT								C1orf94 (73214 upstream) : MIR552 (377257 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	34882527	34882527	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:34882527delA								C1orf94 (197798 upstream) : MIR552 (252673 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	35504171	35504171	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:35504171delA								ZMYM6 (6602 upstream) : ZMYM1 (40801 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	35717758	35717758	+	IGR	DEL	T	-	-	rs143854461		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:35717758delT								SFPQ (59015 upstream) : ZMYM4 (16810 downstream)																																			---	---	---	---
ZMYM4	9202	broad.mit.edu	37	1	35741633	35741633	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:35741633delT	uc001byt.2	+						ZMYM4_uc009vuu.2_Intron|ZMYM4_uc001byu.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)																---	---	---	---
KIAA0319L	79932	broad.mit.edu	37	1	35922411	35922411	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:35922411delA	uc001byx.2	-						KIAA0319L_uc001byw.2_5'Flank|KIAA0319L_uc010ohv.1_Intron	NM_024874	NP_079150			dyslexia susceptibility 2-like							cytoplasmic vesicle part|integral to membrane	protein binding			skin(2)	2		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0887)																---	---	---	---
KIAA0319L	79932	broad.mit.edu	37	1	36019914	36019914	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:36019914delA	uc001byx.2	-						KIAA0319L_uc010ohw.1_Intron|KIAA0319L_uc001byz.2_Intron|KIAA0319L_uc010ohx.1_Intron	NM_024874	NP_079150			dyslexia susceptibility 2-like							cytoplasmic vesicle part|integral to membrane	protein binding			skin(2)	2		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0887)																---	---	---	---
NCDN	23154	broad.mit.edu	37	1	36027122	36027123	+	Intron	DEL	AC	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:36027122_36027123delAC	uc001bza.2	+						NCDN_uc001bzb.2_Intron|NCDN_uc001bzc.2_Intron	NM_001014839	NP_001014839			neurochondrin isoform 1						neuron projection development	cytosol|dendrite|neuronal cell body				large_intestine(2)|pancreas(1)	3		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0887)																---	---	---	---
TFAP2E	339488	broad.mit.edu	37	1	36055095	36055096	+	Intron	DEL	GT	-	-	rs67449985		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:36055095_36055096delGT	uc010ohy.1	+						PSMB2_uc001bzd.1_Intron	NM_178548	NP_848643			transcription factor AP-2 epsilon (activating							nucleus	DNA binding|sequence-specific DNA binding transcription factor activity				0		Myeloproliferative disorder(586;0.0393)|all_neural(195;0.196)																---	---	---	---
CLSPN	63967	broad.mit.edu	37	1	36203850	36203850	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:36203850delA	uc001bzi.2	-						CLSPN_uc009vux.2_Intron	NM_022111	NP_071394			claspin						activation of protein kinase activity|cell cycle|cellular component disassembly involved in apoptosis|DNA repair|DNA replication|G2/M transition DNA damage checkpoint|mitotic cell cycle DNA replication checkpoint|peptidyl-serine phosphorylation	nucleoplasm	anaphase-promoting complex binding|DNA binding			breast(2)|ovary(2)|central_nervous_system(1)|lung(1)|skin(1)|kidney(1)	8		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0887)																---	---	---	---
EIF2C4	192670	broad.mit.edu	37	1	36312775	36312776	+	Intron	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:36312775_36312776delAA	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)																---	---	---	---
TRAPPC3	27095	broad.mit.edu	37	1	36603019	36603019	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:36603019delA	uc001bzx.2	-						TRAPPC3_uc001bzy.2_Intron	NM_014408	NP_055223			trafficking protein particle complex 3							endoplasmic reticulum	guanylate cyclase activity|heme binding			central_nervous_system(1)	1		Myeloproliferative disorder(586;0.0393)																---	---	---	---
CSF3R	1441	broad.mit.edu	37	1	36937440	36937440	+	Intron	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:36937440delG	uc001caw.1	-						CSF3R_uc001cat.1_5'Flank|CSF3R_uc009vvc.1_5'Flank|CSF3R_uc001cau.1_Intron|CSF3R_uc001cav.1_Intron|CSF3R_uc001cax.1_Intron|CSF3R_uc001cay.1_Intron	NM_000760	NP_000751			colony stimulating factor 3 receptor isoform a						cell adhesion|defense response	extracellular region|integral to plasma membrane	cytokine receptor activity			central_nervous_system(2)|ovary(1)	3		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.164)			Filgrastim(DB00099)|Pegfilgrastim(DB00019)													---	---	---	---
GRIK3	2899	broad.mit.edu	37	1	37486238	37486238	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:37486238delA	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	37772845	37772846	+	IGR	INS	-	A	A	rs145223392	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:37772845_37772846insA								GRIK3 (273001 upstream) : ZC3H12A (167273 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	37808432	37808433	+	IGR	INS	-	T	T	rs147276472	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:37808432_37808433insT								GRIK3 (308588 upstream) : ZC3H12A (131686 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	37985890	37985890	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:37985890delA								MEAF6 (5526 upstream) : SNIP1 (16255 downstream)																																			---	---	---	---
C1orf109	54955	broad.mit.edu	37	1	38147951	38147951	+	3'UTR	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:38147951delG	uc001cbp.2	-	5					C1orf109_uc001cbn.2_RNA|C1orf109_uc010oig.1_3'UTR|C1orf109_uc001cbo.2_3'UTR	NM_017850	NP_060320			hypothetical protein LOC54955												0		Myeloproliferative disorder(586;0.0393)														OREG0013382	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
EPHA10	284656	broad.mit.edu	37	1	38182851	38182851	+	3'UTR	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:38182851delC	uc009vvi.2	-	17					EPHA10_uc001cbt.2_Intron|EPHA10_uc009vvh.1_Intron|EPHA10_uc001cbu.2_Intron|EPHA10_uc001cbv.1_Intron	NM_001099439	NP_001092909			EPH receptor A10 isofom 3							extracellular region|integral to membrane|integral to plasma membrane	ATP binding|ephrin receptor activity|protein binding|transmembrane-ephrin receptor activity			breast(4)|stomach(3)|lung(1)	8	Acute lymphoblastic leukemia(166;0.074)|all_hematologic(146;0.197)	Myeloproliferative disorder(586;0.0255)|all_neural(195;0.164)																---	---	---	---
INPP5B	3633	broad.mit.edu	37	1	38352957	38352957	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:38352957delA	uc001ccg.1	-						INPP5B_uc009vvk.1_Intron|INPP5B_uc001ccf.1_Intron|INPP5B_uc010oij.1_Intron	NM_005540	NP_005531			inositol polyphosphate-5-phosphatase, 75kDa						regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol|integral to membrane|microtubule cytoskeleton	GTPase activator activity|inositol-polyphosphate 5-phosphatase activity|phosphatidylinositol-4,5-bisphosphate 5-phosphatase activity|protein binding			urinary_tract(1)	1	Acute lymphoblastic leukemia(166;0.074)|all_hematologic(146;0.197)	Myeloproliferative disorder(586;0.0255)																---	---	---	---
Unknown	0	broad.mit.edu	37	1	38641821	38641821	+	IGR	DEL	C	-	-	rs112360134		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:38641821delC								POU3F1 (129371 upstream) : RRAGC (663194 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	38715048	38715049	+	IGR	DEL	TG	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:38715048_38715049delTG								POU3F1 (202598 upstream) : RRAGC (589966 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	38807810	38807811	+	IGR	DEL	AA	-	-	rs150047037		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:38807810_38807811delAA								POU3F1 (295360 upstream) : RRAGC (497204 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	38808274	38808274	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:38808274delT								POU3F1 (295824 upstream) : RRAGC (496741 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	38934567	38934567	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:38934567delA								POU3F1 (422117 upstream) : RRAGC (370448 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	39414545	39414545	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:39414545delA								RHBDL2 (7089 upstream) : AKIRIN1 (42371 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	39441215	39441215	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:39441215delT								RHBDL2 (33759 upstream) : AKIRIN1 (15701 downstream)																																			---	---	---	---
MACF1	23499	broad.mit.edu	37	1	39633386	39633386	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:39633386delA	uc010ois.1	+						MACF1_uc001cda.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)															---	---	---	---
MACF1	23499	broad.mit.edu	37	1	39803450	39803450	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:39803450delT	uc010oiu.1	+						MACF1_uc010ois.1_Intron|MACF1_uc001cda.1_Intron|MACF1_uc001cdc.1_Intron|MACF1_uc001cdb.1_Intron	NM_033044	NP_149033			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)															---	---	---	---
MACF1	23499	broad.mit.edu	37	1	39829277	39829278	+	Intron	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:39829277_39829278delTT	uc010oiu.1	+						MACF1_uc010ois.1_Intron|MACF1_uc001cda.1_Intron|MACF1_uc001cdc.1_Intron|MACF1_uc001cdb.1_Intron	NM_033044	NP_149033			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)															---	---	---	---
MACF1	23499	broad.mit.edu	37	1	39898480	39898480	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:39898480delT	uc010oiu.1	+						MACF1_uc010ois.1_Intron|MACF1_uc001cda.1_Intron|MACF1_uc001cdc.1_Intron	NM_033044	NP_149033			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)															---	---	---	---
Unknown	0	broad.mit.edu	37	1	40398949	40398949	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:40398949delA								MYCL1 (31262 upstream) : MFSD2A (21835 downstream)																																			---	---	---	---
MFSD2A	84879	broad.mit.edu	37	1	40429116	40429116	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:40429116delA	uc001cev.2	+						MFSD2A_uc010ojb.1_Intron|MFSD2A_uc001ceu.2_Intron|MFSD2A_uc010ojc.1_Intron|MFSD2A_uc009vvy.2_Intron	NM_001136493	NP_001129965			major facilitator superfamily domain containing						transmembrane transport	endoplasmic reticulum membrane|integral to membrane				ovary(1)|pancreas(1)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	1	40799407	40799407	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:40799407delT								COL9A2 (16347 upstream) : SMAP2 (40321 downstream)																																			---	---	---	---
SCMH1	22955	broad.mit.edu	37	1	41552240	41552241	+	Intron	INS	-	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:41552240_41552241insC	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)																---	---	---	---
SCMH1	22955	broad.mit.edu	37	1	41617397	41617397	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:41617397delA	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)																---	---	---	---
Unknown	0	broad.mit.edu	37	1	41729280	41729280	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:41729280delT								SCMH1 (21492 upstream) : EDN2 (215169 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	41798713	41798713	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:41798713delA								SCMH1 (90925 upstream) : EDN2 (145736 downstream)																																			---	---	---	---
HIVEP3	59269	broad.mit.edu	37	1	42068369	42068369	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:42068369delT	uc001cgz.3	-						HIVEP3_uc001cha.3_Intron	NM_024503	NP_078779			human immunodeficiency virus type I enhancer						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	42573960	42573961	+	IGR	INS	-	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:42573960_42573961insC								HIVEP3 (72364 upstream) : GUCA2B (45131 downstream)																																			---	---	---	---
CCDC30	728621	broad.mit.edu	37	1	43010889	43010889	+	Intron	DEL	A	-	-	rs141597374		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:43010889delA	uc009vwk.1	+						CCDC30_uc001chm.2_Intron|CCDC30_uc001chn.2_Intron|CCDC30_uc010oju.1_Intron|CCDC30_uc001chp.2_Intron	NM_001080850	NP_001074319			coiled-coil domain containing 30												0																		---	---	---	---
CCDC30	728621	broad.mit.edu	37	1	43021760	43021760	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:43021760delT	uc009vwk.1	+						CCDC30_uc001chm.2_Intron|CCDC30_uc001chn.2_Intron|CCDC30_uc010oju.1_Intron|CCDC30_uc001chp.2_Intron	NM_001080850	NP_001074319			coiled-coil domain containing 30												0																		---	---	---	---
LEPRE1	64175	broad.mit.edu	37	1	43223043	43223045	+	Intron	DEL	GAA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:43223043_43223045delGAA	uc001chv.2	-						LEPRE1_uc001chw.2_Intron|LEPRE1_uc001chx.3_Intron	NM_022356	NP_071751			leprecan 1 isoform 1						negative regulation of cell proliferation	endoplasmic reticulum|proteinaceous extracellular matrix	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			ovary(3)|lung(1)	4	Ovarian(52;0.00744)|all_hematologic(146;0.0977)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0505)			L-Proline(DB00172)|Succinic acid(DB00139)|Vitamin C(DB00126)											OREG0013423	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	43490247	43490248	+	IGR	DEL	GT	-	-	rs149497291	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:43490247_43490248delGT								SLC2A1 (65400 upstream) : FAM183A (123346 downstream)																																			---	---	---	---
MED8	112950	broad.mit.edu	37	1	43850143	43850143	+	Frame_Shift_Del	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:43850143delT	uc001cje.1	-	8	932	c.884delA	c.(883-885)AATfs	p.N295fs		NM_052877	NP_443109	Q96G25	MED8_HUMAN	mediator complex subunit 8 isoform 3	Error:Variant_position_missing_in_Q96G25_after_alignment					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)																---	---	---	---
ST3GAL3	6487	broad.mit.edu	37	1	44344991	44344991	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:44344991delT	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)																---	---	---	---
Unknown	0	broad.mit.edu	37	1	44406415	44406415	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:44406415delA								ARTN (3504 upstream) : IPO13 (6063 downstream)																																			---	---	---	---
KIF2C	11004	broad.mit.edu	37	1	45215808	45215809	+	Intron	DEL	TC	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:45215808_45215809delTC	uc001cmg.3	+						KIF2C_uc010olb.1_Intron|KIF2C_uc010olc.1_Intron|KIF2C_uc001cmh.3_Intron	NM_006845	NP_006836			kinesin family member 2C						blood coagulation|cell division|cell proliferation|chromosome segregation|establishment or maintenance of microtubule cytoskeleton polarity|microtubule depolymerization|microtubule-based movement|mitotic prometaphase|regulation of chromosome segregation	condensed chromosome kinetochore|cytosol|kinesin complex|microtubule|nucleus	ATP binding|centromeric DNA binding|microtubule motor activity|microtubule plus-end binding			ovary(1)	1	Acute lymphoblastic leukemia(166;0.155)																	---	---	---	---
EIF2B3	8891	broad.mit.edu	37	1	45392811	45392812	+	Intron	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:45392811_45392812delAA	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)																	---	---	---	---
ZSWIM5	57643	broad.mit.edu	37	1	45553513	45553513	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:45553513delA	uc001cnd.2	-							NM_020883	NP_065934			zinc finger, SWIM domain containing 5								zinc ion binding				0	Acute lymphoblastic leukemia(166;0.155)																	---	---	---	---
Unknown	0	broad.mit.edu	37	1	45716467	45716468	+	IGR	DEL	AA	-	-	rs66680489		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:45716467_45716468delAA								ZSWIM5 (44217 upstream) : LOC400752 (53114 downstream)																																			---	---	---	---
TOE1	114034	broad.mit.edu	37	1	45807064	45807064	+	Intron	DEL	G	-	-	rs3811432	byFrequency	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-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)																	---	---	---	---
GPBP1L1	60313	broad.mit.edu	37	1	46142716	46142716	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:46142716delA	uc001coq.2	-							NM_021639	NP_067652			GC-rich promoter binding protein 1-like 1						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding			ovary(1)	1	Acute lymphoblastic leukemia(166;0.155)																	---	---	---	---
Unknown	0	broad.mit.edu	37	1	46221918	46221918	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:46221918delT								IPP (5433 upstream) : MAST2 (47367 downstream)																																			---	---	---	---
MKNK1	8569	broad.mit.edu	37	1	47053490	47053490	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:47053490delA	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|MKNK1_uc010omf.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)																	---	---	---	---
MOBKL2C	148932	broad.mit.edu	37	1	47074907	47074908	+	3'UTR	DEL	CA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:47074907_47074908delCA	uc001cqf.3	-	4					MKNK1_uc010omf.1_Intron|MOBKL2C_uc001cqe.3_3'UTR	NM_201403	NP_958805			MOB1, Mps One Binder kinase activator-like 2C								metal ion binding			pancreas(1)	1	Acute lymphoblastic leukemia(166;0.155)																	---	---	---	---
CYP4Z2P	163720	broad.mit.edu	37	1	47339125	47339125	+	Intron	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:47339125delC	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																		---	---	---	---
CYP4Z2P	163720	broad.mit.edu	37	1	47339172	47339172	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:47339172delT	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																		---	---	---	---
Unknown	0	broad.mit.edu	37	1	47616605	47616605	+	IGR	DEL	G	-	-	rs72637981		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:47616605delG								CYP4A22 (2079 upstream) : PDZK1IP1 (32657 downstream)																																			---	---	---	---
STIL	6491	broad.mit.edu	37	1	47737729	47737729	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:47737729delA	uc001crc.1	-						TAL1_uc001crb.1_Intron|STIL_uc010omn.1_Intron|STIL_uc010omo.1_Intron|STIL_uc001crd.1_Intron|STIL_uc001cre.1_Intron|STIL_uc001crf.1_Intron|STIL_uc001crg.1_Intron	NM_003035	NP_003026			SCL/TAL1 interrupting locus isoform 2						cell proliferation|multicellular organismal development	centrosome|cytosol				lung(2)|skin(1)	3		Acute lymphoblastic leukemia(5;0.00116)|all_hematologic(5;0.00444)																---	---	---	---
STIL	6491	broad.mit.edu	37	1	47759445	47759446	+	Intron	DEL	GA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:47759445_47759446delGA	uc001crc.1	-						TAL1_uc001crb.1_Intron|STIL_uc010omn.1_Intron|STIL_uc010omo.1_Intron|STIL_uc001crd.1_Intron|STIL_uc001cre.1_Intron|STIL_uc001crg.1_Intron	NM_003035	NP_003026			SCL/TAL1 interrupting locus isoform 2						cell proliferation|multicellular organismal development	centrosome|cytosol				lung(2)|skin(1)	3		Acute lymphoblastic leukemia(5;0.00116)|all_hematologic(5;0.00444)																---	---	---	---
Unknown	0	broad.mit.edu	37	1	48111004	48111005	+	IGR	INS	-	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:48111004_48111005insT								FOXD2 (204642 upstream) : SKINTL (456382 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	48554990	48554990	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:48554990delT								FOXD2 (648628 upstream) : SKINTL (12397 downstream)																																			---	---	---	---
SKINTL	391037	broad.mit.edu	37	1	48595028	48595028	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:48595028delT	uc010omr.1	-							NR_026749				Homo sapiens Skint-like (pseudogene) (SKINTL), non-coding RNA.												0																		---	---	---	---
AGBL4	84871	broad.mit.edu	37	1	49272331	49272332	+	Intron	INS	-	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:49272331_49272332insG	uc001cru.2	-						AGBL4_uc010omw.1_Intron|AGBL4_uc010omx.1_Intron|AGBL4_uc001crv.1_Intron|AGBL4_uc010omy.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	49450748	49450749	+	Intron	INS	-	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:49450748_49450749insA	uc001cru.2	-						AGBL4_uc010omw.1_Intron|AGBL4_uc010omx.1_Intron|AGBL4_uc001crv.1_Intron|AGBL4_uc010omy.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	49575525	49575525	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:49575525delT	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	49871411	49871411	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:49871411delT	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	50572178	50572178	+	5'Flank	DEL	A	-	-	rs79810783		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:50572178delA	uc001csb.2	+						ELAVL4_uc001cry.3_Intron|ELAVL4_uc001crz.3_Intron|ELAVL4_uc001csa.3_Intron|ELAVL4_uc001csc.3_5'Flank	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																		---	---	---	---
Unknown	0	broad.mit.edu	37	1	50681744	50681744	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:50681744delA								ELAVL4 (14204 upstream) : DMRTA2 (201485 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	50732274	50732274	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:50732274delA								ELAVL4 (64734 upstream) : DMRTA2 (150955 downstream)																																			---	---	---	---
DMRTA2	63950	broad.mit.edu	37	1	50886249	50886249	+	Intron	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:50886249delG	uc010ona.1	-						DMRTA2_uc010onb.1_Intron	NM_032110	NP_115486			DMRT-like family A2						sex differentiation	nucleus	DNA binding|metal ion binding|sequence-specific DNA binding transcription factor activity				0																		---	---	---	---
FAF1	11124	broad.mit.edu	37	1	51061719	51061719	+	Intron	DEL	A	-	-	rs74080024	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:51061719delA	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)														---	---	---	---
FAF1	11124	broad.mit.edu	37	1	51306135	51306135	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:51306135delA	uc009vyx.1	-						FAF1_uc009vyw.1_Intron|FAF1_uc001cse.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	p.0?(2)		ovary(1)|pancreas(1)	2				GBM - Glioblastoma multiforme(3;3.18e-11)|all cancers(3;0.00526)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	51501942	51501942	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:51501942delT								CDKN2C (61635 upstream) : C1orf185 (65964 downstream)														p.0?(1)																					---	---	---	---
Unknown	0	broad.mit.edu	37	1	51683069	51683072	+	IGR	DEL	TTTT	-	-	rs34623961		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:51683069_51683072delTTTT								C1orf185 (69317 upstream) : RNF11 (18873 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	52038885	52038886	+	IGR	DEL	AA	-	-	rs5774102		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:52038885_52038886delAA								EPS15 (53890 upstream) : OSBPL9 (3965 downstream)																																			---	---	---	---
NRD1	4898	broad.mit.edu	37	1	52261563	52261563	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:52261563delA	uc001ctc.3	-						NRD1_uc009vzb.2_Intron|NRD1_uc001ctd.3_Intron|NRD1_uc001cte.2_Intron|NRD1_uc001ctf.2_Intron|NRD1_uc010ong.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																		---	---	---	---
Unknown	0	broad.mit.edu	37	1	52474054	52474055	+	IGR	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:52474054_52474055delAA								RAB3B (17706 upstream) : TXNDC12 (11752 downstream)																																			---	---	---	---
BTF3L4	91408	broad.mit.edu	37	1	52548724	52548724	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:52548724delA	uc001ctk.2	+						BTF3L4_uc001ctl.2_Intron|BTF3L4_uc010onh.1_Intron|BTF3L4_uc001ctm.2_Intron	NM_152265	NP_689478			basic transcription factor 3-like 4 isoform 1											large_intestine(1)	1																		---	---	---	---
ZCCHC11	23318	broad.mit.edu	37	1	52923972	52923972	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:52923972delA	uc001ctx.2	-						ZCCHC11_uc001cty.2_Intron|ZCCHC11_uc001ctz.2_Intron|ZCCHC11_uc009vze.1_Intron|ZCCHC11_uc009vzf.1_Intron|ZCCHC11_uc001cua.1_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	52956483	52956483	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:52956483delA	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																		---	---	---	---
ZCCHC11	23318	broad.mit.edu	37	1	52959246	52959248	+	Intron	DEL	AAA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:52959246_52959248delAAA	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																		---	---	---	---
Unknown	0	broad.mit.edu	37	1	53039570	53039570	+	IGR	DEL	A	-	-	rs113441580		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:53039570delA								ZCCHC11 (20440 upstream) : GPX7 (28473 downstream)																																			---	---	---	---
FAM159A	348378	broad.mit.edu	37	1	53129433	53129433	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:53129433delA	uc001cug.1	+						FAM159A_uc001cuh.2_Intron	NM_001042693				hypothetical protein LOC348378							integral to membrane					0																		---	---	---	---
Unknown	0	broad.mit.edu	37	1	53144101	53144101	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:53144101delA								FAM159A (8764 upstream) : C1orf163 (8413 downstream)																																			---	---	---	---
ZYG11B	79699	broad.mit.edu	37	1	53287007	53287007	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:53287007delA	uc001cuj.2	+						ZYG11B_uc010onj.1_Intron|ZYG11B_uc009vzh.2_Intron	NM_024646	NP_078922			zyg-11 homolog B								protein binding			upper_aerodigestive_tract(2)|ovary(1)|pancreas(1)	4																		---	---	---	---
LRP8	7804	broad.mit.edu	37	1	53770934	53770934	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:53770934delA	uc001cvi.1	-						LRP8_uc001cvh.1_Intron|LRP8_uc001cvk.1_Intron|LRP8_uc001cvj.1_Intron|LRP8_uc001cvl.1_Intron	NM_004631	NP_004622			low density lipoprotein receptor-related protein						cytokine-mediated signaling pathway|endocytosis|lipid metabolic process|platelet activation|proteolysis	caveola	calcium ion binding|very-low-density lipoprotein particle receptor activity				0																		---	---	---	---
GLIS1	148979	broad.mit.edu	37	1	54147582	54147582	+	Intron	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:54147582delG	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																		---	---	---	---
DIO1	1733	broad.mit.edu	37	1	54372336	54372336	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:54372336delT	uc010onx.1	+						DIO1_uc010onw.1_Intron|DIO1_uc009vzl.2_Intron|DIO1_uc001cwb.2_Intron|DIO1_uc010ony.1_Intron|DIO1_uc001cwd.2_Intron|DIO1_uc001cwe.2_Intron|DIO1_uc001cwf.2_Intron|DIO1_uc001cwg.2_Intron	NM_000792	NP_000783			deiodinase, iodothyronine, type I isoform a						hormone biosynthetic process|thyroid hormone generation	endoplasmic reticulum membrane|integral to membrane|plasma membrane	selenium binding|thyroxine 5'-deiodinase activity				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	1	54450310	54450311	+	IGR	INS	-	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:54450310_54450311insA								LRRC42 (16471 upstream) : LDLRAD1 (24195 downstream)																																			---	---	---	---
C1orf83	127428	broad.mit.edu	37	1	54519996	54519996	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:54519996delA	uc001cwt.1	+						C1orf83_uc001cwu.1_Intron|TMEM59_uc001cwp.2_5'Flank|TMEM59_uc001cwq.2_5'Flank|TMEM59_uc001cwr.2_5'Flank|TMEM59_uc001cws.1_5'Flank	NM_153035	NP_694580			hypothetical protein LOC127428						transcription, DNA-dependent	nucleus	DNA binding				0																		---	---	---	---
SSBP3	23648	broad.mit.edu	37	1	54816517	54816517	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:54816517delT	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																		---	---	---	---
SSBP3	23648	broad.mit.edu	37	1	54845615	54845615	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:54845615delT	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	54896993	54896993	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:54896993delT								SSBP3 (24901 upstream) : ACOT11 (110937 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	54990771	54990771	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:54990771delA								SSBP3 (118679 upstream) : ACOT11 (17159 downstream)																																			---	---	---	---
ACOT11	26027	broad.mit.edu	37	1	55070504	55070504	+	Intron	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:55070504delG	uc001cxm.1	+						ACOT11_uc001cxj.1_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																		---	---	---	---
C1orf177	163747	broad.mit.edu	37	1	55282852	55282852	+	Intron	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:55282852delG	uc001cyb.3	+						C1orf177_uc001cya.3_Intron	NM_001110533	NP_001104003			hypothetical protein LOC163747 isoform 2												0																		---	---	---	---
DHCR24	1718	broad.mit.edu	37	1	55325148	55325148	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:55325148delT	uc001cyc.1	-						DHCR24_uc010ooi.1_Intron|DHCR24_uc010ooj.1_Intron|DHCR24_uc010ook.1_Intron	NM_014762	NP_055577			24-dehydrocholesterol reductase precursor						anti-apoptosis|apoptosis|cell cycle arrest|cholesterol biosynthetic process|negative regulation of caspase activity|neuroprotection|response to oxidative stress|skin development	endoplasmic reticulum membrane|Golgi membrane|integral to membrane|nucleus	delta24-sterol reductase activity|enzyme binding|flavin adenine dinucleotide binding|peptide antigen binding			pancreas(1)	1																		---	---	---	---
USP24	23358	broad.mit.edu	37	1	55604597	55604597	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-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																		---	---	---	---
USP24	23358	broad.mit.edu	37	1	55632130	55632130	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:55632130delT	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	55685617	55685617	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:55685617delA								USP24 (4855 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	55852585	55852585	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:55852585delA								USP24 (171823 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	56211629	56211629	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:56211629delT								USP24 (530867 upstream) : PPAP2B (748804 downstream)																																			---	---	---	---
PPAP2B	8613	broad.mit.edu	37	1	56983832	56983833	+	Intron	INS	-	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:56983832_56983833insA	uc001cyj.1	-							NM_177414	NP_803133			phosphatidic acid phosphatase type 2B						canonical Wnt receptor signaling pathway involved in positive regulation of cell-cell adhesion|canonical Wnt receptor signaling pathway involved in positive regulation of endothelial cell migration|canonical Wnt receptor signaling pathway involved in positive regulation of wound healing|germ cell migration|homotypic cell-cell adhesion|negative regulation of protein phosphorylation|positive regulation of sequence-specific DNA binding transcription factor activity|protein stabilization|sphingolipid metabolic process	adherens junction|Golgi apparatus|integral to membrane	phosphatidate phosphatase activity|phosphoprotein phosphatase activity|protein binding|sphingosine-1-phosphate phosphatase activity				0																		---	---	---	---
PPAP2B	8613	broad.mit.edu	37	1	56989381	56989381	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:56989381delT	uc001cyj.1	-							NM_177414	NP_803133			phosphatidic acid phosphatase type 2B						canonical Wnt receptor signaling pathway involved in positive regulation of cell-cell adhesion|canonical Wnt receptor signaling pathway involved in positive regulation of endothelial cell migration|canonical Wnt receptor signaling pathway involved in positive regulation of wound healing|germ cell migration|homotypic cell-cell adhesion|negative regulation of protein phosphorylation|positive regulation of sequence-specific DNA binding transcription factor activity|protein stabilization|sphingolipid metabolic process	adherens junction|Golgi apparatus|integral to membrane	phosphatidate phosphatase activity|phosphoprotein phosphatase activity|protein binding|sphingosine-1-phosphate phosphatase activity				0																		---	---	---	---
DAB1	1600	broad.mit.edu	37	1	58160968	58160971	+	Intron	DEL	GAAG	-	-	rs7553249		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:58160968_58160971delGAAG	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	58281342	58281343	+	Intron	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:58281342_58281343delAA	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	58325854	58325854	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:58325854delA	uc001cys.1	-						DAB1_uc001cyt.1_Intron|uc001cyu.1_5'Flank|uc001cyv.1_5'Flank	NM_021080	NP_066566			disabled homolog 1						cell differentiation|nervous system development					skin(2)|ovary(1)	3																		---	---	---	---
DAB1	1600	broad.mit.edu	37	1	58861808	58861808	+	Intron	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:58861808delG	uc001cyt.1	-							NM_021080	NP_066566			disabled homolog 1						cell differentiation|nervous system development					skin(2)|ovary(1)	3																		---	---	---	---
DAB1	1600	broad.mit.edu	37	1	58971951	58971951	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:58971951delT	uc001cyt.1	-						OMA1_uc001cyx.1_Intron|OMA1_uc001cyy.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	59309480	59309480	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:59309480delT	uc001czf.2	+						uc010oop.1_Intron					Homo sapiens cDNA FLJ30588 fis, clone BRAWH2008128.																														---	---	---	---
Unknown	0	broad.mit.edu	37	1	59423309	59423309	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:59423309delT								JUN (173524 upstream) : LOC729467 (174301 downstream)																																			---	---	---	---
FGGY	55277	broad.mit.edu	37	1	59792395	59792395	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:59792395delT	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	59819772	59819773	+	Intron	INS	-	AC	AC	rs72500925		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:59819772_59819773insAC	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	60344051	60344051	+	IGR	DEL	T	-	-	rs78657747		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:60344051delT								HOOK1 (2002 upstream) : CYP2J2 (14930 downstream)																																			---	---	---	---
C1orf87	127795	broad.mit.edu	37	1	60490037	60490037	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:60490037delT	uc001czs.1	-							NM_152377	NP_689590			hypothetical protein LOC127795								calcium ion binding			ovary(1)|breast(1)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	1	60619083	60619084	+	IGR	DEL	AA	-	-	rs77617843		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:60619083_60619084delAA								C1orf87 (79657 upstream) : NFIA (923862 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	60666444	60666445	+	IGR	DEL	AT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:60666444_60666445delAT								C1orf87 (127018 upstream) : NFIA (876501 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	60695025	60695025	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:60695025delA								C1orf87 (155599 upstream) : NFIA (847921 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	61144512	61144513	+	Intron	DEL	AC	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:61144512_61144513delAC	uc001czt.1	-											Homo sapiens cDNA FLJ39874 fis, clone SPLEN2015815.																														---	---	---	---
Unknown	0	broad.mit.edu	37	1	61372520	61372522	+	IGR	DEL	AAA	-	-	rs71823856		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:61372520_61372522delAAA								C1orf87 (833094 upstream) : NFIA (170424 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	61464072	61464073	+	IGR	DEL	AG	-	-	rs144234113		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:61464072_61464073delAG								C1orf87 (924646 upstream) : NFIA (78873 downstream)																																			---	---	---	---
NFIA	4774	broad.mit.edu	37	1	61540514	61540514	+	5'Flank	DEL	A	-	-	rs80140085		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:61540514delA	uc001czy.2	+							NM_001145511	NP_001138983			nuclear factor I/A isoform 3						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	61623092	61623093	+	Intron	INS	-	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:61623092_61623093insA	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	61906338	61906338	+	Intron	DEL	T	-	-	rs72060162		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:61906338delT	uc001czw.2	+						NFIA_uc001czy.2_Intron|NFIA_uc010oos.1_Intron|NFIA_uc001czv.2_Intron|NFIA_uc001czx.2_Intron|NFIA_uc009wae.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	62234929	62234929	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:62234929delT	uc001dab.2	+						INADL_uc009waf.1_Intron|INADL_uc001daa.2_Intron|INADL_uc001dad.3_5'Flank	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	62441128	62441128	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:62441128delT	uc001dab.2	+						INADL_uc009waf.1_Intron|INADL_uc001daa.2_Intron|INADL_uc001dad.3_Intron|INADL_uc001dac.2_Intron|INADL_uc010oot.1_Intron|INADL_uc009wag.2_Intron|INADL_uc010oou.1_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	62478997	62478997	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:62478997delT	uc001dab.2	+						INADL_uc009waf.1_Intron|INADL_uc001daa.2_Intron|INADL_uc001dad.3_Intron|INADL_uc001dac.2_Intron|INADL_uc010oot.1_Intron|INADL_uc009wag.2_Intron|INADL_uc010oou.1_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	62631411	62631412	+	Intron	INS	-	TG	TG	rs149000891	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:62631411_62631412insTG	uc009wag.2	+							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																		---	---	---	---
KANK4	163782	broad.mit.edu	37	1	62777079	62777079	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:62777079delA	uc001dah.3	-						KANK4_uc001dai.3_Intron	NM_181712	NP_859063			ankyrin repeat domain 38											ovary(3)|skin(2)|lung(1)	6																		---	---	---	---
DOCK7	85440	broad.mit.edu	37	1	62941104	62941104	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-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																		---	---	---	---
Unknown	0	broad.mit.edu	37	1	63349315	63349315	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:63349315delT								ATG4C (19266 upstream) : FOXD3 (439415 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	63761163	63761164	+	Intron	DEL	CA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:63761163_63761164delCA	uc001daw.1	-											Homo sapiens cDNA clone IMAGE:4838722.																														---	---	---	---
EFCAB7	84455	broad.mit.edu	37	1	64015237	64015237	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:64015237delA	uc001dbf.2	+						DLEU2L_uc001dbg.1_RNA	NM_032437	NP_115813			EF-hand calcium binding domain 7								calcium ion binding				0																		---	---	---	---
EFCAB7	84455	broad.mit.edu	37	1	64017378	64017378	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:64017378delT	uc001dbf.2	+							NM_032437	NP_115813			EF-hand calcium binding domain 7								calcium ion binding				0																		---	---	---	---
PGM1	5236	broad.mit.edu	37	1	64061518	64061519	+	Intron	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:64061518_64061519delAA	uc001dbh.2	+						PGM1_uc010ooy.1_Intron	NM_002633	NP_002624			phosphoglucomutase 1						cellular calcium ion homeostasis|galactose catabolic process|glucose 1-phosphate metabolic process|glycogen biosynthetic process|glycogen catabolic process	cytosol	magnesium ion binding|phosphoglucomutase activity			ovary(2)|kidney(1)	3																		---	---	---	---
Unknown	0	broad.mit.edu	37	1	64789971	64789971	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:64789971delT								UBE2U (79944 upstream) : CACHD1 (146505 downstream)																																			---	---	---	---
CACHD1	57685	broad.mit.edu	37	1	65151238	65151238	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:65151238delT	uc001dbo.1	+						CACHD1_uc001dbp.1_Intron|CACHD1_uc001dbq.1_Intron|CACHD1_uc010opa.1_Intron	NM_020925	NP_065976			cache domain containing 1						calcium ion transport	integral to membrane				ovary(2)	2																		---	---	---	---
JAK1	3716	broad.mit.edu	37	1	65421548	65421548	+	Intron	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:65421548delG	uc001dbu.1	-						JAK1_uc009wam.1_Intron	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								---	---	---	---
LEPR	3953	broad.mit.edu	37	1	65906125	65906125	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:65906125delA	uc001dci.2	+						LEPR_uc001dcg.2_Intron|LEPR_uc001dch.2_Intron|LEPR_uc009waq.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)														---	---	---	---
PDE4B	5142	broad.mit.edu	37	1	66369103	66369104	+	Intron	DEL	CA	-	-	rs67594381		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:66369103_66369104delCA	uc001dcn.2	+						PDE4B_uc009war.2_Intron|PDE4B_uc001dco.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)													---	---	---	---
PDE4B	5142	broad.mit.edu	37	1	66584400	66584400	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:66584400delA	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)													---	---	---	---
PDE4B	5142	broad.mit.edu	37	1	66589267	66589267	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:66589267delT	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)													---	---	---	---
PDE4B	5142	broad.mit.edu	37	1	66720942	66720942	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:66720942delT	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)													---	---	---	---
PDE4B	5142	broad.mit.edu	37	1	66834325	66834325	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:66834325delT	uc001dcn.2	+						PDE4B_uc009war.2_Intron|PDE4B_uc001dco.2_Intron|PDE4B_uc001dcp.2_Intron|PDE4B_uc001dcq.2_Intron|PDE4B_uc009was.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)													---	---	---	---
SGIP1	84251	broad.mit.edu	37	1	67099769	67099769	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:67099769delA	uc001dcr.2	+							NM_032291	NP_115667			SH3-domain GRB2-like (endophilin) interacting						positive regulation of energy homeostasis|positive regulation of feeding behavior|positive regulation of receptor-mediated endocytosis|response to dietary excess	AP-2 adaptor complex	microtubule binding|phospholipid binding|SH3 domain binding			ovary(3)	3																		---	---	---	---
SGIP1	84251	broad.mit.edu	37	1	67147679	67147679	+	Frame_Shift_Del	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:67147679delT	uc001dcr.2	+	15	1159	c.942delT	c.(940-942)CATfs	p.H314fs	SGIP1_uc010opd.1_Intron|SGIP1_uc001dcs.2_Intron|SGIP1_uc001dct.2_Intron|SGIP1_uc009wat.2_Frame_Shift_Del_p.H81fs	NM_032291	NP_115667	Q9BQI5	SGIP1_HUMAN	SH3-domain GRB2-like (endophilin) interacting	314	Pro-rich.				positive regulation of energy homeostasis|positive regulation of feeding behavior|positive regulation of receptor-mediated endocytosis|response to dietary excess	AP-2 adaptor complex	microtubule binding|phospholipid binding|SH3 domain binding			ovary(3)	3																		---	---	---	---
MIER1	57708	broad.mit.edu	37	1	67425196	67425196	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:67425196delT	uc001dde.2	+						MIER1_uc010opf.1_Intron|MIER1_uc009way.2_Intron|MIER1_uc001ddc.2_Intron|MIER1_uc001ddh.2_Intron|MIER1_uc001ddf.2_Intron|MIER1_uc001ddg.2_Intron|MIER1_uc010opg.1_Intron|MIER1_uc001ddj.1_Intron|MIER1_uc001ddi.2_Intron	NM_001077700	NP_001071168			mesoderm induction early response 1 isoform b						positive regulation of I-kappaB kinase/NF-kappaB cascade|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	DNA binding|signal transducer activity			ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	1	68058344	68058344	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:68058344delA								SERBP1 (162221 upstream) : GADD45A (92539 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	68068049	68068049	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:68068049delA								SERBP1 (171926 upstream) : GADD45A (82834 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	68069632	68069632	+	IGR	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:68069632delG								SERBP1 (173509 upstream) : GADD45A (81251 downstream)																																			---	---	---	---
GNG12	55970	broad.mit.edu	37	1	68180640	68180640	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:68180640delT	uc001dea.1	-							NM_018841	NP_061329			G-protein gamma-12 subunit precursor						cellular response to glucagon stimulus|energy reserve metabolic process|G-protein coupled receptor protein signaling pathway|synaptic transmission	heterotrimeric G-protein complex	signal transducer activity				0																		---	---	---	---
GNG12	55970	broad.mit.edu	37	1	68223665	68223665	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:68223665delT	uc001dea.1	-							NM_018841	NP_061329			G-protein gamma-12 subunit precursor						cellular response to glucagon stimulus|energy reserve metabolic process|G-protein coupled receptor protein signaling pathway|synaptic transmission	heterotrimeric G-protein complex	signal transducer activity				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	1	68352140	68352140	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:68352140delA	uc001deb.1	+						uc001dec.1_Intron					Homo sapiens cDNA FLJ38762 fis, clone KIDNE2013801.																														---	---	---	---
Unknown	0	broad.mit.edu	37	1	68442772	68442772	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:68442772delT	uc001deb.1	+						uc001dec.1_Intron					Homo sapiens cDNA FLJ38762 fis, clone KIDNE2013801.																														---	---	---	---
Unknown	0	broad.mit.edu	37	1	68818649	68818649	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:68818649delT								WLS (120396 upstream) : RPE65 (75858 downstream)																																			---	---	---	---
RPE65	6121	broad.mit.edu	37	1	68905368	68905368	+	Intron	DEL	T	-	-	rs61752894		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:68905368delT	uc001dei.1	-							NM_000329	NP_000320			retinal pigment epithelium-specific protein						visual perception	cytoplasm|plasma membrane	all-trans-retinyl-palmitate hydrolase activity|metal ion binding|retinol isomerase activity			ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	1	69333002	69333002	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:69333002delT								DEPDC1 (370203 upstream) : LRRC7 (699866 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	69772869	69772869	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:69772869delT								DEPDC1 (810070 upstream) : LRRC7 (259999 downstream)																																			---	---	---	---
LRRC7	57554	broad.mit.edu	37	1	70089119	70089119	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:70089119delA	uc001deo.1	+											SubName: Full=Leucine rich repeat containing 7; SubName: Full=cDNA FLJ54846, highly similar to Leucine-rich repeat-containing protein 7;							centrosome|focal adhesion|nucleolus	protein binding			ovary(9)|breast(2)|central_nervous_system(2)|liver(1)	14																		---	---	---	---
LRRC7	57554	broad.mit.edu	37	1	70150432	70150432	+	Intron	DEL	A	-	-	rs60828658	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:70150432delA	uc001deo.1	+											SubName: Full=Leucine rich repeat containing 7; SubName: Full=cDNA FLJ54846, highly similar to Leucine-rich repeat-containing protein 7;							centrosome|focal adhesion|nucleolus	protein binding			ovary(9)|breast(2)|central_nervous_system(2)|liver(1)	14																		---	---	---	---
LRRC7	57554	broad.mit.edu	37	1	70443050	70443050	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:70443050delA	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																		---	---	---	---
LRRC7	57554	broad.mit.edu	37	1	70506991	70506991	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:70506991delT	uc001dep.2	+						LRRC7_uc009wbg.2_Intron|LRRC7_uc001deq.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	70652301	70652301	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:70652301delT	uc001der.1	-							NM_017768	NP_060238			leucine rich repeat containing 40											ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	1	73764767	73764767	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:73764767delA								None (None upstream) : LRRIQ3 (726937 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	74483422	74483423	+	IGR	INS	-	TGTG	TGTG	rs143424922	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:74483422_74483423insTGTG								None (None upstream) : LRRIQ3 (8281 downstream)																																			---	---	---	---
LHX8	431707	broad.mit.edu	37	1	75606525	75606525	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:75606525delA	uc001dgo.2	+						LHX8_uc001dgq.2_Intron	NM_001001933	NP_001001933			LIM homeobox 8							nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(3)	3																		---	---	---	---
MSH4	4438	broad.mit.edu	37	1	76288497	76288497	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:76288497delT	uc001dhd.1	+							NM_002440	NP_002431			mutS homolog 4						chiasma assembly|homologous chromosome segregation|mismatch repair|reciprocal meiotic recombination	synaptonemal complex	ATP binding|DNA-dependent ATPase activity|mismatched DNA binding			lung(3)|ovary(2)	5													MMR					---	---	---	---
ST6GALNAC3	256435	broad.mit.edu	37	1	76893068	76893068	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:76893068delT	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																		---	---	---	---
ST6GALNAC3	256435	broad.mit.edu	37	1	76929407	76929407	+	Intron	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:76929407delG	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																		---	---	---	---
ST6GALNAC3	256435	broad.mit.edu	37	1	76947825	76947826	+	Intron	DEL	AC	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:76947825_76947826delAC	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	77163532	77163532	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:77163532delT								ST6GALNAC3 (66863 upstream) : ST6GALNAC5 (169654 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	77546947	77546947	+	IGR	DEL	T	-	-	rs68028325		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:77546947delT								ST6GALNAC5 (15555 upstream) : PIGK (7722 downstream)																																			---	---	---	---
AK5	26289	broad.mit.edu	37	1	77922329	77922329	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:77922329delA	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																		---	---	---	---
ZZZ3	26009	broad.mit.edu	37	1	78042935	78042935	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:78042935delA	uc001dhq.2	-						ZZZ3_uc001dhr.2_Intron|ZZZ3_uc001dhp.2_Intron	NM_015534	NP_056349			zinc finger, ZZ-type containing 3						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(4)|large_intestine(1)	5																		---	---	---	---
ZZZ3	26009	broad.mit.edu	37	1	78068770	78068770	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:78068770delT	uc001dhq.2	-						ZZZ3_uc001dhr.2_Intron|ZZZ3_uc009wbz.1_Intron|ZZZ3_uc001dhp.2_Intron	NM_015534	NP_056349			zinc finger, ZZ-type containing 3						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(4)|large_intestine(1)	5																		---	---	---	---
ZZZ3	26009	broad.mit.edu	37	1	78147585	78147585	+	Intron	DEL	A	-	-	rs71994522		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:78147585delA	uc001dhq.2	-						ZZZ3_uc001dhr.2_Intron|ZZZ3_uc009wbz.1_Intron	NM_015534	NP_056349			zinc finger, ZZ-type containing 3						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(4)|large_intestine(1)	5																		---	---	---	---
FUBP1	8880	broad.mit.edu	37	1	78432648	78432648	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:78432648delA	uc001dii.2	-						FUBP1_uc001dih.3_Intron|FUBP1_uc010orm.1_Intron	NM_003902	NP_003893			far upstream element-binding protein						transcription from RNA polymerase II promoter	nucleus	protein binding|RNA binding|sequence-specific DNA binding transcription factor activity|single-stranded DNA binding			central_nervous_system(2)|lung(1)	3																		---	---	---	---
GIPC2	54810	broad.mit.edu	37	1	78560481	78560481	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:78560481delT	uc001dik.2	+							NM_017655	NP_060125			PDZ domain protein GIPC2							cytoplasm				ovary(1)	1																		---	---	---	---
MGC27382	149047	broad.mit.edu	37	1	78741344	78741345	+	Intron	INS	-	CCA	CCA	rs144243279	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:78741344_78741345insCCA	uc001dil.1	+						MGC27382_uc009wcc.2_Intron					Homo sapiens cDNA FLJ34438 fis, clone HLUNG2001144.												0																		---	---	---	---
ELTD1	64123	broad.mit.edu	37	1	79387475	79387475	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:79387475delA	uc001diq.3	-							NM_022159	NP_071442			EGF, latrophilin and seven transmembrane domain						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)														---	---	---	---
ELTD1	64123	broad.mit.edu	37	1	79474510	79474511	+	5'Flank	INS	-	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:79474510_79474511insA	uc001diq.3	-							NM_022159	NP_071442			EGF, latrophilin and seven transmembrane domain						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)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	79532480	79532480	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:79532480delA								ELTD1 (59985 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	79582584	79582584	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:79582584delA								ELTD1 (110089 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	79835468	79835468	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:79835468delT								ELTD1 (362973 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	80110844	80110844	+	IGR	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:80110844delC								ELTD1 (638349 upstream) : None (None downstream)																																			---	---	---	---
LPHN2	23266	broad.mit.edu	37	1	81865173	81865173	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:81865173delT	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	82208706	82208706	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:82208706delT	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	82241270	82241274	+	Intron	DEL	AAAAA	-	-	rs10874269	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:82241270_82241274delAAAAA	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	82245114	82245114	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:82245114delA	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	82946915	82946915	+	IGR	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:82946915delG								LPHN2 (488809 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	83163029	83163030	+	IGR	INS	-	GTGTGT	GTGTGT			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:83163029_83163030insGTGTGT								LPHN2 (704923 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	83303777	83303778	+	IGR	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:83303777_83303778delTT								LPHN2 (845671 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	83815960	83815960	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:83815960delT								None (None upstream) : TTLL7 (519099 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	84105578	84105579	+	Intron	DEL	AG	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:84105578_84105579delAG	uc001diz.3	-											Homo sapiens cDNA clone IMAGE:4815396.																														---	---	---	---
Unknown	0	broad.mit.edu	37	1	84259638	84259638	+	Intron	DEL	A	-	-	rs111685871		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:84259638delA	uc001diz.3	-											Homo sapiens cDNA clone IMAGE:4815396.																														---	---	---	---
Unknown	0	broad.mit.edu	37	1	84709900	84709900	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:84709900delA								PRKACB (5721 upstream) : SAMD13 (54149 downstream)																																			---	---	---	---
SAMD13	148418	broad.mit.edu	37	1	84769113	84769114	+	Intron	INS	-	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:84769113_84769114insC	uc001djr.2	+						SAMD13_uc010orw.1_Intron|SAMD13_uc010orx.1_Intron	NM_001010971	NP_001010971			sterile alpha motif domain containing 13 isoform												0				all cancers(265;0.00667)|Epithelial(280;0.0219)|OV - Ovarian serous cystadenocarcinoma(397;0.136)														---	---	---	---
SAMD13	148418	broad.mit.edu	37	1	84809762	84809762	+	5'Flank	DEL	T	-	-	rs113728574		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:84809762delT	uc001djs.2	+						SAMD13_uc001djr.2_Intron|SAMD13_uc010orw.1_Intron|SAMD13_uc010orx.1_Intron					SubName: Full=HSD-41;												0				all cancers(265;0.00667)|Epithelial(280;0.0219)|OV - Ovarian serous cystadenocarcinoma(397;0.136)														---	---	---	---
CTBS	1486	broad.mit.edu	37	1	85020568	85020568	+	3'UTR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:85020568delT	uc001dka.2	-	7					SPATA1_uc001djz.1_Intron|CTBS_uc001dkc.2_3'UTR|CTBS_uc001dkd.2_3'UTR|CTBS_uc001dkb.2_3'UTR	NM_004388	NP_004379			chitobiase, di-N-acetyl- precursor							lysosome	cation binding				0				all cancers(265;0.00727)|Epithelial(280;0.0192)|OV - Ovarian serous cystadenocarcinoma(397;0.166)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	85226936	85226938	+	IGR	DEL	AAC	-	-	rs67769172		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:85226936_85226938delAAC								SSX2IP (70496 upstream) : LPAR3 (52148 downstream)																																			---	---	---	---
SYDE2	84144	broad.mit.edu	37	1	85624415	85624415	+	3'UTR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:85624415delA	uc009wcm.2	-	7						NM_032184	NP_115560			synapse defective 1, Rho GTPase, homolog 2						activation of Rho GTPase activity|small GTPase mediated signal transduction	cytosol	Rho GTPase activator activity			ovary(1)|central_nervous_system(1)	2				all cancers(265;0.0126)|Epithelial(280;0.0336)														---	---	---	---
BCL10	8915	broad.mit.edu	37	1	85741445	85741445	+	Intron	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:85741445delC	uc001dkz.2	-						uc001dla.1_5'Flank	NM_003921	NP_003912			B-cell CLL/lymphoma 10						apoptosis|cellular response to mechanical stimulus|innate immune response|interleukin-6 biosynthetic process|lymphotoxin A biosynthetic process|negative regulation of mature B cell apoptosis|neural tube closure|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of interleukin-8 biosynthetic process|positive regulation of mast cell cytokine production|positive regulation of NF-kappaB transcription factor activity|positive regulation of phosphorylation|positive regulation of protein ubiquitination|positive regulation of transcription, DNA-dependent|protein homooligomerization|response to molecule of bacterial origin|T cell receptor signaling pathway	CBM complex|cytosol|lysosome|membrane raft|nucleus|perinuclear region of cytoplasm	NF-kappaB binding|protease binding|protein C-terminus binding|protein kinase B binding|protein self-association|transcription coactivator activity|ubiquitin binding|ubiquitin protein ligase binding			lung(2)	2				all cancers(265;0.0114)|Epithelial(280;0.0311)				T	IGH@	MALT 								---	---	---	---
COL24A1	255631	broad.mit.edu	37	1	86488565	86488565	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:86488565delA	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)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	86692260	86692261	+	IGR	INS	-	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:86692260_86692261insT								COL24A1 (69814 upstream) : ODF2L (122151 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	86695603	86695603	+	IGR	DEL	T	-	-	rs67242862		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:86695603delT								COL24A1 (73157 upstream) : ODF2L (118809 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	86775670	86775670	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:86775670delA								COL24A1 (153224 upstream) : ODF2L (38742 downstream)																																			---	---	---	---
ODF2L	57489	broad.mit.edu	37	1	86820550	86820550	+	Intron	DEL	A	-	-	rs76785175		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:86820550delA	uc001dll.1	-						ODF2L_uc001dlm.1_Intron|ODF2L_uc001dln.2_Intron|ODF2L_uc001dlo.2_Intron|ODF2L_uc001dlp.2_Intron|ODF2L_uc010osg.1_Intron	NM_020729	NP_065780			outer dense fiber of sperm tails 2-like isoform							centrosome				ovary(1)	1				all cancers(265;0.0313)|Epithelial(280;0.0611)														---	---	---	---
CLCA2	9635	broad.mit.edu	37	1	86916592	86916592	+	Intron	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:86916592delG	uc001dlr.3	+							NM_006536	NP_006527			chloride channel accessory 2 precursor						cell adhesion	basal plasma membrane|cell junction|extracellular region|integral to plasma membrane	chloride channel activity			ovary(1)|breast(1)|skin(1)	3		Lung NSC(277;0.238)		all cancers(265;0.0233)|Epithelial(280;0.0452)														---	---	---	---
CLCA1	1179	broad.mit.edu	37	1	86953113	86953114	+	Intron	DEL	GT	-	-	rs1321693	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:86953113_86953114delGT	uc001dlt.2	+						CLCA1_uc001dls.1_Intron	NM_001285	NP_001276			chloride channel accessory 1 precursor						calcium ion transport	extracellular space|integral to plasma membrane	chloride channel activity			ovary(1)	1		Lung NSC(277;0.239)		all cancers(265;0.0249)|Epithelial(280;0.0476)														---	---	---	---
CLCA1	1179	broad.mit.edu	37	1	86965770	86965770	+	3'UTR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:86965770delT	uc001dlt.2	+	14						NM_001285	NP_001276			chloride channel accessory 1 precursor						calcium ion transport	extracellular space|integral to plasma membrane	chloride channel activity			ovary(1)	1		Lung NSC(277;0.239)		all cancers(265;0.0249)|Epithelial(280;0.0476)														---	---	---	---
CLCA4	22802	broad.mit.edu	37	1	87043983	87043983	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:87043983delT	uc009wcs.2	+						CLCA4_uc009wct.2_Intron|CLCA4_uc009wcu.2_Intron	NM_012128	NP_036260			chloride channel accessory 4							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)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	87144764	87144764	+	IGR	DEL	T	-	-	rs71862397		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:87144764delT								CLCA3P (23706 upstream) : SH3GLB1 (25493 downstream)																																			---	---	---	---
HS2ST1	9653	broad.mit.edu	37	1	87570130	87570130	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:87570130delT	uc010osk.1	+						LOC339524_uc001dme.1_Intron	NM_012262	NP_036394			heparan sulfate 2-O-sulfotransferase 1 isoform							Golgi membrane|integral to membrane				central_nervous_system(1)	1		Lung NSC(277;0.153)		all cancers(265;0.00699)|Epithelial(280;0.0261)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	87985549	87985550	+	IGR	INS	-	TG	TG			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:87985549_87985550insTG								LMO4 (170946 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	88922642	88922642	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:88922642delT								None (None upstream) : PKN2 (227280 downstream)																																			---	---	---	---
PKN2	5586	broad.mit.edu	37	1	89240305	89240305	+	Intron	DEL	T	-	-	rs12061887	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:89240305delT	uc001dmn.2	+						PKN2_uc001dmm.1_Intron|PKN2_uc010osp.1_Intron|PKN2_uc010osq.1_Intron|PKN2_uc009wcv.2_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	89272841	89272841	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:89272841delA	uc001dmn.2	+						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)														---	---	---	---
GTF2B	2959	broad.mit.edu	37	1	89331544	89331545	+	Intron	INS	-	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:89331544_89331545insA	uc001dmo.3	-						GTF2B_uc009wcw.1_Intron	NM_001514	NP_001505			general transcription factor IIB						interspecies interaction between organisms|regulation of transcription, DNA-dependent|transcription elongation from RNA polymerase II promoter|transcription initiation from RNA polymerase II promoter|viral reproduction	nucleoplasm	thyroid hormone receptor binding|translation initiation factor activity|zinc ion binding			large_intestine(1)|ovary(1)	2		Lung NSC(277;0.123)		all cancers(265;0.0131)|Epithelial(280;0.0255)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	89755803	89755803	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:89755803delT								GBP5 (17259 upstream) : GBP6 (73633 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	90764098	90764098	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:90764098delT								ZNF326 (270004 upstream) : BARHL2 (413482 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	91135139	91135139	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:91135139delA								ZNF326 (641045 upstream) : BARHL2 (42441 downstream)																																			---	---	---	---
ZNF644	84146	broad.mit.edu	37	1	91448053	91448053	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:91448053delA	uc001dnw.2	-						ZNF644_uc001dnv.2_Intron|ZNF644_uc001dnx.2_Intron|ZNF644_uc001dny.1_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)														---	---	---	---
HFM1	164045	broad.mit.edu	37	1	91829750	91829750	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:91829750delA	uc001doa.3	-						HFM1_uc010osu.1_Intron|HFM1_uc010osv.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	91883726	91883726	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:91883726delT								HFM1 (13300 upstream) : CDC7 (82678 downstream)																																			---	---	---	---
TGFBR3	7049	broad.mit.edu	37	1	92267927	92267927	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:92267927delT	uc001doh.2	-						TGFBR3_uc009wde.2_Intron|TGFBR3_uc010osy.1_Intron|TGFBR3_uc001doi.2_Intron|TGFBR3_uc001doj.2_Intron	NM_003243	NP_003234			transforming growth factor, beta receptor III						BMP signaling pathway|cardiac epithelial to mesenchymal transition|cardiac muscle cell proliferation|cell growth|cell migration|definitive erythrocyte differentiation|heart trabecula formation|immune response|intracellular protein kinase cascade|liver development|negative regulation of cellular component movement|negative regulation of epithelial cell proliferation|palate development|pathway-restricted SMAD protein phosphorylation|response to follicle-stimulating hormone stimulus|response to luteinizing hormone stimulus|response to prostaglandin E stimulus|transforming growth factor beta receptor signaling pathway|ventricular cardiac muscle tissue morphogenesis	external side of plasma membrane|extracellular space|inhibin-betaglycan-ActRII complex|integral to plasma membrane|intracellular membrane-bounded organelle	coreceptor activity|heparin binding|PDZ domain binding|SMAD binding|transforming growth factor beta binding|transforming growth factor beta receptor activity, type III|type II transforming growth factor beta receptor binding			ovary(3)	3		all_lung(203;0.00719)|Lung NSC(277;0.0268)		all cancers(265;0.0108)|Epithelial(280;0.0825)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	92377749	92377749	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:92377749delA								TGFBR3 (6190 upstream) : BRDT (37179 downstream)																																			---	---	---	---
EPHX4	253152	broad.mit.edu	37	1	92510850	92510851	+	Intron	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:92510850_92510851delTT	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	92568324	92568324	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:92568324delT	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	92618218	92618218	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:92618218delT								BTBD8 (4823 upstream) : KIAA1107 (14391 downstream)																																			---	---	---	---
KIAA1107	23285	broad.mit.edu	37	1	92642576	92642576	+	Frame_Shift_Del	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:92642576delA	uc010otd.1	+	5	610	c.512delA	c.(511-513)GAAfs	p.E171fs	KIAA1107_uc001dop.2_Frame_Shift_Del_p.E96fs	NM_015237	NP_056052	Q9UPP5	K1107_HUMAN	hypothetical protein LOC23285	226											0																		---	---	---	---
RPAP2	79871	broad.mit.edu	37	1	92765881	92765882	+	Intron	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:92765881_92765882delTT	uc001dot.2	+						RPAP2_uc009wdh.2_Intron|GLMN_uc001dor.2_5'Flank|GLMN_uc009wdg.2_5'Flank|GLMN_uc001dos.2_5'Flank	NM_024813	NP_079089			RNA polymerase II associated protein 2							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)														---	---	---	---
RPAP2	79871	broad.mit.edu	37	1	92823094	92823094	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:92823094delT	uc001dot.2	+						RPAP2_uc009wdh.2_Intron	NM_024813	NP_079089			RNA polymerase II associated protein 2							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)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	93501600	93501600	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:93501600delT								FAM69A (74521 upstream) : MTF2 (43192 downstream)																																			---	---	---	---
MTF2	22823	broad.mit.edu	37	1	93553499	93553499	+	Intron	DEL	T	-	-	rs66667421		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:93553499delT	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	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)														---	---	---	---
MTF2	22823	broad.mit.edu	37	1	93556586	93556586	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:93556586delT	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	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)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	93794271	93794271	+	Intron	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:93794271delG	uc001dps.2	-						uc001dpt.1_Intron					Homo sapiens cDNA FLJ42965 fis, clone BRSTN2014751.																														---	---	---	---
Unknown	0	broad.mit.edu	37	1	93896397	93896398	+	IGR	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:93896397_93896398delTT								DR1 (68251 upstream) : FNBP1L (17441 downstream)																																			---	---	---	---
BCAR3	8412	broad.mit.edu	37	1	94123285	94123286	+	Intron	DEL	AA	-	-	rs35976570		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:94123285_94123286delAA	uc001dpz.2	-						BCAR3_uc001dqa.2_Intron|BCAR3_uc001dqb.2_Intron	NM_003567	NP_003558			breast cancer antiestrogen resistance 3						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)														---	---	---	---
GCLM	2730	broad.mit.edu	37	1	94356436	94356438	+	Intron	DEL	TTT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:94356436_94356438delTTT	uc001dqg.1	-							NM_002061	NP_002052			glutamate-cysteine ligase regulatory protein						glutamate metabolic process|glutathione biosynthetic process|regulation of blood vessel size|response to drug|response to oxidative stress|xenobiotic metabolic process	cytosol|soluble fraction	glutamate-cysteine ligase catalytic subunit binding			ovary(1)	1		all_lung(203;0.000815)|Lung NSC(277;0.00363)		all cancers(265;0.00566)|GBM - Glioblastoma multiforme(16;0.0203)|Epithelial(280;0.131)	L-Cysteine(DB00151)|L-Glutamic Acid(DB00142)													---	---	---	---
Unknown	0	broad.mit.edu	37	1	94416750	94416751	+	IGR	DEL	GA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:94416750_94416751delGA								GCLM (41738 upstream) : ABCA4 (41645 downstream)																																			---	---	---	---
ARHGAP29	9411	broad.mit.edu	37	1	94643144	94643144	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-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)														---	---	---	---
ABCD3	5825	broad.mit.edu	37	1	94892104	94892105	+	Intron	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:94892104_94892105delTT	uc001dqn.3	+						ABCD3_uc001dqm.3_Intron|ABCD3_uc010oto.1_Intron|ABCD3_uc010otp.1_Intron|ABCD3_uc009wdr.2_Intron	NM_002858	NP_002849			ATP-binding cassette, sub-family D, member 3						peroxisomal long-chain fatty acid import|peroxisome organization	cytosol|integral to peroxisomal membrane	ATP binding|ATPase activity, coupled to transmembrane movement of substances			skin(1)	1		all_lung(203;0.000434)|Lung NSC(277;0.0019)		all cancers(265;0.0261)|Epithelial(280;0.165)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	96554880	96554880	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:96554880delT								RWDD3 (842107 upstream) : PTBP2 (632295 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	96634993	96634994	+	IGR	INS	-	G	G	rs1146557	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:96634993_96634994insG								RWDD3 (922220 upstream) : PTBP2 (552181 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	96637693	96637693	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:96637693delA								RWDD3 (924920 upstream) : PTBP2 (549482 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	96673448	96673448	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:96673448delT								RWDD3 (960675 upstream) : PTBP2 (513727 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	96693100	96693100	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:96693100delT								RWDD3 (980327 upstream) : PTBP2 (494075 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	96921077	96921077	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:96921077delT								None (None upstream) : PTBP2 (266098 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	96952511	96952511	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:96952511delT								None (None upstream) : PTBP2 (234664 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	97043717	97043718	+	IGR	INS	-	A	A	rs138656744	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:97043717_97043718insA								None (None upstream) : PTBP2 (143457 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	97110151	97110152	+	IGR	INS	-	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:97110151_97110152insA								None (None upstream) : PTBP2 (77023 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	97282806	97282806	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:97282806delT								PTBP2 (2207 upstream) : DPYD (260496 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	97385024	97385024	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:97385024delT								PTBP2 (104425 upstream) : DPYD (158278 downstream)																																			---	---	---	---
DPYD	1806	broad.mit.edu	37	1	97727534	97727534	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:97727534delT	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	97913403	97913403	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:97913403delT	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	98157419	98157419	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:98157419delA	uc001drv.2	-						DPYD_uc010oub.1_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)													---	---	---	---
DPYD	1806	broad.mit.edu	37	1	98362169	98362169	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:98362169delT	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)													---	---	---	---
Unknown	0	broad.mit.edu	37	1	99022218	99022218	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:99022218delA								MIR137 (510491 upstream) : SNX7 (105018 downstream)																																			---	---	---	---
LPPR4	9890	broad.mit.edu	37	1	99773807	99773807	+	3'UTR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:99773807delA	uc001dse.2	+	7					LPPR4_uc010oue.1_3'UTR	NM_014839	NP_055654			plasticity related gene 1								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)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	100101986	100101987	+	IGR	DEL	AA	-	-	rs834965	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:100101986_100101987delAA								LPPR4 (326850 upstream) : PALMD (9444 downstream)																																			---	---	---	---
HIAT1	64645	broad.mit.edu	37	1	100508617	100508617	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:100508617delT	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)														---	---	---	---
HIAT1	64645	broad.mit.edu	37	1	100522239	100522239	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:100522239delT	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)														---	---	---	---
SASS6	163786	broad.mit.edu	37	1	100576114	100576114	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:100576114delA	uc001dsu.2	-						SASS6_uc009wdz.2_Intron	NM_194292	NP_919268			spindle assembly abnormal protein 6						centriole replication	centriole				upper_aerodigestive_tract(1)|ovary(1)	2		all_epithelial(167;4.58e-06)|all_lung(203;0.00125)|Lung NSC(277;0.00131)		Epithelial(280;0.085)|all cancers(265;0.139)|COAD - Colon adenocarcinoma(174;0.15)|Lung(183;0.197)														---	---	---	---
CCDC76	54482	broad.mit.edu	37	1	100602758	100602758	+	Intron	DEL	T	-	-	rs79825452		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:100602758delT	uc001dsv.2	+						CCDC76_uc010ouf.1_Intron|CCDC76_uc009wea.2_Intron	NM_019083	NP_061956			coiled-coil domain containing 76						tRNA processing		metal ion binding|methyltransferase activity			ovary(1)	1		all_epithelial(167;0.000542)|all_lung(203;0.0154)|Lung NSC(277;0.0155)		Epithelial(280;0.0814)|all cancers(265;0.133)|COAD - Colon adenocarcinoma(174;0.146)|Lung(183;0.194)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	100991057	100991057	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:100991057delT								CDC14A (5225 upstream) : GPR88 (12671 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	101262580	101262580	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:101262580delA								VCAM1 (57981 upstream) : EXTL2 (75361 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	101767374	101767375	+	IGR	INS	-	G	G	rs149694094	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:101767374_101767375insG								S1PR1 (60298 upstream) : OLFM3 (500752 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	103035717	103035717	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:103035717delA								OLFM3 (572927 upstream) : COL11A1 (306307 downstream)																																			---	---	---	---
COL11A1	1301	broad.mit.edu	37	1	103376439	103376439	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:103376439delA	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	103473926	103473926	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:103473926delA	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)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	103615951	103615952	+	IGR	INS	-	AACA	AACA	rs141059892	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:103615951_103615952insAACA								COL11A1 (41899 upstream) : RNPC3 (452626 downstream)																																			---	---	---	---
AMY1A	276	broad.mit.edu	37	1	104296957	104296958	+	Intron	DEL	TG	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:104296957_104296958delTG	uc001duy.2	+						AMY1A_uc001duz.2_Intron	NM_001008221	NP_001008222			salivary amylase alpha 1A precursor						carbohydrate metabolic process|digestion	extracellular region	alpha-amylase activity|metal ion binding|protein binding				0		all_epithelial(167;3.05e-05)|all_lung(203;0.000199)|Lung NSC(277;0.000451)		Colorectal(144;0.0654)|all cancers(265;0.0808)|Epithelial(280;0.0921)|Lung(183;0.111)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	105085882	105085882	+	IGR	DEL	T	-	-	rs11336473		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:105085882delT								AMY1A (878710 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	105165101	105165101	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:105165101delA								AMY1A (957929 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	105307506	105307506	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:105307506delT								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	105571431	105571432	+	IGR	DEL	AA	-	-	rs35073777		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:105571431_105571432delAA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	105819552	105819552	+	IGR	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:105819552delG								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	107494873	107494874	+	IGR	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:107494873_107494874delAA								None (None upstream) : PRMT6 (104393 downstream)																																			---	---	---	---
NTNG1	22854	broad.mit.edu	37	1	107779383	107779383	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:107779383delT	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	108092403	108092403	+	IGR	DEL	T	-	-	rs34330018		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:108092403delT								NTNG1 (67932 upstream) : VAV3 (21379 downstream)																																			---	---	---	---
NBPF4	148545	broad.mit.edu	37	1	108766518	108766518	+	Intron	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:108766518delG	uc009weo.2	-						NBPF4_uc001dvo.2_Intron	NM_001143989	NP_001137461			neuroblastoma breakpoint family, member 4							cytoplasm					0																		---	---	---	---
KIAA1324	57535	broad.mit.edu	37	1	109728698	109728700	+	Intron	DEL	AAA	-	-	rs111462175		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:109728698_109728700delAAA	uc001dwq.2	+						KIAA1324_uc009wex.1_Intron|KIAA1324_uc009wey.2_Intron|KIAA1324_uc010ovg.1_Intron|KIAA1324_uc001dwr.2_5'Flank	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)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	110068722	110068722	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:110068722delA								AMIGO1 (16386 upstream) : GPR61 (13772 downstream)																																			---	---	---	---
GNAI3	2773	broad.mit.edu	37	1	110104431	110104431	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:110104431delT	uc001dxz.2	+							NM_006496	NP_006487			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	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)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	110140078	110140078	+	5'Flank	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:110140078delT	uc010ovq.1	+						MIR197_hsa-mir-197|MI0000239_5'Flank					DM004264																														---	---	---	---
AHCYL1	10768	broad.mit.edu	37	1	110547612	110547612	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:110547612delT	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)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	110666346	110666346	+	IGR	DEL	T	-	-	rs76248103		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:110666346delT								UBL4B (9778 upstream) : SLC6A17 (26786 downstream)																																			---	---	---	---
HBXIP	10542	broad.mit.edu	37	1	110951691	110951691	+	5'Flank	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:110951691delA	uc001dzr.2	-							NM_006402	NP_006393			hepatitis B virus x-interacting protein						anti-apoptosis|negative regulation of caspase activity|response to virus|viral genome replication	cytosol	protein binding			large_intestine(1)|ovary(1)|pancreas(1)	3		all_cancers(81;4.08e-06)|all_epithelial(167;4.38e-06)|all_lung(203;0.000152)|Lung NSC(277;0.000301)		Lung(183;0.0237)|all cancers(265;0.0675)|Epithelial(280;0.0732)|Colorectal(144;0.102)|LUSC - Lung squamous cell carcinoma(189;0.134)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	111009589	111009589	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:111009589delA								PROK1 (9615 upstream) : CYMP (6789 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	111065230	111065230	+	IGR	DEL	A	-	-	rs146296248		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:111065230delA								KCNA10 (3433 upstream) : KCNA2 (70973 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	111106170	111106170	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:111106170delT								KCNA10 (44373 upstream) : KCNA2 (30033 downstream)																																			---	---	---	---
CEPT1	10390	broad.mit.edu	37	1	111695807	111695807	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:111695807delT	uc001eah.1	+						CEPT1_uc001eag.2_Intron|CEPT1_uc001eai.1_Intron|CEPT1_uc001eaj.1_Intron	NM_001007794	NP_001007795			choline/ethanolaminephosphotransferase							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)													---	---	---	---
ADORA3	140	broad.mit.edu	37	1	112054297	112054298	+	Intron	DEL	AC	-	-	rs150737451		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:112054297_112054298delAC	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	112079261	112079261	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:112079261delT	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)													---	---	---	---
Unknown	0	broad.mit.edu	37	1	112542024	112542025	+	IGR	DEL	TC	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:112542024_112542025delTC								KCND3 (10247 upstream) : CTTNBP2NL (396775 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	112560740	112560741	+	IGR	DEL	TC	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:112560740_112560741delTC								KCND3 (28963 upstream) : CTTNBP2NL (378059 downstream)																																			---	---	---	---
WNT2B	7482	broad.mit.edu	37	1	113015578	113015579	+	Intron	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:113015578_113015579delAA	uc001eca.2	+						WNT2B_uc009wgg.2_Intron	NM_004185	NP_004176			wingless-type MMTV integration site family,						chondrocyte differentiation|cornea development in camera-type eye|dorsal/ventral axis specification|forebrain regionalization|hemopoietic stem cell proliferation|iris morphogenesis|lens development in camera-type eye|lung induction|male gonad development|neuron differentiation|positive regulation of branching involved in ureteric bud morphogenesis|positive regulation of canonical Wnt receptor signaling pathway|Wnt receptor signaling pathway, calcium modulating pathway	extracellular space|plasma membrane|proteinaceous extracellular matrix	frizzled-2 binding|signal transducer activity			ovary(2)|breast(2)|skin(1)	5	Lung SC(450;0.246)	all_cancers(81;7.31e-07)|all_epithelial(167;4.59e-06)|all_lung(203;2.56e-05)|Lung NSC(69;4.38e-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)														---	---	---	---
CAPZA1	829	broad.mit.edu	37	1	113181799	113181799	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:113181799delT	uc001ecj.1	+							NM_006135	NP_006126			F-actin capping protein alpha-1 subunit						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)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	113329926	113329926	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:113329926delA								FAM19A3 (60072 upstream) : SLC16A1 (124546 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	113408795	113408795	+	IGR	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:113408795delC								FAM19A3 (138941 upstream) : SLC16A1 (45677 downstream)																																			---	---	---	---
SLC16A1	6566	broad.mit.edu	37	1	113487327	113487327	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:113487327delT	uc001ecx.2	-						SLC16A1_uc001ecy.2_Intron|SLC16A1_uc001ecz.2_Intron	NM_003051	NP_003042			solute carrier family 16, member 1						blood coagulation|leukocyte migration|organic anion transport|pyruvate metabolic process	integral to membrane|membrane fraction|plasma membrane	mevalonate transmembrane transporter activity|protein binding|secondary active monocarboxylate transmembrane transporter activity|symporter activity			central_nervous_system(1)	1	Lung SC(450;0.246)	all_cancers(81;7.6e-08)|all_epithelial(167;3.82e-07)|all_lung(203;3.07e-05)|Lung NSC(69;5.51e-05)|Prostate(1639;0.00232)		Epithelial(280;7.31e-13)|all cancers(265;5.1e-10)|Kidney(133;5.29e-07)|KIRC - Kidney renal clear cell carcinoma(1967;8.63e-06)|OV - Ovarian serous cystadenocarcinoma(397;1.48e-05)|BRCA - Breast invasive adenocarcinoma(282;0.003)|LUSC - Lung squamous cell carcinoma(189;0.008)|Lung(183;0.00948)|Colorectal(144;0.0325)|COAD - Colon adenocarcinoma(174;0.0643)	Pyruvic acid(DB00119)													---	---	---	---
SLC16A1	6566	broad.mit.edu	37	1	113497880	113497880	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:113497880delA	uc001ecx.2	-						uc001edc.1_5'Flank|uc001edd.2_5'Flank|SLC16A1_uc001ecy.2_Intron|SLC16A1_uc001ecz.2_Intron|uc001edb.2_5'Flank	NM_003051	NP_003042			solute carrier family 16, member 1						blood coagulation|leukocyte migration|organic anion transport|pyruvate metabolic process	integral to membrane|membrane fraction|plasma membrane	mevalonate transmembrane transporter activity|protein binding|secondary active monocarboxylate transmembrane transporter activity|symporter activity			central_nervous_system(1)	1	Lung SC(450;0.246)	all_cancers(81;7.6e-08)|all_epithelial(167;3.82e-07)|all_lung(203;3.07e-05)|Lung NSC(69;5.51e-05)|Prostate(1639;0.00232)		Epithelial(280;7.31e-13)|all cancers(265;5.1e-10)|Kidney(133;5.29e-07)|KIRC - Kidney renal clear cell carcinoma(1967;8.63e-06)|OV - Ovarian serous cystadenocarcinoma(397;1.48e-05)|BRCA - Breast invasive adenocarcinoma(282;0.003)|LUSC - Lung squamous cell carcinoma(189;0.008)|Lung(183;0.00948)|Colorectal(144;0.0325)|COAD - Colon adenocarcinoma(174;0.0643)	Pyruvic acid(DB00119)													---	---	---	---
Unknown	0	broad.mit.edu	37	1	113759829	113759829	+	IGR	DEL	C	-	-	rs11307865		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:113759829delC								LRIG2 (92487 upstream) : MAGI3 (173646 downstream)																																			---	---	---	---
MAGI3	260425	broad.mit.edu	37	1	113936799	113936799	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:113936799delT	uc001edk.2	+						MAGI3_uc001edh.3_Intron|MAGI3_uc001edi.3_Intron|MAGI3_uc010owm.1_Intron	NM_001142782	NP_001136254			membrane-associated guanylate kinase-related  3						apoptosis|interspecies interaction between organisms|intracellular signal transduction	nucleus|tight junction	ATP binding|guanylate kinase activity|protein binding			lung(3)|ovary(2)|central_nervous_system(1)	6	Lung SC(450;0.184)	all_cancers(81;2.34e-09)|all_epithelial(167;7.41e-09)|all_lung(203;7.13e-06)|Lung NSC(69;1.2e-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)														---	---	---	---
MAGI3	260425	broad.mit.edu	37	1	113950195	113950197	+	Intron	DEL	TTT	-	-	rs111639704		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:113950195_113950197delTTT	uc001edk.2	+						MAGI3_uc001edh.3_Intron|MAGI3_uc001edi.3_Intron|MAGI3_uc010owm.1_Intron	NM_001142782	NP_001136254			membrane-associated guanylate kinase-related  3						apoptosis|interspecies interaction between organisms|intracellular signal transduction	nucleus|tight junction	ATP binding|guanylate kinase activity|protein binding			lung(3)|ovary(2)|central_nervous_system(1)	6	Lung SC(450;0.184)	all_cancers(81;2.34e-09)|all_epithelial(167;7.41e-09)|all_lung(203;7.13e-06)|Lung NSC(69;1.2e-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-4200-01A-01D-1126-08	TCGA-BR-4200-11A-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)														---	---	---	---
BCL2L15	440603	broad.mit.edu	37	1	114429118	114429118	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:114429118delA	uc001edw.2	-						uc001edv.1_Intron|BCL2L15_uc001edx.2_Intron|BCL2L15_uc001edy.2_Intron|BCL2L15_uc001edz.1_Intron	NM_001010922	NP_001010922			pro-apoptotic Bcl-2 protein						apoptosis					ovary(1)	1	Lung SC(450;0.184)	all_cancers(81;3.95e-08)|all_epithelial(167;9.95e-08)|all_lung(203;1.31e-05)|Lung NSC(69;2.46e-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)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	114834530	114834531	+	IGR	INS	-	CA	CA	rs150406546	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:114834530_114834531insCA								SYT6 (138058 upstream) : TRIM33 (100870 downstream)																																			---	---	---	---
TRIM33	51592	broad.mit.edu	37	1	114973400	114973401	+	Intron	INS	-	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:114973400_114973401insT	uc001eew.2	-						TRIM33_uc010owr.1_5'Flank|TRIM33_uc010ows.1_Intron|TRIM33_uc001eex.2_Intron	NM_015906	NP_056990			tripartite motif-containing 33 protein isoform						negative regulation of BMP signaling pathway|negative regulation of transcription, DNA-dependent|protein ubiquitination|regulation of transforming growth factor beta receptor signaling pathway|transcription, DNA-dependent	nucleus	co-SMAD binding|DNA binding|ligase activity|R-SMAD binding|zinc ion binding			lung(4)|central_nervous_system(3)|large_intestine(1)|breast(1)|skin(1)|ovary(1)	11	all_epithelial(7;0.000132)|all_lung(7;0.00106)|Lung SC(450;0.184)	all_cancers(81;3.03e-08)|all_epithelial(167;3.24e-08)|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)				T	RET	papillary thyroid								---	---	---	---
AMPD1	270	broad.mit.edu	37	1	115217930	115217930	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-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)													---	---	---	---
Unknown	0	broad.mit.edu	37	1	115382592	115382592	+	IGR	DEL	T	-	-	rs11347162		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:115382592delT								SIKE1 (59284 upstream) : SYCP1 (14863 downstream)																																			---	---	---	---
SYCP1	6847	broad.mit.edu	37	1	115468891	115468891	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:115468891delT	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	115943351	115943351	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:115943351delA								NGF (62494 upstream) : VANGL1 (241223 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	116466585	116466585	+	Intron	DEL	T	-	-	rs11321910		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:116466585delT	uc001efz.2	+											Homo sapiens cDNA clone IMAGE:5296456.																														---	---	---	---
Unknown	0	broad.mit.edu	37	1	116714079	116714080	+	IGR	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:116714079_116714080delTT								C1orf161 (36218 upstream) : ATP1A1 (200924 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	116846174	116846176	+	IGR	DEL	AAA	-	-	rs112233919		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:116846174_116846176delAAA								C1orf161 (168313 upstream) : ATP1A1 (68828 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	116908460	116908462	+	IGR	DEL	TTT	-	-	rs72037361		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:116908460_116908462delTTT								C1orf161 (230599 upstream) : ATP1A1 (6542 downstream)																																			---	---	---	---
IGSF3	3321	broad.mit.edu	37	1	117164228	117164228	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:117164228delT	uc001egr.1	-						IGSF3_uc001egq.1_Intron	NM_001007237	NP_001007238			immunoglobulin superfamily, member 3 isoform 2							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)														---	---	---	---
IGSF3	3321	broad.mit.edu	37	1	117202221	117202221	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:117202221delT	uc001egr.1	-						IGSF3_uc001egq.1_Intron	NM_001007237	NP_001007238			immunoglobulin superfamily, member 3 isoform 2							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)														---	---	---	---
TTF2	8458	broad.mit.edu	37	1	117626815	117626815	+	Intron	DEL	G	-	-	rs116064890	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:117626815delG	uc001egy.2	+							NM_003594	NP_003585			transcription termination factor, RNA polymerase						mRNA processing|regulation of transcription, DNA-dependent|RNA splicing|termination of RNA polymerase II transcription	cytoplasm|spliceosomal complex|transcription elongation factor complex	ATP binding|ATP-dependent helicase activity|DNA binding|DNA-dependent ATPase activity|protein binding|zinc ion binding			ovary(1)	1	Lung SC(450;0.225)	all_cancers(81;4.23e-06)|all_epithelial(167;3.65e-07)|all_lung(203;2.81e-06)|Lung NSC(69;1.98e-05)		Lung(183;0.0553)|Colorectal(144;0.179)|LUSC - Lung squamous cell carcinoma(189;0.19)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	117674733	117674733	+	IGR	DEL	A	-	-	rs116702135	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:117674733delA								TRIM45 (10319 upstream) : VTCN1 (11477 downstream)																																			---	---	---	---
VTCN1	79679	broad.mit.edu	37	1	117715263	117715263	+	Intron	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:117715263delC	uc001ehb.2	-						VTCN1_uc001ehc.2_Intron|VTCN1_uc009whf.1_Intron	NM_024626	NP_078902			V-set domain containing T cell activation							integral to membrane|plasma membrane					0	Lung SC(450;0.225)	all_cancers(81;6.05e-06)|all_epithelial(167;5.59e-07)|all_lung(203;2.85e-06)|Lung NSC(69;2e-05)		Lung(183;0.0664)|LUSC - Lung squamous cell carcinoma(189;0.214)|Colorectal(144;0.23)														---	---	---	---
FAM46C	54855	broad.mit.edu	37	1	118166787	118166791	+	3'UTR	DEL	TTTTT	-	-	rs76688747		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:118166787_118166791delTTTTT	uc001ehe.2	+	2						NM_017709	NP_060179			hypothetical protein LOC54855												0	Lung SC(450;0.225)	all_cancers(81;0.000101)|all_lung(203;3.4e-06)|all_epithelial(167;4.98e-06)|Lung NSC(69;2.33e-05)		Lung(183;0.0576)|LUSC - Lung squamous cell carcinoma(189;0.192)|Colorectal(144;0.247)											Multiple Myeloma(3;1.13e-06)			---	---	---	---
Unknown	0	broad.mit.edu	37	1	118203082	118203083	+	IGR	DEL	AC	-	-	rs66934245		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:118203082_118203083delAC								FAM46C (32072 upstream) : GDAP2 (203025 downstream)																																			---	---	---	---
GDAP2	54834	broad.mit.edu	37	1	118459659	118459660	+	Intron	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:118459659_118459660delAA	uc001ehf.2	-						GDAP2_uc001ehg.2_Intron	NM_017686	NP_060156			ganglioside induced differentiation associated											ovary(2)	2		all_cancers(81;0.0156)|all_lung(203;5.81e-05)|Lung NSC(69;0.000446)|all_epithelial(167;0.00295)		Lung(183;0.0583)|LUSC - Lung squamous cell carcinoma(189;0.194)														---	---	---	---
WDR3	10885	broad.mit.edu	37	1	118491606	118491606	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:118491606delT	uc010oxe.1	+						WDR3_uc001ehi.2_Intron	NM_006784	NP_006775			WD repeat-containing protein 3							nuclear membrane|nucleolus				upper_aerodigestive_tract(1)	1	Esophageal squamous(2;0.162)	all_cancers(81;2.72e-05)|Acute lymphoblastic leukemia(138;1e-08)|all_epithelial(167;4.4e-07)|all_lung(203;1.7e-06)|Lung NSC(69;1.98e-05)|Prostate(1639;0.00955)|Breast(1374;0.244)		OV - Ovarian serous cystadenocarcinoma(397;1.39e-08)|Epithelial(280;1.82e-07)|all cancers(265;2.04e-05)|Lung(183;0.0525)|BRCA - Breast invasive adenocarcinoma(282;0.0695)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.185)														---	---	---	---
WDR3	10885	broad.mit.edu	37	1	118495529	118495529	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:118495529delT	uc010oxe.1	+						WDR3_uc001ehi.2_Intron	NM_006784	NP_006775			WD repeat-containing protein 3							nuclear membrane|nucleolus				upper_aerodigestive_tract(1)	1	Esophageal squamous(2;0.162)	all_cancers(81;2.72e-05)|Acute lymphoblastic leukemia(138;1e-08)|all_epithelial(167;4.4e-07)|all_lung(203;1.7e-06)|Lung NSC(69;1.98e-05)|Prostate(1639;0.00955)|Breast(1374;0.244)		OV - Ovarian serous cystadenocarcinoma(397;1.39e-08)|Epithelial(280;1.82e-07)|all cancers(265;2.04e-05)|Lung(183;0.0525)|BRCA - Breast invasive adenocarcinoma(282;0.0695)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.185)														---	---	---	---
SPAG17	200162	broad.mit.edu	37	1	118534238	118534238	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:118534238delA	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)														---	---	---	---
SPAG17	200162	broad.mit.edu	37	1	118616767	118616767	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:118616767delT	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	119079680	119079681	+	IGR	INS	-	TC	TC			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:119079680_119079681insTC								SPAG17 (351832 upstream) : TBX15 (345985 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	119296796	119296796	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:119296796delT								SPAG17 (568948 upstream) : TBX15 (128870 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	119369503	119369503	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:119369503delA								SPAG17 (641655 upstream) : TBX15 (56163 downstream)																																			---	---	---	---
TBX15	6913	broad.mit.edu	37	1	119442739	119442739	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:119442739delA	uc001ehl.1	-						TBX15_uc009whj.1_5'Flank	NM_152380	NP_689593			T-box 15							nucleus	DNA binding|sequence-specific DNA binding transcription factor activity			large_intestine(1)|pancreas(1)	2	all_neural(166;0.117)	all_cancers(81;0.000692)|all_lung(203;3.05e-06)|Lung NSC(69;2.13e-05)|all_epithelial(167;0.000237)		Lung(183;0.044)|LUSC - Lung squamous cell carcinoma(189;0.141)														---	---	---	---
NOTCH2	4853	broad.mit.edu	37	1	120567627	120567628	+	Intron	INS	-	T	T	rs144108943		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:120567627_120567628insT	uc001eik.2	-						NOTCH2_uc001eil.2_Intron|NOTCH2_uc001eim.3_Intron	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				---	---	---	---
HIST2H2BA	337875	broad.mit.edu	37	1	120912062	120912062	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:120912062delT	uc001eio.2	+							NR_027337				Homo sapiens histone cluster 2, H2ba, mRNA (cDNA clone IMAGE:40032208).												0																		---	---	---	---
LOC647121	647121	broad.mit.edu	37	1	121296499	121296500	+	Intron	DEL	TG	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:121296499_121296500delTG	uc001eiu.1	+							NR_003955				Homo sapiens cDNA FLJ46881 fis, clone UTERU3015647, moderately similar to Embigin precursor.												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	1	142611721	142611721	+	IGR	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:142611721delC								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	142805096	142805099	+	Intron	DEL	CTGC	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:142805096_142805099delCTGC	uc001eiw.1	+						uc001ejb.2_RNA|uc001ejd.1_RNA|uc001ejc.2_Intron					Homo sapiens PNAS-130 mRNA, complete cds.																														---	---	---	---
Unknown	0	broad.mit.edu	37	1	142860697	142860697	+	Intron	DEL	A	-	-	rs139169457		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:142860697delA	uc001eiw.1	+						uc001ejb.2_Intron|uc001ejd.1_Intron					Homo sapiens PNAS-130 mRNA, complete cds.																														---	---	---	---
Unknown	0	broad.mit.edu	37	1	142942923	142942924	+	Intron	DEL	GT	-	-	rs147098887		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:142942923_142942924delGT	uc001eiw.1	+											Homo sapiens PNAS-130 mRNA, complete cds.																														---	---	---	---
Unknown	0	broad.mit.edu	37	1	143165873	143165873	+	Intron	DEL	C	-	-	rs112938103		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:143165873delC	uc001eiw.1	+											Homo sapiens PNAS-130 mRNA, complete cds.																														---	---	---	---
Unknown	0	broad.mit.edu	37	1	143412865	143412865	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:143412865delA								None (None upstream) : LOC100286793 (234774 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	143486948	143486953	+	IGR	DEL	TGTGTG	-	-	rs113342785		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:143486948_143486953delTGTGTG								None (None upstream) : LOC100286793 (160686 downstream)																																			---	---	---	---
PDE4DIP	9659	broad.mit.edu	37	1	144944990	144944990	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:144944990delT	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	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	145009535	145009535	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:145009535delT	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	145054268	145054269	+	Intron	INS	-	G	G	rs149978567		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:145054268_145054269insG	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	145056193	145056193	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:145056193delA	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	145058201	145058201	+	Intron	DEL	A	-	-	rs11347217		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:145058201delA	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	145146794	145146794	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:145146794delT	uc010oye.1	+						NBPF10_uc009wir.2_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron					RecName: Full=Neuroblastoma breakpoint family member 8;							cytoplasm					0																		---	---	---	---
NBPF10	100132406	broad.mit.edu	37	1	145231553	145231554	+	Intron	INS	-	C	C	rs142041832		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:145231553_145231554insC	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	145424581	145424582	+	Intron	DEL	AA	-	-	rs112272313		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:145424581_145424582delAA	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	145498328	145498330	+	Intron	DEL	ATA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:145498328_145498330delATA	uc001emp.3	+						LIX1L_uc001enr.2_Intron|LIX1L_uc009wiu.1_5'Flank	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	145505301	145505301	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:145505301delA	uc001emp.3	+						RBM8A_uc001ent.1_5'Flank|RBM8A_uc001enu.1_5'Flank	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	145572567	145572570	+	Intron	DEL	GTTT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:145572567_145572570delGTTT	uc001emp.3	+						PIAS3_uc010oyy.1_5'Flank	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	145581645	145581645	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:145581645delT	uc001emp.3	+						PIAS3_uc001eoc.1_Intron|PIAS3_uc001eod.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	145640869	145640869	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:145640869delT	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	145686358	145686359	+	Intron	INS	-	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:145686358_145686359insT	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	145731228	145731230	+	Intron	DEL	AAA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:145731228_145731230delAAA	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	145816543	145816543	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:145816543delT	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)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	146615099	146615099	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:146615099delT								LOC728989 (100500 upstream) : PRKAB2 (11588 downstream)																																			---	---	---	---
PRKAB2	5565	broad.mit.edu	37	1	146637373	146637373	+	Intron	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:146637373delG	uc001epe.2	-						PRKAB2_uc010ozm.1_Intron|PRKAB2_uc010ozn.1_Intron|PRKAB2_uc009wjf.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	146859177	146859178	+	Intron	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:146859177_146859178delTT	uc001epp.2	-											Homo sapiens cDNA clone IMAGE:5266739.																														---	---	---	---
Unknown	0	broad.mit.edu	37	1	147350290	147350290	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:147350290delA								GJA5 (104806 upstream) : GJA8 (24646 downstream)																																			---	---	---	---
LOC200030	200030	broad.mit.edu	37	1	147790692	147790692	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:147790692delT	uc001eqf.2	-						LOC200030_uc010ozz.1_Intron|LOC200030_uc001eqe.2_Intron|LOC200030_uc001eqg.2_Intron	NM_017940	NP_060410			hypothetical protein LOC55672							cytoplasm					0																		---	---	---	---
Unknown	0	broad.mit.edu	37	1	148538283	148538283	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:148538283delT								NBPF14 (191492 upstream) : NBPF15 (19986 downstream)																																			---	---	---	---
NBPF15	284565	broad.mit.edu	37	1	148560488	148560488	+	5'Flank	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:148560488delT	uc001esc.2	+						NBPF15_uc001esb.1_Intron	NM_173638	NP_775909			hypothetical protein LOC284565							cytoplasm					0	all_hematologic(923;0.032)																	---	---	---	---
Unknown	0	broad.mit.edu	37	1	148898510	148898510	+	Intron	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:148898510delG	uc009wkv.1	+											Homo sapiens cDNA, FLJ17483.																														---	---	---	---
LOC645166	645166	broad.mit.edu	37	1	148935053	148935055	+	Intron	DEL	TTC	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:148935053_148935055delTTC	uc010pbc.1	+						LOC645166_uc010pbd.1_Intron|LOC645166_uc009wkw.1_Intron	NR_027355				Homo sapiens cDNA, FLJ18771.												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	1	149204922	149204922	+	IGR	DEL	T	-	-	rs5777595		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:149204922delT								LOC645166 (251868 upstream) : LOC388692 (74554 downstream)																																	OREG0013773	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	149246473	149246473	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:149246473delT								LOC645166 (293419 upstream) : LOC388692 (33003 downstream)																																			---	---	---	---
LOC388692	388692	broad.mit.edu	37	1	149291174	149291174	+	RNA	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:149291174delT	uc010pbf.1	+	1		c.11699delT			LOC388692_uc001esg.3_Intron	NR_027002				Homo sapiens cDNA FLJ13580 fis, clone PLACE1008851.												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	1	149689121	149689121	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:149689121delA								HIST2H2BF (289892 upstream) : FCGR1A (65129 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	149893915	149893915	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:149893915delA								SV2A (4481 upstream) : SF3B4 (1296 downstream)																																			---	---	---	---
MTMR11	10903	broad.mit.edu	37	1	149902648	149902648	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:149902648delA	uc001etl.3	-						SF3B4_uc001etj.1_5'Flank|SF3B4_uc001etk.1_5'Flank|SF3B4_uc009wll.1_5'Flank|MTMR11_uc001etm.1_Intron|MTMR11_uc010pbm.1_3'UTR	NM_001145862	NP_001139334			myotubularin related protein 11 isoform a								phosphatase activity			central_nervous_system(1)	1	Breast(34;0.0009)|Ovarian(49;0.0377)|all_hematologic(923;0.0597)|Hepatocellular(266;0.161)|Colorectal(459;0.171)		LUSC - Lung squamous cell carcinoma(543;0.221)|STAD - Stomach adenocarcinoma(528;0.247)															---	---	---	---
PLEKHO1	51177	broad.mit.edu	37	1	150130459	150130459	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:150130459delT	uc001ett.2	+						PLEKHO1_uc001etr.2_Intron|PLEKHO1_uc001ets.2_Intron|PLEKHO1_uc001etu.2_Intron	NM_016274	NP_057358			pleckstrin homology domain containing, family O							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)															---	---	---	---
ANP32E	81611	broad.mit.edu	37	1	150199259	150199259	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:150199259delT	uc001etw.2	-						ANP32E_uc010pbt.1_5'Flank|ANP32E_uc010pbu.1_Intron|ANP32E_uc010pbv.1_Intron|ANP32E_uc001etv.3_Intron|ANP32E_uc010pbw.1_Intron	NM_030920	NP_112182			acidic (leucine-rich) nuclear phosphoprotein 32							cytoplasmic membrane-bounded vesicle|nucleus	phosphatase inhibitor activity				0	Lung NSC(24;7.29e-29)|Breast(34;0.00211)|Ovarian(49;0.0167)|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	150216291	150216291	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:150216291delA								ANP32E (7787 upstream) : CA14 (13927 downstream)																																			---	---	---	---
RPRD2	23248	broad.mit.edu	37	1	150335024	150335026	+	5'Flank	DEL	AAA	-	-	rs71578486		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:150335024_150335026delAAA	uc009wlr.2	+						RPRD2_uc010pcc.1_5'Flank|RPRD2_uc001eup.3_5'Flank	NM_015203	NP_056018			Regulation of nuclear pre-mRNA domain containing								protein binding			ovary(1)	1																		---	---	---	---
RPRD2	23248	broad.mit.edu	37	1	150412447	150412448	+	Intron	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:150412447_150412448delTT	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																		---	---	---	---
MCL1	4170	broad.mit.edu	37	1	150550110	150550110	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:150550110delA	uc001euz.2	-						MCL1_uc010pch.1_Intron|MCL1_uc001eva.2_Intron	NM_021960	NP_068779			myeloid cell leukemia sequence 1 isoform 1						anti-apoptosis|apoptosis|cell fate determination|cellular homeostasis|multicellular organismal development|response to cytokine stimulus	integral to membrane|mitochondrial outer membrane|nucleoplasm	BH3 domain binding|protein binding|protein channel activity|protein heterodimerization activity				0	all_cancers(9;1.69e-53)|all_epithelial(9;1.95e-43)|all_lung(15;1.09e-34)|Lung NSC(24;4.04e-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)															---	---	---	---
ENSA	2029	broad.mit.edu	37	1	150601455	150601455	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:150601455delT	uc001eve.2	-						ENSA_uc001evd.2_Intron|ENSA_uc009wly.2_Intron|ENSA_uc001evg.2_Intron|ENSA_uc001evh.2_Intron|ENSA_uc009wlz.1_Intron|ENSA_uc001evi.2_Intron|ENSA_uc001evb.2_Intron|ENSA_uc001evc.2_Intron|ENSA_uc001evf.2_Intron	NM_004436	NP_004427			endosulfine alpha isoform 3						cell division|G2/M transition of mitotic cell cycle|mitosis|response to nutrient|transport	cytoplasm	ion channel inhibitor activity|protein phosphatase 2A binding|protein phosphatase inhibitor activity|protein phosphatase type 2A regulator activity|receptor binding			central_nervous_system(1)	1	all_cancers(9;3.09e-52)|all_epithelial(9;4.47e-43)|all_lung(15;1.09e-34)|Lung NSC(24;4.04e-31)|Breast(34;0.000615)|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;9.85e-23)|all cancers(9;5.06e-22)|OV - Ovarian serous cystadenocarcinoma(6;1.67e-14)|BRCA - Breast invasive adenocarcinoma(12;0.000701)|LUSC - Lung squamous cell carcinoma(543;0.171)															---	---	---	---
HORMAD1	84072	broad.mit.edu	37	1	150686600	150686600	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:150686600delA	uc001evk.1	-						HORMAD1_uc001evl.1_Intron|HORMAD1_uc001evm.1_Intron	NM_032132	NP_115508			HORMA domain containing 1						blastocyst development|cell differentiation|meiotic DNA double-strand break formation|meiotic recombination checkpoint|meiotic sister chromatid cohesion|mitosis|oogenesis|regulation of homologous chromosome segregation|spermatogenesis|synaptonemal complex assembly	chromosome|nucleus				ovary(2)|central_nervous_system(1)	3	all_cancers(9;3.23e-52)|all_epithelial(9;4.68e-43)|all_lung(15;5.74e-35)|Lung NSC(24;2.09e-31)|Breast(34;0.0009)|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;2.32e-23)|all cancers(9;5.21e-23)|OV - Ovarian serous cystadenocarcinoma(6;6.72e-15)|BRCA - Breast invasive adenocarcinoma(12;0.000479)|LUSC - Lung squamous cell carcinoma(543;0.171)															---	---	---	---
ARNT	405	broad.mit.edu	37	1	150836292	150836293	+	Intron	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:150836292_150836293delAA	uc001evr.1	-						ARNT_uc001evs.1_Intron|ARNT_uc009wmb.1_Intron|ARNT_uc009wmc.1_Intron|ARNT_uc009wmd.1_Intron|ARNT_uc009wme.1_Intron|ARNT_uc010pcl.1_Intron	NM_001668	NP_001659			aryl hydrocarbon receptor nuclear translocator						positive regulation of hormone biosynthetic process|positive regulation vascular endothelial growth factor production|regulation of transcription from RNA polymerase II promoter in response to oxidative stress|response to hypoxia		aryl hydrocarbon receptor binding|protein heterodimerization activity|sequence-specific DNA binding transcription factor activity|signal transducer activity|transcription coactivator activity			skin(4)|lung(3)|central_nervous_system(1)|kidney(1)	9	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;0.02)|BRCA - Breast invasive adenocarcinoma(12;0.00606)|LUSC - Lung squamous cell carcinoma(543;0.211)					T	ETV6	AML								---	---	---	---
ARNT	405	broad.mit.edu	37	1	150845444	150845444	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:150845444delA	uc001evr.1	-						ARNT_uc001evs.1_Intron|ARNT_uc009wmb.1_Intron|ARNT_uc009wmc.1_Intron|ARNT_uc009wmd.1_Intron|ARNT_uc009wme.1_Intron|ARNT_uc010pcl.1_Intron	NM_001668	NP_001659			aryl hydrocarbon receptor nuclear translocator						positive regulation of hormone biosynthetic process|positive regulation vascular endothelial growth factor production|regulation of transcription from RNA polymerase II promoter in response to oxidative stress|response to hypoxia		aryl hydrocarbon receptor binding|protein heterodimerization activity|sequence-specific DNA binding transcription factor activity|signal transducer activity|transcription coactivator activity			skin(4)|lung(3)|central_nervous_system(1)|kidney(1)	9	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;0.02)|BRCA - Breast invasive adenocarcinoma(12;0.00606)|LUSC - Lung squamous cell carcinoma(543;0.211)					T	ETV6	AML								---	---	---	---
Unknown	0	broad.mit.edu	37	1	150881267	150881267	+	IGR	DEL	A	-	-	rs79741383		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:150881267delA								ARNT (32081 upstream) : SETDB1 (17548 downstream)																																			---	---	---	---
SETDB1	9869	broad.mit.edu	37	1	150917624	150917624	+	Intron	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:150917624delG	uc001evu.2	+						SETDB1_uc009wmf.2_Intron|SETDB1_uc001evv.2_Intron|SETDB1_uc001evw.3_Frame_Shift_Del_p.G394fs|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)															---	---	---	---
SETDB1	9869	broad.mit.edu	37	1	150925703	150925703	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:150925703delA	uc001evu.2	+						SETDB1_uc001evv.2_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	150990220	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:150990220delA	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)															---	---	---	---
SEMA6C	10500	broad.mit.edu	37	1	151121250	151121250	+	5'Flank	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:151121250delA	uc001ewu.2	-						SEMA6C_uc001ewv.2_5'Flank|SEMA6C_uc001eww.2_5'Flank|SEMA6C_uc010pcq.1_5'Flank|SEMA6C_uc009wml.1_5'Flank	NM_030913	NP_112175			semaphorin Y precursor							integral to membrane	receptor activity			ovary(1)|skin(1)	2	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;0.211)															---	---	---	---
PIP5K1A	8394	broad.mit.edu	37	1	151204488	151204488	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:151204488delA	uc001exj.2	+						PIP5K1A_uc001exi.2_Intron|PIP5K1A_uc010pcu.1_Intron|PIP5K1A_uc001exk.2_Intron|PIP5K1A_uc010pcv.1_5'Flank	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)															---	---	---	---
RFX5	5993	broad.mit.edu	37	1	151318741	151318741	+	Frame_Shift_Del	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:151318741delG	uc001exv.1	-	3	270	c.56delC	c.(55-57)CCAfs	p.P19fs	RFX5_uc001exw.1_Frame_Shift_Del_p.P19fs|RFX5_uc009wmr.1_Frame_Shift_Del_p.P19fs|RFX5_uc010pcx.1_Frame_Shift_Del_p.P19fs	NM_001025603	NP_001020774	P48382	RFX5_HUMAN	regulatory factor X, 5	19						nucleus	DNA binding|protein binding|sequence-specific DNA binding transcription factor activity			ovary(1)	1	Lung SC(34;0.00471)|Ovarian(49;0.0147)|Hepatocellular(266;0.0997)|all_hematologic(923;0.127)|Melanoma(130;0.185)		UCEC - Uterine corpus endometrioid carcinoma (35;0.112)|LUSC - Lung squamous cell carcinoma(543;0.181)															---	---	---	---
POGZ	23126	broad.mit.edu	37	1	151384306	151384306	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:151384306delA	uc001eyd.1	-						POGZ_uc001eye.1_Intron|POGZ_uc010pdb.1_Intron|POGZ_uc001eyf.1_Intron|POGZ_uc010pdc.1_Intron|POGZ_uc009wmv.1_Intron|POGZ_uc010pdd.1_Intron	NM_015100	NP_055915			pogo transposable element with ZNF domain						cell division|kinetochore assembly|mitotic sister chromatid cohesion|regulation of transcription, DNA-dependent	cytoplasm|nuclear chromatin	DNA binding|protein binding|zinc ion binding			ovary(3)	3	Lung SC(34;0.00471)|Ovarian(49;0.00672)|Hepatocellular(266;0.0997)|all_hematologic(923;0.127)|Melanoma(130;0.185)		UCEC - Uterine corpus endometrioid carcinoma (35;0.112)|LUSC - Lung squamous cell carcinoma(543;0.181)															---	---	---	---
CGN	57530	broad.mit.edu	37	1	151492628	151492628	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-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)															---	---	---	---
SNX27	81609	broad.mit.edu	37	1	151634967	151634967	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:151634967delT	uc001eyn.1	+						SNX27_uc001eyo.2_Intron|SNX27_uc001eyp.2_Intron	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	151921809	151921809	+	IGR	DEL	A	-	-	rs6678366	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:151921809delA								THEM4 (39696 upstream) : S100A10 (33578 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	152317836	152317837	+	Intron	INS	-	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:152317836_152317837insT	uc001ezv.2	+											Homo sapiens cDNA FLJ31869 fis, clone NT2RP7002151.																														---	---	---	---
LCE1E	353135	broad.mit.edu	37	1	152756550	152756551	+	5'Flank	INS	-	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:152756550_152756551insT	uc001fan.2	+							NM_178353	NP_848130			late cornified envelope 1E						keratinization						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;0.206)															---	---	---	---
LCE1D	353134	broad.mit.edu	37	1	152767221	152767222	+	5'Flank	INS	-	A	A	rs139530442	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:152767221_152767222insA	uc009wnp.2	+							NM_178352	NP_848129			late cornified envelope 1D						cellular response to calcium ion|keratinization	cornified envelope|perinuclear region of cytoplasm					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;0.206)															---	---	---	---
SPRR2D	6703	broad.mit.edu	37	1	153019497	153019497	+	Intron	DEL	A	-	-	rs74883464		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:153019497delA	uc009wnz.2	-											Homo sapiens cDNA FLJ76407 complete cds, highly similar to Homo sapiens small proline-rich protein 2D (SPRR2D), mRNA.						keratinization	cornified envelope|cytoplasm					0	Lung NSC(65;1.49e-28)|Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		LUSC - Lung squamous cell carcinoma(543;0.171)															---	---	---	---
SPRR2D	6703	broad.mit.edu	37	1	153025847	153025847	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:153025847delA	uc009wnz.2	-											Homo sapiens cDNA FLJ76407 complete cds, highly similar to Homo sapiens small proline-rich protein 2D (SPRR2D), mRNA.						keratinization	cornified envelope|cytoplasm					0	Lung NSC(65;1.49e-28)|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	153163346	153163346	+	IGR	DEL	T	-	-	rs148770718		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:153163346delT								SPRR2G (39919 upstream) : LELP1 (12573 downstream)																																			---	---	---	---
GATAD2B	57459	broad.mit.edu	37	1	153810982	153810982	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:153810982delT	uc001fdb.3	-							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	153836107	153836107	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:153836107delT	uc001fdb.3	-							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	153843049	153843049	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:153843049delA	uc001fdb.3	-							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	153849933	153849933	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:153849933delA	uc001fdb.3	-							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)															---	---	---	---
UBAP2L	9898	broad.mit.edu	37	1	154207835	154207835	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:154207835delT	uc001fep.3	+						UBAP2L_uc009wot.2_Intron|UBAP2L_uc010pek.1_Intron|UBAP2L_uc010pel.1_Intron|UBAP2L_uc001fen.1_Intron|UBAP2L_uc010pen.1_Intron	NM_014847	NP_055662			ubiquitin associated protein 2-like isoform a						binding of sperm to zona pellucida		protein binding			ovary(1)|central_nervous_system(1)	2	all_lung(78;1.09e-30)|Lung NSC(65;1.66e-28)|Hepatocellular(266;0.0877)		LUSC - Lung squamous cell carcinoma(543;0.185)															---	---	---	---
HAX1	10456	broad.mit.edu	37	1	154245558	154245558	+	Intron	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:154245558delG	uc001fes.2	+						HAX1_uc001fet.2_Intron|HAX1_uc010peo.1_Intron|HAX1_uc009wou.2_Intron|HAX1_uc009wov.2_Intron	NM_006118	NP_006109			HCLS1 associated protein X-1 isoform a							actin cytoskeleton|cytoplasmic membrane-bounded vesicle|lamellipodium|mitochondrion|nuclear membrane|sarcoplasmic reticulum|soluble fraction	interleukin-1 binding|protein N-terminus binding				0	all_lung(78;2.62e-30)|Lung NSC(65;3.94e-28)|Hepatocellular(266;0.0877)		LUSC - Lung squamous cell carcinoma(543;0.185)											Kostmann_syndrome				---	---	---	---
Unknown	0	broad.mit.edu	37	1	154283194	154283195	+	IGR	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:154283194_154283195delTT								HAX1 (34845 upstream) : AQP10 (10397 downstream)																																			---	---	---	---
KCNN3	3782	broad.mit.edu	37	1	154728263	154728264	+	Intron	INS	-	A	A	rs150370646	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:154728263_154728264insA	uc001ffp.2	-						KCNN3_uc001ffo.2_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)															---	---	---	---
DCST2	127579	broad.mit.edu	37	1	154998707	154998707	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:154998707delA	uc001fgm.2	-						DCST2_uc009wpb.2_Intron	NM_144622	NP_653223			DC-STAMP domain containing 2							integral to membrane				ovary(2)|central_nervous_system(1)	3	all_epithelial(22;2.77e-30)|all_lung(78;4.1e-28)|all_hematologic(923;0.0359)|Hepatocellular(266;0.0877)		BRCA - Breast invasive adenocarcinoma(34;0.00034)															---	---	---	---
MTX1	4580	broad.mit.edu	37	1	155178591	155178591	+	5'UTR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:155178591delA	uc001fjb.2	+	1					RAG1AP1_uc010pey.1_Intron|THBS3_uc001fix.2_5'Flank|THBS3_uc009wqi.2_5'Flank|THBS3_uc001fiz.2_5'Flank|THBS3_uc001fiy.2_5'Flank|THBS3_uc010pfu.1_5'Flank|THBS3_uc010pfv.1_5'Flank|THBS3_uc001fja.2_Intron|THBS3_uc009wqj.1_Intron|MTX1_uc001fjc.2_5'UTR	NM_002455	NP_002446			metaxin 1 isoform 1						protein targeting to mitochondrion	integral to membrane|mitochondrial outer membrane	protein binding			skin(1)	1	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)															---	---	---	---
ASH1L	55870	broad.mit.edu	37	1	155347853	155347854	+	Intron	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:155347853_155347854delAA	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)															---	---	---	---
YY1AP1	55249	broad.mit.edu	37	1	155644954	155644954	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:155644954delT	uc001fln.2	-						YY1AP1_uc010pgg.1_Intron|YY1AP1_uc010pgh.1_Intron|YY1AP1_uc010pgi.1_Intron|YY1AP1_uc001flh.2_Intron|YY1AP1_uc009wqt.2_Intron|YY1AP1_uc001flk.2_Intron|YY1AP1_uc001fll.2_Intron|YY1AP1_uc009wqv.2_Intron|YY1AP1_uc001flm.2_Intron|YY1AP1_uc001fli.2_Intron|YY1AP1_uc009wqu.2_Intron|YY1AP1_uc001flj.2_Intron|YY1AP1_uc009wqw.2_Intron|YY1AP1_uc001flo.2_Intron|YY1AP1_uc001flp.2_Intron|YY1AP1_uc010pgj.1_Intron|YY1AP1_uc009wqx.2_Intron|YY1AP1_uc010pgk.1_Intron	NM_139118	NP_620829			YY1-associated protein isoform 2						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)																	---	---	---	---
GON4L	54856	broad.mit.edu	37	1	155781844	155781844	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:155781844delA	uc001flz.2	-						GON4L_uc001fly.1_Intron|GON4L_uc009wrh.1_Intron|GON4L_uc001fma.1_Intron|GON4L_uc001fmc.2_Intron|GON4L_uc001fmd.3_Intron|GON4L_uc009wri.2_Intron|GON4L_uc001fme.2_Intron|GON4L_uc001fmf.2_Intron	NM_001037533	NP_001032622			gon-4-like isoform a						regulation of transcription, DNA-dependent	cytoplasm|nucleus	DNA binding			ovary(3)	3	Hepatocellular(266;0.0997)|all_hematologic(923;0.145)|all_neural(408;0.195)																	---	---	---	---
GON4L	54856	broad.mit.edu	37	1	155825155	155825156	+	Intron	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:155825155_155825156delTT	uc001flz.2	-						GON4L_uc001fly.1_Intron|GON4L_uc009wrh.1_Intron|GON4L_uc001fma.1_Intron|GON4L_uc001fmc.2_Intron|GON4L_uc001fmd.3_Intron|GON4L_uc009wri.2_Intron	NM_001037533	NP_001032622			gon-4-like isoform a						regulation of transcription, DNA-dependent	cytoplasm|nucleus	DNA binding			ovary(3)	3	Hepatocellular(266;0.0997)|all_hematologic(923;0.145)|all_neural(408;0.195)																	---	---	---	---
LMNA	4000	broad.mit.edu	37	1	156083114	156083115	+	5'Flank	INS	-	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:156083114_156083115insA	uc001fni.2	+						LMNA_uc001fnf.1_Intron|LMNA_uc001fng.2_5'Flank|LMNA_uc001fnh.2_5'Flank|LMNA_uc009wro.1_5'Flank	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				---	---	---	---
LMNA	4000	broad.mit.edu	37	1	156109034	156109034	+	3'UTR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:156109034delT	uc001fni.2	+	12					LMNA_uc001fnh.2_3'UTR|LMNA_uc009wro.1_3'UTR|LMNA_uc001fnk.2_3'UTR|LMNA_uc010phb.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				---	---	---	---
SEMA4A	64218	broad.mit.edu	37	1	156135456	156135457	+	Intron	INS	-	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:156135456_156135457insT	uc001fnl.2	+						SEMA4A_uc009wrq.2_Intron|SEMA4A_uc001fnm.2_Intron|SEMA4A_uc001fnn.2_Intron|SEMA4A_uc001fno.2_Intron	NM_022367	NP_071762			semaphorin B precursor						axon guidance	integral to membrane|plasma membrane	receptor activity			ovary(1)|skin(1)	2	Hepatocellular(266;0.158)																	---	---	---	---
Unknown	0	broad.mit.edu	37	1	156151165	156151165	+	IGR	DEL	A	-	-	rs74548425		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:156151165delA								SEMA4A (3631 upstream) : SLC25A44 (12565 downstream)																																			---	---	---	---
TMEM79	84283	broad.mit.edu	37	1	156258132	156258132	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:156258132delT	uc010phi.1	+						TMEM79_uc001fod.2_Intron|TMEM79_uc009wrw.2_Intron	NM_032323	NP_115699			transmembrane protein 79							integral to membrane				central_nervous_system(1)	1	Hepatocellular(266;0.158)																	---	---	---	---
TMEM79	84283	broad.mit.edu	37	1	156261416	156261416	+	3'UTR	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:156261416delG	uc010phi.1	+	4					TMEM79_uc001fod.2_3'UTR|TMEM79_uc009wrw.2_3'UTR|C1orf85_uc001fof.3_Intron|C1orf85_uc001fog.1_Intron	NM_032323	NP_115699			transmembrane protein 79							integral to membrane				central_nervous_system(1)	1	Hepatocellular(266;0.158)																	---	---	---	---
C1orf85	112770	broad.mit.edu	37	1	156264123	156264123	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:156264123delT	uc001foh.2	-						C1orf85_uc001fof.3_5'Flank|C1orf85_uc001fog.1_Intron|C1orf85_uc001foi.2_Intron|C1orf85_uc009wrx.2_Intron|C1orf85_uc001foj.2_Intron	NM_144580	NP_653181			kidney predominant protein NCU-G1 precursor						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)																	---	---	---	---
VHLL	391104	broad.mit.edu	37	1	156271831	156271832	+	5'Flank	DEL	AA	-	-	rs75439990		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:156271831_156271832delAA	uc001fok.2	-							NM_001004319	NP_001004319			von Hippel-Lindau tumor suppressor-like						protein ubiquitination	nucleus				ovary(1)	1	Hepatocellular(266;0.158)																	---	---	---	---
CCT3	7203	broad.mit.edu	37	1	156279226	156279226	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:156279226delT	uc001fol.1	-						CCT3_uc001fom.1_Intron|CCT3_uc001fon.1_Intron|CCT3_uc010phj.1_Intron|CCT3_uc010phk.1_Intron|CCT3_uc010phl.1_Intron	NM_005998	NP_005989			chaperonin containing TCP1, subunit 3 isoform a						'de novo' posttranslational protein folding	cytoskeleton|cytosol|plasma membrane	ATP binding|unfolded protein binding			ovary(1)|skin(1)	2	Hepatocellular(266;0.158)																	---	---	---	---
IQGAP3	128239	broad.mit.edu	37	1	156536653	156536654	+	Intron	DEL	CT	-	-	rs1778824		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:156536653_156536654delCT	uc001fpf.2	-						IQGAP3_uc009wsb.1_Intron	NM_178229	NP_839943			IQ motif containing GTPase activating protein 3						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)																	---	---	---	---
Unknown	0	broad.mit.edu	37	1	156651661	156651661	+	IGR	DEL	C	-	-	rs36101248		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:156651661delC								NES (4472 upstream) : CRABP2 (17749 downstream)																																			---	---	---	---
ARHGEF11	9826	broad.mit.edu	37	1	156920442	156920442	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:156920442delA	uc001fqo.2	-						ARHGEF11_uc010phu.1_5'Flank|ARHGEF11_uc001fqn.2_Intron|ARHGEF11_uc001fqp.1_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	156953003	156953003	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:156953003delT	uc001fqo.2	-						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	157088339	157088344	+	IGR	DEL	TTTCTT	-	-	rs10522191		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:157088339_157088344delTTTCTT								ETV3L (18739 upstream) : ETV3 (6115 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	157278936	157278937	+	IGR	INS	-	TG	TG			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:157278936_157278937insTG								ETV3 (170553 upstream) : FCRL5 (204231 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	157322763	157322763	+	IGR	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:157322763delC								ETV3 (214380 upstream) : FCRL5 (160405 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	158124069	158124069	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:158124069delT								KIRREL (58227 upstream) : CD1D (25668 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	158580421	158580421	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:158580421delA								OR10Z1 (3252 upstream) : SPTA1 (75 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	159069702	159069702	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:159069702delA								AIM2 (23055 upstream) : CADM3 (71675 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	159316871	159316871	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:159316871delA	uc001fts.3	-											Homo sapiens, clone IMAGE:3917623, mRNA.																														---	---	---	---
Unknown	0	broad.mit.edu	37	1	159363527	159363528	+	Intron	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:159363527_159363528delAA	uc001fts.3	-											Homo sapiens, clone IMAGE:3917623, mRNA.																														---	---	---	---
Unknown	0	broad.mit.edu	37	1	159546313	159546313	+	IGR	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:159546313delC								OR10J5 (40516 upstream) : APCS (11303 downstream)																																			---	---	---	---
DCAF8	50717	broad.mit.edu	37	1	160204933	160204933	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:160204933delT	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	160208555	160208555	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:160208555delA	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																		---	---	---	---
DCAF8	50717	broad.mit.edu	37	1	160215932	160215933	+	Intron	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:160215932_160215933delAA	uc001fvo.2	-						DCAF8_uc001fvn.2_Intron|DCAF8_uc009wth.2_Intron|DCAF8_uc010pjb.1_Intron|DCAF8_uc010pjc.1_Intron|DCAF8_uc001fvq.3_Intron|DCAF8_uc001fvp.3_Intron|DCAF8_uc001fvr.2_Intron	NM_015726	NP_056541			DDB1 and CUL4 associated factor 8							CUL4 RING ubiquitin ligase complex	protein binding			skin(2)	2																		---	---	---	---
NHLH1	4807	broad.mit.edu	37	1	160341681	160341681	+	3'UTR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:160341681delA	uc001fwa.2	+	2						NM_005598	NP_005589			nescient helix loop helix 1						cell differentiation|central nervous system development|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding			ovary(1)	1	all_cancers(52;7.11e-19)|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-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:160640798delT								SLAMF1 (23717 upstream) : CD48 (7740 downstream)																																			---	---	---	---
CD244	51744	broad.mit.edu	37	1	160806114	160806114	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:160806114delA	uc009wtq.2	-						CD244_uc001fxa.2_Intron|CD244_uc009wtp.2_Intron|CD244_uc009wtr.2_Intron	NM_016382	NP_057466			CD244 natural killer cell receptor 2B4						blood coagulation|leukocyte migration	integral to membrane|plasma membrane	protein binding|receptor activity			ovary(1)	1	all_cancers(52;2.72e-17)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.00737)															---	---	---	---
Unknown	0	broad.mit.edu	37	1	160905990	160905991	+	IGR	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:160905990_160905991delTT								ITLN1 (51030 upstream) : ITLN2 (8826 downstream)																																			---	---	---	---
DEDD	9191	broad.mit.edu	37	1	161103856	161103856	+	5'Flank	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:161103856delA	uc001fxz.2	-						DEDD_uc001fya.2_5'Flank|DEDD_uc001fyb.2_5'Flank|DEDD_uc010pkb.1_5'Flank|DEDD_uc001fyc.2_5'Flank	NM_001039712	NP_001034801			death effector domain-containing protein						apoptosis|induction of apoptosis via death domain receptors|negative regulation of transcription, DNA-dependent|spermatogenesis|transcription, DNA-dependent	cytoplasm|nucleolus	DNA binding|protein binding				0	all_cancers(52;3.39e-19)|Breast(13;0.000577)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.00165)															---	---	---	---
B4GALT3	8703	broad.mit.edu	37	1	161149192	161149193	+	5'Flank	INS	-	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:161149192_161149193insT	uc001fyq.1	-						B4GALT3_uc001fyr.1_5'Flank|B4GALT3_uc001fys.1_5'Flank|B4GALT3_uc009wud.1_5'Flank	NM_003779	NP_003770			UDP-Gal:betaGlcNAc beta 1,4-						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)													---	---	---	---
PCP4L1	654790	broad.mit.edu	37	1	161238055	161238055	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:161238055delA	uc001gad.2	+							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)															---	---	---	---
FCRLB	127943	broad.mit.edu	37	1	161690064	161690064	+	5'Flank	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:161690064delA	uc001gbh.2	+						FCRLB_uc009wus.2_5'Flank|FCRLB_uc001gbj.2_5'Flank|FCRLB_uc001gbk.2_5'Flank|FCRLB_uc001gbl.2_5'Flank|FCRLB_uc001gbm.2_5'Flank|FCRLB_uc001gbi.2_5'Flank	NM_001002901	NP_001002901			Fc receptor-like B							endoplasmic reticulum					0	all_hematologic(112;0.0359)		BRCA - Breast invasive adenocarcinoma(70;0.00634)															---	---	---	---
ATF6	22926	broad.mit.edu	37	1	161826512	161826512	+	Intron	DEL	T	-	-	rs3835612		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:161826512delT	uc001gbr.2	+						ATF6_uc001gbq.1_Intron	NM_007348	NP_031374			activating transcription factor 6						positive regulation of transcription from RNA polymerase II promoter involved in unfolded protein response|protein folding	endoplasmic reticulum membrane|Golgi membrane|integral to membrane|nuclear envelope|nucleoplasm	protein dimerization activity|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription coactivator activity			ovary(2)|skin(1)	3	all_hematologic(112;0.156)		BRCA - Breast invasive adenocarcinoma(70;0.00953)															---	---	---	---
ATF6	22926	broad.mit.edu	37	1	161917858	161917858	+	Intron	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:161917858delC	uc001gbr.2	+							NM_007348	NP_031374			activating transcription factor 6						positive regulation of transcription from RNA polymerase II promoter involved in unfolded protein response|protein folding	endoplasmic reticulum membrane|Golgi membrane|integral to membrane|nuclear envelope|nucleoplasm	protein dimerization activity|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription coactivator activity			ovary(2)|skin(1)	3	all_hematologic(112;0.156)		BRCA - Breast invasive adenocarcinoma(70;0.00953)															---	---	---	---
SH2D1B	117157	broad.mit.edu	37	1	162372712	162372715	+	Intron	DEL	TTTC	-	-	rs3122549	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:162372712_162372715delTTTC	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	162473698	162473698	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:162473698delT	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)															---	---	---	---
Unknown	0	broad.mit.edu	37	1	162923432	162923433	+	IGR	DEL	TT	-	-	rs75944824		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:162923432_162923433delTT								C1orf110 (84827 upstream) : RGS4 (114963 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	163014562	163014565	+	IGR	DEL	CCTT	-	-	rs67487115		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:163014562_163014565delCCTT								C1orf110 (175957 upstream) : RGS4 (23831 downstream)																																			---	---	---	---
RGS5	8490	broad.mit.edu	37	1	163137887	163137887	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:163137887delA	uc001gcn.2	-						RGS5_uc009wvb.2_Intron	NM_003617	NP_003608			regulator of G-protein signalling 5						negative regulation of signal transduction|regulation of G-protein coupled receptor protein signaling pathway	cytoplasm|plasma membrane	GTPase activator activity|signal transducer activity				0			LUSC - Lung squamous cell carcinoma(543;0.187)															---	---	---	---
Unknown	0	broad.mit.edu	37	1	163494706	163494707	+	IGR	INS	-	GC	GC	rs71681156		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:163494706_163494707insGC								NUF2 (169153 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	164203983	164203984	+	IGR	INS	-	AG	AG	rs35026099		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:164203983_164203984insAG								NUF2 (878430 upstream) : PBX1 (324818 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	164339749	164339749	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:164339749delT								None (None upstream) : PBX1 (189053 downstream)																																			---	---	---	---
PBX1	5087	broad.mit.edu	37	1	164591072	164591072	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:164591072delT	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	164789505	164789506	+	Intron	DEL	AG	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:164789505_164789506delAG	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	164893267	164893267	+	IGR	DEL	T	-	-	rs77912724		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:164893267delT								PBX1 (38967 upstream) : LMX1A (277838 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	165589653	165589654	+	IGR	INS	-	C	C	rs35092535	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:165589653_165589654insC								LOC400794 (38312 upstream) : MGST3 (10796 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	165680307	165680307	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:165680307delT								ALDH9A1 (12407 upstream) : TMCO1 (13223 downstream)																																			---	---	---	---
FAM78B	149297	broad.mit.edu	37	1	166054407	166054407	+	Intron	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:166054407delC	uc001gdr.2	-						FAM78B_uc010plc.1_Intron	NM_001017961	NP_001017961			hypothetical protein LOC149297											central_nervous_system(1)|skin(1)	2	all_hematologic(923;0.0813)|Acute lymphoblastic leukemia(8;0.155)																	---	---	---	---
Unknown	0	broad.mit.edu	37	1	166260957	166260957	+	IGR	DEL	T	-	-	rs72156784		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:166260957delT								FAM78B (124751 upstream) : FMO9P (312196 downstream)																																			---	---	---	---
MAEL	84944	broad.mit.edu	37	1	166990103	166990103	+	Intron	DEL	A	-	-	rs148294601	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:166990103delA	uc001gdy.1	+						MAEL_uc001gdz.1_Intron|MAEL_uc009wvf.1_Intron	NM_032858	NP_116247			maelstrom homolog						cell differentiation|DNA methylation involved in gamete generation|gene silencing by RNA|multicellular organismal development|piRNA metabolic process|spermatogenesis	piP-body	DNA binding			skin(1)	1																		---	---	---	---
CD247	919	broad.mit.edu	37	1	167407407	167407407	+	Intron	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:167407407delC	uc001gei.3	-						CD247_uc001gej.3_Intron|CD247_uc001gek.2_Intron	NM_198053	NP_932170			T-cell receptor zeta chain isoform 1 precursor						interspecies interaction between organisms|regulation of defense response to virus by virus|T cell costimulation|T cell receptor signaling pathway|viral reproduction	cytoplasm|integral to membrane	protein homodimerization activity|transmembrane receptor activity				0			LUSC - Lung squamous cell carcinoma(543;0.236)															---	---	---	---
DCAF6	55827	broad.mit.edu	37	1	167976517	167976517	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:167976517delT	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																		---	---	---	---
GPR161	23432	broad.mit.edu	37	1	168054506	168054506	+	3'UTR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:168054506delT	uc001gfc.2	-	8					GPR161_uc001gfb.2_3'UTR|GPR161_uc010pll.1_3'UTR|GPR161_uc010plm.1_3'UTR|GPR161_uc009wvo.2_3'UTR|GPR161_uc001gfd.2_3'UTR|GPR161_uc010pln.1_3'UTR	NM_153832	NP_722561			G protein-coupled receptor 161 isoform 2						multicellular organismal development	integral to membrane|plasma membrane	G-protein coupled receptor activity				0	all_hematologic(923;0.215)															OREG0013978	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
GPR161	23432	broad.mit.edu	37	1	168086739	168086739	+	Intron	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:168086739delC	uc001gfc.2	-						GPR161_uc001gfb.2_Intron|GPR161_uc010pll.1_Intron|GPR161_uc010plm.1_Intron|GPR161_uc009wvo.2_Intron|GPR161_uc001gfd.2_Intron|GPR161_uc010pln.1_Intron	NM_153832	NP_722561			G protein-coupled receptor 161 isoform 2						multicellular organismal development	integral to membrane|plasma membrane	G-protein coupled receptor activity				0	all_hematologic(923;0.215)																	---	---	---	---
TIPRL	261726	broad.mit.edu	37	1	168146104	168146104	+	5'Flank	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:168146104delA	uc001gfg.2	+						TIPRL_uc001gfh.2_5'Flank|TIPRL_uc001gff.2_5'Flank	NM_152902	NP_690866			TIP41, TOR signalling pathway regulator-like						DNA damage checkpoint|negative regulation of protein phosphatase type 2A activity	cytoplasm	protein binding			ovary(1)	1	all_hematologic(923;0.215)																	---	---	---	---
TBX19	9095	broad.mit.edu	37	1	168245267	168245267	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:168245267delT	uc001gfj.3	+							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	168364392	168364395	+	IGR	DEL	TTTT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:168364392_168364395delTTTT								MIR557 (19533 upstream) : XCL2 (145610 downstream)																																			---	---	---	---
F5	2153	broad.mit.edu	37	1	169484915	169484915	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:169484915delT	uc001ggg.1	-							NM_000130	NP_000121			coagulation factor V precursor						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)													---	---	---	---
F5	2153	broad.mit.edu	37	1	169520687	169520687	+	Intron	DEL	G	-	-	rs145185031		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:169520687delG	uc001ggg.1	-						F5_uc010plr.1_Intron	NM_000130	NP_000121			coagulation factor V precursor						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)													---	---	---	---
SELL	6402	broad.mit.edu	37	1	169670640	169670640	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:169670640delT	uc001ggk.2	-						C1orf112_uc001ggj.2_Intron|SELL_uc010pls.1_Intron	NM_000655	NP_000646			selectin L precursor						blood coagulation|cell adhesion|leukocyte migration|regulation of immune response	integral to plasma membrane	glycosphingolipid binding|heparin binding|protease binding|sugar binding				0	all_hematologic(923;0.208)																	---	---	---	---
C1orf112	55732	broad.mit.edu	37	1	169817057	169817057	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:169817057delA	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)																	---	---	---	---
Unknown	0	broad.mit.edu	37	1	170052275	170052275	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:170052275delA								KIFAP3 (8396 upstream) : METTL11B (62913 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	170090974	170090975	+	IGR	DEL	AC	-	-	rs34427780		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:170090974_170090975delAC								KIFAP3 (47095 upstream) : METTL11B (24213 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	170771651	170771652	+	IGR	INS	-	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:170771651_170771652insT								PRRX1 (63111 upstream) : C1orf129 (132960 downstream)																																			---	---	---	---
C1orf129	80133	broad.mit.edu	37	1	170975963	170975963	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:170975963delT	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)																	---	---	---	---
C1orf129	80133	broad.mit.edu	37	1	170998366	170998366	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:170998366delT	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)																	---	---	---	---
FMO1	2326	broad.mit.edu	37	1	171252450	171252450	+	Intron	DEL	A	-	-	rs67171509		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:171252450delA	uc009wvz.2	+						FMO1_uc010pme.1_Intron|FMO1_uc001ghl.2_Intron|FMO1_uc001ghm.2_Intron|FMO1_uc001ghn.2_Intron	NM_002021	NP_002012			flavin containing monooxygenase 1						NADPH oxidation|organic acid metabolic process|toxin metabolic process|xenobiotic metabolic process	endoplasmic reticulum lumen|integral to membrane|intrinsic to endoplasmic reticulum 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)																	---	---	---	---
Unknown	0	broad.mit.edu	37	1	171351888	171351888	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:171351888delT								FMO4 (40666 upstream) : BAT2L2 (102778 downstream)																																			---	---	---	---
BAT2L2	23215	broad.mit.edu	37	1	171452363	171452364	+	5'Flank	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:171452363_171452364delAA	uc010pmg.1	+						BAT2L2_uc001ghq.1_5'Flank|BAT2L2_uc001ghr.1_5'Flank	NM_015172	NP_055987			HBxAg transactivated protein 2								protein C-terminus binding				0																		---	---	---	---
VAMP4	8674	broad.mit.edu	37	1	171697650	171697650	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:171697650delA	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	171901456	171901457	+	Intron	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:171901456_171901457delTT	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																		---	---	---	---
DNM3	26052	broad.mit.edu	37	1	172165809	172165809	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:172165809delT	uc001gie.2	+						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																		---	---	---	---
C1orf9	51430	broad.mit.edu	37	1	172571102	172571102	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:172571102delA	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	172688306	172688306	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:172688306delT								FASLG (52296 upstream) : TNFSF18 (322054 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	172989892	172989892	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:172989892delT								FASLG (353882 upstream) : TNFSF18 (20468 downstream)																																			---	---	---	---
TNFSF18	8995	broad.mit.edu	37	1	173020270	173020270	+	5'Flank	DEL	A	-	-	rs72718913	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:173020270delA	uc001giu.2	-							NM_005092	NP_005083			tumor necrosis factor (ligand) superfamily,						anti-apoptosis|cell-cell signaling|immune response|signal transduction	extracellular space|integral to membrane	cytokine activity|tumor necrosis factor receptor binding			central_nervous_system(1)	1																		---	---	---	---
SLC9A11	284525	broad.mit.edu	37	1	173556683	173556683	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-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	173657723	173657724	+	IGR	DEL	CT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:173657723_173657724delCT								ANKRD45 (18722 upstream) : KLHL20 (26356 downstream)																																			---	---	---	---
DARS2	55157	broad.mit.edu	37	1	173798343	173798344	+	Intron	DEL	GT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:173798343_173798344delGT	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	173879823	173879823	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:173879823delA	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)													---	---	---	---
RC3H1	149041	broad.mit.edu	37	1	173910258	173910259	+	Intron	INS	-	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:173910258_173910259insA	uc001gju.3	-						RC3H1_uc010pms.1_Intron|RC3H1_uc001gjv.2_Intron|RC3H1_uc010pmt.1_Intron	NM_172071	NP_742068			roquin						cytoplasmic mRNA processing body assembly|negative regulation of activated T cell proliferation|negative regulation of B cell proliferation|negative regulation of germinal center formation|negative regulation of T-helper cell differentiation|nuclear-transcribed mRNA catabolic process|regulation of mRNA stability|regulation of T cell receptor signaling pathway	cytoplasmic mRNA processing body|stress granule	mRNA 3'-UTR binding|ubiquitin-protein ligase activity|zinc ion binding			ovary(2)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	1	173966054	173966054	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:173966054delT								RC3H1 (3844 upstream) : RABGAP1L (162580 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	174077496	174077497	+	IGR	INS	-	AC	AC	rs145301621	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:174077496_174077497insAC								RC3H1 (115286 upstream) : RABGAP1L (51137 downstream)																																			---	---	---	---
RABGAP1L	9910	broad.mit.edu	37	1	174219938	174219938	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:174219938delT	uc001gjx.2	+						RABGAP1L_uc009wwq.1_Intron|RABGAP1L_uc001gjw.2_Intron|RABGAP1L_uc001gjy.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	174341836	174341836	+	Intron	DEL	T	-	-	rs74128374	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:174341836delT	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	174353443	174353443	+	Intron	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:174353443delG	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	174759348	174759349	+	Intron	DEL	AA	-	-	rs112964112		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:174759348_174759349delAA	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	174786172	174786172	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:174786172delT	uc001gjx.2	+						RABGAP1L_uc001gkb.3_Intron|RABGAP1L_uc001gkc.3_Intron|RABGAP1L_uc001gkd.3_Intron|RABGAP1L_uc001gke.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	174914708	174914708	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:174914708delT	uc001gjx.2	+						RABGAP1L_uc001gkb.3_Intron|RABGAP1L_uc001gkc.3_Intron|RABGAP1L_uc001gkd.3_Intron|RABGAP1L_uc001gke.3_Intron|RABGAP1L_uc001gkf.2_Intron|RABGAP1L_uc001gkg.2_Intron|RABGAP1L_uc001gkh.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																		---	---	---	---
TNR	7143	broad.mit.edu	37	1	175296106	175296106	+	Intron	DEL	T	-	-	rs77303805		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:175296106delT	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)																	---	---	---	---
TNR	7143	broad.mit.edu	37	1	175390133	175390133	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:175390133delT	uc009wwu.1	-						TNR_uc010pmz.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)																	---	---	---	---
TNR	7143	broad.mit.edu	37	1	175449431	175449431	+	Intron	DEL	A	-	-	rs34031344		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:175449431delA	uc009wwu.1	-						TNR_uc010pmz.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)																	---	---	---	---
RFWD2	64326	broad.mit.edu	37	1	175958359	175958359	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:175958359delA	uc001gku.1	-						RFWD2_uc001gkv.1_Intron|RFWD2_uc001gkw.1_Intron|RFWD2_uc009wwv.2_Intron|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																		---	---	---	---
RFWD2	64326	broad.mit.edu	37	1	176033799	176033799	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:176033799delT	uc001gku.1	-						RFWD2_uc001gkv.1_Intron|RFWD2_uc001gkw.1_Intron|RFWD2_uc009wwv.2_Intron|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																		---	---	---	---
RFWD2	64326	broad.mit.edu	37	1	176145160	176145160	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:176145160delA	uc001gku.1	-						RFWD2_uc001gkv.1_Intron|RFWD2_uc001gkw.1_Intron|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																		---	---	---	---
RFWD2	64326	broad.mit.edu	37	1	176150978	176150979	+	Intron	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:176150978_176150979delAA	uc001gku.1	-						RFWD2_uc001gkv.1_Intron|RFWD2_uc001gkw.1_Intron|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	176815423	176815423	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:176815423delA								PAPPA2 (3455 upstream) : ASTN1 (11018 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	177321426	177321427	+	IGR	DEL	AA	-	-	rs111489100		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:177321426_177321427delAA								FAM5B (69869 upstream) : SEC16B (576062 downstream)																																			---	---	---	---
SEC16B	89866	broad.mit.edu	37	1	177963158	177963158	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:177963158delA	uc001glj.1	-						SEC16B_uc001glk.1_Intron	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	178663404	178663404	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:178663404delT								C1orf220 (145380 upstream) : RALGPS2 (30896 downstream)																																			---	---	---	---
RALGPS2	55103	broad.mit.edu	37	1	178753846	178753846	+	Intron	DEL	T	-	-	rs77811423		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:178753846delT	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																		---	---	---	---
Unknown	0	broad.mit.edu	37	1	178917226	178917227	+	IGR	INS	-	C	C	rs142096720	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:178917226_178917227insC								RALGPS2 (27991 upstream) : FAM20B (77847 downstream)																																			---	---	---	---
SOAT1	6646	broad.mit.edu	37	1	179269310	179269311	+	Intron	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:179269310_179269311delAA	uc001gml.2	+						SOAT1_uc010pni.1_Intron|SOAT1_uc001gmm.2_Intron|SOAT1_uc010pnj.1_Intron	NM_003101	NP_003092			sterol O-acyltransferase 1						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)													---	---	---	---
C1orf125	126859	broad.mit.edu	37	1	179402038	179402038	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:179402038delA	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																		---	---	---	---
TDRD5	163589	broad.mit.edu	37	1	179586760	179586760	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:179586760delT	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	179612461	179612461	+	Intron	DEL	A	-	-	rs10913844	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:179612461delA	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																		---	---	---	---
TOR1AIP2	163590	broad.mit.edu	37	1	179844102	179844103	+	Intron	DEL	TC	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-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																		---	---	---	---
Unknown	0	broad.mit.edu	37	1	179904131	179904131	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-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	180028389	180028389	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:180028389delA	uc001gnt.2	+						CEP350_uc009wxl.2_Intron	NM_014810	NP_055625			centrosome-associated protein 350							centrosome|nucleus|spindle				ovary(4)	4																		---	---	---	---
Unknown	0	broad.mit.edu	37	1	180177868	180177868	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:180177868delT								FLJ23867 (8011 upstream) : LHX4 (21574 downstream)																																			---	---	---	---
ACBD6	84320	broad.mit.edu	37	1	180400660	180400660	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:180400660delA	uc001gog.2	-							NM_032360	NP_115736			acyl-coenzyme A binding domain containing 6							cytoplasm|nucleus	fatty-acyl-CoA binding			ovary(1)	1																		---	---	---	---
XPR1	9213	broad.mit.edu	37	1	180685391	180685392	+	Intron	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:180685391_180685392delTT	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																		---	---	---	---
STX6	10228	broad.mit.edu	37	1	180953685	180953685	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:180953685delA	uc010pnq.1	-						STX6_uc001goo.2_Intron|STX6_uc010pnr.1_Intron	NM_005819	NP_005810			syntaxin 6						Golgi vesicle transport|intracellular protein transport|vesicle fusion	clathrin-coated vesicle|early endosome|integral to membrane|perinuclear region of cytoplasm|plasma membrane|trans-Golgi network membrane	SNAP receptor activity			ovary(1)	1																		---	---	---	---
MR1	3140	broad.mit.edu	37	1	181017671	181017671	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:181017671delA	uc001goq.1	+						MR1_uc001gop.2_Intron|MR1_uc001gor.1_Intron|MR1_uc001gos.1_Intron|MR1_uc010pns.1_Intron	NM_001531	NP_001522			major histocompatibility complex, class						antigen processing and presentation of peptide antigen via MHC class I|immune response	endoplasmic reticulum|extracellular region|integral to membrane|MHC class I protein complex	MHC class I receptor activity			skin(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	1	181073487	181073489	+	IGR	DEL	ACA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:181073487_181073489delACA								IER5 (13510 upstream) : CACNA1E (379227 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	181093653	181093653	+	IGR	DEL	T	-	-	rs60841769		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:181093653delT								IER5 (33676 upstream) : CACNA1E (359063 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	181099943	181099943	+	IGR	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:181099943delG								IER5 (39966 upstream) : CACNA1E (352773 downstream)																																			---	---	---	---
CACNA1E	777	broad.mit.edu	37	1	181507802	181507802	+	Intron	DEL	A	-	-	rs34351318		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:181507802delA	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	181549518	181549519	+	Intron	INS	-	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:181549518_181549519insT	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	181629171	181629172	+	Intron	INS	-	CA	CA			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:181629171_181629172insCA	uc001gow.2	+						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	181642359	181642366	+	Intron	DEL	TGTGTGTG	-	-	rs112579035		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:181642359_181642366delTGTGTGTG	uc001gow.2	+						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	181680214	181680214	+	Intron	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:181680214delG	uc001gow.2	+						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	181758171	181758171	+	Intron	DEL	T	-	-	rs11353754		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:181758171delT	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	181966261	181966261	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:181966261delT								CACNA1E (195548 upstream) : ZNF648 (57446 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	182216558	182216558	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:182216558delA								ZNF648 (185711 upstream) : GLUL (135111 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	182285643	182285645	+	IGR	DEL	AAG	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:182285643_182285645delAAG								ZNF648 (254796 upstream) : GLUL (66024 downstream)																																			---	---	---	---
RGSL1	353299	broad.mit.edu	37	1	182473901	182473901	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:182473901delA	uc009wxw.2	+						RGSL1_uc010pnu.1_Intron|RGSL1_uc009wxx.1_Intron	NM_001137669	NP_001131141			regulator of G-protein signaling like 1							integral to membrane	signal transducer activity			central_nervous_system(1)	1																		---	---	---	---
RGSL1	353299	broad.mit.edu	37	1	182488146	182488146	+	Intron	DEL	G	-	-	rs151228309		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:182488146delG	uc009wxw.2	+						RGSL1_uc010pnu.1_Intron|RGSL1_uc009wxx.1_Intron	NM_001137669	NP_001131141			regulator of G-protein signaling like 1							integral to membrane	signal transducer activity			central_nervous_system(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	1	182746088	182746088	+	IGR	DEL	A	-	-	rs79367307		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:182746088delA								RGS8 (104021 upstream) : NPL (12784 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	182978125	182978125	+	IGR	DEL	T	-	-	rs35286047		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:182978125delT								C1orf14 (55572 upstream) : LAMC1 (14470 downstream)																																			---	---	---	---
LAMC2	3918	broad.mit.edu	37	1	183211975	183211978	+	Intron	DEL	TTTT	-	-	rs34898091		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:183211975_183211978delTTTT	uc001gqa.2	+							NM_005562	NP_005553			laminin, gamma 2 isoform a precursor						cell adhesion|epidermis development|hemidesmosome assembly		heparin binding			skin(2)|ovary(1)	3																		---	---	---	---
RGL1	23179	broad.mit.edu	37	1	183691364	183691366	+	Intron	DEL	AAA	-	-	rs79769872		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:183691364_183691366delAAA	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																		---	---	---	---
Unknown	0	broad.mit.edu	37	1	184220369	184220370	+	IGR	DEL	CT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:184220369_184220370delCT								TSEN15 (177028 upstream) : C1orf21 (135780 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	184320812	184320815	+	IGR	DEL	AGGA	-	-	rs71904036	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:184320812_184320815delAGGA								TSEN15 (277471 upstream) : C1orf21 (35335 downstream)																																			---	---	---	---
C1orf21	81563	broad.mit.edu	37	1	184387511	184387511	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:184387511delT	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)														---	---	---	---
C1orf21	81563	broad.mit.edu	37	1	184562406	184562407	+	Intron	DEL	TG	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:184562406_184562407delTG	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)														---	---	---	---
EDEM3	80267	broad.mit.edu	37	1	184681066	184681067	+	Intron	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:184681066_184681067delTT	uc010pok.1	-						EDEM3_uc010pol.1_Intron|EDEM3_uc010pom.1_Intron	NM_025191	NP_079467			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	calcium ion binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity|misfolded protein binding			skin(1)	1																		---	---	---	---
FAM129A	116496	broad.mit.edu	37	1	184799628	184799628	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:184799628delA	uc001gra.2	-						FAM129A_uc001grb.1_Intron|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																		---	---	---	---
C1orf26	54823	broad.mit.edu	37	1	185140797	185140797	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-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	185261461	185261461	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:185261461delT								C1orf26 (549 upstream) : IVNS1ABP (4063 downstream)																																			---	---	---	---
IVNS1ABP	10625	broad.mit.edu	37	1	185269101	185269101	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:185269101delA	uc001grl.2	-						IVNS1ABP_uc001gri.2_Intron|IVNS1ABP_uc001grj.2_Intron|IVNS1ABP_uc009wyj.2_Intron|IVNS1ABP_uc009wyk.2_Intron|IVNS1ABP_uc001grm.2_Intron	NM_006469	NP_006460			influenza virus NS1A binding protein						interspecies interaction between organisms|response to virus|RNA splicing|transcription from RNA polymerase III promoter	cytoplasm|cytoskeleton|spliceosomal complex|transcription factor complex				ovary(4)|central_nervous_system(1)	5																		---	---	---	---
Unknown	0	broad.mit.edu	37	1	185463324	185463324	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:185463324delT								IVNS1ABP (176863 upstream) : HMCN1 (240359 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	185636983	185636983	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:185636983delT								IVNS1ABP (350522 upstream) : HMCN1 (66700 downstream)																																			---	---	---	---
HMCN1	83872	broad.mit.edu	37	1	185953284	185953284	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:185953284delT	uc001grq.1	+						HMCN1_uc001grr.1_Intron	NM_031935	NP_114141			hemicentin 1 precursor						response to stimulus|visual perception	basement membrane	calcium ion binding			ovary(22)|skin(1)	23																		---	---	---	---
HMCN1	83872	broad.mit.edu	37	1	186042923	186042923	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:186042923delA	uc001grq.1	+							NM_031935	NP_114141			hemicentin 1 precursor						response to stimulus|visual perception	basement membrane	calcium ion binding			ovary(22)|skin(1)	23																		---	---	---	---
HMCN1	83872	broad.mit.edu	37	1	186076225	186076226	+	Intron	DEL	TT	-	-	rs79076408		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:186076225_186076226delTT	uc001grq.1	+							NM_031935	NP_114141			hemicentin 1 precursor						response to stimulus|visual perception	basement membrane	calcium ion binding			ovary(22)|skin(1)	23																		---	---	---	---
HMCN1	83872	broad.mit.edu	37	1	186077432	186077432	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:186077432delA	uc001grq.1	+							NM_031935	NP_114141			hemicentin 1 precursor						response to stimulus|visual perception	basement membrane	calcium ion binding			ovary(22)|skin(1)	23																		---	---	---	---
HMCN1	83872	broad.mit.edu	37	1	186115162	186115166	+	Intron	DEL	AAAAA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:186115162_186115166delAAAAA	uc001grq.1	+						HMCN1_uc001grs.1_Intron	NM_031935	NP_114141			hemicentin 1 precursor						response to stimulus|visual perception	basement membrane	calcium ion binding			ovary(22)|skin(1)	23																		---	---	---	---
TPR	7175	broad.mit.edu	37	1	186319227	186319227	+	Intron	DEL	T	-	-	rs115878910	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:186319227delT	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								---	---	---	---
Unknown	0	broad.mit.edu	37	1	186613151	186613151	+	IGR	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:186613151delC								PDC (182912 upstream) : PTGS2 (27794 downstream)																																			---	---	---	---
PLA2G4A	5321	broad.mit.edu	37	1	186955367	186955367	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:186955367delT	uc001gsc.2	+						PLA2G4A_uc010pos.1_Intron	NM_024420	NP_077734			cytosolic phospholipase A2, group IVA						phospholipid catabolic process|platelet activating factor biosynthetic process|platelet activation	cytosol|endoplasmic reticulum membrane	calcium ion binding|calcium-dependent phospholipid binding|lysophospholipase activity			lung(2)|breast(1)	3					Flunisolide(DB00180)|Fluocinolone Acetonide(DB00591)|Fluocinonide(DB01047)|Fluorometholone(DB00324)|Flurandrenolide(DB00846)|Fluticasone Propionate(DB00588)|Medrysone(DB00253)|Quinacrine(DB01103)													---	---	---	---
Unknown	0	broad.mit.edu	37	1	187057899	187057899	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:187057899delT								PLA2G4A (99794 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	187683958	187683958	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:187683958delT								PLA2G4A (725853 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	187863271	187863272	+	IGR	DEL	TT	-	-	rs10602627		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:187863271_187863272delTT								PLA2G4A (905166 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	188033469	188033472	+	IGR	DEL	TTTT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:188033469_188033472delTTTT								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	188561127	188561127	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:188561127delA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	189756870	189756871	+	IGR	DEL	TT	-	-	rs67326976		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:189756870_189756871delTT								None (None upstream) : FAM5C (309926 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	189957424	189957424	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:189957424delT								None (None upstream) : FAM5C (109373 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	190772096	190772096	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:190772096delT								FAM5C (325337 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	190854123	190854124	+	IGR	DEL	AC	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:190854123_190854124delAC								FAM5C (407364 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	192091461	192091461	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:192091461delT								None (None upstream) : RGS18 (36131 downstream)																																			---	---	---	---
RGS18	64407	broad.mit.edu	37	1	192128012	192128012	+	Intron	DEL	A	-	-	rs28417375		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:192128012delA	uc001gsg.2	+							NM_130782	NP_570138			regulator of G-protein signalling 18						negative regulation of signal transduction	cytoplasm|plasma membrane	GTPase activator activity|signal transducer activity			ovary(3)	3																		---	---	---	---
RGS18	64407	broad.mit.edu	37	1	192128076	192128076	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:192128076delA	uc001gsg.2	+							NM_130782	NP_570138			regulator of G-protein signalling 18						negative regulation of signal transduction	cytoplasm|plasma membrane	GTPase activator activity|signal transducer activity			ovary(3)	3																		---	---	---	---
RGS21	431704	broad.mit.edu	37	1	192292721	192292721	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:192292721delA	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	192962650	192962650	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:192962650delT								RGS2 (181244 upstream) : UCHL5 (22250 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	193514529	193514530	+	IGR	DEL	AG	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:193514529_193514530delAG								CDC73 (290589 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	193565574	193565574	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:193565574delA								CDC73 (341634 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	193743266	193743266	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:193743266delT								CDC73 (519326 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	194574512	194574512	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:194574512delT								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	194918305	194918305	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:194918305delA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	194977171	194977171	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:194977171delA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	196717239	196717240	+	IGR	DEL	GT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:196717239_196717240delGT								CFH (608 upstream) : CFHR3 (26690 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	196719526	196719526	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:196719526delA								CFH (2895 upstream) : CFHR3 (24404 downstream)																																			---	---	---	---
CRB1	23418	broad.mit.edu	37	1	197411573	197411573	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:197411573delA	uc001gtz.2	+						CRB1_uc010poz.1_Intron|CRB1_uc010ppa.1_Intron|CRB1_uc009wza.2_Intron|CRB1_uc010ppb.1_Intron|CRB1_uc010ppd.1_Intron|CRB1_uc001gub.1_3'UTR	NM_201253	NP_957705			crumbs homolog 1 precursor						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																		---	---	---	---
CRB1	23418	broad.mit.edu	37	1	197427490	197427490	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:197427490delT	uc001gtz.2	+						CRB1_uc010poz.1_Intron|CRB1_uc010ppa.1_Intron|CRB1_uc009wza.2_Intron|CRB1_uc010ppb.1_Intron|CRB1_uc010ppd.1_Intron	NM_201253	NP_957705			crumbs homolog 1 precursor						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																		---	---	---	---
DENND1B	163486	broad.mit.edu	37	1	197721108	197721110	+	Intron	DEL	AGA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:197721108_197721110delAGA	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	198002846	198002847	+	IGR	DEL	TG	-	-	rs113411653		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:198002846_198002847delTG								LHX9 (101131 upstream) : NEK7 (123261 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	198097080	198097080	+	IGR	DEL	T	-	-	rs59967617	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:198097080delT								LHX9 (195365 upstream) : NEK7 (29028 downstream)																																			---	---	---	---
NEK7	140609	broad.mit.edu	37	1	198163430	198163430	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:198163430delT	uc001gun.3	+							NM_133494	NP_598001			NIMA-related kinase 7							cytoplasm	ATP binding|metal ion binding|protein binding|protein serine/threonine kinase activity			stomach(2)|lung(1)|ovary(1)	4																		---	---	---	---
Unknown	0	broad.mit.edu	37	1	198952999	198953001	+	IGR	DEL	TTT	-	-	rs71915875		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:198952999_198953001delTTT								MIR181A1 (124717 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	199186858	199186858	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:199186858delT								MIR181A1 (358576 upstream) : NR5A2 (809912 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	199927123	199927123	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:199927123delA								None (None upstream) : NR5A2 (69647 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	199969266	199969267	+	IGR	INS	-	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:199969266_199969267insT								None (None upstream) : NR5A2 (27503 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	199980161	199980162	+	IGR	INS	-	A	A	rs144087824	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:199980161_199980162insA								None (None upstream) : NR5A2 (16608 downstream)																																			---	---	---	---
NR5A2	2494	broad.mit.edu	37	1	200124658	200124660	+	Intron	DEL	TCA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:200124658_200124660delTCA	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)																	---	---	---	---
KIF14	9928	broad.mit.edu	37	1	200544882	200544882	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:200544882delA	uc010ppk.1	-						KIF14_uc010ppj.1_Intron	NM_014875	NP_055690			kinesin family member 14						microtubule-based movement	cytoplasm|microtubule|nucleus|spindle	ATP binding|microtubule motor activity|protein binding			breast(3)|ovary(2)|skin(2)	7																		---	---	---	---
DDX59	83479	broad.mit.edu	37	1	200632979	200632979	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-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																		---	---	---	---
CAMSAP1L1	23271	broad.mit.edu	37	1	200788755	200788755	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:200788755delT	uc001gvl.2	+						CAMSAP1L1_uc001gvk.2_Intron|CAMSAP1L1_uc001gvm.2_Intron	NM_203459	NP_982284			calmodulin regulated spectrin-associated protein							cytoplasm|microtubule	protein binding			ovary(2)|large_intestine(1)|pancreas(1)	4																		---	---	---	---
CACNA1S	779	broad.mit.edu	37	1	201063292	201063292	+	Intron	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:201063292delC	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)													---	---	---	---
NAV1	89796	broad.mit.edu	37	1	201685143	201685144	+	Intron	INS	-	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:201685143_201685144insA	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																		---	---	---	---
NAV1	89796	broad.mit.edu	37	1	201694922	201694922	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:201694922delA	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	201820591	201820591	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:201820591delT	uc001gwz.2	+							NM_018085	NP_060555			importin 9						protein import into nucleus	cytoplasm|nucleus	histone binding|protein transporter activity			ovary(2)	2																		---	---	---	---
ELF3	1999	broad.mit.edu	37	1	201985745	201985745	+	3'UTR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:201985745delT	uc001gxg.3	+	8					ELF3_uc001gxi.3_3'UTR|ELF3_uc001gxh.3_3'UTR	NM_004433	NP_004424			E74-like factor 3 (ets domain transcription						epidermis development|epithelial cell differentiation|inflammatory response|mammary gland involution|negative regulation of transcription, DNA-dependent|positive regulation of transcription, DNA-dependent|transcription from RNA polymerase II promoter	Golgi apparatus|nucleus	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription coactivator activity				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	1	202025488	202025488	+	IGR	DEL	T	-	-	rs67454679		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:202025488delT								ELF3 (39182 upstream) : GPR37L1 (66541 downstream)																																			---	---	---	---
PPP1R12B	4660	broad.mit.edu	37	1	202407190	202407190	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:202407190delT	uc001gya.1	+						PPP1R12B_uc001gxy.2_Frame_Shift_Del_p.V499fs|PPP1R12B_uc009xad.1_Frame_Shift_Del_p.V305fs|PPP1R12B_uc009xae.1_3'UTR|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)															---	---	---	---
PPP1R12B	4660	broad.mit.edu	37	1	202510276	202510278	+	Intron	DEL	AAG	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:202510276_202510278delAAG	uc001gya.1	+						PPP1R12B_uc001gxz.1_Intron|PPP1R12B_uc001gyb.1_Intron|PPP1R12B_uc001gyc.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)															---	---	---	---
SYT2	127833	broad.mit.edu	37	1	202589595	202589595	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:202589595delT	uc001gye.2	-						SYT2_uc010pqb.1_Intron|SYT2_uc009xaf.2_Intron	NM_001136504	NP_001129976			synaptotagmin II						neurotransmitter secretion	cell junction|chromaffin granule membrane|endocytic vesicle membrane|integral to membrane|synaptic vesicle membrane	protein binding|transporter activity			ovary(2)|skin(1)	3			BRCA - Breast invasive adenocarcinoma(75;0.169)		Botulinum Toxin Type B(DB00042)													---	---	---	---
Unknown	0	broad.mit.edu	37	1	202784593	202784594	+	IGR	DEL	TT	-	-	rs71709459		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:202784593_202784594delTT								KDM5B (7044 upstream) : LOC148709 (46288 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	202945296	202945296	+	IGR	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:202945296delC								CYB5R1 (8892 upstream) : TMEM183A (31238 downstream)																																			---	---	---	---
FMOD	2331	broad.mit.edu	37	1	203294666	203294667	+	Intron	INS	-	T	T	rs75081001		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:203294666_203294667insT	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	203330661	203330661	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:203330661delT								FMOD (10372 upstream) : PRELP (114222 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	203479734	203479734	+	IGR	DEL	A	-	-	rs113135253		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:203479734delA								OPTC (1657 upstream) : ATP2B4 (116194 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	203563704	203563707	+	IGR	DEL	TGTG	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:203563704_203563707delTGTG								OPTC (85627 upstream) : ATP2B4 (32221 downstream)																																			---	---	---	---
KISS1	3814	broad.mit.edu	37	1	204166153	204166153	+	5'Flank	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:204166153delT	uc001har.2	-							NM_002256	NP_002247			KiSS-1 metastasis-suppressor						cytoskeleton organization	extracellular region	protein binding			ovary(1)	1	all_cancers(21;0.0165)|Breast(84;0.179)|all_epithelial(62;0.242)	Breast(1374;9.42e-05)	KIRC - Kidney renal clear cell carcinoma(13;0.0584)|BRCA - Breast invasive adenocarcinoma(75;0.069)|Kidney(21;0.0934)|Epithelial(59;0.239)	Colorectal(1306;0.0129)														---	---	---	---
PLEKHA6	22874	broad.mit.edu	37	1	204260562	204260562	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:204260562delA	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)															---	---	---	---
LRRN2	10446	broad.mit.edu	37	1	204638870	204638871	+	Intron	INS	-	AA	AA	rs142423324	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:204638870_204638871insAA	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)															---	---	---	---
NUAK2	81788	broad.mit.edu	37	1	205282795	205282796	+	Intron	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:205282795_205282796delTT	uc001hce.2	-							NM_030952	NP_112214			NUAK family, SNF1-like kinase, 2						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)															---	---	---	---
MFSD4	148808	broad.mit.edu	37	1	205553347	205553353	+	Intron	DEL	TTTTTTT	-	-	rs67135708		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:205553347_205553353delTTTTTTT	uc001hcv.3	+						MFSD4_uc010prk.1_Intron|MFSD4_uc010prl.1_Intron|MFSD4_uc010prm.1_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)															---	---	---	---
Unknown	0	broad.mit.edu	37	1	205572698	205572698	+	IGR	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:205572698delG								MFSD4 (653 upstream) : ELK4 (12537 downstream)																																			---	---	---	---
NUCKS1	64710	broad.mit.edu	37	1	205698104	205698104	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:205698104delT	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)															---	---	---	---
C1orf186	440712	broad.mit.edu	37	1	206285884	206285884	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:206285884delT	uc001hdt.1	-							NM_001007544	NP_001007545			hypothetical protein LOC440712							integral to membrane					0			BRCA - Breast invasive adenocarcinoma(75;0.0754)															---	---	---	---
Unknown	0	broad.mit.edu	37	1	206486301	206486303	+	IGR	DEL	TTG	-	-	rs75022360		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:206486301_206486303delTTG								CTSE (154198 upstream) : SRGAP2 (29897 downstream)																																			---	---	---	---
SRGAP2	23380	broad.mit.edu	37	1	206558364	206558364	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:206558364delT	uc001hdy.2	+						SRGAP2_uc009xbt.2_Intron|SRGAP2_uc010prt.1_Intron|SRGAP2_uc001hdx.2_Intron|SRGAP2_uc010pru.1_Intron|SRGAP2_uc010prv.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)																	---	---	---	---
IKBKE	9641	broad.mit.edu	37	1	206644743	206644743	+	Intron	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:206644743delG	uc001hdz.1	+						IKBKE_uc009xbu.1_Intron|IKBKE_uc009xbv.1_Intron|IKBKE_uc001hea.1_Intron	NM_014002	NP_054721			IKK-related kinase epsilon						DNA damage response, signal transduction resulting in induction of apoptosis|innate immune response|MyD88-independent toll-like receptor signaling pathway|negative regulation of type I interferon production|positive regulation of I-kappaB kinase/NF-kappaB cascade|Toll signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway	cytosol|endosome membrane|plasma membrane|PML body	ATP binding|IkappaB kinase activity|NF-kappaB-inducing kinase activity|protein binding			ovary(3)|lung(3)|central_nervous_system(1)|skin(1)	8	Breast(84;0.137)																	---	---	---	---
RASSF5	83593	broad.mit.edu	37	1	206698194	206698195	+	Intron	DEL	AC	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:206698194_206698195delAC	uc001hed.2	+						RASSF5_uc001hec.1_Intron|RASSF5_uc001hee.2_Intron	NM_182663	NP_872604			Ras association (RalGDS/AF-6) domain family 5						apoptosis|intracellular signal transduction	cytoplasm|microtubule	metal ion binding|protein binding			ovary(1)	1	Breast(84;0.183)		BRCA - Breast invasive adenocarcinoma(75;0.166)															---	---	---	---
Unknown	0	broad.mit.edu	37	1	206926194	206926194	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:206926194delT								MAPKAPK2 (18568 upstream) : IL10 (14754 downstream)																																			---	---	---	---
C4BPA	722	broad.mit.edu	37	1	207286219	207286219	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:207286219delT	uc001hfo.2	+							NM_000715	NP_000706			complement component 4 binding protein, alpha						complement activation, classical pathway|innate immune response	extracellular region	protein binding			large_intestine(1)|ovary(1)|central_nervous_system(1)	3																		---	---	---	---
CR2	1380	broad.mit.edu	37	1	207641700	207641700	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:207641700delT	uc001hfw.2	+						CR2_uc001hfv.2_Intron|CR2_uc009xch.2_Intron|CR2_uc009xci.1_5'Flank	NM_001877	NP_001868			complement component (3d/Epstein Barr virus)						complement activation, classical pathway|innate immune response	integral to membrane|plasma membrane	complement receptor activity|protein homodimerization activity			upper_aerodigestive_tract(3)|skin(3)|urinary_tract(1)|ovary(1)	8																		---	---	---	---
CD34	947	broad.mit.edu	37	1	208080582	208080582	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:208080582delA	uc001hgw.1	-						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																		---	---	---	---
PLXNA2	5362	broad.mit.edu	37	1	208320541	208320542	+	Intron	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:208320541_208320542delTT	uc001hgz.2	-							NM_025179	NP_079455			plexin A2 precursor						axon guidance	integral to membrane|intracellular|plasma membrane				ovary(2)|central_nervous_system(1)	3				OV - Ovarian serous cystadenocarcinoma(81;0.199)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	208515535	208515537	+	IGR	DEL	TTT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:208515535_208515537delTTT								PLXNA2 (97870 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	208979125	208979125	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:208979125delT								PLXNA2 (561460 upstream) : LOC642587 (623043 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	209028051	209028051	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:209028051delT								PLXNA2 (610386 upstream) : LOC642587 (574117 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	209222453	209222453	+	IGR	DEL	T	-	-	rs67437582		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:209222453delT								PLXNA2 (804788 upstream) : LOC642587 (379715 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	209305451	209305451	+	IGR	DEL	A	-	-	rs75850212		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:209305451delA								PLXNA2 (887786 upstream) : LOC642587 (296717 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	209414675	209414675	+	IGR	DEL	A	-	-	rs79679187		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:209414675delA								PLXNA2 (997010 upstream) : LOC642587 (187493 downstream)																																			---	---	---	---
SERTAD4	56256	broad.mit.edu	37	1	210411505	210411505	+	Intron	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:210411505delC	uc001hhy.2	+						SERTAD4_uc009xcw.2_Intron	NM_019605	NP_062551			SERTA domain containing 4								protein binding			ovary(1)|pancreas(1)	2				OV - Ovarian serous cystadenocarcinoma(81;0.0237)|all cancers(67;0.127)														---	---	---	---
HHAT	55733	broad.mit.edu	37	1	210642206	210642207	+	Intron	INS	-	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:210642206_210642207insT	uc009xcx.2	+						HHAT_uc010psq.1_Intron|HHAT_uc001hhz.3_Intron|HHAT_uc010psr.1_Intron|HHAT_uc010pss.1_Intron|HHAT_uc009xcy.2_Intron|HHAT_uc010pst.1_Intron|HHAT_uc010psu.1_Intron|HHAT_uc001hia.3_Intron	NM_001122834	NP_001116306			hedgehog acyltransferase						multicellular organismal development	endoplasmic reticulum membrane|integral to membrane	GTP binding			ovary(2)	2				OV - Ovarian serous cystadenocarcinoma(81;0.0136)|all cancers(67;0.161)|KIRC - Kidney renal clear cell carcinoma(1967;0.215)														---	---	---	---
HHAT	55733	broad.mit.edu	37	1	210682995	210682996	+	Intron	DEL	TG	-	-	rs147233450	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:210682995_210682996delTG	uc009xcx.2	+						HHAT_uc010psq.1_Intron|HHAT_uc001hhz.3_Intron|HHAT_uc010psr.1_Intron|HHAT_uc010pss.1_Intron|HHAT_uc009xcy.2_Intron|HHAT_uc010pst.1_Intron|HHAT_uc010psu.1_Intron|HHAT_uc001hia.3_Intron	NM_001122834	NP_001116306			hedgehog acyltransferase						multicellular organismal development	endoplasmic reticulum membrane|integral to membrane	GTP binding			ovary(2)	2				OV - Ovarian serous cystadenocarcinoma(81;0.0136)|all cancers(67;0.161)|KIRC - Kidney renal clear cell carcinoma(1967;0.215)														---	---	---	---
KCNH1	3756	broad.mit.edu	37	1	210857741	210857741	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:210857741delT	uc001hib.2	-						KCNH1_uc001hic.2_Intron	NM_172362	NP_758872			potassium voltage-gated channel, subfamily H,						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)														---	---	---	---
KCNH1	3756	broad.mit.edu	37	1	210874980	210874980	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:210874980delT	uc001hib.2	-						KCNH1_uc001hic.2_Intron	NM_172362	NP_758872			potassium voltage-gated channel, subfamily H,						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)														---	---	---	---
KCNH1	3756	broad.mit.edu	37	1	211200946	211200946	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:211200946delA	uc001hib.2	-						KCNH1_uc001hic.2_Intron	NM_172362	NP_758872			potassium voltage-gated channel, subfamily H,						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)														---	---	---	---
KCNH1	3756	broad.mit.edu	37	1	211231950	211231950	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:211231950delA	uc001hib.2	-						KCNH1_uc001hic.2_Intron	NM_172362	NP_758872			potassium voltage-gated channel, subfamily H,						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	211431935	211431935	+	5'Flank	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:211431935delA	uc001hig.2	+						RCOR3_uc010psv.1_5'Flank|RCOR3_uc001hie.2_5'Flank|RCOR3_uc010psw.1_5'Flank|RCOR3_uc001hif.2_5'Flank	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)												OREG0014230	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
TRAF5	7188	broad.mit.edu	37	1	211511975	211511975	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:211511975delT	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)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	211744346	211744346	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:211744346delT								RD3 (78087 upstream) : SLC30A1 (4035 downstream)																																			---	---	---	---
LPGAT1	9926	broad.mit.edu	37	1	211960832	211960836	+	Intron	DEL	AAAAA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:211960832_211960836delAAAAA	uc001hiu.2	-						LPGAT1_uc001hiv.2_Intron	NM_014873	NP_055688			lysophosphatidylglycerol acyltransferase 1						phospholipid biosynthetic process	endoplasmic reticulum membrane|integral to membrane	acyltransferase activity			ovary(1)|skin(1)	2				OV - Ovarian serous cystadenocarcinoma(81;0.00773)|all cancers(67;0.0765)|Epithelial(68;0.114)														---	---	---	---
DTL	51514	broad.mit.edu	37	1	212224846	212224846	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:212224846delT	uc009xdc.2	+						DTL_uc010ptb.1_Intron|DTL_uc001hiz.3_Intron	NM_016448	NP_057532			denticleless homolog						DNA replication|G2/M transition DNA damage checkpoint|protein monoubiquitination|protein polyubiquitination|response to UV|translesion synthesis|ubiquitin-dependent protein catabolic process	centrosome|Cul4A-RING ubiquitin ligase complex|Cul4B-RING ubiquitin ligase complex|nuclear membrane	protein binding				0				OV - Ovarian serous cystadenocarcinoma(81;0.00796)|all cancers(67;0.0385)|Epithelial(68;0.102)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	212350852	212350852	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:212350852delA								DTL (72666 upstream) : PPP2R5A (108027 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	212699768	212699769	+	IGR	DEL	AA	-	-	rs72431178		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:212699768_212699769delAA								NENF (80049 upstream) : ATF3 (38928 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	212730686	212730686	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:212730686delA								NENF (110967 upstream) : ATF3 (8011 downstream)																																			---	---	---	---
ATF3	467	broad.mit.edu	37	1	212748351	212748352	+	Intron	DEL	CA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:212748351_212748352delCA	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)														---	---	---	---
C1orf227	149643	broad.mit.edu	37	1	213014500	213014500	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:213014500delT	uc001hjq.2	-							NM_001024601	NP_001019772			hypothetical protein LOC149643												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	1	213216576	213216577	+	IGR	INS	-	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:213216576_213216577insA								ANGEL2 (27408 upstream) : RPS6KC1 (8011 downstream)																																			---	---	---	---
RPS6KC1	26750	broad.mit.edu	37	1	213329008	213329008	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:213329008delT	uc010ptr.1	+						RPS6KC1_uc001hkd.2_Intron|RPS6KC1_uc010pts.1_Intron|RPS6KC1_uc010ptt.1_Intron|RPS6KC1_uc010ptu.1_Intron|RPS6KC1_uc010ptv.1_Intron|RPS6KC1_uc001hke.2_Intron	NM_012424	NP_036556			ribosomal protein S6 kinase, 52kDa, polypeptide						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)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	213483785	213483785	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:213483785delT								RPS6KC1 (36978 upstream) : PROX1 (677501 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	213645091	213645091	+	IGR	DEL	T	-	-	rs71674963		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:213645091delT								RPS6KC1 (198284 upstream) : PROX1 (516195 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	214025731	214025731	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:214025731delT	uc001hkf.1	-											Homo sapiens cDNA FLJ34932 fis, clone NT2RP7005631.																														---	---	---	---
Unknown	0	broad.mit.edu	37	1	214249585	214249585	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:214249585delA								PROX1 (39825 upstream) : SMYD2 (204980 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	214407801	214407801	+	IGR	DEL	G	-	-	rs113741070		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:214407801delG								PROX1 (198041 upstream) : SMYD2 (46764 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	214997755	214997755	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:214997755delT								CENPF (159843 upstream) : KCNK2 (181130 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	215071517	215071517	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:215071517delA								CENPF (233605 upstream) : KCNK2 (107368 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	215113300	215113301	+	IGR	INS	-	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:215113300_215113301insT								CENPF (275388 upstream) : KCNK2 (65584 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	215148715	215148715	+	IGR	DEL	G	-	-	rs146568055	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:215148715delG								CENPF (310803 upstream) : KCNK2 (30170 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	215163117	215163117	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:215163117delT								CENPF (325205 upstream) : KCNK2 (15768 downstream)																																			---	---	---	---
USH2A	7399	broad.mit.edu	37	1	215953518	215953519	+	Intron	INS	-	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:215953518_215953519insT	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	216459901	216459901	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:216459901delA	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)			---	---	---	---
Unknown	0	broad.mit.edu	37	1	217423617	217423617	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:217423617delT								ESRRG (112520 upstream) : GPATCH2 (180217 downstream)																																			---	---	---	---
GPATCH2	55105	broad.mit.edu	37	1	217649578	217649579	+	Intron	DEL	GT	-	-	rs141872592		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:217649578_217649579delGT	uc001hlf.1	-						GPATCH2_uc009xdq.1_Intron	NM_018040	NP_060510			G patch domain containing 2							intracellular	nucleic acid binding			ovary(1)	1				OV - Ovarian serous cystadenocarcinoma(81;0.0397)|all cancers(67;0.0744)|GBM - Glioblastoma multiforme(131;0.0872)														---	---	---	---
GPATCH2	55105	broad.mit.edu	37	1	217787674	217787674	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:217787674delT	uc001hlf.1	-						GPATCH2_uc001hlg.3_Intron	NM_018040	NP_060510			G patch domain containing 2							intracellular	nucleic acid binding			ovary(1)	1				OV - Ovarian serous cystadenocarcinoma(81;0.0397)|all cancers(67;0.0744)|GBM - Glioblastoma multiforme(131;0.0872)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	218259869	218259869	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:218259869delT								SPATA17 (219367 upstream) : RRP15 (198760 downstream)																																			---	---	---	---
RRP15	51018	broad.mit.edu	37	1	218464308	218464308	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:218464308delA	uc001hlj.2	+							NM_016052	NP_057136			ribosomal RNA processing 15 homolog							mitochondrion|nucleolus	protein binding				0				all cancers(67;0.0315)|OV - Ovarian serous cystadenocarcinoma(81;0.0411)|GBM - Glioblastoma multiforme(131;0.06)|Epithelial(68;0.248)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	218664283	218664283	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:218664283delT								TGFB2 (46324 upstream) : LYPLAL1 (682909 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	218971568	218971569	+	IGR	DEL	TT	-	-	rs68162355		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:218971568_218971569delTT								TGFB2 (353609 upstream) : LYPLAL1 (375623 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	219599944	219599944	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:219599944delT								LYPLAL1 (213738 upstream) : SLC30A10 (258825 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	219743463	219743463	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:219743463delA								LYPLAL1 (357257 upstream) : SLC30A10 (115306 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	219785370	219785370	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:219785370delA								LYPLAL1 (399164 upstream) : SLC30A10 (73399 downstream)																																			---	---	---	---
SLC30A10	55532	broad.mit.edu	37	1	220070945	220070946	+	Intron	INS	-	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:220070945_220070946insA	uc001hlu.1	-											Synthetic construct DNA, clone: pF1KB7405, Homo sapiens SLC30A10 gene for solute carrier family 30, member 10, without stop codon, in Flexi system.						zinc ion transport	integral to membrane|plasma membrane	cation transmembrane transporter activity				0				GBM - Glioblastoma multiforme(131;0.051)|all cancers(67;0.209)														---	---	---	---
SLC30A10	55532	broad.mit.edu	37	1	220074237	220074237	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:220074237delA	uc001hlu.1	-											Synthetic construct DNA, clone: pF1KB7405, Homo sapiens SLC30A10 gene for solute carrier family 30, member 10, without stop codon, in Flexi system.						zinc ion transport	integral to membrane|plasma membrane	cation transmembrane transporter activity				0				GBM - Glioblastoma multiforme(131;0.051)|all cancers(67;0.209)														---	---	---	---
SLC30A10	55532	broad.mit.edu	37	1	220115031	220115032	+	Intron	DEL	TC	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:220115031_220115032delTC	uc001hlu.1	-											Synthetic construct DNA, clone: pF1KB7405, Homo sapiens SLC30A10 gene for solute carrier family 30, member 10, without stop codon, in Flexi system.						zinc ion transport	integral to membrane|plasma membrane	cation transmembrane transporter activity				0				GBM - Glioblastoma multiforme(131;0.051)|all cancers(67;0.209)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	220140459	220140466	+	IGR	DEL	TTTTTTTT	-	-	rs72237453		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:220140459_220140466delTTTTTTTT								SLC30A10 (8470 upstream) : EPRS (1476 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	220225557	220225557	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:220225557delT								EPRS (5557 upstream) : BPNT1 (5269 downstream)																																			---	---	---	---
RAB3GAP2	25782	broad.mit.edu	37	1	220324483	220324483	+	3'UTR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:220324483delA	uc010puk.1	-	35					RAB3GAP2_uc001hmf.2_RNA|RAB3GAP2_uc001hmg.2_3'UTR|RAB3GAP2_uc001hmh.2_3'UTR	NM_012414	NP_036546			rab3 GTPase-activating protein, non-catalytic						intracellular protein transport	cytoplasm|soluble fraction	GTPase activator activity|protein heterodimerization activity			central_nervous_system(1)	1				GBM - Glioblastoma multiforme(131;0.0443)														---	---	---	---
RAB3GAP2	25782	broad.mit.edu	37	1	220331787	220331789	+	Intron	DEL	TTT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:220331787_220331789delTTT	uc010puk.1	-						RAB3GAP2_uc001hmf.2_Intron|RAB3GAP2_uc001hmg.2_Intron|RAB3GAP2_uc001hmh.2_Intron	NM_012414	NP_036546			rab3 GTPase-activating protein, non-catalytic						intracellular protein transport	cytoplasm|soluble fraction	GTPase activator activity|protein heterodimerization activity			central_nervous_system(1)	1				GBM - Glioblastoma multiforme(131;0.0443)														---	---	---	---
RAB3GAP2	25782	broad.mit.edu	37	1	220346115	220346115	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:220346115delA	uc010puk.1	-						RAB3GAP2_uc001hmf.2_Intron|RAB3GAP2_uc001hmg.2_Intron	NM_012414	NP_036546			rab3 GTPase-activating protein, non-catalytic						intracellular protein transport	cytoplasm|soluble fraction	GTPase activator activity|protein heterodimerization activity			central_nervous_system(1)	1				GBM - Glioblastoma multiforme(131;0.0443)														---	---	---	---
RAB3GAP2	25782	broad.mit.edu	37	1	220379362	220379362	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:220379362delA	uc010puk.1	-						RAB3GAP2_uc001hmf.2_Intron|RAB3GAP2_uc001hmg.2_Intron	NM_012414	NP_036546			rab3 GTPase-activating protein, non-catalytic						intracellular protein transport	cytoplasm|soluble fraction	GTPase activator activity|protein heterodimerization activity			central_nervous_system(1)	1				GBM - Glioblastoma multiforme(131;0.0443)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	220840515	220840516	+	IGR	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:220840515_220840516delAA								MARK1 (2717 upstream) : C1orf115 (23112 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	220845031	220845031	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:220845031delA								MARK1 (7233 upstream) : C1orf115 (18597 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	221616378	221616378	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:221616378delT								LOC400804 (106740 upstream) : DUSP10 (258388 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	221660604	221660604	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:221660604delT								LOC400804 (150966 upstream) : DUSP10 (214162 downstream)																																			---	---	---	---
MIA3	375056	broad.mit.edu	37	1	222798358	222798359	+	Intron	DEL	TT	-	-	rs74885819		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:222798358_222798359delTT	uc001hnl.2	+						MIA3_uc009xea.1_5'Flank	NM_198551	NP_940953			melanoma inhibitory activity family, member 3						exocytosis|negative regulation of cell adhesion|negative regulation of cell migration|positive regulation of leukocyte migration|protein transport|wound healing	endoplasmic reticulum membrane|integral to membrane	protein binding			ovary(4)|central_nervous_system(1)	5				GBM - Glioblastoma multiforme(131;0.0199)														---	---	---	---
MIA3	375056	broad.mit.edu	37	1	222806607	222806607	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:222806607delT	uc001hnl.2	+						MIA3_uc009xea.1_Intron	NM_198551	NP_940953			melanoma inhibitory activity family, member 3						exocytosis|negative regulation of cell adhesion|negative regulation of cell migration|positive regulation of leukocyte migration|protein transport|wound healing	endoplasmic reticulum membrane|integral to membrane	protein binding			ovary(4)|central_nervous_system(1)	5				GBM - Glioblastoma multiforme(131;0.0199)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	223251266	223251266	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:223251266delA								DISP1 (71931 upstream) : TLR5 (32318 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	223282491	223282492	+	IGR	DEL	GC	-	-	rs35153461		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:223282491_223282492delGC								DISP1 (103156 upstream) : TLR5 (1092 downstream)																																			---	---	---	---
SUSD4	55061	broad.mit.edu	37	1	223408527	223408527	+	Intron	DEL	A	-	-	rs67943821		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:223408527delA	uc001hnx.2	-						SUSD4_uc001hny.3_Intron|SUSD4_uc010puw.1_Intron|SUSD4_uc001hnz.2_Intron	NM_017982	NP_060452			sushi domain containing 4 isoform a							integral to membrane					0				GBM - Glioblastoma multiforme(131;0.0611)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	223862994	223862994	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:223862994delT								CAPN8 (9558 upstream) : CAPN2 (26301 downstream)																																			---	---	---	---
CAPN2	824	broad.mit.edu	37	1	223890136	223890136	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:223890136delA	uc010puy.1	+							NM_001146068	NP_001139540			calpain 2 isoform 2						proteolysis	cytoplasm|plasma membrane				lung(3)|breast(1)|skin(1)	5				GBM - Glioblastoma multiforme(131;0.109)														---	---	---	---
CAPN2	824	broad.mit.edu	37	1	223918042	223918044	+	Intron	DEL	TTT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:223918042_223918044delTTT	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)														---	---	---	---
CAPN2	824	broad.mit.edu	37	1	223949716	223949717	+	Intron	INS	-	T	T	rs146172055	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:223949716_223949717insT	uc001hob.3	+						CAPN2_uc010puy.1_Intron|CAPN2_uc001hoc.2_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)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	224262236	224262237	+	IGR	INS	-	CCTC	CCTC	rs60087320	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:224262236_224262237insCCTC								TP53BP2 (228562 upstream) : FBXO28 (39554 downstream)																																			---	---	---	---
NVL	4931	broad.mit.edu	37	1	224480456	224480456	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:224480456delT	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)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	224530184	224530191	+	IGR	DEL	TCTCTCTG	-	-	rs59776293		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:224530184_224530191delTCTCTCTG								NVL (12312 upstream) : CNIH4 (14404 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	224751161	224751164	+	IGR	DEL	GGGT	-	-	rs146173308	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:224751161_224751164delGGGT								WDR26 (129429 upstream) : CNIH3 (53015 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	224940455	224940456	+	IGR	DEL	TT	-	-	rs78380729		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:224940455_224940456delTT								CNIH3 (12206 upstream) : DNAH14 (176900 downstream)																																			---	---	---	---
DNAH14	127602	broad.mit.edu	37	1	225177718	225177718	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:225177718delT	uc001how.2	+						DNAH14_uc001hou.3_Intron|DNAH14_uc001hot.3_Intron	NM_001373	NP_001364			dynein, axonemal, heavy polypeptide 14 isoform						microtubule-based movement	cilium axoneme|cytoplasm|dynein complex|microtubule	ATP binding|microtubule motor activity			central_nervous_system(1)	1																		---	---	---	---
DNAH14	127602	broad.mit.edu	37	1	225586072	225586072	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:225586072delA	uc001how.2	+							NM_001373	NP_001364			dynein, axonemal, heavy polypeptide 14 isoform						microtubule-based movement	cilium axoneme|cytoplasm|dynein complex|microtubule	ATP binding|microtubule motor activity			central_nervous_system(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	1	225629811	225629811	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:225629811delA								LBR (13292 upstream) : ENAH (44723 downstream)																																			---	---	---	---
ENAH	55740	broad.mit.edu	37	1	225695604	225695604	+	Intron	DEL	T	-	-	rs76873734		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:225695604delT	uc001hpc.1	-						ENAH_uc001hpd.1_Intron|ENAH_uc001hpb.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)														---	---	---	---
ENAH	55740	broad.mit.edu	37	1	225758091	225758091	+	Intron	DEL	T	-	-	rs112014685		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:225758091delT	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)														---	---	---	---
ENAH	55740	broad.mit.edu	37	1	225796108	225796109	+	Intron	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:225796108_225796109delTT	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)														---	---	---	---
LEFTY1	10637	broad.mit.edu	37	1	226112555	226112555	+	5'Flank	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:226112555delC	uc010pvj.1	-						PYCR2_uc001hpp.2_5'Flank|PYCR2_uc001hpq.2_5'Flank|PYCR2_uc001hpr.2_5'Flank|PYCR2_uc001hps.1_5'Flank					SubName: Full=cDNA FLJ54750, moderately similar to Pyrroline-5-carboxylate reductase 2 (EC 1.5.1.2);						cell growth|multicellular organismal development|transforming growth factor beta receptor signaling pathway	extracellular space	cytokine activity|growth factor activity|transforming growth factor beta receptor binding				0	Breast(184;0.197)																	---	---	---	---
Unknown	0	broad.mit.edu	37	1	226165886	226165887	+	IGR	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:226165886_226165887delAA								LEFTY2 (36966 upstream) : C1orf55 (4517 downstream)																																			---	---	---	---
LIN9	286826	broad.mit.edu	37	1	226438518	226438518	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:226438518delA	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	226547817	226547817	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:226547817delA								LIN9 (50247 upstream) : PARP1 (576 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	226723707	226723708	+	RNA	INS	-	AG	AG	rs150434687	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:226723707_226723708insAG	uc001hqe.1	-	3		c.2942_2943insCT								Homo sapiens cDNA FLJ31294 fis, clone KIDNE2007810, weakly similar to DEOXYURIDINE 5'-TRIPHOSPHATE NUCLEOTIDOHYDROLASE (EC 3.6.1.23).																														---	---	---	---
C1orf95	375057	broad.mit.edu	37	1	226754053	226754053	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:226754053delT	uc010pvn.1	+							NM_001003665	NP_001003665			hypothetical protein LOC375057							integral to membrane				ovary(1)	1	Breast(184;0.133)	Prostate(94;0.0885)		GBM - Glioblastoma multiforme(131;0.113)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	226798412	226798413	+	IGR	INS	-	AG	AG	rs78947639		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:226798412_226798413insAG								C1orf95 (5109 upstream) : ITPKB (20979 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	226818851	226818851	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:226818851delA								C1orf95 (25548 upstream) : ITPKB (541 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	226971102	226971103	+	IGR	DEL	CA	-	-	rs148321812		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:226971102_226971103delCA								ITPKB (44226 upstream) : PSEN2 (87170 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	227573038	227573039	+	IGR	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:227573038_227573039delAA								CDC42BPA (67212 upstream) : ZNF678 (178205 downstream)																																			---	---	---	---
RHOU	58480	broad.mit.edu	37	1	228873641	228873641	+	Intron	DEL	T	-	-	rs35672194		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:228873641delT	uc001htf.2	+							NM_021205	NP_067028			ras homolog gene family, member U						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)																---	---	---	---
URB2	9816	broad.mit.edu	37	1	229770586	229770586	+	Intron	DEL	T	-	-	rs113038970		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:229770586delT	uc001hts.1	+						URB2_uc009xfd.1_Intron	NM_014777	NP_055592			URB2 ribosome biogenesis 2 homolog							nucleolus				central_nervous_system(2)|ovary(1)	3																		---	---	---	---
Unknown	0	broad.mit.edu	37	1	230189203	230189203	+	IGR	DEL	T	-	-	rs77193603		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:230189203delT								URB2 (393257 upstream) : GALNT2 (4333 downstream)																																			---	---	---	---
PGBD5	79605	broad.mit.edu	37	1	230462963	230462964	+	Intron	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:230462963_230462964delTT	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)														---	---	---	---
PGBD5	79605	broad.mit.edu	37	1	230480866	230480866	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:230480866delT	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)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	230582992	230582992	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:230582992delT								PGBD5 (69625 upstream) : COG2 (195210 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	230747922	230747922	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:230747922delA								PGBD5 (234555 upstream) : COG2 (30280 downstream)																																			---	---	---	---
CAPN9	10753	broad.mit.edu	37	1	230918770	230918770	+	Intron	DEL	T	-	-	rs4847018	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:230918770delT	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)																---	---	---	---
GNPAT	8443	broad.mit.edu	37	1	231404693	231404693	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:231404693delT	uc001hup.3	+						GNPAT_uc009xfp.2_Intron	NM_014236	NP_055051			glyceronephosphate O-acyltransferase						ether lipid biosynthetic process|fatty acid metabolic process|organ morphogenesis	peroxisomal matrix|peroxisomal membrane	glycerone-phosphate O-acyltransferase activity			ovary(3)|breast(1)	4	Breast(184;0.0871)	all_cancers(173;0.2)|Prostate(94;0.183)																---	---	---	---
EGLN1	54583	broad.mit.edu	37	1	231529528	231529528	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:231529528delA	uc001huv.2	-						EGLN1_uc001huu.3_Intron	NM_022051	NP_071334			egl nine homolog 1						negative regulation of sequence-specific DNA binding transcription factor activity|oxygen homeostasis|response to hypoxia	cytosol	iron ion binding|L-ascorbic acid binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|peptidyl-proline dioxygenase activity|protein binding|zinc ion binding				0		Prostate(94;0.194)|Acute lymphoblastic leukemia(190;0.244)			Vitamin C(DB00126)													---	---	---	---
EGLN1	54583	broad.mit.edu	37	1	231551914	231551914	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:231551914delT	uc001huv.2	-						EGLN1_uc001huu.3_Intron	NM_022051	NP_071334			egl nine homolog 1						negative regulation of sequence-specific DNA binding transcription factor activity|oxygen homeostasis|response to hypoxia	cytosol	iron ion binding|L-ascorbic acid binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|peptidyl-proline dioxygenase activity|protein binding|zinc ion binding				0		Prostate(94;0.194)|Acute lymphoblastic leukemia(190;0.244)			Vitamin C(DB00126)													---	---	---	---
DISC1	27185	broad.mit.edu	37	1	231817152	231817153	+	Intron	DEL	TG	-	-	rs111605762		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:231817152_231817153delTG	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	231890959	231890959	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:231890959delT	uc001huz.2	+						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_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	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	231912496	231912496	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:231912496delA	uc001huz.2	+						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_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	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	232099000	232099000	+	Intron	DEL	T	-	-	rs5781681		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:232099000delT	uc001huz.2	+						TSNAX-DISC1_uc010pwl.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	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	232430223	232430223	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:232430223delT								DISC1 (253207 upstream) : SIPA1L2 (103491 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	232520303	232520304	+	IGR	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:232520303_232520304delTT								DISC1 (343287 upstream) : SIPA1L2 (13410 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	232714459	232714459	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:232714459delA								SIPA1L2 (63216 upstream) : KIAA1383 (226179 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	232912051	232912055	+	IGR	DEL	TTTTT	-	-	rs112009541		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:232912051_232912055delTTTTT								SIPA1L2 (260808 upstream) : KIAA1383 (28583 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	232937369	232937369	+	IGR	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:232937369delG								SIPA1L2 (286126 upstream) : KIAA1383 (3269 downstream)																																			---	---	---	---
PCNXL2	80003	broad.mit.edu	37	1	233127146	233127147	+	Intron	DEL	GA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:233127146_233127147delGA	uc001hvl.2	-						PCNXL2_uc001hvk.1_Intron|PCNXL2_uc001hvm.1_Intron	NM_014801	NP_055616			pecanex-like 2							integral to membrane				central_nervous_system(1)|pancreas(1)	2		all_cancers(173;0.0347)|Prostate(94;0.137)																---	---	---	---
Unknown	0	broad.mit.edu	37	1	233456097	233456098	+	IGR	DEL	GT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:233456097_233456098delGT								PCNXL2 (24638 upstream) : KIAA1804 (7416 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	233717944	233717944	+	IGR	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:233717944delG								KIAA1804 (197051 upstream) : KCNK1 (31806 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	234002041	234002042	+	IGR	INS	-	GA	GA	rs140599280	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:234002041_234002042insGA								KCNK1 (193783 upstream) : SLC35F3 (38637 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	234629801	234629802	+	IGR	INS	-	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:234629801_234629802insA								TARBP1 (14952 upstream) : IRF2BP2 (110215 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	234698122	234698122	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:234698122delT								TARBP1 (83273 upstream) : IRF2BP2 (41895 downstream)																																			---	---	---	---
GNG4	2786	broad.mit.edu	37	1	235732094	235732094	+	Intron	DEL	T	-	-	rs66748179		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:235732094delT	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)															---	---	---	---
GNG4	2786	broad.mit.edu	37	1	235732829	235732829	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:235732829delT	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	235850045	235850045	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:235850045delA	uc001hxj.2	-						LYST_uc001hxi.2_Intron	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				---	---	---	---
LYST	1130	broad.mit.edu	37	1	235854216	235854218	+	Intron	DEL	TTT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:235854216_235854218delTTT	uc001hxj.2	-						LYST_uc001hxi.2_Intron	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				---	---	---	---
LYST	1130	broad.mit.edu	37	1	235993743	235993743	+	Intron	DEL	A	-	-	rs72106995		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:235993743delA	uc001hxj.2	-						LYST_uc009xgb.1_Intron|LYST_uc010pxs.1_Intron|LYST_uc001hxl.1_Intron|LYST_uc001hxm.2_Intron|LYST_uc001hxn.1_Intron	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				---	---	---	---
LYST	1130	broad.mit.edu	37	1	236039586	236039586	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:236039586delA	uc001hxl.1	-						LYST_uc009xgb.1_Intron|LYST_uc010pxs.1_Intron|LYST_uc001hxm.2_Intron	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	236084444	236084445	+	IGR	DEL	CA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:236084444_236084445delCA								LYST (37504 upstream) : NID1 (54696 downstream)																																			---	---	---	---
NID1	4811	broad.mit.edu	37	1	236180690	236180690	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-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	236293033	236293033	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:236293033delT								NID1 (64552 upstream) : GPR137B (12799 downstream)																																			---	---	---	---
ERO1LB	56605	broad.mit.edu	37	1	236393400	236393400	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-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)															---	---	---	---
MTR	4548	broad.mit.edu	37	1	236965979	236965979	+	Intron	DEL	A	-	-	rs71559983		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:236965979delA	uc001hyi.3	+						MTR_uc010pxv.1_Intron|MTR_uc010pxw.1_Intron|MTR_uc010pxx.1_Intron|MTR_uc010pxy.1_Intron	NM_000254	NP_000245			5-methyltetrahydrofolate-homocysteine						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	237850667	237850674	+	Intron	DEL	TTTTTTTT	-	-	rs66467386		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:237850667_237850674delTTTTTTTT	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)															---	---	---	---
RYR2	6262	broad.mit.edu	37	1	237924231	237924231	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:237924231delT	uc001hyl.1	+						RYR2_uc010pya.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)															---	---	---	---
RYR2	6262	broad.mit.edu	37	1	237925016	237925016	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:237925016delA	uc001hyl.1	+						RYR2_uc010pya.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	238541237	238541238	+	IGR	INS	-	C	C	rs34660441	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:238541237_238541238insC								LOC100130331 (449620 upstream) : LOC339535 (102448 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	239446051	239446051	+	IGR	DEL	T	-	-	rs34620944		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:239446051delT								LOC339535 (796734 upstream) : CHRM3 (103814 downstream)																																			---	---	---	---
CHRM3	1131	broad.mit.edu	37	1	239569187	239569187	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:239569187delT	uc001hyo.1	+											Homo sapiens clone N10 NTera2D1 teratocarcinoma, m3 muscarinic acetylcholine receptor mRNA, partial cds.						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)													---	---	---	---
FMN2	56776	broad.mit.edu	37	1	240295015	240295015	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:240295015delA	uc010pyd.1	+						FMN2_uc010pye.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)															---	---	---	---
FMN2	56776	broad.mit.edu	37	1	240465065	240465065	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:240465065delT	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)															---	---	---	---
Unknown	0	broad.mit.edu	37	1	240909261	240909261	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:240909261delT								GREM2 (133799 upstream) : RGS7 (22294 downstream)																																			---	---	---	---
RGS7	6000	broad.mit.edu	37	1	241308322	241308322	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:241308322delT	uc001hyv.2	-						RGS7_uc010pyh.1_5'Flank|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)															---	---	---	---
RGS7	6000	broad.mit.edu	37	1	241309524	241309525	+	Intron	INS	-	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:241309524_241309525insA	uc001hyv.2	-						RGS7_uc010pyh.1_5'Flank|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)															---	---	---	---
RGS7	6000	broad.mit.edu	37	1	241340258	241340258	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:241340258delA	uc001hyv.2	-						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)															---	---	---	---
RGS7	6000	broad.mit.edu	37	1	241427801	241427801	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:241427801delA	uc001hyv.2	-						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)															---	---	---	---
RGS7	6000	broad.mit.edu	37	1	241489060	241489060	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:241489060delT	uc001hyv.2	-						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)															---	---	---	---
Unknown	0	broad.mit.edu	37	1	241607976	241607977	+	IGR	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:241607976_241607977delAA								RGS7 (87498 upstream) : FH (52929 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	241642413	241642413	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:241642413delA								RGS7 (121935 upstream) : FH (18493 downstream)																																			---	---	---	---
KMO	8564	broad.mit.edu	37	1	241750769	241750769	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:241750769delT	uc009xgp.2	+						KMO_uc001hyy.2_Intron|KMO_uc009xgo.1_Intron	NM_003679	NP_003670			kynurenine 3-monooxygenase						pyridine nucleotide biosynthetic process|response to salt stress	cytosol|integral to membrane|mitochondrial outer membrane	electron carrier activity|flavin adenine dinucleotide binding|kynurenine 3-monooxygenase activity|NAD(P)H oxidase activity			ovary(2)	2	Ovarian(103;0.103)|all_lung(81;0.23)		OV - Ovarian serous cystadenocarcinoma(106;0.0176)															---	---	---	---
Unknown	0	broad.mit.edu	37	1	241995108	241995109	+	IGR	DEL	CA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:241995108_241995109delCA								WDR64 (30151 upstream) : EXO1 (16426 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	242093390	242093390	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:242093390delA								EXO1 (40343 upstream) : MAP1LC3C (65402 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	242093395	242093396	+	IGR	INS	-	AAAG	AAAG	rs144020915	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:242093395_242093396insAAAG								EXO1 (40348 upstream) : MAP1LC3C (65396 downstream)																																			---	---	---	---
PLD5	200150	broad.mit.edu	37	1	242460186	242460189	+	Intron	DEL	TAAT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:242460186_242460189delTAAT	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	242503804	242503804	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:242503804delA	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	242559351	242559351	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:242559351delA	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)															---	---	---	---
SDCCAG8	10806	broad.mit.edu	37	1	243434124	243434126	+	Intron	DEL	TTT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:243434124_243434126delTTT	uc001hzw.2	+						SDCCAG8_uc010pyk.1_Intron|SDCCAG8_uc010pyl.1_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	243850917	243850917	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:243850917delT	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	244210654	244210654	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:244210654delT								AKT3 (204101 upstream) : ZNF238 (3907 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	244418962	244418963	+	IGR	DEL	AA	-	-	rs111886327		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:244418962_244418963delAA								ZNF238 (198186 upstream) : C1orf100 (96974 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	244496570	244496570	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:244496570delT								ZNF238 (275794 upstream) : C1orf100 (19367 downstream)																																			---	---	---	---
C1orf101	257044	broad.mit.edu	37	1	244751608	244751608	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:244751608delA	uc001iam.2	+						C1orf101_uc001iak.1_Intron|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	244857682	244857682	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:244857682delT	uc001iao.2	+						PPPDE1_uc001iap.2_Intron	NM_016076	NP_057160			PPPDE peptidase domain containing 1											breast(3)	3																		---	---	---	---
Unknown	0	broad.mit.edu	37	1	244907594	244907595	+	IGR	DEL	TT	-	-	rs78475951		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:244907594_244907595delTT								PPPDE1 (35262 upstream) : FAM36A (91044 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	244973374	244973375	+	IGR	INS	-	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:244973374_244973375insA								PPPDE1 (101042 upstream) : FAM36A (25264 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	244977118	244977118	+	IGR	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:244977118delC								PPPDE1 (104786 upstream) : FAM36A (21521 downstream)																																			---	---	---	---
KIF26B	55083	broad.mit.edu	37	1	245689992	245689992	+	Intron	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:245689992delC	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)															---	---	---	---
SMYD3	64754	broad.mit.edu	37	1	246041669	246041669	+	Intron	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:246041669delG	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	246314672	246314672	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:246314672delT	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	246428749	246428749	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:246428749delT	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	246448844	246448844	+	Intron	DEL	A	-	-	rs113468004		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:246448844delA	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)														---	---	---	---
CNST	163882	broad.mit.edu	37	1	246779182	246779182	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:246779182delA	uc001ibp.2	+						CNST_uc001ibo.3_Intron	NM_152609	NP_689822			hypothetical protein LOC163882 isoform 1						positive regulation of Golgi to plasma membrane protein transport	integral to membrane|plasma membrane|protein complex|trans-Golgi network|transport vesicle	connexin binding				0																		---	---	---	---
ZNF695	57116	broad.mit.edu	37	1	247120684	247120685	+	Intron	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:247120684_247120685delAA	uc001ibx.2	-						ZNF695_uc001ica.2_Intron|ZNF695_uc009xgt.1_Intron|ZNF695_uc001iby.2_Intron					RecName: Full=Zinc finger protein 695; AltName: Full=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)															---	---	---	---
NLRP3	114548	broad.mit.edu	37	1	247604428	247604437	+	Intron	DEL	TTTCTCTTTC	-	-	rs140812979	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:247604428_247604437delTTTCTCTTTC	uc001icr.2	+						NLRP3_uc001ics.2_Intron|NLRP3_uc001icu.2_Intron|NLRP3_uc001icw.2_Intron|NLRP3_uc001icv.2_Intron|NLRP3_uc010pyw.1_Intron	NM_001079821	NP_001073289			NLR family, pyrin domain containing 3 isoform a						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)															---	---	---	---
OR2L13	284521	broad.mit.edu	37	1	248218704	248218704	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:248218704delT	uc001ids.2	+							NM_175911	NP_787107			olfactory receptor, family 2, subfamily L,						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)															---	---	---	---
OR2G6	391211	broad.mit.edu	37	1	248684814	248684814	+	5'Flank	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:248684814delT	uc001ien.1	+							NM_001013355	NP_001013373			olfactory receptor, family 2, subfamily G,						sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(2)|skin(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)	all_cancers(173;0.0156)	OV - Ovarian serous cystadenocarcinoma(106;0.0265)															---	---	---	---
Unknown	0	broad.mit.edu	37	1	248844550	248844550	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:248844550delT								OR2T27 (30365 upstream) : OR14I1 (120 downstream)																																			---	---	---	---
SH3YL1	26751	broad.mit.edu	37	2	239569	239569	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:239569delA	uc002qvx.2	-						SH3YL1_uc002qvy.2_Intron|SH3YL1_uc002qvz.2_Intron|SH3YL1_uc002qwa.2_Intron|SH3YL1_uc010ewe.2_Intron|SH3YL1_uc002qvu.2_Intron|SH3YL1_uc002qvv.2_Intron|SH3YL1_uc002qvw.2_Intron|uc002qwb.2_RNA	NM_015677	NP_056492			SH3 domain containing, Ysc84-like 1 isoform 1											ovary(1)	1	all_hematologic(175;0.0429)|Acute lymphoblastic leukemia(172;0.0627)	all_cancers(51;0.034)		all cancers(51;0.000647)|Epithelial(75;0.0043)|OV - Ovarian serous cystadenocarcinoma(76;0.00871)|GBM - Glioblastoma multiforme(21;0.148)														---	---	---	---
Unknown	0	broad.mit.edu	37	2	319287	319288	+	IGR	DEL	GT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:319287_319288delGT								FAM150B (30979 upstream) : TMEM18 (348687 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	866013	866013	+	5'Flank	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:866013delA	uc002qwn.1	-						uc002qwo.1_5'Flank					Homo sapiens cDNA clone IMAGE:5174186.																														---	---	---	---
TPO	7173	broad.mit.edu	37	2	1521524	1521524	+	Intron	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:1521524delC	uc002qww.2	+						TPO_uc010ewj.2_Intron|TPO_uc002qwu.2_Intron|TPO_uc002qwr.2_Intron|TPO_uc002qwx.2_Intron|TPO_uc010yio.1_Intron|TPO_uc010yip.1_Intron|TPO_uc002qwy.1_Intron|TPO_uc002qwz.2_Intron	NM_000547	NP_000538			thyroid peroxidase isoform a						cellular nitrogen compound metabolic process|hormone biosynthetic process|hydrogen peroxide catabolic process	cell surface|cytoplasm|integral to plasma membrane	calcium ion binding|heme binding|iodide peroxidase activity			ovary(7)|pancreas(6)|skin(5)|lung(1)|kidney(1)	20	all_hematologic(175;0.0487)|Acute lymphoblastic leukemia(172;0.0627)	all_cancers(51;0.0338)		all cancers(51;0.0356)|OV - Ovarian serous cystadenocarcinoma(76;0.0748)|Epithelial(75;0.12)	Carbimazole(DB00389)|Methimazole(DB00763)|Propylthiouracil(DB00550)													---	---	---	---
Unknown	0	broad.mit.edu	37	2	2349160	2349160	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:2349160delA								MYT1L (14115 upstream) : TSSC1 (843581 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	2668601	2668602	+	IGR	DEL	CA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:2668601_2668602delCA								MYT1L (333556 upstream) : TSSC1 (524139 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	2700579	2700599	+	IGR	DEL	ACAGGAGCACCAGGGATGTGA	-	-	rs67501163		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:2700579_2700599delACAGGAGCACCAGGGATGTGA								MYT1L (365534 upstream) : TSSC1 (492142 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	2853191	2853191	+	IGR	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:2853191delC								MYT1L (518146 upstream) : TSSC1 (339550 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	2885745	2885745	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:2885745delT								MYT1L (550700 upstream) : TSSC1 (306996 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	3063094	3063094	+	Intron	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:3063094delG	uc002qxh.1	-											Homo sapiens cDNA FLJ37991 fis, clone CTONG2011765.																														---	---	---	---
Unknown	0	broad.mit.edu	37	2	4091862	4091862	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:4091862delT								ALLC (341604 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	4500242	4500253	+	IGR	DEL	TCTTCTTCTCCT	-	-	rs70939917		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:4500242_4500253delTCTTCTTCTCCT								ALLC (749984 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	4742280	4742280	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:4742280delT								ALLC (992022 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	5455401	5455402	+	IGR	DEL	AA	-	-	rs5828998		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:5455401_5455402delAA								None (None upstream) : SOX11 (377397 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	5883896	5883896	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:5883896delA								SOX11 (42380 upstream) : LOC150622 (188923 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	5978701	5978703	+	IGR	DEL	AAA	-	-	rs79928499		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:5978701_5978703delAAA								SOX11 (137185 upstream) : LOC150622 (94116 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	6179185	6179185	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:6179185delT								LOC400940 (50821 upstream) : CMPK2 (801318 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	6532752	6532753	+	IGR	DEL	GC	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:6532752_6532753delGC								LOC400940 (404388 upstream) : CMPK2 (447750 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	7249845	7249845	+	IGR	DEL	G	-	-	rs77531103		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:7249845delG								RNF144A (65538 upstream) : LOC339788 (812713 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	7449508	7449509	+	IGR	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:7449508_7449509delTT								RNF144A (265201 upstream) : LOC339788 (613049 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	8124041	8124041	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:8124041delT								LOC339788 (7064 upstream) : ID2 (695299 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	8304671	8304671	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:8304671delA	uc010eww.1	-											Homo sapiens cDNA FLJ45673 fis, clone D9OST2003989.																														---	---	---	---
Unknown	0	broad.mit.edu	37	2	8691362	8691362	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:8691362delT								LOC339788 (574385 upstream) : ID2 (127978 downstream)																																			---	---	---	---
KIDINS220	57498	broad.mit.edu	37	2	8931444	8931444	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:8931444delA	uc002qzc.2	-						KIDINS220_uc010yiv.1_Intron|KIDINS220_uc002qzd.2_Intron|KIDINS220_uc010yiw.1_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	8965503	8965504	+	Intron	DEL	AA	-	-	rs35919758		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:8965503_8965504delAA	uc002qzc.2	-						KIDINS220_uc010yiv.1_Intron|KIDINS220_uc002qzd.2_Intron|KIDINS220_uc010yiw.1_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)																	---	---	---	---
MBOAT2	129642	broad.mit.edu	37	2	9007192	9007192	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:9007192delT	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)																	---	---	---	---
Unknown	0	broad.mit.edu	37	2	9218937	9218937	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:9218937delA								MBOAT2 (75061 upstream) : ASAP2 (127957 downstream)																																			---	---	---	---
ASAP2	8853	broad.mit.edu	37	2	9541001	9541001	+	Intron	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:9541001delG	uc002qzh.2	+						ASAP2_uc002qzi.2_Intron	NM_003887	NP_003878			ArfGAP with SH3 domain, ankyrin repeat and PH						regulation of ARF GTPase activity	Golgi cisterna membrane|plasma membrane	ARF GTPase activator activity|protein binding|zinc ion binding				0																		---	---	---	---
CPSF3	51692	broad.mit.edu	37	2	9604199	9604200	+	Intron	DEL	TG	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:9604199_9604200delTG	uc002qzo.1	+						CPSF3_uc002qzp.1_Intron|CPSF3_uc002qzq.1_Intron	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)														---	---	---	---
ADAM17	6868	broad.mit.edu	37	2	9657946	9657947	+	Intron	INS	-	A	A	rs2298763	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:9657946_9657947insA	uc002qzu.2	-						ADAM17_uc010ewy.2_Intron|ADAM17_uc010ewz.2_Intron	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)														---	---	---	---
ADAM17	6868	broad.mit.edu	37	2	9664609	9664610	+	Intron	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:9664609_9664610delAA	uc002qzu.2	-						ADAM17_uc010ewy.2_Intron|ADAM17_uc010ewz.2_Intron|ADAM17_uc010exa.2_5'Flank	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)														---	---	---	---
ADAM17	6868	broad.mit.edu	37	2	9694209	9694210	+	Intron	INS	-	A	A	rs143833624	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:9694209_9694210insA	uc002qzu.2	-						ADAM17_uc010ewy.2_Intron|ADAM17_uc010ewz.2_Intron|ADAM17_uc010exb.1_Intron|ADAM17_uc002qzv.2_Intron	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	9862880	9862880	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:9862880delA								YWHAQ (91774 upstream) : TAF1B (120691 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	9864492	9864492	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:9864492delT								YWHAQ (93386 upstream) : TAF1B (119079 downstream)																																			---	---	---	---
TAF1B	9014	broad.mit.edu	37	2	10025873	10025873	+	Intron	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:10025873delC	uc002qzz.2	+						TAF1B_uc010exc.2_Intron|TAF1B_uc002qzy.3_Intron|TAF1B_uc010yja.1_Intron|TAF1B_uc010exd.2_Intron	NM_005680	NP_005671			TBP-associated factor 1B						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)																	---	---	---	---
GRHL1	29841	broad.mit.edu	37	2	10098620	10098620	+	Intron	DEL	T	-	-	rs150498125		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:10098620delT	uc002raa.2	+						GRHL1_uc002rab.2_Intron|GRHL1_uc002rad.2_Intron|GRHL1_uc010yjb.1_Intron|uc002rac.2_5'Flank	NM_198182	NP_937825			grainyhead-like 1						cellular lipid metabolic process|multicellular organismal development|regulation of transcription, DNA-dependent|transcription, DNA-dependent	Golgi apparatus|nucleus	DNA binding			pancreas(1)|skin(1)	2	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)			Epithelial(75;0.172)|OV - Ovarian serous cystadenocarcinoma(76;0.246)														---	---	---	---
Unknown	0	broad.mit.edu	37	2	10230545	10230554	+	IGR	DEL	AAAAAAAAAA	-	-	rs139996085		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:10230545_10230554delAAAAAAAAAA								CYS1 (10007 upstream) : RRM2 (32181 downstream)																																			---	---	---	---
HPCAL1	3241	broad.mit.edu	37	2	10500955	10500957	+	Intron	DEL	CTC	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:10500955_10500957delCTC	uc002raj.2	+						HPCAL1_uc002rak.2_Intron|HPCAL1_uc002ral.2_Intron|HPCAL1_uc010exe.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	10696198	10696199	+	IGR	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:10696198_10696199delTT								ODC1 (107745 upstream) : NOL10 (14695 downstream)																																			---	---	---	---
NOL10	79954	broad.mit.edu	37	2	10749726	10749726	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:10749726delA	uc002raq.2	-						NOL10_uc010yje.1_Intron|NOL10_uc010yjf.1_Intron|NOL10_uc002rap.2_Intron	NM_024894	NP_079170			nucleolar protein 10							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	10795333	10795333	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:10795333delA	uc002raq.2	-						NOL10_uc010yje.1_Intron|NOL10_uc010yjf.1_Intron|NOL10_uc002rap.2_Intron|NOL10_uc002rar.2_Intron	NM_024894	NP_079170			nucleolar protein 10							nucleolus					0	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.191)			Epithelial(75;0.172)|OV - Ovarian serous cystadenocarcinoma(76;0.207)														---	---	---	---
Unknown	0	broad.mit.edu	37	2	11169133	11169133	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:11169133delA								KCNF1 (114783 upstream) : C2orf50 (104046 downstream)																																			---	---	---	---
PQLC3	130814	broad.mit.edu	37	2	11300940	11300948	+	Intron	DEL	AAAAAAAAT	-	-	rs59329825	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:11300940_11300948delAAAAAAAAT	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)														---	---	---	---
GREB1	9687	broad.mit.edu	37	2	11769307	11769308	+	Intron	INS	-	G	G	rs140954854	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:11769307_11769308insG	uc002rbk.1	+						GREB1_uc002rbp.1_Intron	NM_014668	NP_055483			growth regulation by estrogen in breast cancer 1							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)														---	---	---	---
Unknown	0	broad.mit.edu	37	2	12073963	12073964	+	IGR	DEL	AG	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:12073963_12073964delAG								LPIN1 (106432 upstream) : TRIB2 (783034 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	12289063	12289064	+	Intron	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:12289063_12289064delTT	uc002rbu.1	+											Homo sapiens cDNA FLJ10696 fis, clone NT2RP3000484.																														---	---	---	---
Unknown	0	broad.mit.edu	37	2	12515495	12515495	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:12515495delA	uc002rbu.1	+											Homo sapiens cDNA FLJ10696 fis, clone NT2RP3000484.																														---	---	---	---
Unknown	0	broad.mit.edu	37	2	12708678	12708678	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:12708678delA	uc002rbu.1	+											Homo sapiens cDNA FLJ10696 fis, clone NT2RP3000484.																														---	---	---	---
Unknown	0	broad.mit.edu	37	2	13231956	13231956	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:13231956delT								TRIB2 (349100 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	13978964	13978964	+	IGR	DEL	A	-	-	rs5829414		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:13978964delA								None (None upstream) : FAM84A (793892 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	14974603	14974603	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:14974603delA								FAM84A (183670 upstream) : NBAS (332429 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	15015364	15015364	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:15015364delA								FAM84A (224431 upstream) : NBAS (291668 downstream)																																			---	---	---	---
NBAS	51594	broad.mit.edu	37	2	15459834	15459835	+	Intron	INS	-	TTA	TTA	rs139764145	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:15459834_15459835insTTA	uc002rcc.1	-						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	15503209	15503209	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:15503209delA	uc002rcc.1	-						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	15536618	15536618	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:15536618delA	uc002rcc.1	-						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	15655365	15655365	+	Intron	DEL	A	-	-	rs66629513		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:15655365delA	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	15716171	15716171	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:15716171delT								NBAS (14717 upstream) : DDX1 (15599 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	16145619	16145620	+	IGR	INS	-	T	T	rs146333707	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:16145619_16145620insT								MYCN (58491 upstream) : FAM49A (588281 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	16188421	16188429	+	IGR	DEL	AAAAAAAAA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:16188421_16188429delAAAAAAAAA								MYCN (101293 upstream) : FAM49A (545472 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	16492663	16492664	+	IGR	DEL	AA	-	-	rs111484553		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:16492663_16492664delAA								MYCN (405535 upstream) : FAM49A (241237 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	17129290	17129291	+	IGR	DEL	AC	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:17129290_17129291delAC								FAM49A (282194 upstream) : RAD51AP2 (562695 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	17193609	17193609	+	IGR	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:17193609delG								FAM49A (346513 upstream) : RAD51AP2 (498377 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	17383546	17383547	+	IGR	DEL	GT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:17383546_17383547delGT								FAM49A (536450 upstream) : RAD51AP2 (308439 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	17509146	17509146	+	IGR	DEL	G	-	-	rs67132078		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:17509146delG								FAM49A (662050 upstream) : RAD51AP2 (182840 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	17553965	17553965	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:17553965delT								FAM49A (706869 upstream) : RAD51AP2 (138021 downstream)																																			---	---	---	---
VSNL1	7447	broad.mit.edu	37	2	17725107	17725107	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:17725107delT	uc002rcm.2	+							NM_003385	NP_003376			visinin-like 1								calcium ion binding			ovary(1)	1	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.158)																	---	---	---	---
SMC6	79677	broad.mit.edu	37	2	17907884	17907884	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:17907884delA	uc002rco.2	-						SMC6_uc010exo.2_Intron|SMC6_uc002rcn.2_Intron|SMC6_uc002rcp.1_Intron|SMC6_uc002rcq.2_Intron|SMC6_uc002rcr.1_Intron	NM_001142286	NP_001135758			SMC6 protein						DNA recombination|DNA repair	chromosome|nucleus	ATP binding			breast(4)|upper_aerodigestive_tract(1)|kidney(1)	6	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.158)																	---	---	---	---
SMC6	79677	broad.mit.edu	37	2	17983854	17983854	+	5'Flank	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:17983854delT	uc010exo.2	-							NM_024624	NP_078900			SMC6 protein						DNA recombination|DNA repair	chromosome|nucleus	ATP binding			breast(4)|upper_aerodigestive_tract(1)|kidney(1)	6	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.158)																	---	---	---	---
Unknown	0	broad.mit.edu	37	2	18972407	18972410	+	IGR	DEL	TCTT	-	-	rs6715976		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:18972407_18972410delTCTT								NT5C1B (201569 upstream) : OSR1 (578837 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	19334139	19334140	+	IGR	INS	-	GAAAGGAAGGAA	GAAAGGAAGGAA	rs149711577	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:19334139_19334140insGAAAGGAAGGAA								NT5C1B (563301 upstream) : OSR1 (217107 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	19571373	19571373	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:19571373delT								OSR1 (13001 upstream) : TTC32 (525145 downstream)																																			---	---	---	---
WDR35	57539	broad.mit.edu	37	2	20130442	20130442	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:20130442delT	uc002rdi.2	-						WDR35_uc002rdj.2_Intron|WDR35_uc010ext.2_Intron|WDR35_uc002rdh.2_Intron	NM_001006657	NP_001006658			WD repeat domain 35 isoform 1											ovary(1)	1	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)																	---	---	---	---
Unknown	0	broad.mit.edu	37	2	20320490	20320493	+	IGR	DEL	AAGG	-	-	rs28380549	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:20320490_20320493delAAGG								LAPTM4A (68701 upstream) : SDC1 (80065 downstream)																																			---	---	---	---
PUM2	23369	broad.mit.edu	37	2	20492688	20492689	+	Intron	INS	-	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:20492688_20492689insA	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)																	---	---	---	---
PUM2	23369	broad.mit.edu	37	2	20518224	20518224	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:20518224delA	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)																	---	---	---	---
PUM2	23369	broad.mit.edu	37	2	20526999	20526999	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:20526999delA	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	20766719	20766719	+	IGR	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:20766719delC								RHOB (117519 upstream) : HS1BP3 (50845 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	21495777	21495777	+	IGR	DEL	A	-	-	rs72350440		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:21495777delA								APOB (228832 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	21694107	21694109	+	IGR	DEL	AAA	-	-	rs111832951		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:21694107_21694109delAAA								APOB (427162 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	22037748	22037749	+	IGR	INS	-	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:22037748_22037749insA								APOB (770803 upstream) : None (None downstream)																																			---	---	---	---
KLHL29	114818	broad.mit.edu	37	2	23918223	23918223	+	Intron	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:23918223delG	uc002reg.2	+						KLHL29_uc010ykg.1_Intron|KLHL29_uc010ykh.1_Intron					RecName: Full=Kelch-like protein 29; AltName: Full=Kelch repeat and BTB domain-containing protein 9;											ovary(1)|lung(1)	2																		---	---	---	---
ITSN2	50618	broad.mit.edu	37	2	24450764	24450764	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:24450764delA	uc002rfe.2	-						ITSN2_uc002rff.2_Intron|ITSN2_uc002rfg.2_Intron	NM_006277	NP_006268			intersectin 2 isoform 1						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)																	---	---	---	---
Unknown	0	broad.mit.edu	37	2	24722400	24722400	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:24722400delT								ITSN2 (139003 upstream) : NCOA1 (64779 downstream)																																			---	---	---	---
ADCY3	109	broad.mit.edu	37	2	25043917	25043917	+	Intron	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:25043917delC	uc002rfs.3	-						ADCY3_uc002rfr.3_Intron|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)																	---	---	---	---
ADCY3	109	broad.mit.edu	37	2	25052634	25052635	+	Intron	INS	-	A	A	rs144052640	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:25052634_25052635insA	uc002rfs.3	-						ADCY3_uc002rfr.3_Intron|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)																	---	---	---	---
EFR3B	22979	broad.mit.edu	37	2	25283997	25284000	+	Intron	DEL	TTTT	-	-	rs77971362		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:25283997_25284000delTTTT	uc010eyh.2	+						EFR3B_uc002rfw.2_Intron	NM_014971	NP_055786			EFR3 homolog B								binding				0																		---	---	---	---
DNMT3A	1788	broad.mit.edu	37	2	25476941	25476944	+	Intron	DEL	AAAA	-	-	rs74738948		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:25476941_25476944delAAAA	uc002rgc.2	-						DNMT3A_uc002rgd.2_Intron|DNMT3A_uc010eyi.2_Intron|DNMT3A_uc002rgb.2_5'Flank	NM_022552	NP_072046			DNA cytosine methyltransferase 3 alpha isoform						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								---	---	---	---
Unknown	0	broad.mit.edu	37	2	25579749	25579749	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:25579749delT								DNMT3A (14290 upstream) : DTNB (20365 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	25580935	25580935	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:25580935delA								DNMT3A (15476 upstream) : DTNB (19179 downstream)																																			---	---	---	---
DTNB	1838	broad.mit.edu	37	2	25651055	25651055	+	Intron	DEL	T	-	-	rs79373015		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:25651055delT	uc002rgh.2	-						DTNB_uc002rgg.2_Intron|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|DTNB_uc002rgp.1_5'Flank	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	25881960	25881960	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:25881960delA	uc002rgh.2	-						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_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)																	---	---	---	---
Unknown	0	broad.mit.edu	37	2	26118269	26118271	+	IGR	DEL	TTT	-	-	rs71399330		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:26118269_26118271delTTT								ASXL2 (16957 upstream) : KIF3C (31184 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	26362986	26362988	+	IGR	DEL	TTT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:26362986_26362988delTTT								RAB10 (2664 upstream) : HADHA (50517 downstream)																																			---	---	---	---
HADHA	3030	broad.mit.edu	37	2	26435360	26435360	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:26435360delT	uc002rgy.2	-						HADHA_uc010yks.1_Intron|HADHA_uc010ykt.1_3'UTR	NM_000182	NP_000173			mitochondrial trifunctional protein, alpha						fatty acid beta-oxidation	fatty acid beta-oxidation multienzyme complex|mitochondrial nucleoid|nucleolus	3-hydroxyacyl-CoA dehydrogenase activity|acetyl-CoA C-acetyltransferase activity|coenzyme binding|enoyl-CoA hydratase activity|long-chain-3-hydroxyacyl-CoA dehydrogenase activity|protein binding			ovary(1)	1	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)				NADH(DB00157)													---	---	---	---
HADHB	3032	broad.mit.edu	37	2	26486167	26486170	+	Intron	DEL	AAAA	-	-	rs139107013		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:26486167_26486170delAAAA	uc002rgz.2	+						HADHB_uc010yku.1_Intron|HADHB_uc010ykv.1_Intron|HADHB_uc010ykw.1_Intron|HADHB_uc002rha.2_Intron	NM_000183	NP_000174			mitochondrial trifunctional protein, beta						fatty acid beta-oxidation	mitochondrial nucleoid	3-hydroxyacyl-CoA dehydrogenase activity|acetyl-CoA C-acyltransferase activity|enoyl-CoA hydratase activity|protein binding			ovary(1)|breast(1)	2	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)																	---	---	---	---
Unknown	0	broad.mit.edu	37	2	26619291	26619291	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:26619291delA								EPT1 (532 upstream) : C2orf39 (5493 downstream)																																			---	---	---	---
OTOF	9381	broad.mit.edu	37	2	26689208	26689208	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:26689208delT	uc002rhk.2	-						OTOF_uc010yla.1_Intron|OTOF_uc002rhh.2_Intron|OTOF_uc002rhi.2_Intron|OTOF_uc002rhj.2_Intron	NM_194248	NP_919224			otoferlin isoform a						cellular membrane fusion|sensory perception of sound|synaptic vesicle exocytosis	basolateral plasma membrane|cell junction|cytosol|endoplasmic reticulum membrane|integral to membrane|membrane fraction|synaptic vesicle membrane	calcium ion binding			ovary(3)|breast(2)|central_nervous_system(1)|pancreas(1)	7	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)																	---	---	---	---
OTOF	9381	broad.mit.edu	37	2	26773867	26773868	+	Intron	DEL	CC	-	-	rs6547102	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:26773867_26773868delCC	uc002rhk.2	-							NM_194248	NP_919224			otoferlin isoform a						cellular membrane fusion|sensory perception of sound|synaptic vesicle exocytosis	basolateral plasma membrane|cell junction|cytosol|endoplasmic reticulum membrane|integral to membrane|membrane fraction|synaptic vesicle membrane	calcium ion binding			ovary(3)|breast(2)|central_nervous_system(1)|pancreas(1)	7	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)																	---	---	---	---
OTOF	9381	broad.mit.edu	37	2	26780145	26780145	+	Intron	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:26780145delG	uc002rhk.2	-							NM_194248	NP_919224			otoferlin isoform a						cellular membrane fusion|sensory perception of sound|synaptic vesicle exocytosis	basolateral plasma membrane|cell junction|cytosol|endoplasmic reticulum membrane|integral to membrane|membrane fraction|synaptic vesicle membrane	calcium ion binding			ovary(3)|breast(2)|central_nervous_system(1)|pancreas(1)	7	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)																	---	---	---	---
DPYSL5	56896	broad.mit.edu	37	2	27132738	27132739	+	Intron	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:27132738_27132739delAA	uc002rhu.3	+						DPYSL5_uc002rhv.3_Intron	NM_020134	NP_064519			dihydropyrimidinase-like 5						axon guidance|pyrimidine base catabolic process|signal transduction	cytosol	hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amides			ovary(2)	2	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)																	---	---	---	---
EMILIN1	11117	broad.mit.edu	37	2	27308518	27308518	+	Intron	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:27308518delC	uc002rii.3	+						EMILIN1_uc002rik.3_Intron|KHK_uc002ril.2_5'Flank|KHK_uc002rim.2_5'Flank|KHK_uc002rin.2_5'Flank|KHK_uc002rio.2_5'Flank	NM_007046	NP_008977			elastin microfibril interfacer 1 precursor						cell adhesion	collagen				pancreas(1)	1	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)																	---	---	---	---
Unknown	0	broad.mit.edu	37	2	27475892	27475892	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:27475892delT								CAD (9239 upstream) : SLC30A3 (1549 downstream)																																			---	---	---	---
GTF3C2	2976	broad.mit.edu	37	2	27563496	27563498	+	Intron	DEL	TTT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:27563496_27563498delTTT	uc002rjv.1	-						GTF3C2_uc002rju.1_Intron|GTF3C2_uc002rjw.1_Intron|GTF3C2_uc010eyz.1_Intron	NM_001521	NP_001512			general transcription factor IIIC, polypeptide							transcription factor TFIIIC complex				ovary(1)|skin(1)	2	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)																	---	---	---	---
GCKR	2646	broad.mit.edu	37	2	27724825	27724825	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:27724825delT	uc002rky.2	+						GCKR_uc010ezd.2_Intron|GCKR_uc010ylu.1_Intron	NM_001486	NP_001477			glucokinase regulatory protein						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)																	---	---	---	---
GPN1	11321	broad.mit.edu	37	2	27864187	27864187	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:27864187delA	uc010ymc.1	+						GPN1_uc010ezf.2_Intron|GPN1_uc010yma.1_Intron|GPN1_uc010ymb.1_Intron|GPN1_uc010ymd.1_Intron|GPN1_uc010yme.1_Intron|GPN1_uc010ezg.1_Intron	NM_007266	NP_009197			GPN-loop GTPase 1 isoform a							cytoplasm	GTP binding|nucleoside-triphosphatase activity|protein binding				0																		---	---	---	---
RBKS	64080	broad.mit.edu	37	2	28062888	28062890	+	Intron	DEL	TTT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:28062888_28062890delTTT	uc002rlo.1	-						RBKS_uc010ezi.1_Intron|RBKS_uc010ymg.1_Intron	NM_022128	NP_071411			ribokinase						D-ribose metabolic process		ATP binding|ribokinase activity			ovary(1)|skin(1)	2	Acute lymphoblastic leukemia(172;0.155)																	---	---	---	---
Unknown	0	broad.mit.edu	37	2	28970322	28970322	+	IGR	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:28970322delG								PLB1 (103709 upstream) : PPP1CB (4290 downstream)																																			---	---	---	---
SPDYA	245711	broad.mit.edu	37	2	29048612	29048612	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:29048612delT	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)																	---	---	---	---
CLIP4	79745	broad.mit.edu	37	2	29393665	29393666	+	Intron	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:29393665_29393666delTT	uc002rmv.2	+						CLIP4_uc002rmu.2_Intron|CLIP4_uc002rmw.2_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	29785502	29785502	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:29785502delA	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				---	---	---	---
LCLAT1	253558	broad.mit.edu	37	2	30857627	30857627	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:30857627delT	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	31393674	31393679	+	IGR	DEL	TTTTTT	-	-	rs112123106		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:31393674_31393679delTTTTTT								GALNT14 (15606 upstream) : CAPN14 (2245 downstream)																																			---	---	---	---
EHD3	30845	broad.mit.edu	37	2	31470700	31470700	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:31470700delA	uc002rnu.2	+						EHD3_uc010ymt.1_Intron	NM_014600	NP_055415			EH-domain containing 3						blood coagulation|endocytic recycling|protein homooligomerization	nucleus|plasma membrane|recycling endosome membrane	ATP binding|calcium ion binding|GTP binding|GTPase activity|nucleic acid binding|protein binding			skin(2)	2	Acute lymphoblastic leukemia(172;0.155)																	---	---	---	---
XDH	7498	broad.mit.edu	37	2	31600308	31600309	+	Intron	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:31600308_31600309delAA	uc002rnv.1	-							NM_000379	NP_000370			xanthine dehydrogenase						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)													---	---	---	---
Unknown	0	broad.mit.edu	37	2	32080645	32080645	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:32080645delT								SRD5A2 (274605 upstream) : MEMO1 (12251 downstream)																																			---	---	---	---
MEMO1	51072	broad.mit.edu	37	2	32172885	32172886	+	Intron	DEL	CA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:32172885_32172886delCA	uc002rnx.2	-						MEMO1_uc010ymu.1_Intron|MEMO1_uc010ezq.2_Intron|MEMO1_uc002rny.2_Intron|MEMO1_uc002rnz.2_Intron|MEMO1_uc010ymv.1_Intron	NM_015955	NP_057039			mediator of cell motility 1 isoform 1						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	32299569	32299569	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:32299569delT	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)																	---	---	---	---
LTBP1	4052	broad.mit.edu	37	2	33522402	33522402	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:33522402delT	uc002ros.2	+						LTBP1_uc002rot.2_Intron|LTBP1_uc002rou.2_Intron|LTBP1_uc002rov.2_Intron|LTBP1_uc010ymz.1_Intron|LTBP1_uc010yna.1_Intron|LTBP1_uc010ynb.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)																---	---	---	---
Unknown	0	broad.mit.edu	37	2	34146643	34146646	+	IGR	DEL	TATG	-	-	rs74708446	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:34146643_34146646delTATG								MYADML (193359 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	34211194	34211195	+	IGR	INS	-	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:34211194_34211195insT								MYADML (257910 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	35295863	35295863	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:35295863delA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	35630515	35630515	+	IGR	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:35630515delC								None (None upstream) : CRIM1 (952882 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	36470294	36470294	+	IGR	DEL	A	-	-	rs76426899		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:36470294delA								None (None upstream) : CRIM1 (113103 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	36497114	36497114	+	IGR	DEL	A	-	-	rs113492163		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:36497114delA								None (None upstream) : CRIM1 (86283 downstream)																																			---	---	---	---
FEZ2	9637	broad.mit.edu	37	2	36817798	36817799	+	Intron	DEL	AA	-	-	rs146856068		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:36817798_36817799delAA	uc002rph.2	-						FEZ2_uc002rpf.2_Intron|FEZ2_uc002rpg.2_Intron|FEZ2_uc002rpi.2_Intron|FEZ2_uc002rpj.2_Intron	NM_005102	NP_005093			zygin 2 isoform 1						axon guidance|signal transduction		protein binding			ovary(1)	1		all_hematologic(82;0.21)																---	---	---	---
HEATR5B	54497	broad.mit.edu	37	2	37277042	37277043	+	Intron	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:37277042_37277043delTT	uc002rpp.1	-							NM_019024	NP_061897			HEAT repeat containing 5B								binding			ovary(5)|skin(2)|breast(1)	8		all_hematologic(82;0.21)																---	---	---	---
Unknown	0	broad.mit.edu	37	2	37327280	37327280	+	IGR	DEL	A	-	-	rs111469570		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:37327280delA								CCDC75 (3544 upstream) : EIF2AK2 (6419 downstream)																																			---	---	---	---
EIF2AK2	5610	broad.mit.edu	37	2	37365252	37365257	+	Intron	DEL	AAAAAA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:37365252_37365257delAAAAAA	uc010ynh.1	-						EIF2AK2_uc010fab.1_Intron|EIF2AK2_uc010yng.1_Intron|EIF2AK2_uc010fac.2_Intron|EIF2AK2_uc010fad.2_Intron	NM_002759	NP_002750			eukaryotic translation initiation factor 2-alpha						evasion by virus of host immune response|modulation by virus of host cellular process|negative regulation of osteoblast proliferation|protein autophosphorylation|response to virus|viral infectious cycle	cytosol	ATP binding|double-stranded RNA binding|eukaryotic translation initiation factor 2alpha kinase activity|protein binding|protein phosphatase type 2A regulator activity			ovary(2)|lung(2)|pancreas(1)	5		all_hematologic(82;0.248)																---	---	---	---
EIF2AK2	5610	broad.mit.edu	37	2	37366106	37366109	+	Intron	DEL	TTTT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:37366106_37366109delTTTT	uc010ynh.1	-						EIF2AK2_uc010fab.1_Intron|EIF2AK2_uc010yng.1_Intron|EIF2AK2_uc010fac.2_Intron|EIF2AK2_uc010fad.2_Intron	NM_002759	NP_002750			eukaryotic translation initiation factor 2-alpha						evasion by virus of host immune response|modulation by virus of host cellular process|negative regulation of osteoblast proliferation|protein autophosphorylation|response to virus|viral infectious cycle	cytosol	ATP binding|double-stranded RNA binding|eukaryotic translation initiation factor 2alpha kinase activity|protein binding|protein phosphatase type 2A regulator activity			ovary(2)|lung(2)|pancreas(1)	5		all_hematologic(82;0.248)																---	---	---	---
Unknown	0	broad.mit.edu	37	2	37393745	37393746	+	IGR	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:37393745_37393746delTT								EIF2AK2 (9555 upstream) : SULT6B1 (1218 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	37568651	37568651	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:37568651delT								PRKD3 (24429 upstream) : QPCT (3102 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	37643810	37643811	+	IGR	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:37643810_37643811delTT								QPCT (43346 upstream) : CDC42EP3 (226932 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	37967092	37967098	+	IGR	DEL	GAAAAAA	-	-	rs67500259		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:37967092_37967098delGAAAAAA								CDC42EP3 (67766 upstream) : FAM82A1 (185364 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	37976146	37976146	+	IGR	DEL	T	-	-	rs67724115		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:37976146delT								CDC42EP3 (76820 upstream) : FAM82A1 (176316 downstream)																																			---	---	---	---
FAM82A1	151393	broad.mit.edu	37	2	38271715	38271716	+	Intron	DEL	TT	-	-	rs74935042		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:38271715_38271716delTT	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	38741707	38741707	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:38741707delA								ATL2 (137275 upstream) : HNRPLL (48621 downstream)																																			---	---	---	---
GALM	130589	broad.mit.edu	37	2	38944988	38944988	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:38944988delT	uc002rqy.2	+							NM_138801	NP_620156			galactose mutarotase						hexose metabolic process	cytoplasm	aldose 1-epimerase activity|carbohydrate binding				0		all_hematologic(82;0.248)																---	---	---	---
SFRS7	6432	broad.mit.edu	37	2	38973132	38973133	+	Intron	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:38973132_38973133delAA	uc002rqz.2	-						SFRS7_uc002rra.2_Intron|SFRS7_uc010ynp.1_Intron	NM_001031684	NP_001026854			splicing factor, arginine/serine-rich 7						mRNA 3'-end processing|mRNA export from nucleus|nuclear mRNA splicing, via spliceosome|termination of RNA polymerase II transcription	nucleoplasm	nucleotide binding|protein binding|RNA binding|zinc ion binding				0		all_hematologic(82;0.248)																---	---	---	---
DHX57	90957	broad.mit.edu	37	2	39041084	39041084	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:39041084delT	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)																---	---	---	---
SOS1	6654	broad.mit.edu	37	2	39299051	39299054	+	Intron	DEL	TTTT	-	-	rs75838859		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:39299051_39299054delTTTT	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				---	---	---	---
CDKL4	344387	broad.mit.edu	37	2	39423757	39423757	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:39423757delT	uc002rrm.2	-						CDKL4_uc010fal.1_Intron	NM_001009565	NP_001009565			cyclin-dependent kinase-like 4							cytoplasm	ATP binding|cyclin-dependent protein kinase activity			ovary(1)	1		all_hematologic(82;0.248)																---	---	---	---
Unknown	0	broad.mit.edu	37	2	40021989	40021989	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:40021989delT								THUMPD2 (15573 upstream) : SLC8A1 (317298 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	40143292	40143292	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:40143292delT								THUMPD2 (136876 upstream) : SLC8A1 (195995 downstream)																																			---	---	---	---
SLC8A1	6546	broad.mit.edu	37	2	40487560	40487560	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:40487560delT	uc002rrx.2	-						SLC8A1_uc002rry.2_Intron|SLC8A1_uc002rrz.2_Intron|SLC8A1_uc002rsa.2_Intron|SLC8A1_uc002rsd.3_Intron|SLC8A1_uc002rsb.1_Intron	NM_021097	NP_066920			solute carrier family 8 (sodium/calcium						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)													---	---	---	---
SLC8A1	6546	broad.mit.edu	37	2	40677877	40677878	+	Intron	DEL	GA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:40677877_40677878delGA	uc002rsa.2	-						SLC8A1_uc002rsd.3_Intron|SLC8A1_uc010fan.1_Intron|SLC8A1_uc002rsc.1_Intron	NM_001112802	NP_001106273			solute carrier family 8 (sodium/calcium						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)													---	---	---	---
Unknown	0	broad.mit.edu	37	2	40862969	40862969	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:40862969delT								SLC8A1 (123394 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	40932997	40932997	+	IGR	DEL	T	-	-	rs75959954		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-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	41029365	41029365	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:41029365delA								SLC8A1 (289790 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	41638868	41638869	+	IGR	DEL	TC	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:41638868_41638869delTC								SLC8A1 (899293 upstream) : PKDCC (636292 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	41738722	41738723	+	IGR	INS	-	TG	TG	rs144745113	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:41738722_41738723insTG								SLC8A1 (999147 upstream) : PKDCC (536438 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	42384590	42384590	+	IGR	DEL	G	-	-	rs6708175	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:42384590delG								PKDCC (98924 upstream) : EML4 (11900 downstream)																																			---	---	---	---
EML4	27436	broad.mit.edu	37	2	42508205	42508205	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:42508205delA	uc002rsi.2	+						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								---	---	---	---
EML4	27436	broad.mit.edu	37	2	42526415	42526415	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:42526415delT	uc002rsi.2	+						EML4_uc010fap.2_Intron|EML4_uc002rsj.2_Intron|EML4_uc010faq.2_5'Flank|EML4_uc010ynv.1_5'Flank	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-4200-01A-01D-1126-08	TCGA-BR-4200-11A-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	42763259	42763260	+	Intron	INS	-	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:42763259_42763260insA	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	42805909	42805909	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:42805909delT	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	42936306	42936306	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:42936306delT	uc002rso.1	+						MTA3_uc002rsp.1_Intron|MTA3_uc002rsq.2_3'UTR|MTA3_uc002rsr.2_3'UTR	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																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	43263109	43263109	+	Intron	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:43263109delC	uc002rsu.1	-											full-length cDNA clone CS0DE006YH09 of Placenta of Homo sapiens (human).																														---	---	---	---
Unknown	0	broad.mit.edu	37	2	43372997	43372997	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:43372997delT								HAAO (353246 upstream) : ZFP36L2 (76545 downstream)																																			---	---	---	---
DYNC2LI1	51626	broad.mit.edu	37	2	44007229	44007230	+	Intron	INS	-	G	G	rs115742272	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:44007229_44007230insG	uc002rtk.2	+						DYNC2LI1_uc002rth.2_Intron|DYNC2LI1_uc002rti.2_Intron|DYNC2LI1_uc002rtj.2_Intron|DYNC2LI1_uc002rtl.2_Intron|DYNC2LI1_uc010ynz.1_Intron	NM_016008	NP_057092			dynein 2 light intermediate chain isoform 1							apical part of cell|axonemal dynein complex|cilium axoneme|cytoplasm|microtubule|motile primary cilium	motor activity			ovary(1)	1		all_hematologic(82;0.151)|Acute lymphoblastic leukemia(82;0.175)																---	---	---	---
ABCG5	64240	broad.mit.edu	37	2	44053306	44053308	+	Intron	DEL	TTT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:44053306_44053308delTTT	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)																---	---	---	---
Unknown	0	broad.mit.edu	37	2	44268163	44268163	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:44268163delT								LRPPRC (45019 upstream) : PPM1B (127837 downstream)																																			---	---	---	---
PPM1B	5495	broad.mit.edu	37	2	44414385	44414385	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:44414385delT	uc002rtt.2	+						PPM1B_uc002rts.2_Intron|PPM1B_uc002rtu.2_Intron|PPM1B_uc002rtv.2_Intron|PPM1B_uc002rtw.2_Intron|PPM1B_uc002rtx.2_Intron	NM_002706	NP_002697			protein phosphatase 1B isoform 1						protein dephosphorylation	protein serine/threonine phosphatase complex	magnesium ion binding|manganese ion binding|protein binding|protein serine/threonine phosphatase activity			kidney(1)|skin(1)	2		all_hematologic(82;0.151)|Acute lymphoblastic leukemia(82;0.175)																---	---	---	---
PREPL	9581	broad.mit.edu	37	2	44553635	44553637	+	Intron	DEL	TTT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:44553635_44553637delTTT	uc002ruf.2	-						PREPL_uc002rug.2_Intron|PREPL_uc002ruh.2_Intron|PREPL_uc010fax.2_Intron|PREPL_uc002rui.3_Intron|PREPL_uc002ruj.1_Intron|PREPL_uc002ruk.1_Intron	NM_006036	NP_006027			prolyl endopeptidase-like isoform C						proteolysis	cytosol	serine-type endopeptidase activity			ovary(1)	1		all_hematologic(82;0.151)|Acute lymphoblastic leukemia(82;0.175)																---	---	---	---
C2orf34	79823	broad.mit.edu	37	2	44751664	44751664	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:44751664delT	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)																---	---	---	---
C2orf34	79823	broad.mit.edu	37	2	44922779	44922779	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:44922779delT	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	45055865	45055868	+	IGR	DEL	AAAA	-	-	rs76804832		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:45055865_45055868delAAAA								C2orf34 (56136 upstream) : SIX3 (113169 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	45096354	45096354	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:45096354delA								C2orf34 (96625 upstream) : SIX3 (72683 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	45415257	45415257	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:45415257delA	uc002ruq.2	-						uc002rur.1_RNA					Homo sapiens cDNA FLJ38231 fis, clone FCBBF2004707.																														---	---	---	---
PRKCE	5581	broad.mit.edu	37	2	46094870	46094871	+	Intron	DEL	GT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:46094870_46094871delGT	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)															---	---	---	---
Unknown	0	broad.mit.edu	37	2	46637325	46637326	+	IGR	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:46637325_46637326delAA								EPAS1 (23490 upstream) : LOC388946 (69378 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	46649103	46649103	+	IGR	DEL	A	-	-	rs6755133	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:46649103delA								EPAS1 (35268 upstream) : LOC388946 (57601 downstream)																																			---	---	---	---
RHOQ	23433	broad.mit.edu	37	2	46772772	46772773	+	Intron	INS	-	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:46772772_46772773insG	uc002rva.2	+							NM_012249	NP_036381			ras-like protein TC10 precursor						cortical actin cytoskeleton organization|insulin receptor signaling pathway|negative regulation of establishment of protein localization in plasma membrane|positive regulation of filopodium assembly|positive regulation of glucose import|positive regulation of transcription from RNA polymerase II promoter|regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	actin filament|cytosol|plasma membrane	GBD domain binding|GTP binding|GTPase activity|profilin binding			skin(2)	2		all_hematologic(82;0.151)|Acute lymphoblastic leukemia(82;0.175)	LUSC - Lung squamous cell carcinoma(58;0.114)															---	---	---	---
SOCS5	9655	broad.mit.edu	37	2	46963177	46963177	+	Intron	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:46963177delC	uc002rvf.2	+						SOCS5_uc010yoe.1_Intron|SOCS5_uc002rvg.2_Intron	NM_014011	NP_054730			suppressor of cytokine signaling 5						cell growth|cytokine-mediated signaling pathway|intracellular signal transduction|negative regulation of signal transduction|negative regulation of T-helper 2 cell differentiation|positive regulation of T-helper 1 cell differentiation|regulation of growth					ovary(1)|lung(1)|central_nervous_system(1)	3		all_hematologic(82;0.151)|Acute lymphoblastic leukemia(82;0.175)	LUSC - Lung squamous cell carcinoma(58;0.114)															---	---	---	---
Unknown	0	broad.mit.edu	37	2	47022997	47022997	+	IGR	DEL	T	-	-	rs67529632		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:47022997delT								SOCS5 (33071 upstream) : LOC100134259 (32006 downstream)																																			---	---	---	---
TTC7A	57217	broad.mit.edu	37	2	47165477	47165477	+	5'Flank	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:47165477delT	uc002rvo.2	+						TTC7A_uc002rvm.2_Intron|TTC7A_uc002rvn.1_5'Flank|TTC7A_uc010fbb.2_5'Flank|TTC7A_uc010fbc.2_5'Flank|MCFD2_uc010fba.2_Intron|MCFD2_uc010yof.1_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	47367576	47367576	+	Intron	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:47367576delC	uc002rvs.2	-						C2orf61_uc010fbd.2_Intron|C2orf61_uc010yog.1_Intron	NM_173649	NP_775920			hypothetical protein LOC285051 isoform 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)															---	---	---	---
Unknown	0	broad.mit.edu	37	2	47481444	47481445	+	Intron	DEL	TT	-	-	rs111606234		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:47481444_47481445delTT	uc002rvu.1	-											Homo sapiens cDNA FLJ37024 fis, clone BRACE2010837.									p.?(1)																					---	---	---	---
Unknown	0	broad.mit.edu	37	2	47540916	47540917	+	Intron	INS	-	TC	TC	rs144575908	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:47540916_47540917insTC	uc002rvu.1	-						uc002rvv.1_5'Flank					Homo sapiens cDNA FLJ37024 fis, clone BRACE2010837.									p.?(1)																					---	---	---	---
Unknown	0	broad.mit.edu	37	2	47564719	47564720	+	Intron	DEL	AA	-	-	rs71399024		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:47564719_47564720delAA	uc002rvu.1	-											Homo sapiens cDNA FLJ37024 fis, clone BRACE2010837.									p.?(1)																					---	---	---	---
EPCAM	4072	broad.mit.edu	37	2	47578344	47578345	+	Intron	INS	-	G	G	rs143166896	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:47578344_47578345insG	uc002rvw.2	+							NM_002354	NP_002345			epithelial cell adhesion molecule precursor						positive regulation of cell proliferation	apical plasma membrane|basolateral plasma membrane|integral to membrane|lateral plasma membrane|tight junction	protein binding	p.?(1)		skin(1)	1														Lynch_syndrome				---	---	---	---
MSH2	4436	broad.mit.edu	37	2	47637614	47637614	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:47637614delT	uc002rvy.1	+						MSH2_uc010yoh.1_Intron|MSH2_uc002rvz.2_Intron|MSH2_uc010fbg.2_Intron|MSH2_uc010fbf.1_Intron	NM_000251	NP_000242			mutS homolog 2						B cell differentiation|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|double-strand break repair|intra-S DNA damage checkpoint|isotype switching|maintenance of DNA repeat elements|male gonad development|meiotic gene conversion|meiotic mismatch repair|negative regulation of neuron apoptosis|negative regulation of reciprocal meiotic recombination|positive regulation of helicase activity|postreplication repair|response to UV-B|response to X-ray|somatic hypermutation of immunoglobulin genes	MutSalpha complex|MutSbeta complex|nuclear chromosome	ATP binding|DNA-dependent ATPase activity|double-strand/single-strand DNA junction binding|guanine/thymine mispair binding|loop DNA binding|protein C-terminus binding|protein homodimerization activity|protein kinase binding|Y-form DNA binding			large_intestine(33)|haematopoietic_and_lymphoid_tissue(6)|endometrium(4)|ovary(3)|cervix(2)|central_nervous_system(2)|stomach(1)|small_intestine(1)|breast(1)|skin(1)|prostate(1)	55		all_hematologic(82;0.0359)|Acute lymphoblastic leukemia(82;0.175)	Lung(47;0.101)|LUSC - Lung squamous cell carcinoma(58;0.151)					D|Mis|N|F|S		colorectal|endometrial|ovarian	colorectal|endometrial|ovarian		MMR	Lynch_syndrome|Muir-Torre_syndrome|Turcot_syndrome|Constitutional_Mismatch_Repair_Deficiency_Syndrome				---	---	---	---
MSH2	4436	broad.mit.edu	37	2	47644671	47644671	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:47644671delA	uc002rvy.1	+						MSH2_uc010yoh.1_Intron|MSH2_uc002rvz.2_Intron|MSH2_uc010fbg.2_Intron	NM_000251	NP_000242			mutS homolog 2						B cell differentiation|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|double-strand break repair|intra-S DNA damage checkpoint|isotype switching|maintenance of DNA repeat elements|male gonad development|meiotic gene conversion|meiotic mismatch repair|negative regulation of neuron apoptosis|negative regulation of reciprocal meiotic recombination|positive regulation of helicase activity|postreplication repair|response to UV-B|response to X-ray|somatic hypermutation of immunoglobulin genes	MutSalpha complex|MutSbeta complex|nuclear chromosome	ATP binding|DNA-dependent ATPase activity|double-strand/single-strand DNA junction binding|guanine/thymine mispair binding|loop DNA binding|protein C-terminus binding|protein homodimerization activity|protein kinase binding|Y-form DNA binding			large_intestine(33)|haematopoietic_and_lymphoid_tissue(6)|endometrium(4)|ovary(3)|cervix(2)|central_nervous_system(2)|stomach(1)|small_intestine(1)|breast(1)|skin(1)|prostate(1)	55		all_hematologic(82;0.0359)|Acute lymphoblastic leukemia(82;0.175)	Lung(47;0.101)|LUSC - Lung squamous cell carcinoma(58;0.151)					D|Mis|N|F|S		colorectal|endometrial|ovarian	colorectal|endometrial|ovarian		MMR	Lynch_syndrome|Muir-Torre_syndrome|Turcot_syndrome|Constitutional_Mismatch_Repair_Deficiency_Syndrome				---	---	---	---
MSH2	4436	broad.mit.edu	37	2	47694593	47694594	+	Intron	DEL	TC	-	-	rs70940689		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:47694593_47694594delTC	uc002rvy.1	+						MSH2_uc010yoh.1_Intron|MSH2_uc002rvz.2_Intron|MSH2_uc010fbg.2_Intron|MSH2_uc010fbi.1_Intron	NM_000251	NP_000242			mutS homolog 2						B cell differentiation|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|double-strand break repair|intra-S DNA damage checkpoint|isotype switching|maintenance of DNA repeat elements|male gonad development|meiotic gene conversion|meiotic mismatch repair|negative regulation of neuron apoptosis|negative regulation of reciprocal meiotic recombination|positive regulation of helicase activity|postreplication repair|response to UV-B|response to X-ray|somatic hypermutation of immunoglobulin genes	MutSalpha complex|MutSbeta complex|nuclear chromosome	ATP binding|DNA-dependent ATPase activity|double-strand/single-strand DNA junction binding|guanine/thymine mispair binding|loop DNA binding|protein C-terminus binding|protein homodimerization activity|protein kinase binding|Y-form DNA binding	p.?(2)		large_intestine(33)|haematopoietic_and_lymphoid_tissue(6)|endometrium(4)|ovary(3)|cervix(2)|central_nervous_system(2)|stomach(1)|small_intestine(1)|breast(1)|skin(1)|prostate(1)	55		all_hematologic(82;0.0359)|Acute lymphoblastic leukemia(82;0.175)	Lung(47;0.101)|LUSC - Lung squamous cell carcinoma(58;0.151)					D|Mis|N|F|S		colorectal|endometrial|ovarian	colorectal|endometrial|ovarian		MMR	Lynch_syndrome|Muir-Torre_syndrome|Turcot_syndrome|Constitutional_Mismatch_Repair_Deficiency_Syndrome				---	---	---	---
Unknown	0	broad.mit.edu	37	2	48293827	48293827	+	IGR	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:48293827delC								FBXO11 (161013 upstream) : FOXN2 (247968 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	48748641	48748641	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:48748641delA								KLRAQ1 (6117 upstream) : STON1 (8667 downstream)																																			---	---	---	---
STON1	11037	broad.mit.edu	37	2	48792975	48792976	+	Intron	DEL	TG	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:48792975_48792976delTG	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)															---	---	---	---
LHCGR	3973	broad.mit.edu	37	2	48952906	48952906	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:48952906delA	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	49307231	49307231	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:49307231delA	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				---	---	---	---
FSHR	2492	broad.mit.edu	37	2	49334359	49334359	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:49334359delT	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				---	---	---	---
NRXN1	9378	broad.mit.edu	37	2	50637827	50637827	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:50637827delA	uc010fbq.2	-						NRXN1_uc002rxb.3_Intron|NRXN1_uc002rxe.3_Intron|NRXN1_uc002rxc.1_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	50693641	50693641	+	Intron	DEL	A	-	-	rs78516173	byFrequency;by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:50693641delA	uc010fbq.2	-						NRXN1_uc002rxb.3_Intron|NRXN1_uc002rxe.3_Intron|NRXN1_uc002rxc.1_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	51475017	51475018	+	IGR	DEL	TG	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:51475017_51475018delTG								NRXN1 (215343 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	51594138	51594138	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:51594138delA								NRXN1 (334464 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	51737734	51737734	+	IGR	DEL	A	-	-	rs13423125	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:51737734delA								NRXN1 (478060 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	51829874	51829874	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:51829874delT								NRXN1 (570200 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	52294656	52294657	+	IGR	DEL	AG	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:52294656_52294657delAG								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	52624971	52624972	+	IGR	INS	-	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:52624971_52624972insT								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	52993674	52993674	+	IGR	DEL	A	-	-	rs111963573		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:52993674delA								None (None upstream) : ASB3 (903444 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	53083188	53083188	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:53083188delA								None (None upstream) : ASB3 (813930 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	53283876	53283876	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:53283876delA								None (None upstream) : ASB3 (613242 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	53432285	53432285	+	IGR	DEL	C	-	-	rs7593278	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:53432285delC								None (None upstream) : ASB3 (464833 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	53811439	53811439	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:53811439delT								None (None upstream) : ASB3 (85679 downstream)																																			---	---	---	---
ASB3	51130	broad.mit.edu	37	2	53941050	53941050	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:53941050delA	uc002rxg.1	-						ASB3_uc002rxh.1_Intron|ASB3_uc002rxi.3_Intron	NM_016115	NP_057199			ankyrin repeat and SOCS box-containing protein 3						intracellular signal transduction					ovary(1)|kidney(1)	2			Lung(47;0.125)|LUSC - Lung squamous cell carcinoma(58;0.181)															---	---	---	---
ASB3	51130	broad.mit.edu	37	2	54052940	54052941	+	Intron	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:54052940_54052941delAA	uc002rxi.3	-							NM_001164165	NP_001157637			hypothetical protein LOC100302652						intracellular signal transduction					ovary(1)|kidney(1)	2			Lung(47;0.125)|LUSC - Lung squamous cell carcinoma(58;0.181)															---	---	---	---
PSME4	23198	broad.mit.edu	37	2	54133991	54133991	+	Frame_Shift_Del	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:54133991delT	uc002rxp.2	-	25	2855	c.2799delA	c.(2797-2799)AAAfs	p.K933fs	PSME4_uc010yop.1_Frame_Shift_Del_p.K819fs|PSME4_uc010yoq.1_RNA|PSME4_uc010fbu.1_Frame_Shift_Del_p.K308fs|PSME4_uc010fbv.1_Frame_Shift_Del_p.K77fs	NM_014614	NP_055429	Q14997	PSME4_HUMAN	proteasome (prosome, macropain) activator	933					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	54190469	54190469	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:54190469delA	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	54609071	54609071	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:54609071delT								C2orf73 (20357 upstream) : SPTBN1 (74383 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	54652112	54652113	+	IGR	DEL	TC	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:54652112_54652113delTC								C2orf73 (63398 upstream) : SPTBN1 (31341 downstream)																																			---	---	---	---
SPTBN1	6711	broad.mit.edu	37	2	54859486	54859486	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:54859486delA	uc002rxu.2	+						SPTBN1_uc002rxx.2_Intron	NM_003128	NP_003119			spectrin, beta, non-erythrocytic 1 isoform 1						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)															---	---	---	---
EML6	400954	broad.mit.edu	37	2	55119193	55119196	+	Intron	DEL	TTGC	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:55119193_55119196delTTGC	uc002ryb.3	+							NM_001039753	NP_001034842			echinoderm microtubule associated protein like							cytoplasm|microtubule					0																		---	---	---	---
C2orf63	130162	broad.mit.edu	37	2	55428380	55428381	+	Intron	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:55428380_55428381delAA	uc002ryi.2	-						C2orf63_uc002ryh.2_Intron|C2orf63_uc002ryj.2_Intron	NM_152385	NP_689598			hypothetical protein LOC130162 isoform 1								binding			ovary(2)|central_nervous_system(1)	3			LUSC - Lung squamous cell carcinoma(58;0.179)|Lung(47;0.189)															---	---	---	---
C2orf63	130162	broad.mit.edu	37	2	55438639	55438643	+	Intron	DEL	AAAAA	-	-	rs71958882		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:55438639_55438643delAAAAA	uc002ryi.2	-						C2orf63_uc002ryh.2_Intron|C2orf63_uc002ryj.2_Intron	NM_152385	NP_689598			hypothetical protein LOC130162 isoform 1								binding			ovary(2)|central_nervous_system(1)	3			LUSC - Lung squamous cell carcinoma(58;0.179)|Lung(47;0.189)															---	---	---	---
C2orf63	130162	broad.mit.edu	37	2	55449637	55449637	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:55449637delA	uc002ryi.2	-						C2orf63_uc002ryh.2_Intron|C2orf63_uc002ryj.2_Intron	NM_152385	NP_689598			hypothetical protein LOC130162 isoform 1								binding			ovary(2)|central_nervous_system(1)	3			LUSC - Lung squamous cell carcinoma(58;0.179)|Lung(47;0.189)															---	---	---	---
CCDC88A	55704	broad.mit.edu	37	2	55544494	55544494	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:55544494delA	uc002ryv.2	-						CCDC88A_uc010yoz.1_Intron|CCDC88A_uc010ypa.1_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																		---	---	---	---
CCDC88A	55704	broad.mit.edu	37	2	55575891	55575891	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:55575891delA	uc002ryv.2	-						CCDC88A_uc010yoz.1_Intron|CCDC88A_uc010ypa.1_Intron|CCDC88A_uc010ypb.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																		---	---	---	---
SMEK2	57223	broad.mit.edu	37	2	55826951	55826955	+	Intron	DEL	AAGAT	-	-	rs76818433		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:55826951_55826955delAAGAT	uc002rzc.2	-						SMEK2_uc002rzb.2_Intron|SMEK2_uc002rzd.2_Intron|SMEK2_uc002rza.2_Intron	NM_001122964	NP_001116436			SMEK homolog 2, suppressor of mek1 isoform 1							microtubule organizing center|nucleus	protein binding			skin(1)	1			LUSC - Lung squamous cell carcinoma(58;0.127)|Lung(47;0.132)															---	---	---	---
PNPT1	87178	broad.mit.edu	37	2	55884886	55884887	+	Intron	INS	-	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:55884886_55884887insG	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	56241802	56241802	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:56241802delT	uc002rzk.2	+											Homo sapiens, clone IMAGE:3873411, mRNA.																														---	---	---	---
CCDC85A	114800	broad.mit.edu	37	2	56611387	56611387	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:56611387delT	uc002rzn.2	+							NM_001080433	NP_001073902			coiled-coil domain containing 85A											breast(3)|ovary(2)	5			LUSC - Lung squamous cell carcinoma(58;0.127)|Lung(47;0.132)															---	---	---	---
Unknown	0	broad.mit.edu	37	2	57235892	57235892	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:57235892delA								CCDC85A (622584 upstream) : VRK2 (898894 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	57271058	57271058	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:57271058delT								CCDC85A (657750 upstream) : VRK2 (863728 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	57631732	57631732	+	IGR	DEL	T	-	-	rs71835031		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:57631732delT								None (None upstream) : VRK2 (503054 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	58025159	58025159	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:58025159delA								None (None upstream) : VRK2 (109627 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	58121858	58121858	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:58121858delA								None (None upstream) : VRK2 (12928 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	58130296	58130296	+	IGR	DEL	A	-	-	rs11287568		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:58130296delA								None (None upstream) : VRK2 (4490 downstream)																																			---	---	---	---
VRK2	7444	broad.mit.edu	37	2	58171871	58171871	+	Intron	DEL	A	-	-	rs75556867		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:58171871delA	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																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	58587081	58587081	+	IGR	DEL	T	-	-	rs72071537		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:58587081delT								FANCL (118566 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	59099053	59099056	+	Intron	DEL	TTTT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:59099053_59099056delTTTT	uc002rzy.2	+						uc002rzz.2_Intron					Homo sapiens cDNA FLJ30838 fis, clone FEBRA2002399.																														---	---	---	---
Unknown	0	broad.mit.edu	37	2	59129752	59129753	+	Intron	DEL	AG	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:59129752_59129753delAG	uc002rzy.2	+						uc002rzz.2_Intron					Homo sapiens cDNA FLJ30838 fis, clone FEBRA2002399.																														---	---	---	---
Unknown	0	broad.mit.edu	37	2	59675456	59675457	+	IGR	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:59675456_59675457delTT								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	59880527	59880527	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:59880527delT								None (None upstream) : BCL11A (797776 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	59886524	59886525	+	IGR	DEL	TG	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:59886524_59886525delTG								None (None upstream) : BCL11A (791778 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	60550706	60550717	+	IGR	DEL	GTGTGTGTGTGT	-	-	rs67709427		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:60550706_60550717delGTGTGTGTGTGT								None (None upstream) : BCL11A (127586 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	60786815	60786815	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:60786815delA								BCL11A (6182 upstream) : PAPOLG (196568 downstream)																																			---	---	---	---
PAPOLG	64895	broad.mit.edu	37	2	61023857	61023857	+	Intron	DEL	T	-	-	rs71400300		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:61023857delT	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)															---	---	---	---
KIAA1841	84542	broad.mit.edu	37	2	61344482	61344482	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:61344482delT	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	61548306	61548306	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:61548306delA	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)															---	---	---	---
Unknown	0	broad.mit.edu	37	2	62032968	62032969	+	IGR	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:62032968_62032969delTT								XPO1 (267550 upstream) : FAM161A (19016 downstream)																																			---	---	---	---
FAM161A	84140	broad.mit.edu	37	2	62079312	62079313	+	Intron	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:62079312_62079313delTT	uc010ypo.1	-						FAM161A_uc002sbm.3_Intron|FAM161A_uc002sbn.3_Intron|FAM161A_uc010fcm.1_Intron|FAM161A_uc010fcn.1_Intron	NM_032180	NP_115556			hypothetical protein LOC84140						response to stimulus|visual perception	centrosome				large_intestine(2)|ovary(1)	3																		---	---	---	---
COMMD1	150684	broad.mit.edu	37	2	62310085	62310085	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:62310085delT	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	62416909	62416911	+	IGR	DEL	AAA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:62416909_62416911delAAA								COMMD1 (53705 upstream) : B3GNT2 (6351 downstream)																																			---	---	---	---
B3GNT2	10678	broad.mit.edu	37	2	62428495	62428495	+	Intron	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:62428495delG	uc002sbs.2	+							NM_006577	NP_006568			UDP-GlcNAc:betaGal							Golgi membrane|integral to membrane	UDP-galactose:beta-N-acetylglucosamine beta-1,3-galactosyltransferase activity			ovary(1)	1	Lung NSC(7;0.031)|all_lung(7;0.0634)		LUSC - Lung squamous cell carcinoma(7;3.55e-06)|Epithelial(17;0.0963)															---	---	---	---
Unknown	0	broad.mit.edu	37	2	62493561	62493562	+	IGR	DEL	AA	-	-	rs67204725		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:62493561_62493562delAA								B3GNT2 (41697 upstream) : TMEM17 (233794 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	62766345	62766347	+	IGR	DEL	TTT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:62766345_62766347delTTT								TMEM17 (3565 upstream) : EHBP1 (134666 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	62829445	62829445	+	IGR	DEL	A	-	-	rs71874963		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:62829445delA								TMEM17 (66665 upstream) : EHBP1 (71568 downstream)																																			---	---	---	---
EHBP1	23301	broad.mit.edu	37	2	62915823	62915823	+	Intron	DEL	T	-	-	rs6719613	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:62915823delT	uc010fcp.2	+							NM_001142615	NP_001136087			EH domain binding protein 1 isoform 3							cytoplasm|membrane				ovary(1)|breast(1)	2	Lung NSC(7;0.0951)|all_lung(7;0.169)		LUSC - Lung squamous cell carcinoma(7;7.74e-05)|Epithelial(17;0.189)											Hereditary_Prostate_Cancer				---	---	---	---
EHBP1	23301	broad.mit.edu	37	2	62974689	62974689	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:62974689delT	uc002sby.2	+						EHBP1_uc010fcp.2_Intron|EHBP1_uc010fcq.1_Intron|EHBP1_uc002sbx.2_Intron|EHBP1_uc002sbz.2_Intron|EHBP1_uc002scb.2_Intron|EHBP1_uc002sca.2_Intron	NM_015252	NP_056067			EH domain binding protein 1 isoform 1							cytoplasm|membrane				ovary(1)|breast(1)	2	Lung NSC(7;0.0951)|all_lung(7;0.169)		LUSC - Lung squamous cell carcinoma(7;7.74e-05)|Epithelial(17;0.189)											Hereditary_Prostate_Cancer				---	---	---	---
EHBP1	23301	broad.mit.edu	37	2	63148684	63148684	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:63148684delA	uc002sby.2	+						EHBP1_uc010fcp.2_Intron|EHBP1_uc002sbz.2_Intron|EHBP1_uc002scb.2_Intron	NM_015252	NP_056067			EH domain binding protein 1 isoform 1							cytoplasm|membrane				ovary(1)|breast(1)	2	Lung NSC(7;0.0951)|all_lung(7;0.169)		LUSC - Lung squamous cell carcinoma(7;7.74e-05)|Epithelial(17;0.189)											Hereditary_Prostate_Cancer				---	---	---	---
EHBP1	23301	broad.mit.edu	37	2	63247028	63247028	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:63247028delA	uc002sby.2	+						EHBP1_uc010fcp.2_Intron|EHBP1_uc002sbz.2_Intron|EHBP1_uc002scb.2_Intron	NM_015252	NP_056067			EH domain binding protein 1 isoform 1							cytoplasm|membrane				ovary(1)|breast(1)	2	Lung NSC(7;0.0951)|all_lung(7;0.169)		LUSC - Lung squamous cell carcinoma(7;7.74e-05)|Epithelial(17;0.189)											Hereditary_Prostate_Cancer				---	---	---	---
C2orf86	51057	broad.mit.edu	37	2	63512206	63512206	+	Intron	DEL	T	-	-	rs7596446	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:63512206delT	uc002sch.2	-						C2orf86_uc002sce.2_Intron|C2orf86_uc002scf.2_Intron|C2orf86_uc010ypu.1_Intron|C2orf86_uc002scg.2_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																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	64062166	64062166	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:64062166delT								LOC388955 (212007 upstream) : UGP2 (5932 downstream)																																			---	---	---	---
VPS54	51542	broad.mit.edu	37	2	64209328	64209329	+	Intron	DEL	TC	-	-	rs79076966	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:64209328_64209329delTC	uc002scq.2	-						VPS54_uc002scp.2_Intron	NM_016516	NP_057600			vacuolar protein sorting 54 isoform 1						protein transport|retrograde transport, endosome to Golgi						0																		---	---	---	---
PELI1	57162	broad.mit.edu	37	2	64331637	64331637	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:64331637delT	uc002scs.3	-						PELI1_uc002sct.3_Intron	NM_020651	NP_065702			pellino protein						innate immune response|MyD88-dependent toll-like receptor signaling pathway|positive regulation of I-kappaB kinase/NF-kappaB cascade|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway	cytosol				ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	64574342	64574343	+	IGR	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:64574342_64574343delTT								PELI1 (202737 upstream) : HSPC159 (106984 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	65019637	65019638	+	IGR	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:65019637_65019638delTT								SERTAD2 (138591 upstream) : SLC1A4 (195941 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	65849958	65849959	+	Intron	DEL	AG	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:65849958_65849959delAG	uc010fcy.1	+											Homo sapiens cDNA FLJ16124 fis, clone BRACE2011677.																														---	---	---	---
Unknown	0	broad.mit.edu	37	2	66008520	66008521	+	Intron	INS	-	AC	AC	rs148823858	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:66008520_66008521insAC	uc010fcy.1	+											Homo sapiens cDNA FLJ16124 fis, clone BRACE2011677.																														---	---	---	---
Unknown	0	broad.mit.edu	37	2	66085756	66085757	+	Intron	INS	-	T	T	rs142454180	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:66085756_66085757insT	uc010fcy.1	+											Homo sapiens cDNA FLJ16124 fis, clone BRACE2011677.																														---	---	---	---
Unknown	0	broad.mit.edu	37	2	66427734	66427734	+	IGR	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:66427734delC								SPRED2 (768078 upstream) : MEIS1 (234798 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	66648200	66648200	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:66648200delA								SPRED2 (988544 upstream) : MEIS1 (14332 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	66932014	66932014	+	IGR	DEL	C	-	-	rs67676633		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:66932014delC								MEIS1 (132124 upstream) : ETAA1 (692428 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	67171953	67171953	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:67171953delA								MEIS1 (372063 upstream) : ETAA1 (452489 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	67379956	67379957	+	Intron	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:67379956_67379957delAA	uc002sdx.2	+						uc002sdy.1_Intron					Homo sapiens, clone IMAGE:5541055, mRNA.																														---	---	---	---
Unknown	0	broad.mit.edu	37	2	67710503	67710503	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:67710503delA								ETAA1 (72970 upstream) : C1D (558830 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	68229946	68229946	+	IGR	DEL	A	-	-	rs143113461		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:68229946delA								ETAA1 (592413 upstream) : C1D (39387 downstream)																																			---	---	---	---
C1D	10438	broad.mit.edu	37	2	68282609	68282610	+	5'Flank	DEL	AA	-	-	rs79786910		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:68282609_68282610delAA	uc002sea.3	-						C1D_uc002seb.2_Intron|C1D_uc002sec.2_Intron|C1D_uc010fdc.2_Intron	NM_173177	NP_775269			nuclear DNA-binding protein						apoptosis|maturation of 5.8S rRNA|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nuclear exosome (RNase complex)|nucleolus	DNA binding|RNA binding				0																		---	---	---	---
PNO1	56902	broad.mit.edu	37	2	68388973	68388975	+	Intron	DEL	AAA	-	-	rs113134222		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:68388973_68388975delAAA	uc002seh.2	+							NM_020143	NP_064528			partner of NOB1							nucleolus	RNA binding				0																		---	---	---	---
PNO1	56902	broad.mit.edu	37	2	68392813	68392813	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:68392813delA	uc002seh.2	+							NM_020143	NP_064528			partner of NOB1							nucleolus	RNA binding				0																		---	---	---	---
PNO1	56902	broad.mit.edu	37	2	68401848	68401848	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:68401848delT	uc002seh.2	+							NM_020143	NP_064528			partner of NOB1							nucleolus	RNA binding				0																		---	---	---	---
PPP3R1	5534	broad.mit.edu	37	2	68414624	68414624	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:68414624delT	uc002sei.1	-							NM_000945	NP_000936			protein phosphatase 3, regulatory subunit B,						activation of pro-apoptotic gene products|induction of apoptosis by intracellular signals	calcineurin complex|cytosol	calcium ion binding|calcium-dependent protein serine/threonine phosphatase activity|calmodulin binding				0					Pimecrolimus(DB00337)													---	---	---	---
PROKR1	10887	broad.mit.edu	37	2	68880558	68880558	+	Intron	DEL	A	-	-	rs72155993		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:68880558delA	uc010yqj.1	+						PROKR1_uc002ses.2_Intron	NM_138964	NP_620414			G protein-coupled receptor 73							integral to membrane|plasma membrane	neuropeptide Y receptor activity			ovary(1)	1																		---	---	---	---
ARHGAP25	9938	broad.mit.edu	37	2	68910534	68910534	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:68910534delT	uc010yqk.1	+							NM_014882	NP_055697			Rho GTPase activating protein 25 isoform b						regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol	GTPase activator activity			ovary(2)|breast(2)	4																		---	---	---	---
BMP10	27302	broad.mit.edu	37	2	69096396	69096396	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:69096396delT	uc002sez.1	-							NM_014482	NP_055297			bone morphogenetic protein 10 preproprotein						activin receptor signaling pathway|adult heart development|atrial cardiac muscle tissue morphogenesis|BMP signaling pathway|cardiac muscle cell proliferation|heart trabecula formation|negative regulation of cardiac muscle hypertrophy|negative regulation of cell growth|negative regulation of endothelial cell migration|Notch signaling pathway|pathway-restricted SMAD protein phosphorylation|positive regulation of cardiac muscle cell proliferation|positive regulation of cardiac muscle hypertrophy|positive regulation of pathway-restricted SMAD protein phosphorylation|positive regulation of transcription, DNA-dependent|sarcomere organization|ventricular cardiac muscle cell development|ventricular cardiac muscle tissue morphogenesis	cell surface|extracellular space|Z disc	cytokine activity|growth factor activity|receptor serine/threonine kinase binding			ovary(2)	2																		---	---	---	---
AAK1	22848	broad.mit.edu	37	2	69703200	69703200	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:69703200delA	uc002sfp.2	-							NM_014911	NP_055726			AP2 associated kinase 1							coated pit|mitochondrion|plasma membrane	ATP binding|protein serine/threonine kinase activity				0																		---	---	---	---
AAK1	22848	broad.mit.edu	37	2	69821810	69821810	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:69821810delT	uc002sfp.2	-						AAK1_uc010fdk.2_Intron|AAK1_uc010yqm.1_Intron|AAK1_uc010fdm.1_Intron	NM_014911	NP_055726			AP2 associated kinase 1							coated pit|mitochondrion|plasma membrane	ATP binding|protein serine/threonine kinase activity				0																		---	---	---	---
ANXA4	307	broad.mit.edu	37	2	70030916	70030916	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-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	70265724	70265724	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:70265724delA	uc002sga.2	-						uc002sgb.1_Intron					Homo sapiens cDNA FLJ32260 fis, clone PROST1000334.						protein maturation by peptide bond cleavage|skin development		aspartic-type endopeptidase activity			ovary(1)	1																		---	---	---	---
MIR1285-2	100302268	broad.mit.edu	37	2	70481272	70481275	+	5'Flank	DEL	TTTT	-	-	rs112545635	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:70481272_70481275delTTTT	hsa-mir-1285-2|MI0006347	-																							0																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	70795507	70795507	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:70795507delA								TGFA (14402 upstream) : ADD2 (39243 downstream)																																			---	---	---	---
ZNF638	27332	broad.mit.edu	37	2	71503065	71503065	+	5'Flank	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:71503065delT	uc010yqw.1	+						ZNF638_uc010fec.2_5'Flank	NM_014497	NP_055312			zinc finger protein 638						RNA splicing	cytoplasm|nuclear speck	double-stranded DNA binding|nucleotide binding|RNA binding|zinc ion binding			pancreas(2)|ovary(1)|skin(1)	4																		---	---	---	---
DYSF	8291	broad.mit.edu	37	2	71844708	71844709	+	Intron	DEL	GT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:71844708_71844709delGT	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|DYSF_uc010yqy.1_Intron|DYSF_uc010yqz.1_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	72043005	72043006	+	IGR	INS	-	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:72043005_72043006insG								DYSF (129113 upstream) : CYP26B1 (313361 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	72323850	72323851	+	IGR	DEL	AA	-	-	rs140793031		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:72323850_72323851delAA								DYSF (409958 upstream) : CYP26B1 (32516 downstream)																																			---	---	---	---
EXOC6B	23233	broad.mit.edu	37	2	72439155	72439156	+	Intron	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:72439155_72439156delAA	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	72557109	72557110	+	Intron	INS	-	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:72557109_72557110insA	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	72572792	72572793	+	Intron	INS	-	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:72572792_72572793insG	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	72968233	72968233	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-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																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	73110201	73110201	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:73110201delA								EXOC6B (57024 upstream) : SPR (4311 downstream)																																			---	---	---	---
CCT7	10574	broad.mit.edu	37	2	73479767	73479767	+	Splice_Site	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:73479767delG	uc002siz.2	+	12	1513	c.1411_splice	c.e12-1	p.G471_splice	CCT7_uc002sja.2_Splice_Site_p.G267_splice|CCT7_uc010yrf.1_Splice_Site_p.G427_splice|CCT7_uc010feu.2_Splice_Site_p.G429_splice|CCT7_uc010yrg.1_Splice_Site_p.G371_splice|CCT7_uc010yrh.1_Splice_Site_p.G343_splice|CCT7_uc010yri.1_Splice_Site_p.G384_splice	NM_006429	NP_006420			chaperonin containing TCP1, subunit 7 isoform a						'de novo' posttranslational protein folding		ATP binding|unfolded protein binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	73560704	73560705	+	IGR	DEL	AA	-	-	rs113844476		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:73560704_73560705delAA								EGR4 (39875 upstream) : ALMS1 (52181 downstream)																																			---	---	---	---
ALMS1	7840	broad.mit.edu	37	2	73624514	73624514	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:73624514delT	uc002sje.1	+						ALMS1_uc002sjf.1_Intron	NM_015120	NP_055935			Alstrom syndrome 1						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	73803202	73803202	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:73803202delT	uc002sje.1	+						ALMS1_uc002sjf.1_Intron|ALMS1_uc002sjh.1_Intron	NM_015120	NP_055935			Alstrom syndrome 1						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	73830582	73830583	+	Intron	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:73830582_73830583delAA	uc002sje.1	+						ALMS1_uc002sjf.1_Intron|ALMS1_uc002sjh.1_3'UTR	NM_015120	NP_055935			Alstrom syndrome 1						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																		---	---	---	---
ALMS1P	200420	broad.mit.edu	37	2	73906762	73906763	+	Intron	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:73906762_73906763delAA	uc010yrl.1	+							NR_003683				RecName: Full=Putative ALMS1-like protein;												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	74047136	74047136	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:74047136delT								C2orf78 (2862 upstream) : STAMBP (8950 downstream)																																			---	---	---	---
TET3	200424	broad.mit.edu	37	2	74312062	74312062	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:74312062delA	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																		---	---	---	---
SLC4A5	57835	broad.mit.edu	37	2	74461210	74461210	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:74461210delA	uc002sko.1	-						SLC4A5_uc002skl.2_Intron|SLC4A5_uc002skn.2_Intron|SLC4A5_uc010ffc.1_Intron|SLC4A5_uc002skp.1_Intron|SLC4A5_uc002sks.1_Intron	NM_021196	NP_067019			sodium bicarbonate transporter 4 isoform a							apical plasma membrane|integral to membrane	inorganic anion exchanger activity|sodium:bicarbonate symporter activity			ovary(5)|skin(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)	9																		---	---	---	---
SEMA4F	10505	broad.mit.edu	37	2	74879048	74879049	+	5'Flank	DEL	TT	-	-	rs67922911		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:74879048_74879049delTT	uc002sna.1	+						SEMA4F_uc010ysb.1_5'Flank|SEMA4F_uc010ffq.1_5'Flank|SEMA4F_uc010ffr.1_5'Flank|SEMA4F_uc002snb.1_5'Flank|SEMA4F_uc002snc.1_5'Flank	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	75064800	75064808	+	Intron	DEL	TTTTTTTTT	-	-	rs67705659		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:75064800_75064808delTTTTTTTTT	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	75081243	+	Intron	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:75081242_75081243delTT	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	75113157	75113157	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:75113157delA	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	75228821	75228821	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:75228821delA								POLE4 (31963 upstream) : TACR1 (44769 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	75869990	75869990	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:75869990delT								FAM176A (73142 upstream) : MRPL19 (3919 downstream)																																			---	---	---	---
C2orf3	6936	broad.mit.edu	37	2	75900439	75900439	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:75900439delA	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	75949441	75949441	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:75949441delT								C2orf3 (11330 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	76347375	76347375	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:76347375delA								C2orf3 (409264 upstream) : LRRTM4 (627483 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	76593086	76593086	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:76593086delT								C2orf3 (654975 upstream) : LRRTM4 (381772 downstream)																																			---	---	---	---
LRRTM4	80059	broad.mit.edu	37	2	77751670	77751671	+	5'Flank	DEL	AC	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:77751670_77751671delAC	uc002snr.2	-						LRRTM4_uc002snq.2_5'Flank|LRRTM4_uc002sns.2_5'Flank|LRRTM4_uc002snt.2_5'Flank	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	78180456	78180456	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:78180456delA								LRRTM4 (430954 upstream) : SNAR-H (1577 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	78908063	78908063	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:78908063delT								SNAR-H (725911 upstream) : REG3G (344763 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	79034898	79034898	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:79034898delA								SNAR-H (852746 upstream) : REG3G (217928 downstream)																																			---	---	---	---
CTNNA2	1496	broad.mit.edu	37	2	79555101	79555102	+	Intron	INS	-	G	G	rs148604984	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:79555101_79555102insG	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	79567376	79567376	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:79567376delA	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	79888188	79888189	+	Intron	INS	-	T	T	rs150053634	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:79888188_79888189insT	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																		---	---	---	---
CTNNA2	1496	broad.mit.edu	37	2	80773597	80773598	+	Intron	INS	-	TT	TT			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:80773597_80773598insTT	uc010ysh.1	+						CTNNA2_uc010yse.1_Intron|CTNNA2_uc010ysf.1_Intron|CTNNA2_uc010ysg.1_Intron|CTNNA2_uc010ysi.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																		---	---	---	---
CTNNA2	1496	broad.mit.edu	37	2	80800047	80800047	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:80800047delT	uc010ysh.1	+						CTNNA2_uc010yse.1_Intron|CTNNA2_uc010ysf.1_Intron|CTNNA2_uc010ysg.1_Intron|CTNNA2_uc010ysi.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	82184195	82184195	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:82184195delA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	82883557	82883557	+	IGR	DEL	A	-	-	rs111976752		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:82883557delA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	82931012	82931012	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:82931012delT								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	83211917	83211917	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:83211917delT								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	83801829	83801830	+	IGR	INS	-	AC	AC	rs145950652	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:83801829_83801830insAC								None (None upstream) : FUNDC2P2 (715976 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	84432171	84432171	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:84432171delA								None (None upstream) : FUNDC2P2 (85635 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	84544207	84544207	+	IGR	DEL	G	-	-	rs66715033		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:84544207delG								FUNDC2P2 (24883 upstream) : SUCLG1 (106447 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	84642807	84642808	+	IGR	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:84642807_84642808delTT								FUNDC2P2 (123483 upstream) : SUCLG1 (7846 downstream)																																			---	---	---	---
SUCLG1	8802	broad.mit.edu	37	2	84650857	84650857	+	3'UTR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:84650857delT	uc002son.2	-	9						NM_003849	NP_003840			succinate-CoA ligase, GDP-forming alpha subunit						tricarboxylic acid cycle		ATP citrate synthase activity|GTP binding|succinate-CoA ligase (GDP-forming) activity				0					Succinic acid(DB00139)													---	---	---	---
DNAH6	1768	broad.mit.edu	37	2	84746748	84746748	+	Intron	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:84746748delC	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																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	85182383	85182383	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:85182383delA								TMSB10 (48584 upstream) : KCMF1 (15848 downstream)																																			---	---	---	---
KCMF1	56888	broad.mit.edu	37	2	85240921	85240921	+	Intron	DEL	A	-	-	rs78630282		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:85240921delA	uc002sox.3	+							NM_020122	NP_064507			potassium channel modulatory factor 1							intracellular	ligase activity|zinc ion binding			ovary(2)	2																		---	---	---	---
KCMF1	56888	broad.mit.edu	37	2	85271184	85271184	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:85271184delT	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	85287455	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:85287455delT								KCMF1 (861 upstream) : TCF7L1 (73279 downstream)																																			---	---	---	---
ELMOD3	84173	broad.mit.edu	37	2	85595705	85595705	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:85595705delA	uc002spf.3	+						ELMOD3_uc010fgg.2_Intron|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	85620164	85620165	+	IGR	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:85620164_85620165delTT								ELMOD3 (1291 upstream) : CAPG (1706 downstream)																																			---	---	---	---
USP39	10713	broad.mit.edu	37	2	85847153	85847153	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:85847153delT	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																		---	---	---	---
USP39	10713	broad.mit.edu	37	2	85856623	85856623	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:85856623delT	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																		---	---	---	---
SFTPB	6439	broad.mit.edu	37	2	85888561	85888561	+	Intron	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:85888561delG	uc002sqh.2	-						SFTPB_uc002sqi.2_Intron|SFTPB_uc002sqj.2_Intron|SFTPB_uc010ysw.1_Intron	NM_198843	NP_942140			surfactant, pulmonary-associated protein B						organ morphogenesis|respiratory gaseous exchange|sphingolipid metabolic process	extracellular space|lysosome				ovary(1)|central_nervous_system(1)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	85960285	85960285	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:85960285delA								GNLY (34411 upstream) : ATOH8 (20624 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	86232064	86232064	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:86232064delA								ST3GAL5 (115907 upstream) : LOC90784 (15275 downstream)																																			---	---	---	---
POLR1A	25885	broad.mit.edu	37	2	86272294	86272295	+	Intron	INS	-	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:86272294_86272295insT	uc002sqs.2	-						POLR1A_uc010ytb.1_Intron|POLR1A_uc002sqt.1_5'Flank	NM_015425	NP_056240			DNA-directed RNA polymerase I A						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																		---	---	---	---
POLR1A	25885	broad.mit.edu	37	2	86285064	86285064	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:86285064delA	uc002sqs.2	-						POLR1A_uc010ytb.1_Intron	NM_015425	NP_056240			DNA-directed RNA polymerase I A						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																		---	---	---	---
IMMT	10989	broad.mit.edu	37	2	86372013	86372013	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:86372013delA	uc002sqz.3	-						IMMT_uc002sqy.3_Intron|IMMT_uc002srb.3_Intron|IMMT_uc002sra.3_Intron|IMMT_uc010ytd.1_Intron|IMMT_uc010yte.1_Intron	NM_006839	NP_006830			inner membrane protein, mitochondrial isoform 1							integral to mitochondrial inner membrane	protein binding			skin(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	86440481	86440481	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:86440481delT								MRPL35 (5 upstream) : REEP1 (641 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	86588705	86588705	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:86588705delT								REEP1 (23928 upstream) : KDM3A (79566 downstream)																																			---	---	---	---
RNF103	7844	broad.mit.edu	37	2	86839484	86839484	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:86839484delA	uc002srn.2	-						VPS24_uc010ytl.1_Intron|RNF103_uc002srm.2_5'UTR|uc002sro.2_Intron	NM_005667	NP_005658			ring finger protein 103						central nervous system development|ER-associated protein catabolic process	endoplasmic reticulum membrane|integral to membrane	protein binding|ubiquitin-protein ligase activity|zinc ion binding			central_nervous_system(1)	1																		---	---	---	---
VPS24	51652	broad.mit.edu	37	2	86856342	86856342	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:86856342delT	uc010ytl.1	-							NM_001005753	NP_001005753			vacuolar protein sorting 24 isoform 2						cell cycle|cell division|cellular membrane organization|endosome transport|protein transport	cytosol|late endosome membrane	protein binding			central_nervous_system(1)	1																		---	---	---	---
VPS24	51652	broad.mit.edu	37	2	86924595	86924595	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:86924595delA	uc010ytl.1	-							NM_001005753	NP_001005753			vacuolar protein sorting 24 isoform 2						cell cycle|cell division|cellular membrane organization|endosome transport|protein transport	cytosol|late endosome membrane	protein binding			central_nervous_system(1)	1																		---	---	---	---
RMND5A	64795	broad.mit.edu	37	2	87644152	87644152	+	Intron	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:87644152delG	uc002srs.3	+											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	88451891	88451891	+	IGR	DEL	A	-	-	rs71378850		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:88451891delA								FABP1 (24313 upstream) : THNSL2 (17944 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	88728729	88728730	+	IGR	INS	-	TTTG	TTTG	rs143332447	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:88728729_88728730insTTTG								THNSL2 (242584 upstream) : FOXI3 (18996 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	88784833	88784835	+	IGR	DEL	AAA	-	-	rs76986836		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:88784833_88784835delAAA								FOXI3 (32780 upstream) : C2orf51 (39334 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	88804180	88804180	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:88804180delA								FOXI3 (52127 upstream) : C2orf51 (19989 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	89277834	89277834	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-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	89472189	89472189	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:89472189delA	uc010ytr.1	-						uc002stl.2_Intron					Parts of antibodies, mostly variable regions.																														---	---	---	---
Unknown	0	broad.mit.edu	37	2	89512751	89512752	+	Intron	INS	-	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:89512751_89512752insC	uc010ytr.1	-						uc002stl.2_Intron					Parts of antibodies, mostly variable regions.																														---	---	---	---
Unknown	0	broad.mit.edu	37	2	89854122	89854126	+	IGR	DEL	ATCAT	-	-	rs149731646	by1000genomes;by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:89854122_89854126delATCAT								FLJ40330 (747997 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	90213817	90213818	+	Intron	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:90213817_90213818delAA	uc010fhm.2	+											Parts of antibodies, mostly variable regions.																														---	---	---	---
Unknown	0	broad.mit.edu	37	2	91727201	91727203	+	IGR	DEL	GAG	-	-	rs139041260		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:91727201_91727203delGAG								None (None upstream) : LOC654342 (77989 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	91910308	91910309	+	IGR	INS	-	AC	AC			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:91910308_91910309insAC								LOC654342 (62333 upstream) : GGT8P (53059 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	91917430	91917431	+	IGR	INS	-	AAA	AAA			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:91917430_91917431insAAA								LOC654342 (69455 upstream) : GGT8P (45937 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	92076694	92076695	+	IGR	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:92076694_92076695delTT								GGT8P (106541 upstream) : FKSG73 (52464 downstream)																																			---	---	---	---
MRPS5	64969	broad.mit.edu	37	2	95756513	95756513	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:95756513delA	uc002sub.2	-						MRPS5_uc002suc.2_Intron	NM_031902	NP_114108			mitochondrial ribosomal protein S5						translation	mitochondrion|ribosome	protein binding|RNA binding|structural constituent of ribosome			ovary(2)|central_nervous_system(1)	3																		---	---	---	---
KCNIP3	30818	broad.mit.edu	37	2	96050854	96050854	+	3'UTR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:96050854delA	uc002sup.2	+	9					KCNIP3_uc002suq.2_3'UTR	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)														---	---	---	---
FAHD2A	51011	broad.mit.edu	37	2	96070043	96070044	+	Intron	DEL	TT	-	-	rs113250091		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:96070043_96070044delTT	uc002sur.2	+						FAHD2A_uc002sus.2_Intron	NM_016044	NP_057128			fumarylacetoacetate hydrolase domain containing								hydrolase activity|metal ion binding			ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	96080655	96080655	+	5'Flank	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:96080655delA	uc002sut.1	+											Homo sapiens cDNA FLJ35661 fis, clone SPLEN2017592.																														---	---	---	---
Unknown	0	broad.mit.edu	37	2	96604246	96604247	+	Intron	INS	-	AGAGA	AGAGA	rs145113787	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:96604246_96604247insAGAGA	uc002sva.1	-						uc010yug.1_Intron					Homo sapiens cDNA FLJ41632 fis, clone FCBBF1000297, highly  similar to Human protein immuno-reactive with anti-PTH polyclonal antibodies mRNA.																														---	---	---	---
Unknown	0	broad.mit.edu	37	2	96610812	96610812	+	5'Flank	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:96610812delA	uc002sva.1	-						uc010yug.1_Intron					Homo sapiens cDNA FLJ41632 fis, clone FCBBF1000297, highly  similar to Human protein immuno-reactive with anti-PTH polyclonal antibodies mRNA.																														---	---	---	---
Unknown	0	broad.mit.edu	37	2	96630168	96630168	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:96630168delT	uc010yug.1	-											Homo sapiens cDNA FLJ54441 complete cds, highly similar to Homo sapiens ankyrin repeat domain 36 (ANKRD36), mRNA.																														---	---	---	---
SNRNP200	23020	broad.mit.edu	37	2	96966575	96966575	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:96966575delT	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	97132088	97132090	+	IGR	DEL	TTT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:97132088_97132090delTTT								NCAPH (90814 upstream) : NEURL3 (31295 downstream)																																			---	---	---	---
FER1L5	90342	broad.mit.edu	37	2	97362036	97362036	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:97362036delT	uc010fia.2	+						FER1L5_uc002sws.3_Intron|FER1L5_uc010fib.1_Intron|FER1L5_uc002swt.3_Intron|FER1L5_uc010yus.1_Intron	NM_001113382	NP_001106853			fer-1-like 5 isoform 2							integral to membrane				ovary(1)	1																		---	---	---	---
CNNM4	26504	broad.mit.edu	37	2	97470143	97470143	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:97470143delT	uc002swx.2	+						CNNM4_uc010yuy.1_Intron	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																		---	---	---	---
ANKRD36	375248	broad.mit.edu	37	2	97819021	97819022	+	Intron	INS	-	A	A	rs142216424	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:97819021_97819022insA	uc010yva.1	+						ANKRD36_uc010yuz.1_Intron|ANKRD36_uc010fic.2_Intron|ANKRD36_uc002sxo.2_Intron|ANKRD36_uc002sxp.3_Intron	NM_001164315	NP_001157787			ankyrin repeat domain 36												0																		---	---	---	---
VWA3B	200403	broad.mit.edu	37	2	98788145	98788145	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:98788145delA	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																		---	---	---	---
VWA3B	200403	broad.mit.edu	37	2	98795365	98795365	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:98795365delA	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																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	98945970	98945970	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:98945970delT								VWA3B (16562 upstream) : CNGA3 (16648 downstream)																																			---	---	---	---
INPP4A	3631	broad.mit.edu	37	2	99078421	99078421	+	Intron	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:99078421delC	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																		---	---	---	---
INPP4A	3631	broad.mit.edu	37	2	99177937	99177937	+	Intron	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:99177937delG	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	99241956	99241956	+	3'UTR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:99241956delA	uc002sze.2	-	16					C2orf64_uc002sza.2_Intron|MGAT4A_uc010yvm.1_Intron|MGAT4A_uc010fil.2_3'UTR	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																		---	---	---	---
TSGA10	80705	broad.mit.edu	37	2	99654534	99654534	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:99654534delA	uc002szg.3	-						TSGA10_uc002szh.3_Intron|TSGA10_uc002szi.3_Intron|TSGA10_uc010fin.1_Intron	NM_182911	NP_878915			testis specific, 10						spermatogenesis	cytoplasm|nuclear membrane				ovary(1)|central_nervous_system(1)	2																		---	---	---	---
TSGA10	80705	broad.mit.edu	37	2	99727132	99727132	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:99727132delA	uc002szg.3	-						TSGA10_uc002szh.3_Intron|TSGA10_uc002szi.3_Intron|TSGA10_uc010fin.1_Intron|TSGA10_uc010yvn.1_Intron	NM_182911	NP_878915			testis specific, 10						spermatogenesis	cytoplasm|nuclear membrane				ovary(1)|central_nervous_system(1)	2																		---	---	---	---
TXNDC9	10190	broad.mit.edu	37	2	99927495	99927495	+	Intron	DEL	T	-	-	rs112705516		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:99927495delT	uc010yvp.1	-						MRPL30_uc002szl.1_Intron	NM_005783	NP_005774			thioredoxin domain containing 9						cell redox homeostasis		protein binding				0																		---	---	---	---
EIF5B	9669	broad.mit.edu	37	2	99966909	99966910	+	Intron	INS	-	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:99966909_99966910insT	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																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	100127467	100127467	+	IGR	DEL	T	-	-	rs78191765		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:100127467delT								REV1 (20987 upstream) : AFF3 (36251 downstream)																																			---	---	---	---
AFF3	3899	broad.mit.edu	37	2	100228015	100228015	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:100228015delT	uc002tag.2	-						AFF3_uc002taf.2_Intron|AFF3_uc010fiq.1_Intron|AFF3_uc010yvr.1_Intron|AFF3_uc002tah.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	100778137	100778137	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:100778137delA								AFF3 (19100 upstream) : LONRF2 (111617 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	100825837	100825837	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:100825837delT	uc002taj.1	+											Homo sapiens cDNA FLJ32078 fis, clone OCBBF1000192.																														---	---	---	---
Unknown	0	broad.mit.edu	37	2	100955056	100955056	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:100955056delT								LONRF2 (15861 upstream) : CHST10 (53267 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	100974737	100974737	+	IGR	DEL	A	-	-	rs11402182		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:100974737delA								LONRF2 (35542 upstream) : CHST10 (33586 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	101288911	101288911	+	IGR	DEL	C	-	-	rs149711975		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:101288911delC								PDCL3 (95710 upstream) : NPAS2 (147702 downstream)																																			---	---	---	---
NPAS2	4862	broad.mit.edu	37	2	101526161	101526161	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:101526161delA	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																		---	---	---	---
NPAS2	4862	broad.mit.edu	37	2	101584647	101584647	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-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																		---	---	---	---
RPL31	6160	broad.mit.edu	37	2	101621479	101621479	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:101621479delT	uc002taq.3	+						RPL31_uc002tar.3_Intron|RPL31_uc010yvu.1_Intron|RPL31_uc010yvv.1_Intron|RPL31_uc010fiu.1_Intron|RPL31_uc002tas.1_Intron|RPL31_uc002tat.1_3'UTR	NM_000993	NP_000984			ribosomal protein L31 isoform 1						endocrine pancreas development|translational elongation|translational termination|viral transcription	cytosolic large ribosomal subunit	protein binding|RNA binding|structural constituent of ribosome				0																		---	---	---	---
TBC1D8	11138	broad.mit.edu	37	2	101666296	101666296	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:101666296delT	uc010fiv.2	-						TBC1D8_uc010yvw.1_Intron|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																		---	---	---	---
RFX8	731220	broad.mit.edu	37	2	102027051	102027052	+	Intron	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:102027051_102027052delTT	uc010yvx.1	-						RFX8_uc002tbb.1_Intron	NM_001145664	NP_001139136			regulatory factor X, 8						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding				0																		---	---	---	---
MAP4K4	9448	broad.mit.edu	37	2	102334417	102334417	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:102334417delA	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	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	102337748	102337748	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:102337748delT	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	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																		---	---	---	---
IL1R2	7850	broad.mit.edu	37	2	102632311	102632311	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:102632311delT	uc002tbm.2	+						IL1R2_uc002tbn.2_Intron|IL1R2_uc002tbo.1_Intron	NM_004633	NP_004624			interleukin 1 receptor, type II precursor						immune response	integral to membrane|plasma membrane	interleukin-1, Type II, blocking receptor activity			ovary(1)|breast(1)	2					Anakinra(DB00026)													---	---	---	---
IL1RL2	8808	broad.mit.edu	37	2	102801215	102801215	+	5'Flank	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:102801215delA	uc002tbs.2	+						IL1RL2_uc002tbt.2_5'Flank	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																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	103160313	103160314	+	IGR	DEL	TG	-	-	rs73944386	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:103160313_103160314delTG								SLC9A4 (9883 upstream) : SLC9A2 (75852 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	104836146	104836146	+	IGR	DEL	A	-	-	rs79455955		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:104836146delA								None (None upstream) : LOC150568 (214659 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	105009231	105009231	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:105009231delA	uc010ywf.1	-											SubName: Full=cDNA FLJ59030;																														---	---	---	---
Unknown	0	broad.mit.edu	37	2	105243988	105243996	+	IGR	DEL	TTTTTTTTT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:105243988_105243996delTTTTTTTTT								LOC150568 (114774 upstream) : POU3F3 (227973 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	105492035	105492035	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:105492035delT								POU3F3 (18565 upstream) : MRPS9 (162448 downstream)																																			---	---	---	---
FHL2	2274	broad.mit.edu	37	2	105985293	105985296	+	Intron	DEL	AAAG	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:105985293_105985296delAAAG	uc002tcu.2	-						FHL2_uc002tdc.2_Intron|FHL2_uc002tdd.2_Intron|FHL2_uc002tct.2_5'Flank|FHL2_uc002tcv.2_Intron|FHL2_uc002tcw.2_Intron|FHL2_uc002tcx.2_Intron|FHL2_uc010fje.2_Intron|FHL2_uc002tcy.2_Intron|FHL2_uc002tcz.2_Intron|FHL2_uc002tda.2_Intron|FHL2_uc002tdb.2_Intron	NM_201557	NP_963851			four and a half LIM domains 2						androgen receptor signaling pathway|cellular lipid metabolic process|positive regulation of transcription, DNA-dependent|response to hormone stimulus|transcription, DNA-dependent	actin cytoskeleton|focal adhesion|nucleus	androgen receptor binding|identical protein binding|transcription coactivator activity|zinc ion binding			ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	106192369	106192370	+	IGR	DEL	GA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:106192369_106192370delGA								FHL2 (137139 upstream) : NCK2 (168984 downstream)																																			---	---	---	---
NCK2	8440	broad.mit.edu	37	2	106447258	106447258	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:106447258delT	uc002tdg.2	+						NCK2_uc002tdh.2_Intron	NM_003581	NP_003572			NCK adaptor protein 2 isoform A						axon guidance|epidermal growth factor receptor signaling pathway|negative regulation of cell proliferation|positive regulation of actin filament polymerization|positive regulation of T cell proliferation|regulation of epidermal growth factor receptor activity|regulation of translation|signal complex assembly|T cell activation	cytosol|endoplasmic reticulum	cytoskeletal adaptor activity|receptor signaling complex scaffold activity			ovary(1)|lung(1)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	106641817	106641817	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:106641817delT								NCK2 (131091 upstream) : C2orf40 (40296 downstream)																																			---	---	---	---
UXS1	80146	broad.mit.edu	37	2	106764691	106764691	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:106764691delT	uc002tdm.2	-						UXS1_uc002tdn.2_Intron|UXS1_uc002tdo.2_Intron|UXS1_uc010ywh.1_Intron	NM_025076	NP_079352			UDP-glucuronate decarboxylase 1						cellular metabolic process	Golgi cisterna membrane|integral to membrane	coenzyme binding|UDP-glucuronate decarboxylase activity			ovary(2)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	106852685	106852687	+	IGR	DEL	AAA	-	-	rs137935919		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:106852685_106852687delAAA								UXS1 (41890 upstream) : PLGLA (150082 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	107683072	107683073	+	IGR	DEL	AC	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:107683072_107683073delAC								ST6GAL2 (179509 upstream) : LOC729121 (756447 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	108014306	108014306	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:108014306delT								ST6GAL2 (510743 upstream) : LOC729121 (425214 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	108666734	108666734	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:108666734delA								SLC5A7 (36295 upstream) : SULT1C3 (196917 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	108940582	108940584	+	IGR	DEL	AAA	-	-	rs111955452		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:108940582_108940584delAAA								SULT1C2 (14212 upstream) : SULT1C4 (53837 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	110405940	110405940	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:110405940delT								ANKRD57 (29377 upstream) : RGPD5 (144395 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	110433266	110433266	+	IGR	DEL	T	-	-	rs12719068	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:110433266delT								ANKRD57 (56703 upstream) : RGPD5 (117069 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	110490058	110490060	+	IGR	DEL	TTT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:110490058_110490060delTTT								ANKRD57 (113495 upstream) : RGPD5 (60275 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	110768177	110768177	+	IGR	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:110768177delG								LIMS3-LOC440895 (42030 upstream) : MALL (73275 downstream)																																			---	---	---	---
NPHP1	4867	broad.mit.edu	37	2	110940609	110940610	+	Intron	INS	-	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:110940609_110940610insA	uc002tfn.3	-						NPHP1_uc002tfm.3_Intron|NPHP1_uc002tfl.3_Intron|NPHP1_uc002tfo.3_Intron|NPHP1_uc010ywx.1_Intron|NPHP1_uc010fjv.1_Intron|NPHP1_uc002tfp.2_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	111611701	111611702	+	Intron	DEL	TG	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:111611701_111611702delTG	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																		---	---	---	---
ACOXL	55289	broad.mit.edu	37	2	111726356	111726357	+	Intron	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:111726356_111726357delAA	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																		---	---	---	---
ACOXL	55289	broad.mit.edu	37	2	111828230	111828230	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:111828230delA	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	111975368	111975368	+	Intron	DEL	A	-	-	rs72242649		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:111975368delA	uc002the.2	-											Homo sapiens hypothetical LOC541471, mRNA (cDNA clone IMAGE:3459303).												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	112443403	112443406	+	IGR	DEL	TTTT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:112443403_112443406delTTTT								LOC541471 (190711 upstream) : ANAPC1 (83235 downstream)																																			---	---	---	---
ANAPC1	64682	broad.mit.edu	37	2	112566375	112566375	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:112566375delT	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	112576822	112576822	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-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	112582852	112582852	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:112582852delA	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	112645761	112645761	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:112645761delT								ANAPC1 (4020 upstream) : MERTK (10430 downstream)																																			---	---	---	---
MERTK	10461	broad.mit.edu	37	2	112705359	112705359	+	Intron	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:112705359delG	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																		---	---	---	---
ZC3H6	376940	broad.mit.edu	37	2	113043562	113043564	+	Intron	DEL	TGT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:113043562_113043564delTGT	uc002thq.1	+							NM_198581	NP_940983			zinc finger CCCH-type domain containing 6								nucleic acid binding|zinc ion binding			ovary(3)|central_nervous_system(1)	4																		---	---	---	---
ZC3H6	376940	broad.mit.edu	37	2	113044025	113044025	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:113044025delT	uc002thq.1	+							NM_198581	NP_940983			zinc finger CCCH-type domain containing 6								nucleic acid binding|zinc ion binding			ovary(3)|central_nervous_system(1)	4																		---	---	---	---
ZC3H6	376940	broad.mit.edu	37	2	113077223	113077224	+	Intron	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:113077223_113077224delAA	uc002thq.1	+							NM_198581	NP_940983			zinc finger CCCH-type domain containing 6								nucleic acid binding|zinc ion binding			ovary(3)|central_nervous_system(1)	4																		---	---	---	---
ZC3H6	376940	broad.mit.edu	37	2	113079278	113079278	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:113079278delA	uc002thq.1	+							NM_198581	NP_940983			zinc finger CCCH-type domain containing 6								nucleic acid binding|zinc ion binding			ovary(3)|central_nervous_system(1)	4																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	113207506	113207506	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:113207506delA								RGPD8 (15444 upstream) : TTL (32237 downstream)																																			---	---	---	---
CKAP2L	150468	broad.mit.edu	37	2	113507541	113507541	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:113507541delT	uc002tie.2	-						CKAP2L_uc002tif.2_Intron|CKAP2L_uc010yxp.1_Intron	NM_152515	NP_689728			cytoskeleton associated protein 2-like							centrosome					0																		---	---	---	---
IL1B	3553	broad.mit.edu	37	2	113590122	113590122	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:113590122delT	uc002tii.1	-						IL1B_uc002tih.1_Intron	NM_000576	NP_000567			interleukin 1, beta proprotein						activation of MAPK activity|anti-apoptosis|apoptosis|cell-cell signaling|cellular response to drug|cellular response to mechanical stimulus|cytokine-mediated signaling pathway|embryo implantation|fever generation|negative regulation of adiponectin secretion|negative regulation of cell proliferation|negative regulation of glucose transport|negative regulation of insulin receptor signaling pathway|negative regulation of lipid catabolic process|negative regulation of MAP kinase activity|positive regulation of angiogenesis|positive regulation of calcidiol 1-monooxygenase activity|positive regulation of cell adhesion molecule production|positive regulation of cell division|positive regulation of fever generation|positive regulation of granulocyte macrophage colony-stimulating factor production|positive regulation of heterotypic cell-cell adhesion|positive regulation of histone acetylation|positive regulation of histone phosphorylation|positive regulation of interferon-gamma production|positive regulation of interleukin-2 biosynthetic process|positive regulation of interleukin-6 production|positive regulation of interleukin-8 production|positive regulation of lipid catabolic process|positive regulation of membrane protein ectodomain proteolysis|positive regulation of mitosis|positive regulation of monocyte chemotactic protein-1 production|positive regulation of myosin light chain kinase activity|positive regulation of NF-kappaB import into nucleus|positive regulation of NF-kappaB transcription factor activity|positive regulation of nitric oxide biosynthetic process|positive regulation of prostaglandin secretion|positive regulation of protein export from nucleus|positive regulation of T cell proliferation|positive regulation vascular endothelial growth factor production|regulation of insulin secretion|sequestering of triglyceride|smooth muscle adaptation	cytosol|extracellular space	cytokine activity|growth factor activity|interleukin-1 receptor binding|protein domain specific binding			lung(3)|breast(1)	4					Anakinra(DB00026)|Minocycline(DB01017)|Procaterol(DB01366)													---	---	---	---
Unknown	0	broad.mit.edu	37	2	113973171	113973171	+	IGR	DEL	G	-	-	rs752591	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:113973171delG								PSD4 (12495 upstream) : PAX8 (404 downstream)																																			---	---	---	---
DPP10	57628	broad.mit.edu	37	2	115987953	115987953	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:115987953delT	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	116572705	116572705	+	Intron	DEL	T	-	-	rs79224686		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:116572705delT	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	116714010	116714010	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:116714010delT								DPP10 (112074 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	116721709	116721709	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:116721709delT								DPP10 (119773 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	117126654	117126654	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:117126654delT								DPP10 (524718 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	117221696	117221696	+	IGR	DEL	T	-	-	rs34642815		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:117221696delT								DPP10 (619760 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	117842399	117842400	+	IGR	INS	-	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:117842399_117842400insA								None (None upstream) : DDX18 (729855 downstream)																																			---	---	---	---
CCDC93	54520	broad.mit.edu	37	2	118688949	118688949	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:118688949delT	uc002tlj.2	-							NM_019044	NP_061917			coiled-coil domain containing 93											large_intestine(1)|ovary(1)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	119333725	119333725	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:119333725delT								INSIG2 (466129 upstream) : EN1 (266023 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	119458234	119458235	+	IGR	DEL	TG	-	-	rs112685198		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:119458234_119458235delTG								INSIG2 (590638 upstream) : EN1 (141513 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	119527273	119527273	+	IGR	DEL	A	-	-	rs34792055		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:119527273delA								INSIG2 (659677 upstream) : EN1 (72475 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	119636588	119636588	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:119636588delA								EN1 (30829 upstream) : MARCO (63157 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	119644285	119644286	+	IGR	DEL	TT	-	-	rs36081872		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:119644285_119644286delTT								EN1 (38526 upstream) : MARCO (55459 downstream)																																			---	---	---	---
MARCO	8685	broad.mit.edu	37	2	119723740	119723740	+	Intron	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:119723740delG	uc002tln.1	+						MARCO_uc010yyf.1_Intron	NM_006770	NP_006761			macrophage receptor with collagenous structure						cell surface receptor linked signaling pathway|innate immune response	collagen|integral to plasma membrane	pattern recognition receptor activity|scavenger receptor activity			ovary(3)|skin(2)|central_nervous_system(1)	6																		---	---	---	---
PTPN4	5775	broad.mit.edu	37	2	120673617	120673617	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:120673617delA	uc002tmf.1	+						PTPN4_uc010flj.1_5'UTR	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)													---	---	---	---
Unknown	0	broad.mit.edu	37	2	121362674	121362675	+	IGR	DEL	GT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:121362674_121362675delGT								LOC84931 (138749 upstream) : GLI2 (130524 downstream)																																			---	---	---	---
GLI2	2736	broad.mit.edu	37	2	121580655	121580655	+	Intron	DEL	A	-	-	rs146034631	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:121580655delA	uc010flp.2	+						GLI2_uc010yyu.1_Intron|GLI2_uc002tmp.1_Intron|GLI2_uc010fln.1_Intron|GLI2_uc002tmq.1_Intron|GLI2_uc002tmr.1_Intron|GLI2_uc002tmt.3_Intron|GLI2_uc002tmu.3_Intron|GLI2_uc002tmv.1_Intron|GLI2_uc010flo.1_Intron|GLI2_uc002tmw.1_Intron	NM_005270	NP_005261			GLI-Kruppel family member GLI2						axon guidance|branching morphogenesis of a tube|cell proliferation|cerebellar cortex morphogenesis|developmental growth|embryonic digestive tract development|epidermal cell differentiation|floor plate formation|heart development|hindgut morphogenesis|kidney development|lung development|negative regulation of transcription from RNA polymerase II promoter|odontogenesis of dentine-containing tooth|osteoblast development|osteoblast differentiation|pituitary gland development|positive regulation of DNA replication|positive regulation of T cell differentiation in thymus|positive regulation of transcription from RNA polymerase II promoter|proximal/distal pattern formation|skeletal system development|smoothened signaling pathway involved in ventral spinal cord interneuron specification|spinal cord ventral commissure morphogenesis	nucleus|nucleus	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(8)|lung(2)|breast(1)|central_nervous_system(1)|pancreas(1)	13	Renal(3;0.0496)	Prostate(154;0.0623)																---	---	---	---
GLI2	2736	broad.mit.edu	37	2	121729619	121729620	+	Frame_Shift_Ins	INS	-	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:121729619_121729620insC	uc010flp.2	+	7	1192_1193	c.1162_1163insC	c.(1162-1164)TCCfs	p.S388fs	GLI2_uc002tmq.1_Frame_Shift_Ins_p.S60fs|GLI2_uc002tmr.1_Frame_Shift_Ins_p.S60fs|GLI2_uc002tmt.3_Frame_Shift_Ins_p.S60fs|GLI2_uc002tmu.3_Frame_Shift_Ins_p.S60fs|GLI2_uc010flo.1_Frame_Shift_Ins_p.S263fs|GLI2_uc002tmw.1_Frame_Shift_Ins_p.S388fs	NM_005270	NP_005261	P10070	GLI2_HUMAN	GLI-Kruppel family member GLI2	388					axon guidance|branching morphogenesis of a tube|cell proliferation|cerebellar cortex morphogenesis|developmental growth|embryonic digestive tract development|epidermal cell differentiation|floor plate formation|heart development|hindgut morphogenesis|kidney development|lung development|negative regulation of transcription from RNA polymerase II promoter|odontogenesis of dentine-containing tooth|osteoblast development|osteoblast differentiation|pituitary gland development|positive regulation of DNA replication|positive regulation of T cell differentiation in thymus|positive regulation of transcription from RNA polymerase II promoter|proximal/distal pattern formation|skeletal system development|smoothened signaling pathway involved in ventral spinal cord interneuron specification|spinal cord ventral commissure morphogenesis	nucleus|nucleus	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(8)|lung(2)|breast(1)|central_nervous_system(1)|pancreas(1)	13	Renal(3;0.0496)	Prostate(154;0.0623)																---	---	---	---
Unknown	0	broad.mit.edu	37	2	121933438	121933438	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:121933438delT								GLI2 (183210 upstream) : TFCP2L1 (40728 downstream)																																			---	---	---	---
TFCP2L1	29842	broad.mit.edu	37	2	122016860	122016860	+	Intron	DEL	A	-	-	rs112843070		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:122016860delA	uc002tmx.2	-						TFCP2L1_uc010flr.2_Intron	NM_014553	NP_055368			LBP-9						female pregnancy|steroid biosynthetic process	mitochondrion|nucleolus	DNA binding|sequence-specific DNA binding transcription factor activity|transcription corepressor activity			pancreas(2)|ovary(1)	3	Renal(3;0.01)																	---	---	---	---
CLASP1	23332	broad.mit.edu	37	2	122136792	122136795	+	Intron	DEL	AAAA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:122136792_122136795delAAAA	uc002tnc.2	-						CLASP1_uc010yyv.1_Intron|CLASP1_uc002tmz.2_Intron|CLASP1_uc002tna.2_Intron|CLASP1_uc010yyw.1_Intron|CLASP1_uc002tnb.2_Intron|CLASP1_uc010yyx.1_Intron|CLASP1_uc010yyy.1_Intron|CLASP1_uc010yyz.1_Intron|CLASP1_uc010yza.1_Intron|CLASP1_uc010yzb.1_Intron|CLASP1_uc010yzc.1_Intron|CLASP1_uc002tmy.2_5'Flank|CLASP1_uc002tnf.2_Intron	NM_015282	NP_056097			CLIP-associating protein 1 isoform 1						axon guidance|cell division|establishment or maintenance of cell polarity|exit from mitosis|G2/M transition of mitotic cell cycle|microtubule anchoring|microtubule bundle formation|microtubule nucleation|microtubule organizing center organization|mitotic prometaphase|negative regulation of microtubule depolymerization	centrosomal corona|condensed chromosome kinetochore|cortical microtubule cytoskeleton|cytoplasmic microtubule|cytosol|Golgi apparatus|kinetochore microtubule	kinetochore binding|microtubule plus-end binding			ovary(1)|central_nervous_system(1)	2	Renal(3;0.0496)																	---	---	---	---
CLASP1	23332	broad.mit.edu	37	2	122320737	122320738	+	Intron	DEL	TC	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:122320737_122320738delTC	uc002tnc.2	-						CLASP1_uc010yyy.1_Intron|CLASP1_uc010yyz.1_Intron|CLASP1_uc010yza.1_Intron|CLASP1_uc010yzb.1_Intron|CLASP1_uc010yzc.1_Intron|CLASP1_uc002tng.1_Intron	NM_015282	NP_056097			CLIP-associating protein 1 isoform 1						axon guidance|cell division|establishment or maintenance of cell polarity|exit from mitosis|G2/M transition of mitotic cell cycle|microtubule anchoring|microtubule bundle formation|microtubule nucleation|microtubule organizing center organization|mitotic prometaphase|negative regulation of microtubule depolymerization	centrosomal corona|condensed chromosome kinetochore|cortical microtubule cytoskeleton|cytoplasmic microtubule|cytosol|Golgi apparatus|kinetochore microtubule	kinetochore binding|microtubule plus-end binding			ovary(1)|central_nervous_system(1)	2	Renal(3;0.0496)																	---	---	---	---
CLASP1	23332	broad.mit.edu	37	2	122349449	122349451	+	Intron	DEL	CTT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:122349449_122349451delCTT	uc002tnc.2	-						CLASP1_uc010yyy.1_Intron|CLASP1_uc010yyz.1_Intron|CLASP1_uc010yza.1_Intron|CLASP1_uc010yzb.1_Intron|CLASP1_uc010yzc.1_Intron|CLASP1_uc002tng.1_Intron	NM_015282	NP_056097			CLIP-associating protein 1 isoform 1						axon guidance|cell division|establishment or maintenance of cell polarity|exit from mitosis|G2/M transition of mitotic cell cycle|microtubule anchoring|microtubule bundle formation|microtubule nucleation|microtubule organizing center organization|mitotic prometaphase|negative regulation of microtubule depolymerization	centrosomal corona|condensed chromosome kinetochore|cortical microtubule cytoskeleton|cytoplasmic microtubule|cytosol|Golgi apparatus|kinetochore microtubule	kinetochore binding|microtubule plus-end binding			ovary(1)|central_nervous_system(1)	2	Renal(3;0.0496)																	---	---	---	---
Unknown	0	broad.mit.edu	37	2	122466740	122466741	+	Intron	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:122466740_122466741delTT	uc002tnj.1	+											Homo sapiens cDNA FLJ40945 fis, clone UTERU2008747.																														---	---	---	---
MKI67IP	84365	broad.mit.edu	37	2	122484578	122484578	+	3'UTR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:122484578delT	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	123016255	123016256	+	IGR	INS	-	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:123016255_123016256insT								TSN (490829 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	123351359	123351360	+	IGR	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:123351359_123351360delTT								TSN (825933 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	124044782	124044782	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:124044782delT								None (None upstream) : CNTNAP5 (738082 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	124195165	124195165	+	IGR	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:124195165delG								None (None upstream) : CNTNAP5 (587699 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	124343819	124343819	+	IGR	DEL	A	-	-	rs5834006		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:124343819delA								None (None upstream) : CNTNAP5 (439045 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	124396775	124396775	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:124396775delT								None (None upstream) : CNTNAP5 (386089 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	124405673	124405674	+	IGR	INS	-	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:124405673_124405674insA								None (None upstream) : CNTNAP5 (377190 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	124495742	124495742	+	IGR	DEL	T	-	-	rs79511014		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:124495742delT								None (None upstream) : CNTNAP5 (287122 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	124517217	124517217	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:124517217delT								None (None upstream) : CNTNAP5 (265647 downstream)																																			---	---	---	---
CNTNAP5	129684	broad.mit.edu	37	2	125221512	125221513	+	Intron	INS	-	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:125221512_125221513insT	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	125824743	125824743	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:125824743delA								CNTNAP5 (151882 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	126255538	126255539	+	IGR	INS	-	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:126255538_126255539insT								CNTNAP5 (582677 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	127178146	127178147	+	IGR	DEL	TC	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:127178146_127178147delTC								None (None upstream) : GYPC (235537 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	127269003	127269003	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:127269003delT								None (None upstream) : GYPC (144681 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	127775089	127775089	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:127775089delA								GYPC (320844 upstream) : BIN1 (30518 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	128007517	128007517	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:128007517delA								CYP27C1 (44174 upstream) : ERCC3 (7349 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	128146147	128146148	+	IGR	INS	-	AA	AA	rs142704142	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:128146147_128146148insAA								MAP3K2 (45342 upstream) : PROC (29869 downstream)																																			---	---	---	---
PROC	5624	broad.mit.edu	37	2	128185290	128185290	+	Intron	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:128185290delG	uc002tok.2	+						PROC_uc002tol.2_Intron|PROC_uc010yzi.1_Intron|PROC_uc010yzj.1_Intron|PROC_uc010yzk.1_Intron|PROC_uc002tom.2_Intron	NM_000312	NP_000303			protein C						blood coagulation|leukocyte migration|negative regulation of apoptosis|negative regulation of blood coagulation|peptidyl-glutamic acid carboxylation|post-translational protein modification|proteolysis	endoplasmic reticulum lumen|Golgi lumen|plasma membrane	calcium ion binding|protein binding|serine-type endopeptidase activity				0	Colorectal(110;0.1)			BRCA - Breast invasive adenocarcinoma(221;0.0673)	Antihemophilic Factor(DB00025)|Drotrecogin alfa(DB00055)|Menadione(DB00170)|Sodium Tetradecyl Sulfate(DB00464)													---	---	---	---
IWS1	55677	broad.mit.edu	37	2	128248327	128248327	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:128248327delA	uc002ton.2	-							NM_017969	NP_060439			IWS1 homolog						transcription, DNA-dependent	nucleus	DNA binding			ovary(1)	1	Colorectal(110;0.1)			BRCA - Breast invasive adenocarcinoma(221;0.0735)														---	---	---	---
Unknown	0	broad.mit.edu	37	2	128672700	128672700	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:128672700delA								AMMECR1L (29186 upstream) : SAP130 (26091 downstream)																																			---	---	---	---
UGGT1	56886	broad.mit.edu	37	2	128877330	128877330	+	Intron	DEL	C	-	-	rs113984747		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:128877330delC	uc002tps.2	+						UGGT1_uc010fme.1_Intron|UGGT1_uc002tpr.2_Intron	NM_020120	NP_064505			UDP-glucose ceramide glucosyltransferase-like 1						'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																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	129214517	129214518	+	IGR	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:129214517_129214518delAA								HS6ST1 (138346 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	129303702	129303703	+	IGR	INS	-	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:129303702_129303703insT								HS6ST1 (227531 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	129524162	129524162	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:129524162delT								HS6ST1 (447991 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	129554368	129554369	+	IGR	INS	-	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:129554368_129554369insT								HS6ST1 (478197 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	129753962	129753962	+	IGR	DEL	T	-	-	rs34562737		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:129753962delT								HS6ST1 (677791 upstream) : LOC389033 (926473 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	130778009	130778009	+	IGR	DEL	T	-	-	rs75477191		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:130778009delT								RAB6C (37698 upstream) : LOC440905 (5563 downstream)																																			---	---	---	---
POTEF	728378	broad.mit.edu	37	2	130872255	130872256	+	Intron	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:130872255_130872256delAA	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	130893081	130893081	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:130893081delA								POTEF (6286 upstream) : CCDC74B (3781 downstream)																																			---	---	---	---
SMPD4	55627	broad.mit.edu	37	2	130926642	130926643	+	Intron	INS	-	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:130926642_130926643insC	uc002tqq.1	-						SMPD4_uc002tqp.1_Intron|SMPD4_uc010yzy.1_Intron|SMPD4_uc010yzz.1_Intron|SMPD4_uc002tqr.1_Intron|SMPD4_uc002tqs.1_Intron|SMPD4_uc002tqt.1_Intron|SMPD4_uc010zaa.1_Intron|SMPD4_uc010zab.1_Intron|SMPD4_uc010zac.1_Intron|SMPD4_uc010zad.1_Intron	NM_017951	NP_060421			sphingomyelin phosphodiesterase 4 isoform 2						sphingomyelin catabolic process	endoplasmic reticulum membrane|Golgi membrane|integral to membrane|trans-Golgi network	metal ion binding|protein binding|sphingomyelin phosphodiesterase activity|sphingomyelin phosphodiesterase D activity				0	Colorectal(110;0.1)				Phosphatidylserine(DB00144)													---	---	---	---
ARHGEF4	50649	broad.mit.edu	37	2	131715971	131715971	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:131715971delT	uc002tsa.1	+						ARHGEF4_uc010fmw.1_Intron|ARHGEF4_uc002tsb.1_Intron|ARHGEF4_uc010fmx.1_Intron	NM_015320	NP_056135			Rho guanine nucleotide exchange factor 4 isoform						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)														---	---	---	---
PLEKHB2	55041	broad.mit.edu	37	2	131958157	131958157	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:131958157delA	uc002tsh.2	+											SubName: Full=Putative uncharacterized protein PLEKHB2;							membrane	protein binding			ovary(2)	2				BRCA - Breast invasive adenocarcinoma(221;0.0828)														---	---	---	---
LOC150776	150776	broad.mit.edu	37	2	132254562	132254562	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:132254562delA	uc010fna.2	+						LOC150776_uc010zax.1_Intron|LOC150776_uc010zay.1_Intron|LOC150776_uc010zaz.1_Intron|LOC150776_uc002tsy.3_Intron					Homo sapiens cDNA FLJ61219 complete cds, highly similar to Homo sapiens sphingomyelin phosphodiesterase 4, neutral membrane, transcript variant 2, mRNA.												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	132405729	132405730	+	IGR	INS	-	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:132405729_132405730insG								CCDC74A (114492 upstream) : C2orf27A (74334 downstream)																																			---	---	---	---
NCRNA00164	554226	broad.mit.edu	37	2	133014827	133014828	+	Intron	INS	-	A	A	rs146639319		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:133014827_133014828insA	uc002ttj.3	-						MIR663B_hsa-mir-663b|MI0006336_5'Flank	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	133024017	133024018	+	IGR	INS	-	AA	AA			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:133024017_133024018insAA								NCRNA00164 (8475 upstream) : GPR39 (150129 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	133087871	133087872	+	IGR	INS	-	T	T	rs148498305	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:133087871_133087872insT								NCRNA00164 (72329 upstream) : GPR39 (86275 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	133101571	133101572	+	IGR	INS	-	T	T	rs140120478	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:133101571_133101572insT								NCRNA00164 (86029 upstream) : GPR39 (72575 downstream)																																			---	---	---	---
NCKAP5	344148	broad.mit.edu	37	2	133614745	133614745	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:133614745delT	uc002ttp.2	-						NCKAP5_uc002ttq.2_Intron	NM_207363	NP_997246			Nck-associated protein 5 isoform 1								protein binding				0																		---	---	---	---
NCKAP5	344148	broad.mit.edu	37	2	134044378	134044378	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:134044378delA	uc002ttp.2	-						NCKAP5_uc002ttq.2_Intron|NCKAP5_uc002ttt.1_Intron|NCKAP5_uc002tts.1_Intron	NM_207363	NP_997246			Nck-associated protein 5 isoform 1								protein binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	134709159	134709159	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:134709159delT								NCKAP5 (383128 upstream) : MGAT5 (302671 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	134935671	134935672	+	IGR	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:134935671_134935672delAA								NCKAP5 (609640 upstream) : MGAT5 (76158 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	137087942	137087942	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:137087942delT								CXCR4 (212217 upstream) : THSD7B (435173 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	137170736	137170736	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:137170736delT								CXCR4 (295011 upstream) : THSD7B (352379 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	137326815	137326815	+	IGR	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:137326815delC								CXCR4 (451090 upstream) : THSD7B (196300 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	137397835	137397836	+	IGR	INS	-	T	T	rs113118406		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:137397835_137397836insT								CXCR4 (522110 upstream) : THSD7B (125279 downstream)																																			---	---	---	---
THSD7B	80731	broad.mit.edu	37	2	137705999	137705999	+	Intron	DEL	C	-	-	rs67945845		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:137705999delC	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	137735377	137735378	+	Intron	INS	-	TG	TG	rs28886625		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:137735377_137735378insTG	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	138030022	138030022	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:138030022delT	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)														---	---	---	---
THSD7B	80731	broad.mit.edu	37	2	138033617	138033617	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-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)														---	---	---	---
THSD7B	80731	broad.mit.edu	37	2	138386001	138386001	+	Intron	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:138386001delG	uc002tva.1	+						THSD7B_uc010zbj.1_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)														---	---	---	---
Unknown	0	broad.mit.edu	37	2	138933296	138933296	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:138933296delA								HNMT (159363 upstream) : SPOPL (326054 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	139063376	139063377	+	IGR	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:139063376_139063377delTT								HNMT (289443 upstream) : SPOPL (195973 downstream)																																			---	---	---	---
NXPH2	11249	broad.mit.edu	37	2	139502017	139502017	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:139502017delA	uc002tvi.2	-							NM_007226	NP_009157			neurexophilin 2 precursor						neuropeptide signaling pathway	extracellular region				ovary(3)|skin(1)	4				BRCA - Breast invasive adenocarcinoma(221;0.101)														---	---	---	---
NXPH2	11249	broad.mit.edu	37	2	139504433	139504433	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:139504433delA	uc002tvi.2	-							NM_007226	NP_009157			neurexophilin 2 precursor						neuropeptide signaling pathway	extracellular region				ovary(3)|skin(1)	4				BRCA - Breast invasive adenocarcinoma(221;0.101)														---	---	---	---
Unknown	0	broad.mit.edu	37	2	139979261	139979262	+	IGR	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:139979261_139979262delTT								NXPH2 (441450 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	140017996	140017996	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:140017996delA								NXPH2 (480185 upstream) : LRP1B (971000 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	140584215	140584215	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:140584215delT								None (None upstream) : LRP1B (404781 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	140614491	140614491	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:140614491delA								None (None upstream) : LRP1B (374505 downstream)																																			---	---	---	---
LRP1B	53353	broad.mit.edu	37	2	140995858	140995858	+	Frame_Shift_Del	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:140995858delT	uc002tvj.1	-	89	14395	c.13423delA	c.(13423-13425)ACAfs	p.T4475fs		NM_018557	NP_061027	Q9NZR2	LRP1B_HUMAN	low density lipoprotein-related protein 1B	4475	Cytoplasmic (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)			---	---	---	---
LRP1B	53353	broad.mit.edu	37	2	141323917	141323917	+	Intron	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:141323917delC	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	141435287	141435288	+	Intron	INS	-	A	A	rs144986881	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:141435287_141435288insA	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	141473474	141473475	+	Intron	INS	-	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:141473474_141473475insT	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	141598364	141598365	+	Intron	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:141598364_141598365delTT	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	141703263	141703264	+	Intron	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:141703263_141703264delAA	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	142359213	142359213	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:142359213delT	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	142619499	142619499	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:142619499delA	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	143612810	143612810	+	IGR	DEL	A	-	-	rs113478040		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:143612810delA								LRP1B (723540 upstream) : KYNU (22385 downstream)																																			---	---	---	---
KYNU	8942	broad.mit.edu	37	2	143718078	143718078	+	Intron	DEL	A	-	-	rs74847108		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:143718078delA	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)													---	---	---	---
Unknown	0	broad.mit.edu	37	2	144696215	144696215	+	IGR	DEL	T	-	-	rs3832115		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:144696215delT								ARHGAP15 (170295 upstream) : GTDC1 (7368 downstream)																																			---	---	---	---
GTDC1	79712	broad.mit.edu	37	2	144966898	144966898	+	Intron	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:144966898delC	uc002tvp.2	-						GTDC1_uc002tvo.2_Intron|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)														---	---	---	---
GTDC1	79712	broad.mit.edu	37	2	145064229	145064229	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:145064229delA	uc010fnn.2	-						GTDC1_uc002tvq.2_Intron|GTDC1_uc002tvr.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	145094098	145094101	+	IGR	DEL	AAAA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:145094098_145094101delAAAA								GTDC1 (4069 upstream) : ZEB2 (51484 downstream)																																			---	---	---	---
ZEB2	9839	broad.mit.edu	37	2	145164145	145164145	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:145164145delA	uc002tvu.2	-						ZEB2_uc002tvv.2_Intron|ZEB2_uc010zbm.1_Intron|ZEB2_uc010fnp.2_Intron|ZEB2_uc010fnq.1_Intron	NM_014795	NP_055610			zinc finger homeobox 1b							cytoplasm|nucleolus	phosphatase regulator activity|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|SMAD binding|zinc ion binding			ovary(5)|pancreas(2)|upper_aerodigestive_tract(1)|large_intestine(1)	9				BRCA - Breast invasive adenocarcinoma(221;0.112)														---	---	---	---
Unknown	0	broad.mit.edu	37	2	145455889	145455890	+	Intron	DEL	TG	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:145455889_145455890delTG	uc002twc.2	+											Homo sapiens hypothetical gene supported by BC043549; BX648102, mRNA (cDNA clone IMAGE:5172341).																														---	---	---	---
Unknown	0	broad.mit.edu	37	2	146073598	146073598	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:146073598delA								ZEB2 (795667 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	146613712	146613712	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:146613712delT								None (None upstream) : PABPC1P2 (730913 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	146722694	146722694	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:146722694delA								None (None upstream) : PABPC1P2 (621931 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	146856505	146856505	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:146856505delA								None (None upstream) : PABPC1P2 (488120 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	147125645	147125645	+	IGR	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:147125645delC								None (None upstream) : PABPC1P2 (218980 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	147295091	147295092	+	IGR	INS	-	AG	AG			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:147295091_147295092insAG								None (None upstream) : PABPC1P2 (49533 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	147890750	147890750	+	IGR	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:147890750delC								PABPC1P2 (542193 upstream) : ACVR2A (711336 downstream)																																			---	---	---	---
ACVR2A	92	broad.mit.edu	37	2	148683686	148683686	+	Frame_Shift_Del	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-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)														---	---	---	---
ORC4L	5000	broad.mit.edu	37	2	148727198	148727198	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:148727198delA	uc002twi.2	-						ORC4L_uc002twj.2_Intron|ORC4L_uc010zbo.1_Intron|ORC4L_uc010zbp.1_Intron|ORC4L_uc010fnr.2_Intron|ORC4L_uc010zbq.1_Intron|ORC4L_uc002twk.2_Intron|ORC4L_uc010zbr.1_Intron	NM_181741	NP_859525			origin recognition complex subunit 4						cell cycle checkpoint|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	nuclear origin of replication recognition complex|nucleoplasm	ATP binding|DNA replication origin binding|nucleoside-triphosphatase activity|protein binding				0				BRCA - Breast invasive adenocarcinoma(221;0.0963)|COAD - Colon adenocarcinoma(177;0.203)														---	---	---	---
ORC4L	5000	broad.mit.edu	37	2	148745168	148745168	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:148745168delA	uc002twi.2	-						ORC4L_uc002twj.2_Intron|ORC4L_uc010zbo.1_Intron|ORC4L_uc010zbp.1_Intron|ORC4L_uc010fnr.2_Intron|ORC4L_uc010zbq.1_Intron|ORC4L_uc002twk.2_Intron|ORC4L_uc010zbr.1_Intron	NM_181741	NP_859525			origin recognition complex subunit 4						cell cycle checkpoint|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	nuclear origin of replication recognition complex|nucleoplasm	ATP binding|DNA replication origin binding|nucleoside-triphosphatase activity|protein binding				0				BRCA - Breast invasive adenocarcinoma(221;0.0963)|COAD - Colon adenocarcinoma(177;0.203)														---	---	---	---
MBD5	55777	broad.mit.edu	37	2	148792740	148792740	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:148792740delA	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)														---	---	---	---
MBD5	55777	broad.mit.edu	37	2	148881868	148881869	+	Intron	DEL	AC	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:148881868_148881869delAC	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)														---	---	---	---
MBD5	55777	broad.mit.edu	37	2	149019808	149019808	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:149019808delA	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)														---	---	---	---
EPC2	26122	broad.mit.edu	37	2	149429186	149429186	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:149429186delA	uc010zbt.1	+							NM_015630	NP_056445			enhancer of polycomb homolog 2						chromatin modification|DNA repair|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus				ovary(1)|breast(1)|pancreas(1)	3				BRCA - Breast invasive adenocarcinoma(221;0.0516)														---	---	---	---
EPC2	26122	broad.mit.edu	37	2	149517838	149517839	+	Intron	DEL	AC	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:149517838_149517839delAC	uc010zbt.1	+							NM_015630	NP_056445			enhancer of polycomb homolog 2						chromatin modification|DNA repair|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus				ovary(1)|breast(1)|pancreas(1)	3				BRCA - Breast invasive adenocarcinoma(221;0.0516)														---	---	---	---
LYPD6B	130576	broad.mit.edu	37	2	149955561	149955561	+	Intron	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:149955561delC	uc002twv.1	+						LYPD6B_uc002tww.1_Intron|LYPD6B_uc002twx.1_Intron	NM_177964	NP_808879			LY6/PLAUR domain containing 6B							anchored to membrane|plasma membrane					0																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	150554076	150554076	+	IGR	DEL	T	-	-	rs111356256		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:150554076delT								MMADHC (109746 upstream) : RND3 (770636 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	150941376	150941376	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:150941376delA								MMADHC (497046 upstream) : RND3 (383336 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	150979400	150979403	+	IGR	DEL	TTTT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:150979400_150979403delTTTT								MMADHC (535070 upstream) : RND3 (345309 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	150998290	150998290	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:150998290delT								MMADHC (553960 upstream) : RND3 (326422 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	151004770	151004771	+	IGR	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:151004770_151004771delAA								MMADHC (560440 upstream) : RND3 (319941 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	151130981	151130981	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:151130981delA								MMADHC (686651 upstream) : RND3 (193731 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	151268977	151268980	+	IGR	DEL	AAAC	-	-	rs142569316		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:151268977_151268980delAAAC								MMADHC (824647 upstream) : RND3 (55732 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	151606291	151606292	+	IGR	INS	-	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:151606291_151606292insA								RND3 (262111 upstream) : RBM43 (498437 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	151675575	151675575	+	IGR	DEL	A	-	-	rs78393117		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:151675575delA								RND3 (331395 upstream) : RBM43 (429154 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	151676820	151676820	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:151676820delA								RND3 (332640 upstream) : RBM43 (427909 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	152026919	152026919	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:152026919delT								RND3 (682739 upstream) : RBM43 (77810 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	152199186	152199187	+	IGR	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:152199186_152199187delAA								NMI (52756 upstream) : TNFAIP6 (14918 downstream)																																			---	---	---	---
RIF1	55183	broad.mit.edu	37	2	152293643	152293643	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:152293643delT	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	152299937	152299937	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:152299937delA	uc002txm.2	+						RIF1_uc002txl.2_Intron|RIF1_uc010fnv.1_Intron|RIF1_uc002txn.2_Intron|RIF1_uc002txo.2_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)														---	---	---	---
NEB	4703	broad.mit.edu	37	2	152370226	152370226	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:152370226delA	uc010fnx.2	-						NEB_uc002txr.2_Intron|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)														---	---	---	---
NEB	4703	broad.mit.edu	37	2	152516797	152516797	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:152516797delA	uc010fnx.2	-							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)														---	---	---	---
CACNB4	785	broad.mit.edu	37	2	152905674	152905674	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:152905674delT	uc002tya.2	-						CACNB4_uc002txz.2_Intron|CACNB4_uc010fnz.2_Intron	NM_000726	NP_000717			calcium channel, voltage-dependent, beta 4						axon guidance|membrane depolarization|synaptic transmission	cytosol|internal side of plasma membrane|plasma membrane|synapse|voltage-gated calcium channel complex	protein binding|voltage-gated calcium channel activity			ovary(2)	2				BRCA - Breast invasive adenocarcinoma(221;0.156)	Verapamil(DB00661)													---	---	---	---
Unknown	0	broad.mit.edu	37	2	153162389	153162389	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:153162389delA								STAM2 (129883 upstream) : FMNL2 (29362 downstream)																																			---	---	---	---
PRPF40A	55660	broad.mit.edu	37	2	153522576	153522576	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:153522576delT	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	153788322	153788322	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:153788322delA								ARL6IP6 (170555 upstream) : RPRM (545530 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	154372335	154372335	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:154372335delA								RPRM (37013 upstream) : GALNT13 (356091 downstream)																																			---	---	---	---
KCNJ3	3760	broad.mit.edu	37	2	155552462	155552462	+	5'Flank	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:155552462delA	uc002tyv.1	+						KCNJ3_uc010zce.1_5'Flank	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	156166510	156166510	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:156166510delA								KCNJ3 (453496 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	156420445	156420445	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:156420445delT								KCNJ3 (707431 upstream) : NR4A2 (760501 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	156840310	156840311	+	IGR	INS	-	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:156840310_156840311insT								None (None upstream) : NR4A2 (340635 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	156841899	156841899	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:156841899delA								None (None upstream) : NR4A2 (339047 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	157042106	157042109	+	Intron	DEL	TCTC	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:157042106_157042109delTCTC	uc002tyw.2	-											Homo sapiens cDNA clone IMAGE:5209417.																														---	---	---	---
GPD2	2820	broad.mit.edu	37	2	157304631	157304632	+	Intron	INS	-	T	T	rs71402352		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:157304631_157304632insT	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																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	157684960	157684960	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:157684960delA								GPD2 (214713 upstream) : GALNT5 (429380 downstream)																																			---	---	---	---
CYTIP	9595	broad.mit.edu	37	2	158283944	158283944	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:158283944delA	uc002tzj.1	-						CYTIP_uc010zcl.1_Intron	NM_004288	NP_004279			cytohesin 1 interacting protein						regulation of cell adhesion	cell cortex|early endosome	protein binding			ovary(1)|kidney(1)|skin(1)	3																		---	---	---	---
ACVR1	90	broad.mit.edu	37	2	158720380	158720383	+	Intron	DEL	TTTT	-	-	rs76161063		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:158720380_158720383delTTTT	uc002tzn.3	-						ACVR1_uc010fog.2_Intron	NM_001105	NP_001096			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	158822145	158822147	+	IGR	DEL	TTT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:158822145_158822147delTTT								ACVR1 (89771 upstream) : UPP2 (29544 downstream)																																			---	---	---	---
UPP2	151531	broad.mit.edu	37	2	158910898	158910899	+	Intron	DEL	TT	-	-	rs141791650		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:158910898_158910899delTT	uc002tzo.2	+							NM_001135098	NP_001128570			uridine phosphorylase 2 isoform b						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																		---	---	---	---
CCDC148	130940	broad.mit.edu	37	2	159132974	159132974	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:159132974delA	uc002tzq.2	-						CCDC148_uc002tzr.2_Intron|CCDC148_uc010foh.2_Intron	NM_138803	NP_620158			coiled-coil domain containing 148											ovary(2)	2																		---	---	---	---
PKP4	8502	broad.mit.edu	37	2	159416894	159416894	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:159416894delA	uc002tzv.2	+						PKP4_uc002tzt.1_Intron|PKP4_uc002tzu.2_Intron|PKP4_uc002tzw.2_Intron|PKP4_uc002tzx.2_Intron|PKP4_uc002tzy.1_Intron|PKP4_uc002tzz.1_Intron	NM_003628	NP_003619			plakophilin 4 isoform a						cell adhesion	desmosome	protein binding			ovary(5)|skin(2)	7															HNSCC(62;0.18)			---	---	---	---
BAZ2B	29994	broad.mit.edu	37	2	160201326	160201326	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:160201326delA	uc002uao.2	-						BAZ2B_uc002uap.2_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	160286538	160286538	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:160286538delA	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	160338300	160338300	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:160338300delA	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	160885499	160885500	+	Intron	DEL	AA	-	-	rs80051025		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:160885499_160885500delAA	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																		---	---	---	---
ITGB6	3694	broad.mit.edu	37	2	161023422	161023422	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:161023422delA	uc002ubh.2	-						ITGB6_uc010fow.1_Intron|ITGB6_uc010fou.2_Intron|ITGB6_uc010zcq.1_Intron|ITGB6_uc010fov.1_Intron	NM_000888	NP_000879			integrin, beta 6 precursor						cell-matrix adhesion|integrin-mediated signaling pathway|interspecies interaction between organisms|multicellular organismal development	integrin complex	receptor activity			ovary(1)|lung(1)|skin(1)	3																		---	---	---	---
ITGB6	3694	broad.mit.edu	37	2	161053191	161053192	+	Intron	DEL	TG	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:161053191_161053192delTG	uc002ubh.2	-						ITGB6_uc010fow.1_Intron|ITGB6_uc010fou.2_Intron|ITGB6_uc010zcq.1_Intron|ITGB6_uc010fov.1_Intron	NM_000888	NP_000879			integrin, beta 6 precursor						cell-matrix adhesion|integrin-mediated signaling pathway|interspecies interaction between organisms|multicellular organismal development	integrin complex	receptor activity			ovary(1)|lung(1)|skin(1)	3																		---	---	---	---
ITGB6	3694	broad.mit.edu	37	2	161109701	161109702	+	Intron	INS	-	A	A	rs148251773	by1000genomes;byFrequency;by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:161109701_161109702insA	uc010fow.1	-											Synthetic construct DNA, clone: pF1KB8424, Homo sapiens ITGB6 gene for integrin, beta 6, without stop codon, in Flexi system.						cell-matrix adhesion|integrin-mediated signaling pathway|interspecies interaction between organisms|multicellular organismal development	integrin complex	receptor activity			ovary(1)|lung(1)|skin(1)	3																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	161535146	161535146	+	IGR	DEL	A	-	-	rs35126887		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:161535146delA								RBMS1 (184828 upstream) : TANK (458320 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	161607975	161607975	+	IGR	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:161607975delC								RBMS1 (257657 upstream) : TANK (385491 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	161826895	161826896	+	IGR	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:161826895_161826896delAA								RBMS1 (476577 upstream) : TANK (166570 downstream)																																			---	---	---	---
PSMD14	10213	broad.mit.edu	37	2	162251500	162251501	+	Intron	DEL	TT	-	-	rs112832377		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:162251500_162251501delTT	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	162272776	+	5'UTR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:162272776delA	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																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	162360411	162360411	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:162360411delT								TBR1 (78838 upstream) : SLC4A10 (120434 downstream)																																			---	---	---	---
FAP	2191	broad.mit.edu	37	2	163027346	163027347	+	3'UTR	INS	-	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:163027346_163027347insT	uc002ucd.2	-	26					FAP_uc010fpc.2_3'UTR|FAP_uc010zct.1_3'UTR|FAP_uc010fpd.2_3'UTR	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																		---	---	---	---
KCNH7	90134	broad.mit.edu	37	2	163314615	163314616	+	Intron	DEL	GT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:163314615_163314616delGT	uc002uch.1	-						KCNH7_uc002uci.2_Intron	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	164009275	164009284	+	IGR	DEL	TTTTTTTTTT	-	-	rs147504675		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:164009275_164009284delTTTTTTTTTT								KCNH7 (314035 upstream) : FIGN (454834 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	164075671	164075671	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:164075671delT								KCNH7 (380431 upstream) : FIGN (388447 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	164915765	164915765	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:164915765delT								FIGN (323252 upstream) : GRB14 (433568 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	165126666	165126671	+	IGR	DEL	TTTTTT	-	-	rs71393604		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:165126666_165126671delTTTTTT								FIGN (534153 upstream) : GRB14 (222662 downstream)																																			---	---	---	---
GRB14	2888	broad.mit.edu	37	2	165481058	165481059	+	5'Flank	DEL	CT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:165481058_165481059delCT	uc002ucl.2	-						GRB14_uc002ucm.2_5'Flank	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																		---	---	---	---
COBLL1	22837	broad.mit.edu	37	2	165631668	165631669	+	Intron	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:165631668_165631669delAA	uc010zcw.1	-						COBLL1_uc002ucp.2_Intron|COBLL1_uc002ucq.2_Intron|COBLL1_uc010zcx.1_Intron|COBLL1_uc002ucs.1_Intron|COBLL1_uc002uct.2_Intron	NM_014900	NP_055715			COBL-like 1											ovary(2)|pancreas(1)	3																		---	---	---	---
SLC38A11	151258	broad.mit.edu	37	2	165794392	165794392	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:165794392delT	uc002ucv.1	-						SLC38A11_uc002ucu.1_Intron|SLC38A11_uc002ucw.1_Intron	NM_173512	NP_775783			solute carrier family 38, member 11						amino acid transport|sodium ion transport	integral to membrane				ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	165843279	165843280	+	IGR	DEL	AA	-	-	rs80071591		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:165843279_165843280delAA								SLC38A11 (31244 upstream) : SCN3A (100752 downstream)																																			---	---	---	---
SCN3A	6328	broad.mit.edu	37	2	165996280	165996281	+	Intron	DEL	TA	-	-	rs2289400	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:165996280_165996281delTA	uc002ucx.2	-						SCN3A_uc002ucy.2_Intron|SCN3A_uc002ucz.2_Intron|SCN3A_uc002uda.1_Intron|SCN3A_uc002udb.1_Intron	NM_006922	NP_008853			sodium channel, voltage-gated, type III, alpha							voltage-gated sodium channel complex	voltage-gated sodium channel activity			ovary(4)|breast(3)|skin(2)|central_nervous_system(1)	10					Lamotrigine(DB00555)													---	---	---	---
SCN3A	6328	broad.mit.edu	37	2	166054097	166054098	+	Intron	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:166054097_166054098delTT	uc002ucx.2	-						SCN3A_uc002ucy.2_Intron|SCN3A_uc002ucz.2_Intron	NM_006922	NP_008853			sodium channel, voltage-gated, type III, alpha							voltage-gated sodium channel complex	voltage-gated sodium channel activity			ovary(4)|breast(3)|skin(2)|central_nervous_system(1)	10					Lamotrigine(DB00555)													---	---	---	---
TTC21B	79809	broad.mit.edu	37	2	166775663	166775663	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:166775663delT	uc002udk.2	-							NM_024753	NP_079029			tetratricopeptide repeat domain 21B							cilium axoneme|cytoplasm|cytoskeleton	binding			ovary(2)|pancreas(2)|breast(1)	5																		---	---	---	---
SCN9A	6335	broad.mit.edu	37	2	167060861	167060861	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:167060861delT	uc010fpl.2	-						uc002udp.2_Intron	NM_002977	NP_002968			sodium channel, voltage-gated, type IX, alpha							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	167812326	167812326	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:167812326delT	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																		---	---	---	---
XIRP2	129446	broad.mit.edu	37	2	168098519	168098519	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:168098519delA	uc002udx.2	+						XIRP2_uc010fpn.2_Intron|XIRP2_uc010fpo.2_Intron|XIRP2_uc010fpp.2_Intron|XIRP2_uc002udy.2_Intron|XIRP2_uc010fpq.2_Intron|XIRP2_uc010fpr.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	168438769	168438769	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:168438769delA								XIRP2 (322510 upstream) : B3GALT1 (236413 downstream)																																			---	---	---	---
STK39	27347	broad.mit.edu	37	2	168946802	168946805	+	Intron	DEL	TGAA	-	-	rs111727345		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:168946802_168946805delTGAA	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																		---	---	---	---
LASS6	253782	broad.mit.edu	37	2	169461205	169461206	+	Intron	DEL	CT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:169461205_169461206delCT	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																		---	---	---	---
SPC25	57405	broad.mit.edu	37	2	169745701	169745701	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:169745701delA	uc002uel.2	-							NM_020675	NP_065726			spindle pole body component 25						cell division|chromosome segregation|mitotic prometaphase|mitotic spindle organization	condensed chromosome kinetochore|cytosol|Ndc80 complex|nucleus	protein binding			central_nervous_system(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	170294400	170294400	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:170294400delT								LRP2 (75278 upstream) : BBS5 (41606 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	170433856	170433856	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:170433856delA								FASTKD1 (3432 upstream) : PPIG (6994 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	170611501	170611501	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:170611501delT								KLHL23 (5063 upstream) : SSB (43888 downstream)																																			---	---	---	---
UBR3	130507	broad.mit.edu	37	2	170938525	170938525	+	3'UTR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:170938525delT	uc010zdi.1	+	39					UBR3_uc002ufr.3_RNA|UBR3_uc010fqa.2_3'UTR|UBR3_uc002uft.3_3'UTR|UBR3_uc010zdj.1_3'UTR|UBR3_uc002ufu.3_3'UTR	NM_172070	NP_742067			E3 ubiquitin-protein ligase UBR3						sensory perception of smell|suckling behavior|ubiquitin-dependent protein catabolic process	integral to membrane	ubiquitin-protein ligase activity|zinc ion binding				0																		---	---	---	---
MYO3B	140469	broad.mit.edu	37	2	171130600	171130601	+	Intron	DEL	GA	-	-	rs111859976		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:171130600_171130601delGA	uc002ufy.2	+						MYO3B_uc002ufv.2_Intron|MYO3B_uc010fqb.1_Intron|MYO3B_uc002ufz.2_Intron|MYO3B_uc002ufw.2_Intron|MYO3B_uc002ufx.2_Intron|MYO3B_uc002uga.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	171633702	171633702	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:171633702delT								SP5 (59205 upstream) : GAD1 (39498 downstream)																																			---	---	---	---
GORASP2	26003	broad.mit.edu	37	2	171795940	171795940	+	Intron	DEL	A	-	-	rs58288351		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:171795940delA	uc002ugk.2	+						GORASP2_uc002ugj.2_Intron|GORASP2_uc010zdl.1_Intron|GORASP2_uc010zdm.1_Intron	NM_015530	NP_056345			golgi reassembly stacking protein 2							Golgi membrane				breast(1)|central_nervous_system(1)	2																		---	---	---	---
TLK1	9874	broad.mit.edu	37	2	171943149	171943150	+	Intron	DEL	AA	-	-	rs78793589		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:171943149_171943150delAA	uc002ugn.2	-						TLK1_uc002ugo.2_Intron|TLK1_uc002ugp.2_Intron|TLK1_uc002ugq.2_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	172061834	172061837	+	Intron	DEL	TTTT	-	-	rs139902869		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:172061834_172061837delTTTT	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																		---	---	---	---
METTL8	79828	broad.mit.edu	37	2	172217029	172217029	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:172217029delA	uc010zdo.1	-						METTL8_uc002ugu.3_Intron|METTL8_uc002ugv.3_Intron|METTL8_uc002ugt.3_Intron|METTL8_uc002ugs.3_Intron|METTL8_uc010zdp.1_Intron	NM_024770	NP_079046			methyltransferase like 8								methyltransferase activity			ovary(1)	1																		---	---	---	---
DCAF17	80067	broad.mit.edu	37	2	172314775	172314775	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:172314775delA	uc002ugx.2	+						DCAF17_uc010zdq.1_Intron|DCAF17_uc010fqf.1_Intron|DCAF17_uc010zdr.1_Intron|DCAF17_uc010fqg.2_Intron	NM_025000	NP_079276			DDB1 and CUL4 associated factor 17 isoform 1							CUL4 RING ubiquitin ligase complex|integral to membrane|nucleolus					0																		---	---	---	---
DYNC1I2	1781	broad.mit.edu	37	2	172558005	172558005	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:172558005delT	uc002uha.1	+						DYNC1I2_uc002uhc.2_Intron|DYNC1I2_uc002uhb.1_Intron|DYNC1I2_uc010zds.1_Intron|DYNC1I2_uc002uhd.1_Intron|DYNC1I2_uc002uhe.1_Intron|DYNC1I2_uc002uhf.1_Intron|DYNC1I2_uc010zdt.1_Intron	NM_001378	NP_001369			dynein, cytoplasmic 1, intermediate chain 2						G2/M transition of mitotic cell cycle|interspecies interaction between organisms|microtubule-based movement|transport	centrosome|cytosol|dynein complex|microtubule|vesicle	microtubule motor activity			ovary(1)	1			OV - Ovarian serous cystadenocarcinoma(117;0.198)															---	---	---	---
DYNC1I2	1781	broad.mit.edu	37	2	172584624	172584624	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:172584624delT	uc002uha.1	+						DYNC1I2_uc002uhc.2_Intron|DYNC1I2_uc002uhb.1_Intron|DYNC1I2_uc010zds.1_Intron|DYNC1I2_uc002uhe.1_Intron|DYNC1I2_uc002uhf.1_Intron|DYNC1I2_uc010zdt.1_Intron|DYNC1I2_uc002uhg.1_Intron|DYNC1I2_uc010zdu.1_Intron	NM_001378	NP_001369			dynein, cytoplasmic 1, intermediate chain 2						G2/M transition of mitotic cell cycle|interspecies interaction between organisms|microtubule-based movement|transport	centrosome|cytosol|dynein complex|microtubule|vesicle	microtubule motor activity			ovary(1)	1			OV - Ovarian serous cystadenocarcinoma(117;0.198)															---	---	---	---
Unknown	0	broad.mit.edu	37	2	173064354	173064354	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:173064354delT								DLX2 (96876 upstream) : ITGA6 (227728 downstream)																																			---	---	---	---
ZAK	51776	broad.mit.edu	37	2	174024131	174024132	+	Intron	DEL	TT	-	-	rs67029113		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:174024131_174024132delTT	uc002uhz.2	+						ZAK_uc002uhx.2_Intron|ZAK_uc002uhy.2_Intron|ZAK_uc010zei.1_Intron|ZAK_uc002uia.1_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)															---	---	---	---
Unknown	0	broad.mit.edu	37	2	174157790	174157790	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:174157790delA								ZAK (25054 upstream) : CDCA7 (61771 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	174305333	174305334	+	IGR	INS	-	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:174305333_174305334insA								CDCA7 (71615 upstream) : SP3 (467925 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	174509519	174509519	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:174509519delA								CDCA7 (275801 upstream) : SP3 (263740 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	174522495	174522495	+	IGR	DEL	A	-	-	rs76545606		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:174522495delA								CDCA7 (288777 upstream) : SP3 (250764 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	174622548	174622548	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:174622548delT								CDCA7 (388830 upstream) : SP3 (150711 downstream)																																			---	---	---	---
SP3	6670	broad.mit.edu	37	2	174828742	174828744	+	Intron	DEL	CTC	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:174828742_174828744delCTC	uc002uig.2	-						SP3_uc002uie.2_5'UTR|SP3_uc002uif.2_Intron|SP3_uc010zel.1_Intron	NM_003111	NP_003102			Sp3 transcription factor isoform 1						negative regulation of transcription, DNA-dependent|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	PML body	protein binding|zinc ion binding		EWSR1/SP3(3)	soft_tissue(3)|upper_aerodigestive_tract(1)|ovary(1)|skin(1)	6			OV - Ovarian serous cystadenocarcinoma(117;0.185)															---	---	---	---
Unknown	0	broad.mit.edu	37	2	175145430	175145430	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:175145430delT								OLA1 (32065 upstream) : SP9 (54391 downstream)																																			---	---	---	---
CHN1	1123	broad.mit.edu	37	2	175754316	175754316	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:175754316delA	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								---	---	---	---
CHN1	1123	broad.mit.edu	37	2	175794306	175794307	+	Intron	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:175794306_175794307delAA	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	176355914	176355914	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:176355914delA								ATP5G3 (309424 upstream) : KIAA1715 (434496 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	176522104	176522104	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:176522104delT								ATP5G3 (475614 upstream) : KIAA1715 (268306 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	176708091	176708091	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:176708091delT								ATP5G3 (661601 upstream) : KIAA1715 (82319 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	176746746	176746747	+	IGR	DEL	AC	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:176746746_176746747delAC								ATP5G3 (700256 upstream) : KIAA1715 (43663 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	176923439	176923439	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:176923439delA								KIAA1715 (55925 upstream) : EVX2 (21398 downstream)																																			---	---	---	---
HOXD8	3234	broad.mit.edu	37	2	176996025	176996025	+	Intron	DEL	T	-	-	rs111789488		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:176996025delT	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	177065588	177065589	+	IGR	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:177065588_177065589delTT								HOXD1 (9953 upstream) : MTX2 (68534 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	177238465	177238465	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:177238465delT								MTX2 (35714 upstream) : MIR1246 (227243 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	177948167	177948167	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:177948167delT								MIR1246 (482387 upstream) : HNRNPA3 (129255 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	178029384	178029384	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:178029384delA								MIR1246 (563604 upstream) : HNRNPA3 (48038 downstream)																																	OREG0015097	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
AGPS	8540	broad.mit.edu	37	2	178301396	178301396	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-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)															---	---	---	---
AGPS	8540	broad.mit.edu	37	2	178347701	178347701	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:178347701delT	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)															---	---	---	---
AGPS	8540	broad.mit.edu	37	2	178350656	178350656	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:178350656delA	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)															---	---	---	---
PDE11A	50940	broad.mit.edu	37	2	178916417	178916417	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:178916417delA	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				---	---	---	---
OSBPL6	114880	broad.mit.edu	37	2	179215774	179215774	+	Intron	DEL	A	-	-	rs28439459	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:179215774delA	uc002ulx.2	+						OSBPL6_uc002ulw.2_Intron|OSBPL6_uc002uly.2_Intron|OSBPL6_uc010zfe.1_Intron|OSBPL6_uc002ulz.2_Intron|OSBPL6_uc002uma.2_Intron	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)															---	---	---	---
PLEKHA3	65977	broad.mit.edu	37	2	179368841	179368841	+	3'UTR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:179368841delT	uc002umn.2	+	8						NM_019091	NP_061964			pleckstrin homology domain containing, family A							cytoplasm|membrane				ovary(1)|kidney(1)	2			OV - Ovarian serous cystadenocarcinoma(117;0.0112)|Epithelial(96;0.0266)|all cancers(119;0.0865)															---	---	---	---
TTN	7273	broad.mit.edu	37	2	179463795	179463795	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:179463795delA	uc010zfg.1	-						uc002umo.2_Intron|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	179478747	179478747	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:179478747delT	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	179548634	179548634	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:179548634delT	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	179557609	179557609	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:179557609delT	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)															---	---	---	---
SESTD1	91404	broad.mit.edu	37	2	180056424	180056424	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:180056424delA	uc002uni.3	-							NM_178123	NP_835224			SEC14 and spectrin domains 1						regulation of calcium ion transport via voltage-gated calcium channel activity		phosphatidic acid binding|phosphatidylinositol-3,4-bisphosphate binding|phosphatidylinositol-3,5-bisphosphate binding|phosphatidylinositol-3-phosphate binding|phosphatidylinositol-4,5-bisphosphate binding|phosphatidylinositol-4-phosphate binding|phosphatidylinositol-5-phosphate binding|protein binding			ovary(1)	1			OV - Ovarian serous cystadenocarcinoma(117;0.0344)|Epithelial(96;0.0531)|all cancers(119;0.147)															---	---	---	---
Unknown	0	broad.mit.edu	37	2	180300192	180300192	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:180300192delT								SESTD1 (170842 upstream) : ZNF385B (6528 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	180894684	180894684	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:180894684delT								CWC22 (22844 upstream) : UBE2E3 (950428 downstream)																																			---	---	---	---
UBE2E3	10477	broad.mit.edu	37	2	181850679	181850679	+	Intron	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:181850679delC	uc002unq.1	+						UBE2E3_uc002unr.1_Intron|UBE2E3_uc010fri.1_Intron	NM_182678	NP_872619			ubiquitin-conjugating enzyme E2E 3						protein K11-linked ubiquitination|protein K48-linked ubiquitination|protein K63-linked ubiquitination|regulation of growth	cytoplasm|nucleolus	ATP binding|protein binding|ubiquitin-protein ligase activity			ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	182276141	182276142	+	IGR	INS	-	GCT	GCT	rs143371763	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:182276141_182276142insGCT								UBE2E3 (347991 upstream) : ITGA4 (45477 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	182319654	182319654	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:182319654delT								UBE2E3 (391504 upstream) : ITGA4 (1965 downstream)																																			---	---	---	---
CERKL	375298	broad.mit.edu	37	2	182438657	182438657	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:182438657delT	uc002unx.2	-						CERKL_uc002uny.2_Intron|CERKL_uc010zfm.1_Intron|CERKL_uc002unz.2_Intron|CERKL_uc002uoa.2_Intron|CERKL_uc002uob.2_Intron|CERKL_uc002uoc.2_Intron|CERKL_uc010frk.2_Intron|CERKL_uc002uod.1_Intron|CERKL_uc002uoe.2_Intron	NM_001030311	NP_001025482			ceramide kinase-like isoform b						activation of protein kinase C activity by G-protein coupled receptor protein signaling pathway|anti-apoptosis	endoplasmic reticulum|endoplasmic reticulum|Golgi apparatus|Golgi apparatus|nucleolus|nucleolus	diacylglycerol kinase activity			ovary(2)|kidney(1)|skin(1)	4			OV - Ovarian serous cystadenocarcinoma(117;0.088)															---	---	---	---
PDE1A	5136	broad.mit.edu	37	2	183117233	183117246	+	Intron	DEL	CAGAGTAAAGTTTC	-	-	rs36212772		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:183117233_183117246delCAGAGTAAAGTTTC	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)															---	---	---	---
PDE1A	5136	broad.mit.edu	37	2	183327270	183327270	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:183327270delA	uc002uos.2	-						PDE1A_uc010zfp.1_Intron|PDE1A_uc002uoq.1_Intron|PDE1A_uc010zfq.1_Intron|PDE1A_uc002uov.1_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)															---	---	---	---
Unknown	0	broad.mit.edu	37	2	184080862	184080863	+	IGR	INS	-	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:184080862_184080863insT								NUP35 (54455 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	184505756	184505756	+	IGR	DEL	A	-	-	rs76587659		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:184505756delA								NUP35 (479349 upstream) : ZNF804A (957337 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	184812330	184812330	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:184812330delT								NUP35 (785923 upstream) : ZNF804A (650763 downstream)																																			---	---	---	---
ZNF804A	91752	broad.mit.edu	37	2	185500951	185500952	+	Intron	DEL	TT	-	-	rs146807772		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:185500951_185500952delTT	uc002uph.2	+							NM_194250	NP_919226			zinc finger protein 804A							intracellular	zinc ion binding			ovary(6)|skin(3)|large_intestine(1)|pancreas(1)	11																		---	---	---	---
ZNF804A	91752	broad.mit.edu	37	2	185753877	185753877	+	Intron	DEL	T	-	-	rs78978836		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:185753877delT	uc002uph.2	+							NM_194250	NP_919226			zinc finger protein 804A							intracellular	zinc ion binding			ovary(6)|skin(3)|large_intestine(1)|pancreas(1)	11																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	186406970	186406970	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:186406970delA								ZNF804A (602758 upstream) : ZC3H15 (943915 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	187055888	187055891	+	IGR	DEL	AAGG	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:187055888_187055891delAAGG								None (None upstream) : ZC3H15 (294994 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	187159749	187159749	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:187159749delA								None (None upstream) : ZC3H15 (191136 downstream)																																			---	---	---	---
ITGAV	3685	broad.mit.edu	37	2	187488078	187488079	+	Intron	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:187488078_187488079delTT	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)														---	---	---	---
ITGAV	3685	broad.mit.edu	37	2	187532575	187532575	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-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)														---	---	---	---
Unknown	0	broad.mit.edu	37	2	187635293	187635293	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:187635293delA								FAM171B (4609 upstream) : ZSWIM2 (56914 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	187850325	187850325	+	IGR	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:187850325delC								ZSWIM2 (136428 upstream) : CALCRL (357526 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	187883690	187883691	+	IGR	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:187883690_187883691delTT								ZSWIM2 (169793 upstream) : CALCRL (324160 downstream)																																			---	---	---	---
TFPI	7035	broad.mit.edu	37	2	188398347	188398347	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:188398347delA	uc002upy.2	-						TFPI_uc002upz.2_Intron|TFPI_uc002uqa.2_Intron|TFPI_uc002uqb.2_Intron	NM_006287	NP_006278			tissue factor pathway inhibitor isoform a						blood coagulation, extrinsic pathway	extracellular space|plasma membrane	serine-type endopeptidase inhibitor activity			skin(1)	1			OV - Ovarian serous cystadenocarcinoma(117;0.0554)		Coagulation factor VIIa(DB00036)													---	---	---	---
Unknown	0	broad.mit.edu	37	2	190185101	190185102	+	IGR	INS	-	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:190185101_190185102insG								COL5A2 (140496 upstream) : WDR75 (121057 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	190410706	190410706	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:190410706delT								WDR75 (70442 upstream) : SLC40A1 (14612 downstream)																																			---	---	---	---
ANKAR	150709	broad.mit.edu	37	2	190549286	190549287	+	Intron	DEL	AT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:190549286_190549287delAT	uc002uqw.1	+						ANKAR_uc002uqu.2_Intron|ANKAR_uc002uqv.1_Intron	NM_144708	NP_653309			ankyrin and armadillo repeat containing							integral to membrane	binding			ovary(2)|pancreas(1)|skin(1)	4			OV - Ovarian serous cystadenocarcinoma(117;0.00156)|Epithelial(96;0.0256)|all cancers(119;0.0744)															---	---	---	---
PMS1	5378	broad.mit.edu	37	2	190717518	190717518	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:190717518delA	uc002urh.3	+						PMS1_uc010zga.1_Intron|PMS1_uc010zgb.1_Intron|PMS1_uc002urk.3_Intron|PMS1_uc002uri.3_Intron|PMS1_uc010zgc.1_Intron|PMS1_uc010zgd.1_Intron|PMS1_uc002urj.2_Intron|PMS1_uc010fry.1_Intron|PMS1_uc010frz.2_Intron|PMS1_uc002url.2_Intron|PMS1_uc002urm.2_Intron|PMS1_uc002urn.1_5'Flank	NM_000534	NP_000525			postmeiotic segregation 1 isoform a						mismatch repair|reciprocal meiotic recombination	MutLalpha complex	ATP binding|ATPase activity|mismatched DNA binding			ovary(2)|kidney(1)|central_nervous_system(1)	4			OV - Ovarian serous cystadenocarcinoma(117;0.0013)|Epithelial(96;0.0263)|all cancers(119;0.0751)					Mis|N			colorectal|endometrial|ovarian		Direct_reversal_of_damage|MMR					---	---	---	---
HIBCH	26275	broad.mit.edu	37	2	191152424	191152424	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:191152424delA	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)															---	---	---	---
HIBCH	26275	broad.mit.edu	37	2	191182978	191182980	+	Intron	DEL	AAA	-	-	rs11366930		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:191182978_191182980delAAA	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)															---	---	---	---
INPP1	3628	broad.mit.edu	37	2	191231245	191231246	+	Intron	DEL	CT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:191231245_191231246delCT	uc002ury.3	+						INPP1_uc010fsb.2_Intron|INPP1_uc002urx.3_Intron	NM_001128928	NP_001122400			inositol polyphosphate-1-phosphatase						signal transduction		inositol-1,4-bisphosphate 1-phosphatase activity|metal ion binding			ovary(1)|lung(1)	2			OV - Ovarian serous cystadenocarcinoma(117;0.000286)|Epithelial(96;0.0186)|all cancers(119;0.057)		Lithium(DB01356)													---	---	---	---
MFSD6	54842	broad.mit.edu	37	2	191292323	191292323	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:191292323delT	uc002urz.2	+							NM_017694	NP_060164			major facilitator superfamily domain containing						transmembrane transport	integral to membrane				ovary(2)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	191626973	191626973	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:191626973delT								NAB1 (69482 upstream) : GLS (118574 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	192070935	192070935	+	IGR	DEL	C	-	-	rs73056637	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:192070935delC								STAT4 (32033 upstream) : MYO1B (39172 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	192072634	192072634	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:192072634delA								STAT4 (33732 upstream) : MYO1B (37473 downstream)																																			---	---	---	---
SDPR	8436	broad.mit.edu	37	2	192709449	192709449	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:192709449delT	uc002utb.2	-							NM_004657	NP_004648			serum deprivation response protein							caveola|cytosol	phosphatidylserine binding|protein binding			ovary(1)|pancreas(1)	2			OV - Ovarian serous cystadenocarcinoma(117;0.0647)		Phosphatidylserine(DB00144)													---	---	---	---
Unknown	0	broad.mit.edu	37	2	192794194	192794195	+	IGR	INS	-	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:192794194_192794195insT								SDPR (82213 upstream) : TMEFF2 (20554 downstream)																																			---	---	---	---
TMEFF2	23671	broad.mit.edu	37	2	192922645	192922645	+	Intron	DEL	T	-	-	rs79305372		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:192922645delT	uc002utc.2	-							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	193062715	193062715	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:193062715delT								TMEFF2 (3071 upstream) : PCGEM1 (551856 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	193904191	193904191	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:193904191delT								PCGEM1 (262570 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	194640040	194640040	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:194640040delT								PCGEM1 (998419 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	195546762	195546762	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:195546762delA								None (None upstream) : SLC39A10 (974770 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	195816012	195816013	+	IGR	INS	-	T	T	rs7424493		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:195816012_195816013insT								None (None upstream) : SLC39A10 (705519 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	196365273	196365275	+	IGR	DEL	AAA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:196365273_196365275delAAA								None (None upstream) : SLC39A10 (156257 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	196444334	196444336	+	IGR	DEL	AAA	-	-	rs71895650		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:196444334_196444336delAAA								None (None upstream) : SLC39A10 (77196 downstream)																																			---	---	---	---
SLC39A10	57181	broad.mit.edu	37	2	196589805	196589805	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:196589805delA	uc002utg.3	+						SLC39A10_uc002uth.3_Intron|SLC39A10_uc010zgp.1_Intron	NM_001127257	NP_001120729			solute carrier family 39 (zinc transporter),						zinc ion transport	integral to membrane	metal ion transmembrane transporter activity			pancreas(1)|skin(1)	2			OV - Ovarian serous cystadenocarcinoma(117;0.221)															---	---	---	---
DNAH7	56171	broad.mit.edu	37	2	196929912	196929912	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:196929912delT	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																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	196940479	196940479	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:196940479delT								DNAH7 (6943 upstream) : STK17B (57829 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	196940954	196940954	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:196940954delT								DNAH7 (7418 upstream) : STK17B (57354 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	196968602	196968603	+	IGR	INS	-	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:196968602_196968603insT								DNAH7 (35066 upstream) : STK17B (29705 downstream)																																			---	---	---	---
HECW2	57520	broad.mit.edu	37	2	197181221	197181221	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:197181221delT	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																		---	---	---	---
PGAP1	80055	broad.mit.edu	37	2	197725601	197725601	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:197725601delA	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	197999419	197999419	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:197999419delT	uc002uuc.2	-						ANKRD44_uc002uua.1_Intron|ANKRD44_uc002uub.2_Intron|ANKRD44_uc010zgw.1_Intron|ANKRD44_uc002uud.1_3'UTR	NM_153697	NP_710181			ankyrin repeat domain 44								protein binding			ovary(4)|skin(1)	5			OV - Ovarian serous cystadenocarcinoma(117;0.246)															---	---	---	---
HSPD1	3329	broad.mit.edu	37	2	198360212	198360215	+	Intron	DEL	AATT	-	-	rs13432424		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:198360212_198360215delAATT	uc002uui.2	-						HSPD1_uc002uuj.2_Intron|HSPD1_uc010zgx.1_Intron|HSPD1_uc010fsm.2_5'UTR|HSPD1_uc002uuk.2_Intron	NM_002156	NP_002147			chaperonin						'de novo' protein folding|activation of caspase activity|B cell cytokine production|B cell proliferation|chaperone-mediated protein complex assembly|interspecies interaction between organisms|isotype switching to IgG isotypes|MyD88-dependent toll-like receptor signaling pathway|negative regulation of apoptosis|positive regulation of apoptosis|positive regulation of interferon-alpha production|positive regulation of interferon-gamma production|positive regulation of interleukin-10 production|positive regulation of interleukin-12 production|positive regulation of interleukin-6 production|positive regulation of macrophage activation|positive regulation of T cell activation|positive regulation of T cell mediated immune response to tumor cell|protein maturation|protein refolding|protein stabilization|response to unfolded protein|T cell activation	cell surface|coated pit|coated vesicle|cytosol|early endosome|extracellular space|lipopolysaccharide receptor complex|mitochondrial inner membrane|mitochondrial matrix|stored secretory granule	ATP binding|ATPase activity|cell surface binding|chaperone binding|DNA replication origin binding|lipopolysaccharide binding|p53 binding|single-stranded DNA binding				0			Epithelial(96;0.225)															---	---	---	---
HSPE1	3336	broad.mit.edu	37	2	198366972	198366972	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:198366972delT	uc002uul.2	+						HSPD1_uc002uui.2_5'Flank|HSPD1_uc002uuj.2_5'Flank|HSPD1_uc010zgx.1_5'Flank|HSPD1_uc010fsm.2_5'Flank|HSPD1_uc002uuk.2_5'Flank|HSPD1_uc010zgy.1_5'Flank	NM_002157	NP_002148			heat shock 10kDa protein 1						activation of caspase activity|protein folding|response to unfolded protein	mitochondrial matrix	ATP binding|chaperone binding|unfolded protein binding				0			Epithelial(96;0.225)															---	---	---	---
Unknown	0	broad.mit.edu	37	2	198375522	198375522	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:198375522delT								HSPE1 (7336 upstream) : MOBKL3 (4798 downstream)																																			---	---	---	---
RFTN2	130132	broad.mit.edu	37	2	198473692	198473692	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:198473692delT	uc002uuo.3	-							NM_144629	NP_653230			raftlin family member 2							plasma membrane					0																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	199178497	199178497	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:199178497delT	uc002uux.1	-											Homo sapiens cDNA FLJ39180 fis, clone OCBBF2004168.																														---	---	---	---
SATB2	23314	broad.mit.edu	37	2	200151609	200151609	+	Intron	DEL	A	-	-	rs34606797		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:200151609delA	uc002uuy.1	-						SATB2_uc010fsq.1_Intron|SATB2_uc002uuz.1_Intron|SATB2_uc002uva.1_Intron	NM_015265	NP_056080			SATB homeobox 2							cytoplasm|nuclear matrix	sequence-specific DNA binding transcription factor activity			ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	200362526	200362529	+	IGR	DEL	AAAA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:200362526_200362529delAAAA								FLJ32063 (20868 upstream) : C2orf69 (413450 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	200670643	200670646	+	Intron	DEL	AAAA	-	-	rs75544476		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:200670643_200670646delAAAA	uc002uvg.2	-											Homo sapiens hypothetical protein LOC348751, mRNA (cDNA clone IMAGE:5311172).																														---	---	---	---
C2orf60	129450	broad.mit.edu	37	2	200803934	200803935	+	Intron	DEL	TC	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:200803934_200803935delTC	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	200902056	200902057	+	IGR	INS	-	CTG	CTG	rs150312330	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:200902056_200902057insCTG								C2orf47 (73211 upstream) : SPATS2L (268547 downstream)																																			---	---	---	---
AOX1	316	broad.mit.edu	37	2	201495240	201495240	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:201495240delA	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)													---	---	---	---
AOX2P	344454	broad.mit.edu	37	2	201653663	201653663	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:201653663delT	uc002uwa.2	+							NR_001557				Homo sapiens aldehyde oxidase-like protein (AOX2) pseudogene mRNA, partial sequence.												0																		---	---	---	---
CLK1	1195	broad.mit.edu	37	2	201719835	201719835	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:201719835delA	uc002uwe.2	-						CLK1_uc002uwd.2_Intron|CLK1_uc010zhi.1_Intron|CLK1_uc002uwf.2_Intron|CLK1_uc002uwg.2_Intron|CLK1_uc010fsv.2_Intron	NM_004071	NP_004062			CDC-like kinase 1 isoform 1						cell proliferation	nucleus	ATP binding|non-membrane spanning protein tyrosine kinase activity|protein serine/threonine kinase activity			pancreas(2)	2																		---	---	---	---
CLK1	1195	broad.mit.edu	37	2	201724708	201724708	+	Intron	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:201724708delC	uc002uwe.2	-						CLK1_uc002uwd.2_5'Flank|CLK1_uc010zhi.1_Intron|CLK1_uc002uwf.2_Intron|CLK1_uc002uwg.2_5'UTR|CLK1_uc010fsv.2_Intron	NM_004071	NP_004062			CDC-like kinase 1 isoform 1						cell proliferation	nucleus	ATP binding|non-membrane spanning protein tyrosine kinase activity|protein serine/threonine kinase activity			pancreas(2)	2																		---	---	---	---
NIF3L1	60491	broad.mit.edu	37	2	201762893	201762894	+	Intron	DEL	AT	-	-	rs143380182	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:201762893_201762894delAT	uc002uwm.2	+						NIF3L1_uc002uwl.2_Intron|NIF3L1_uc002uwn.2_Intron|NIF3L1_uc002uwo.2_Intron|NIF3L1_uc002uwp.2_Intron|NIF3L1_uc002uwq.2_Intron	NM_001136039	NP_001129511			NIF3 NGG1 interacting factor 3-like 1 isoform 1						positive regulation of transcription, DNA-dependent		transcription factor binding			skin(1)	1																		---	---	---	---
NIF3L1	60491	broad.mit.edu	37	2	201763866	201763866	+	Intron	DEL	A	-	-	rs7588993	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:201763866delA	uc002uwm.2	+						NIF3L1_uc002uwl.2_Intron|NIF3L1_uc002uwn.2_Intron|NIF3L1_uc002uwo.2_Intron|NIF3L1_uc002uwp.2_Intron|NIF3L1_uc002uwq.2_Intron	NM_001136039	NP_001129511			NIF3 NGG1 interacting factor 3-like 1 isoform 1						positive regulation of transcription, DNA-dependent		transcription factor binding			skin(1)	1																		---	---	---	---
FAM126B	285172	broad.mit.edu	37	2	201870854	201870858	+	Intron	DEL	TTTTT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:201870854_201870858delTTTTT	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	202149799	202149799	+	Frame_Shift_Del	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:202149799delT	uc002uxr.1	+	9	1272	c.1063delT	c.(1063-1065)TTTfs	p.F355fs	CASP8_uc002uxp.1_Frame_Shift_Del_p.F372fs|CASP8_uc002uxq.1_Frame_Shift_Del_p.F340fs|CASP8_uc002uxt.1_Frame_Shift_Del_p.F414fs|CASP8_uc002uxu.1_RNA|CASP8_uc002uxw.1_Frame_Shift_Del_p.F340fs|CASP8_uc002uxy.1_Intron|CASP8_uc002uxx.1_Intron|CASP8_uc010ftf.2_Frame_Shift_Del_p.F271fs	NM_033355	NP_203519	Q14790	CASP8_HUMAN	caspase 8 isoform B precursor	355					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	p.S355F(1)		upper_aerodigestive_tract(2)|ovary(1)|breast(1)|skin(1)	5															HNSCC(4;0.00038)			---	---	---	---
TRAK2	66008	broad.mit.edu	37	2	202286967	202286967	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:202286967delA	uc002uyb.3	-						TRAK2_uc002uyc.2_Intron	NM_015049	NP_055864			trafficking protein, kinesin binding 2							early endosome|plasma membrane	GABA receptor binding				0																		---	---	---	---
CDK15	65061	broad.mit.edu	37	2	202672518	202672518	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-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	202844189	202844191	+	IGR	DEL	TTT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:202844189_202844191delTTT								CDK15 (85926 upstream) : FZD7 (55119 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	202880842	202880842	+	IGR	DEL	T	-	-	rs74747871	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:202880842delT								CDK15 (122579 upstream) : FZD7 (18468 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	202906378	202906378	+	IGR	DEL	A	-	-	rs113436236		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:202906378delA								FZD7 (3218 upstream) : SUMO1 (164525 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	203054933	203054933	+	Frame_Shift_Del	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:203054933delA	uc002uyy.1	+	7	3413	c.752delA	c.(751-753)GAAfs	p.E251fs						RecName: Full=Uncharacterized protein KIAA2012;																														---	---	---	---
NOP58	51602	broad.mit.edu	37	2	203152304	203152304	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:203152304delA	uc002uzb.2	+							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																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	203189176	203189176	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:203189176delT								NOP58 (20794 upstream) : BMPR2 (51874 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	203441417	203441417	+	IGR	DEL	T	-	-	rs143388709		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:203441417delT								BMPR2 (8944 upstream) : FAM117B (58484 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	203479083	203479083	+	IGR	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:203479083delC								BMPR2 (46610 upstream) : FAM117B (20818 downstream)																																			---	---	---	---
NBEAL1	65065	broad.mit.edu	37	2	203969591	203969591	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:203969591delT	uc002uzt.3	+							NM_001114132	NP_001107604			neurobeachin-like 1 isoform 3								binding			ovary(1)|skin(1)	2																		---	---	---	---
CYP20A1	57404	broad.mit.edu	37	2	204144676	204144676	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-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	204174686	204174689	+	IGR	DEL	CTGT	-	-	rs10541244		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:204174686_204174689delCTGT								CYP20A1 (4124 upstream) : ABI2 (18314 downstream)																																			---	---	---	---
ABI2	10152	broad.mit.edu	37	2	204270273	204270274	+	Intron	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:204270273_204270274delAA	uc002vaa.2	+						ABI2_uc002uzz.2_Intron|ABI2_uc010zih.1_Intron|ABI2_uc010zii.1_Intron|ABI2_uc010zij.1_Intron|ABI2_uc002vab.2_Intron|ABI2_uc010zik.1_Intron|ABI2_uc010zil.1_Intron|ABI2_uc010zim.1_Intron|ABI2_uc002vac.2_Intron|ABI2_uc010zin.1_Intron	NM_005759	NP_005750			abl interactor 2						actin polymerization or depolymerization|cell migration|peptidyl-tyrosine phosphorylation	cytoskeleton|cytosol|filopodium|lamellipodium	cytoskeletal adaptor activity|DNA binding|kinase binding|proline-rich region binding|SH3 domain binding|ubiquitin protein ligase binding				0																		---	---	---	---
ABI2	10152	broad.mit.edu	37	2	204291747	204291747	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:204291747delA	uc002vaa.2	+						ABI2_uc002uzz.2_Intron|ABI2_uc010zih.1_Intron|ABI2_uc010zii.1_Intron|ABI2_uc010zij.1_Intron|ABI2_uc002vab.2_Intron|ABI2_uc010zik.1_Intron|ABI2_uc010zil.1_Intron|ABI2_uc010zim.1_Intron|ABI2_uc002vac.2_Intron|ABI2_uc010zin.1_Intron	NM_005759	NP_005750			abl interactor 2						actin polymerization or depolymerization|cell migration|peptidyl-tyrosine phosphorylation	cytoskeleton|cytosol|filopodium|lamellipodium	cytoskeletal adaptor activity|DNA binding|kinase binding|proline-rich region binding|SH3 domain binding|ubiquitin protein ligase binding				0																		---	---	---	---
RAPH1	65059	broad.mit.edu	37	2	204323494	204323495	+	Intron	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:204323494_204323495delTT	uc002vad.2	-						RAPH1_uc002vae.2_Intron|RAPH1_uc002vaf.2_Intron	NM_213589	NP_998754			Ras association and pleckstrin homology domains						cell-matrix adhesion|signal transduction	cytoplasm|cytoskeleton|filopodium|lamellipodium|nucleus|plasma membrane				ovary(3)|breast(3)|central_nervous_system(2)|lung(1)|skin(1)	10																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	204749857	204749857	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:204749857delT								CTLA4 (11174 upstream) : ICOS (51614 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	205319685	205319685	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:205319685delT								ICOS (493389 upstream) : PARD3B (90831 downstream)																																			---	---	---	---
PARD3B	117583	broad.mit.edu	37	2	205573868	205573868	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:205573868delA	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	205629438	205629439	+	Intron	INS	-	GT	GT	rs143519227	by1000genomes;byFrequency	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:205629438_205629439insGT	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	205872584	205872584	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:205872584delT	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	206047115	206047115	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:206047115delA	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	206549287	206549287	+	Intron	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:206549287delC	uc002vaw.2	+						NRP2_uc002vat.2_Intron|NRP2_uc002vau.2_Intron|NRP2_uc002vav.2_Intron|NRP2_uc002vax.2_Intron|NRP2_uc002vay.2_Intron|NRP2_uc010fud.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																		---	---	---	---
NRP2	8828	broad.mit.edu	37	2	206640179	206640180	+	Intron	INS	-	CA	CA			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:206640179_206640180insCA	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																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	206759148	206759148	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:206759148delA								NRP2 (96292 upstream) : INO80D (99298 downstream)																																			---	---	---	---
INO80D	54891	broad.mit.edu	37	2	206935439	206935439	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:206935439delA	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																		---	---	---	---
ADAM23	8745	broad.mit.edu	37	2	207314156	207314156	+	Intron	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:207314156delC	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	207594064	207594064	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:207594064delA								DYTN (10944 upstream) : MDH1B (4879 downstream)																																			---	---	---	---
MDH1B	130752	broad.mit.edu	37	2	207604137	207604137	+	Intron	DEL	A	-	-	rs141240854		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:207604137delA	uc002vbs.2	-						MDH1B_uc010ziw.1_Intron|MDH1B_uc010fui.2_Intron|MDH1B_uc010fuj.2_Intron|MDH1B_uc002vbt.2_Intron	NM_001039845	NP_001034934			malate dehydrogenase 1B, NAD (soluble)						carbohydrate metabolic process|malate metabolic process|tricarboxylic acid cycle		binding|malate dehydrogenase activity			ovary(3)|kidney(1)	4				LUSC - Lung squamous cell carcinoma(261;0.0763)|Epithelial(149;0.131)|Lung(261;0.145)														---	---	---	---
Unknown	0	broad.mit.edu	37	2	207794287	207794288	+	IGR	INS	-	A	A	rs77784553		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:207794287_207794288insA								FASTKD2 (133378 upstream) : CPO (9990 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	208356808	208356808	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:208356808delA								MIR1302-4 (222660 upstream) : CREB1 (37808 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	208678959	208678959	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:208678959delT								FZD5 (44816 upstream) : PLEKHM3 (7053 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	208896716	208896718	+	IGR	DEL	TTT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:208896716_208896718delTTT								PLEKHM3 (6432 upstream) : CRYGD (89614 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	208921915	208921915	+	IGR	DEL	T	-	-	rs74577733	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:208921915delT								PLEKHM3 (31631 upstream) : CRYGD (64417 downstream)																																			---	---	---	---
IDH1	3417	broad.mit.edu	37	2	209115979	209115979	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:209115979delT	uc002vcs.2	-						IDH1_uc002vct.2_Intron|IDH1_uc002vcu.2_Intron	NM_005896	NP_005887			isocitrate dehydrogenase 1 (NADP+), soluble						2-oxoglutarate metabolic process|cellular lipid metabolic process|glyoxylate cycle|isocitrate metabolic process|NADPH regeneration|tricarboxylic acid cycle	cytosol|peroxisomal matrix	isocitrate dehydrogenase (NADP+) activity|magnesium ion binding|NAD binding|protein homodimerization activity			central_nervous_system(2156)|haematopoietic_and_lymphoid_tissue(606)|bone(74)|thyroid(22)|large_intestine(4)|skin(2)|prostate(2)|autonomic_ganglia(1)|soft_tissue(1)	2868				Epithelial(149;0.0322)|LUSC - Lung squamous cell carcinoma(261;0.0711)|Lung(261;0.136)				Mis		gliobastoma 								---	---	---	---
PTH2R	5746	broad.mit.edu	37	2	209562829	209562829	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:209562829delT	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)														---	---	---	---
PTH2R	5746	broad.mit.edu	37	2	209568155	209568155	+	Intron	DEL	T	-	-	rs111865618		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:209568155delT	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)														---	---	---	---
Unknown	0	broad.mit.edu	37	2	210085057	210085058	+	IGR	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:210085057_210085058delAA								PTH2R (380239 upstream) : MAP2 (203713 downstream)																																			---	---	---	---
MAP2	4133	broad.mit.edu	37	2	210366519	210366519	+	Intron	DEL	A	-	-	rs34779878		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:210366519delA	uc002vdc.1	+						MAP2_uc002vdd.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)													---	---	---	---
UNC80	285175	broad.mit.edu	37	2	210736697	210736698	+	Intron	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:210736697_210736698delAA	uc010zjc.1	+						UNC80_uc002vdk.2_Intron	NM_032504	NP_115893			chromosome 2 open reading frame 21 isoform 1							integral to membrane					0																		---	---	---	---
LANCL1	10314	broad.mit.edu	37	2	211302382	211302382	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:211302382delA	uc010zjh.1	-						LANCL1_uc002ved.2_Intron|LANCL1_uc010fuq.2_Intron	NM_001136574	NP_001130046			lanthionine synthetase C-like protein 1							cytoplasm|integral to plasma membrane|microtubule cytoskeleton|nucleus	catalytic activity|G-protein coupled receptor activity|glutathione binding|low-density lipoprotein particle receptor binding|SH3 domain binding|zinc ion binding				0				Epithelial(149;0.00562)|Lung(261;0.0468)|LUSC - Lung squamous cell carcinoma(261;0.0495)|all cancers(144;0.0569)														---	---	---	---
CPS1	1373	broad.mit.edu	37	2	211368748	211368748	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:211368748delT	uc010fur.2	+							NM_001122633	NP_001116105			carbamoyl-phosphate synthetase 1 isoform a						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)														---	---	---	---
CPS1	1373	broad.mit.edu	37	2	211390531	211390532	+	Intron	DEL	GA	-	-	rs67754546		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:211390531_211390532delGA	uc010fur.2	+							NM_001122633	NP_001116105			carbamoyl-phosphate synthetase 1 isoform a						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)														---	---	---	---
CPS1	1373	broad.mit.edu	37	2	211463265	211463265	+	Intron	DEL	A	-	-	rs71395589		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:211463265delA	uc002vee.3	+						CPS1_uc010fur.2_Intron|CPS1_uc010fus.2_Intron	NM_001875	NP_001866			carbamoyl-phosphate synthetase 1 isoform b						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	212361264	212361267	+	Intron	DEL	AAAA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:212361264_212361267delAAAA	uc002veg.1	-						ERBB4_uc002veh.1_Intron|ERBB4_uc010zji.1_Intron|ERBB4_uc010zjj.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)			---	---	---	---
ERBB4	2066	broad.mit.edu	37	2	212443918	212443919	+	Intron	INS	-	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:212443918_212443919insA	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)			---	---	---	---
ERBB4	2066	broad.mit.edu	37	2	213096018	213096018	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:213096018delA	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	213519403	213519404	+	IGR	DEL	AC	-	-	rs111903562		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:213519403_213519404delAC								ERBB4 (116051 upstream) : IKZF2 (345009 downstream)																																			---	---	---	---
SPAG16	79582	broad.mit.edu	37	2	214934805	214934805	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:214934805delT	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)														---	---	---	---
BARD1	580	broad.mit.edu	37	2	215670492	215670493	+	Intron	DEL	AA	-	-	rs113953659		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:215670492_215670493delAA	uc002veu.2	-						BARD1_uc010zjm.1_Intron	NM_000465	NP_000456			BRCA1 associated RING domain 1						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	215819844	215819844	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:215819844delT	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	215866486	215866486	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-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)														---	---	---	---
Unknown	0	broad.mit.edu	37	2	216106918	216106919	+	IGR	INS	-	T	T	rs143081257	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:216106918_216106919insT								ABCA12 (103767 upstream) : ATIC (69773 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	216161829	216161830	+	IGR	DEL	AA	-	-	rs67495145		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:216161829_216161830delAA								ABCA12 (158678 upstream) : ATIC (14862 downstream)																																			---	---	---	---
FN1	2335	broad.mit.edu	37	2	216226406	216226406	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:216226406delA	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	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	216308923	216308923	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:216308923delT								FN1 (8132 upstream) : MREG (498392 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	216561935	216561936	+	Intron	INS	-	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:216561935_216561936insT	uc002vfm.1	-						uc002vfn.1_Intron					Homo sapiens cDNA FLJ34546 fis, clone HLUNG2008959.																														---	---	---	---
PECR	55825	broad.mit.edu	37	2	216884749	216884749	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:216884749delA	uc010zjq.1	-											Synthetic construct DNA, clone: pF1KB6394, Homo sapiens PECR gene for peroxisomal trans-2-enoyl-CoA reductase, without stop codon, in Flexi system.						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)													---	---	---	---
Unknown	0	broad.mit.edu	37	2	217258489	217258490	+	IGR	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:217258489_217258490delAA								MARCH4 (21739 upstream) : SMARCAL1 (18647 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	217669179	217669181	+	IGR	DEL	AGG	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:217669179_217669181delAGG								IGFBP5 (108907 upstream) : TNP1 (55003 downstream)																																			---	---	---	---
DIRC3	729582	broad.mit.edu	37	2	218495299	218495299	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:218495299delT	uc002vgo.2	-							NR_026597				Homo sapiens cDNA FLJ14199 fis, clone NT2RP3002713.												0																		---	---	---	---
DIRC3	729582	broad.mit.edu	37	2	218548372	218548373	+	Intron	DEL	TG	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:218548372_218548373delTG	uc002vgo.2	-							NR_026597				Homo sapiens cDNA FLJ14199 fis, clone NT2RP3002713.												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	218642624	218642624	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:218642624delA								DIRC3 (21308 upstream) : TNS1 (21888 downstream)																																			---	---	---	---
TNS1	7145	broad.mit.edu	37	2	218844252	218844255	+	Intron	DEL	ACAC	-	-	rs72360012		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:218844252_218844255delACAC	uc010fvk.1	-						TNS1_uc002vgv.1_5'Flank	NM_022648	NP_072174			tensin							cytoplasm|cytoskeleton|focal adhesion	actin binding			ovary(3)|breast(1)	4		Renal(207;0.0483)|Lung NSC(271;0.213)		Epithelial(149;4.43e-06)|all cancers(144;0.000653)|LUSC - Lung squamous cell carcinoma(224;0.0091)|Lung(261;0.013)														---	---	---	---
USP37	57695	broad.mit.edu	37	2	219372919	219372920	+	Intron	DEL	TG	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:219372919_219372920delTG	uc002vie.2	-						USP37_uc010fvs.1_Intron|USP37_uc010zkf.1_Intron|USP37_uc002vif.2_Intron|USP37_uc002vig.2_Intron	NM_020935	NP_065986			ubiquitin specific peptidase 37						ubiquitin-dependent protein catabolic process	nucleus	cysteine-type peptidase activity|ubiquitin thiolesterase activity			skin(3)|ovary(1)|prostate(1)	5		Renal(207;0.0915)		Epithelial(149;1.08e-06)|all cancers(144;0.000197)|LUSC - Lung squamous cell carcinoma(224;0.00375)|Lung(261;0.00487)														---	---	---	---
STK36	27148	broad.mit.edu	37	2	219564651	219564652	+	Intron	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:219564651_219564652delTT	uc002viu.2	+						STK36_uc002viv.2_Intron|STK36_uc002viw.2_Intron|STK36_uc002vix.2_Intron	NM_015690	NP_056505			serine/threonine kinase 36						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)														---	---	---	---
TTLL4	9654	broad.mit.edu	37	2	219616611	219616611	+	Intron	DEL	T	-	-	rs72405125		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:219616611delT	uc002viy.2	+						TTLL4_uc010zkl.1_Intron|TTLL4_uc010fvx.2_Intron|TTLL4_uc010zkm.1_Intron	NM_014640	NP_055455			tubulin tyrosine ligase-like family, member 4						protein polyglutamylation	cilium|microtubule basal body	ATP binding|tubulin binding|tubulin-tyrosine ligase activity			ovary(2)|skin(1)	3		Renal(207;0.0915)		Epithelial(149;5.03e-07)|all cancers(144;0.000106)|LUSC - Lung squamous cell carcinoma(224;0.00829)|Lung(261;0.0101)														---	---	---	---
Unknown	0	broad.mit.edu	37	2	219829889	219829893	+	IGR	DEL	AAAAA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:219829889_219829893delAAAAA								CDK5R2 (3013 upstream) : LOC151300 (11113 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	221214984	221214984	+	IGR	DEL	A	-	-	rs111408733		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:221214984delA								SLC4A3 (708283 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	221448781	221448781	+	IGR	DEL	T	-	-	rs111294314		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:221448781delT								SLC4A3 (942080 upstream) : EPHA4 (833968 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	221572103	221572104	+	IGR	INS	-	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:221572103_221572104insA								None (None upstream) : EPHA4 (710645 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	221789004	221789005	+	IGR	DEL	AA	-	-	rs111950361		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:221789004_221789005delAA								None (None upstream) : EPHA4 (493744 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	221902587	221902587	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:221902587delA								None (None upstream) : EPHA4 (380162 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	222028125	222028125	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:222028125delT								None (None upstream) : EPHA4 (254624 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	222030993	222030993	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:222030993delT								None (None upstream) : EPHA4 (251756 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	222171042	222171042	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:222171042delT								None (None upstream) : EPHA4 (111707 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	222228177	222228177	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:222228177delT								None (None upstream) : EPHA4 (54572 downstream)																																			---	---	---	---
EPHA4	2043	broad.mit.edu	37	2	222427639	222427639	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:222427639delA	uc002vmq.2	-						EPHA4_uc002vmr.2_Intron|EPHA4_uc010zlm.1_Intron|EPHA4_uc010zln.1_Intron	NM_004438	NP_004429			ephrin receptor EphA4 precursor							integral to plasma membrane	ATP binding|ephrin receptor activity			lung(6)|large_intestine(2)|central_nervous_system(2)|urinary_tract(1)|skin(1)	12		Renal(207;0.0183)		Epithelial(121;5.38e-09)|all cancers(144;2.47e-06)|LUSC - Lung squamous cell carcinoma(224;0.0115)|Lung(261;0.0154)														---	---	---	---
Unknown	0	broad.mit.edu	37	2	222812625	222812625	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:222812625delA								EPHA4 (373703 upstream) : PAX3 (251982 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	222997642	222997643	+	IGR	INS	-	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:222997642_222997643insA								EPHA4 (558720 upstream) : PAX3 (66964 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	223061449	223061452	+	IGR	DEL	TCTC	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:223061449_223061452delTCTC								EPHA4 (622527 upstream) : PAX3 (3155 downstream)																																			---	---	---	---
PAX3	5077	broad.mit.edu	37	2	223155646	223155647	+	Intron	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:223155646_223155647delAA	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						---	---	---	---
PAX3	5077	broad.mit.edu	37	2	223159091	223159091	+	Intron	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:223159091delC	uc010fwo.2	-						PAX3_uc002vmt.1_Intron|PAX3_uc002vmy.1_Intron|PAX3_uc002vmv.1_Intron|PAX3_uc002vmw.1_Intron|PAX3_uc002vmx.1_Intron|PAX3_uc002vmz.1_Intron|PAX3_uc002vna.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						---	---	---	---
Unknown	0	broad.mit.edu	37	2	223615605	223615605	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:223615605delT								MOGAT1 (40956 upstream) : ACSL3 (110127 downstream)																																			---	---	---	---
KCNE4	23704	broad.mit.edu	37	2	223918634	223918634	+	3'UTR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:223918634delA	uc002vnl.3	+	2						NM_080671	NP_542402			potassium voltage-gated channel, Isk-related							integral to membrane	voltage-gated potassium channel activity			ovary(1)	1		Renal(207;0.0183)|Lung NSC(271;0.137)|all_lung(227;0.175)		Epithelial(121;4.48e-11)|all cancers(144;2.88e-08)|Lung(261;0.00688)|LUSC - Lung squamous cell carcinoma(224;0.008)														---	---	---	---
AP1S3	130340	broad.mit.edu	37	2	224663146	224663146	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:224663146delA	uc010fwx.1	-						AP1S3_uc002vnn.2_Intron|AP1S3_uc010fww.2_Intron|AP1S3_uc002vno.2_Intron	NM_001039569	NP_001034658			adaptor-related protein complex 1, sigma 3						endocytosis|intracellular protein transport|post-Golgi vesicle-mediated transport|regulation of defense response to virus by virus|viral reproduction	coated pit|cytoplasmic vesicle membrane|cytosol|Golgi membrane|lysosomal membrane|membrane coat	protein transporter activity				0		Renal(207;0.0112)|Lung NSC(271;0.0186)|all_lung(227;0.0272)		Epithelial(121;7.6e-10)|all cancers(144;3.62e-07)|Lung(261;0.0086)|LUSC - Lung squamous cell carcinoma(224;0.00902)														---	---	---	---
WDFY1	57590	broad.mit.edu	37	2	224742023	224742023	+	3'UTR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:224742023delT	uc002vnq.2	-	12						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)														---	---	---	---
WDFY1	57590	broad.mit.edu	37	2	224763643	224763643	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:224763643delA	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)														---	---	---	---
SERPINE2	5270	broad.mit.edu	37	2	224856138	224856138	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:224856138delA	uc002vnu.2	-						SERPINE2_uc002vnt.2_Intron|SERPINE2_uc010zlr.1_Intron|SERPINE2_uc002vnv.2_Intron	NM_006216	NP_006207			plasminogen activator inhibitor type 1, member 2						negative regulation of blood coagulation|negative regulation of plasminogen activation|negative regulation of platelet aggregation|positive regulation of astrocyte differentiation|regulation of cell migration	cytosol|extracellular matrix|extracellular space|extrinsic to external side of plasma membrane|neuromuscular junction|platelet alpha granule	heparin binding|receptor binding|serine-type endopeptidase inhibitor activity			breast(2)|ovary(1)|central_nervous_system(1)	4		Renal(207;0.025)|all_lung(227;0.0586)|Lung NSC(271;0.0682)|all_hematologic(139;0.0797)		Epithelial(121;5.68e-10)|all cancers(144;1.9e-07)|Lung(261;0.0088)|LUSC - Lung squamous cell carcinoma(224;0.00902)														---	---	---	---
CUL3	8452	broad.mit.edu	37	2	225386151	225386153	+	Intron	DEL	TTT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:225386151_225386153delTTT	uc002vny.2	-						CUL3_uc010zls.1_Intron|CUL3_uc010fwy.1_Intron	NM_003590	NP_003581			cullin 3						cell cycle arrest|cell migration|cyclin catabolic process|cytokinesis|G1/S transition of mitotic cell cycle|induction of apoptosis by intracellular signals|mitotic anaphase|negative regulation of Rho protein signal transduction|positive regulation of cell proliferation|protein ubiquitination|stress fiber assembly	Cul3-RING ubiquitin ligase complex|Golgi apparatus|nucleus|polar microtubule	ubiquitin protein ligase binding			upper_aerodigestive_tract(1)|ovary(1)|liver(1)|kidney(1)	4		all_lung(227;0.00877)|Lung NSC(271;0.011)|Renal(207;0.0112)|all_hematologic(139;0.138)		Epithelial(121;1.58e-11)|all cancers(144;1.43e-08)|Lung(261;0.00863)|LUSC - Lung squamous cell carcinoma(224;0.00902)														---	---	---	---
Unknown	0	broad.mit.edu	37	2	225462796	225462796	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:225462796delT								CUL3 (12686 upstream) : DOCK10 (167011 downstream)																																			---	---	---	---
DOCK10	55619	broad.mit.edu	37	2	225652810	225652810	+	Intron	DEL	A	-	-	rs35501042		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:225652810delA	uc010fwz.1	-						DOCK10_uc002vob.2_Intron|DOCK10_uc002voa.2_Intron|DOCK10_uc002voc.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	226002636	226002637	+	IGR	INS	-	AGA	AGA			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:226002636_226002637insAGA								DOCK10 (95306 upstream) : KIAA1486 (262965 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	226014895	226014895	+	IGR	DEL	T	-	-	rs11348430		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:226014895delT								DOCK10 (107565 upstream) : KIAA1486 (250707 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	226894832	226894834	+	IGR	DEL	ATT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:226894832_226894834delATT								KIAA1486 (299361 upstream) : IRS1 (701200 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	227311423	227311424	+	IGR	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:227311423_227311424delAA								KIAA1486 (715952 upstream) : IRS1 (284610 downstream)																																			---	---	---	---
IRS1	3667	broad.mit.edu	37	2	227623463	227623463	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-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)														---	---	---	---
COL4A3	1285	broad.mit.edu	37	2	228052942	228052942	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:228052942delA	uc002vom.1	+						COL4A3_uc002von.1_Intron|COL4A3_uc002voo.1_Intron|COL4A3_uc002vop.1_Intron	NM_000091	NP_000082			alpha 3 type IV collagen isoform 1 precursor						activation of caspase activity|axon guidance|blood circulation|cell adhesion|cell proliferation|cell surface receptor linked signaling pathway|glomerular basement membrane development|induction of apoptosis|negative regulation of angiogenesis|negative regulation of cell proliferation|sensory perception of sound	collagen type IV	extracellular matrix structural constituent|integrin binding|metalloendopeptidase inhibitor activity			skin(2)|ovary(1)	3		all_lung(227;0.00101)|Lung NSC(271;0.00278)|Renal(207;0.0112)|Ovarian(221;0.0129)|all_hematologic(139;0.211)|Esophageal squamous(248;0.247)		Epithelial(121;1.17e-46)|all cancers(144;6.87e-42)|Lung(261;0.0137)|LUSC - Lung squamous cell carcinoma(224;0.0187)														---	---	---	---
MFF	56947	broad.mit.edu	37	2	228191501	228191501	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:228191501delT	uc002vos.2	+						MFF_uc002vot.2_Intron|MFF_uc002vou.2_Intron|MFF_uc002vov.2_Intron|MFF_uc002vow.2_Intron|MFF_uc002vox.2_Intron|MFF_uc002voy.2_5'Flank|MFF_uc002voz.2_5'Flank|uc002voq.1_5'Flank|uc002vor.1_5'Flank	NM_020194	NP_064579			mitochondrial fission factor							integral to membrane|mitochondrial outer membrane				large_intestine(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	228270281	228270281	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:228270281delA								TM4SF20 (26259 upstream) : AGFG1 (66607 downstream)																																			---	---	---	---
AGFG1	3267	broad.mit.edu	37	2	228354536	228354536	+	Intron	DEL	T	-	-	rs35139576		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:228354536delT	uc002vpc.2	+						AGFG1_uc002vpd.2_Intron|AGFG1_uc002vpe.2_Intron|AGFG1_uc002vpf.2_Intron	NM_004504	NP_004495			HIV-1 Rev binding protein isoform 2						cell differentiation|mRNA export from nucleus|multicellular organismal development|regulation of ARF GTPase activity|spermatogenesis	cytoplasmic membrane-bounded vesicle|Golgi apparatus|nuclear pore	ARF GTPase activator activity|DNA binding|protein binding|RNA binding|zinc ion binding			skin(2)|ovary(1)|central_nervous_system(1)	4																		---	---	---	---
AGFG1	3267	broad.mit.edu	37	2	228365813	228365813	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:228365813delT	uc002vpc.2	+						AGFG1_uc002vpd.2_Intron|AGFG1_uc002vpe.2_Intron|AGFG1_uc002vpf.2_Intron	NM_004504	NP_004495			HIV-1 Rev binding protein isoform 2						cell differentiation|mRNA export from nucleus|multicellular organismal development|regulation of ARF GTPase activity|spermatogenesis	cytoplasmic membrane-bounded vesicle|Golgi apparatus|nuclear pore	ARF GTPase activator activity|DNA binding|protein binding|RNA binding|zinc ion binding			skin(2)|ovary(1)|central_nervous_system(1)	4																		---	---	---	---
AGFG1	3267	broad.mit.edu	37	2	228412912	228412912	+	Intron	DEL	G	-	-	rs143722091		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:228412912delG	uc002vpc.2	+						AGFG1_uc002vpd.2_Intron|AGFG1_uc002vpe.2_Intron|AGFG1_uc002vpf.2_Intron	NM_004504	NP_004495			HIV-1 Rev binding protein isoform 2						cell differentiation|mRNA export from nucleus|multicellular organismal development|regulation of ARF GTPase activity|spermatogenesis	cytoplasmic membrane-bounded vesicle|Golgi apparatus|nuclear pore	ARF GTPase activator activity|DNA binding|protein binding|RNA binding|zinc ion binding			skin(2)|ovary(1)|central_nervous_system(1)	4																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	228614557	228614558	+	IGR	INS	-	TCCTTCCTTCCTTCCT	TCCTTCCTTCCTTCCT	rs141805638	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:228614557_228614558insTCCTTCCTTCCTTCCT								SLC19A3 (31812 upstream) : CCL20 (64000 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	228614791	228614792	+	IGR	INS	-	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:228614791_228614792insT								SLC19A3 (32046 upstream) : CCL20 (63766 downstream)																																			---	---	---	---
SPHKAP	80309	broad.mit.edu	37	2	228966962	228966962	+	Intron	DEL	T	-	-	rs78894847		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:228966962delT	uc002vpq.2	-						SPHKAP_uc002vpp.2_Intron|SPHKAP_uc010zlx.1_Intron	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	229516484	229516485	+	IGR	INS	-	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:229516484_229516485insA								SPHKAP (470123 upstream) : PID1 (372205 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	230198439	230198439	+	IGR	DEL	T	-	-	rs11301152		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:230198439delT								PID1 (62382 upstream) : DNER (23907 downstream)																																			---	---	---	---
FBXO36	130888	broad.mit.edu	37	2	230871313	230871313	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:230871313delA	uc002vqa.2	+						FBXO36_uc002vqb.2_Intron|FBXO36_uc010fxi.1_Intron|FBXO36_uc002vqc.2_Intron	NM_174899	NP_777559			F-box protein 36											ovary(1)	1		Renal(207;0.0112)|all_lung(227;0.0179)|Lung NSC(271;0.0804)|all_hematologic(139;0.103)|Acute lymphoblastic leukemia(138;0.167)		Epithelial(121;7.56e-14)|all cancers(144;7.74e-11)|Lung(119;0.00488)|LUSC - Lung squamous cell carcinoma(224;0.008)														---	---	---	---
SLC16A14	151473	broad.mit.edu	37	2	230931021	230931021	+	Intron	DEL	A	-	-	rs74867332		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:230931021delA	uc002vqd.1	-						FBXO36_uc010fxi.1_Intron|SLC16A14_uc002vqe.2_Intron|SLC16A14_uc002vqf.2_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)														---	---	---	---
SP100	6672	broad.mit.edu	37	2	231338600	231338601	+	Intron	DEL	AA	-	-	rs78675331		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:231338600_231338601delAA	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	231528724	231528724	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:231528724delA								SP100 (118407 upstream) : CAB39 (48833 downstream)																																			---	---	---	---
CAB39	51719	broad.mit.edu	37	2	231661063	231661063	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:231661063delT	uc002vqx.2	+						CAB39_uc010fxr.2_Intron|CAB39_uc010fxq.2_Intron	NM_016289	NP_057373			calcium binding protein 39						cell cycle arrest|insulin receptor signaling pathway|regulation of fatty acid oxidation	cytosol	kinase binding			central_nervous_system(1)	1		all_lung(227;4.63e-07)|all_hematologic(139;1.83e-06)|Lung NSC(271;2.11e-05)|Acute lymphoblastic leukemia(138;5.51e-05)|Hepatocellular(293;0.0207)|Lung SC(224;0.187)		all cancers(144;1.64e-12)|Epithelial(121;5.29e-11)|LUSC - Lung squamous cell carcinoma(224;0.0154)|Lung(119;0.0177)|COAD - Colon adenocarcinoma(134;0.226)														---	---	---	---
GPR55	9290	broad.mit.edu	37	2	231819438	231819438	+	Intron	DEL	T	-	-	rs111236575	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:231819438delT	uc010fxs.1	-							NM_005683	NP_005674			G protein-coupled receptor 55						activation of phospholipase C activity|bone resorption|negative regulation of osteoclast differentiation|positive regulation of ERK1 and ERK2 cascade|positive regulation of Rho protein signal transduction	integral to plasma membrane	cannabinoid receptor activity			ovary(1)	1		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;1.04e-11)|all cancers(144;4.22e-09)|LUSC - Lung squamous cell carcinoma(224;0.0119)|Lung(119;0.0145)														---	---	---	---
Unknown	0	broad.mit.edu	37	2	231847616	231847616	+	IGR	DEL	A	-	-	rs141383419		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:231847616delA								GPR55 (21925 upstream) : SPATA3 (13223 downstream)																																			---	---	---	---
ARMC9	80210	broad.mit.edu	37	2	232193470	232193471	+	Intron	DEL	AT	-	-	rs34492828		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:232193470_232193471delAT	uc002vrq.3	+						ARMC9_uc002vrp.3_Intron|ARMC9_uc002vrr.1_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)														---	---	---	---
Unknown	0	broad.mit.edu	37	2	232356298	232356298	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:232356298delT								NCL (27093 upstream) : C2orf52 (16839 downstream)																																			---	---	---	---
C2orf52	151477	broad.mit.edu	37	2	232373610	232373617	+	3'UTR	DEL	AAAAAAAA	-	-	rs34321159		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:232373610_232373617delAAAAAAAA	uc002vrx.1	-	3						NR_024079				RecName: Full=Uncharacterized protein C2orf52;												0		Renal(207;0.025)|all_hematologic(139;0.094)|Acute lymphoblastic leukemia(138;0.164)		Epithelial(121;5.72e-11)|LUSC - Lung squamous cell carcinoma(224;0.0115)|Lung(119;0.014)														---	---	---	---
Unknown	0	broad.mit.edu	37	2	232730164	232730164	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:232730164delT								COPS7B (56730 upstream) : MIR1471 (26788 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	232790123	232790123	+	IGR	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:232790123delG								MIR1471 (33115 upstream) : NPPC (12 downstream)																																			---	---	---	---
DIS3L2	129563	broad.mit.edu	37	2	233050382	233050383	+	Intron	INS	-	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:233050382_233050383insA	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)														---	---	---	---
Unknown	0	broad.mit.edu	37	2	233263293	233263293	+	IGR	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:233263293delG								ALPP (15696 upstream) : ALPPL2 (8259 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	233331367	233331367	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:233331367delT								ALPI (6627 upstream) : ECEL1 (13170 downstream)																																			---	---	---	---
EFHD1	80303	broad.mit.edu	37	2	233535150	233535151	+	Intron	INS	-	A	A	rs36101072		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:233535150_233535151insA	uc002vtc.2	+						EFHD1_uc010fyf.2_Intron|EFHD1_uc002vtd.2_Intron	NM_025202	NP_079478			EF-hand domain family, member D1								calcium ion binding|protein binding				0		all_hematologic(139;0.0123)|Acute lymphoblastic leukemia(138;0.0182)|Breast(86;0.0199)|Renal(207;0.025)		Epithelial(121;2.08e-16)|BRCA - Breast invasive adenocarcinoma(100;0.000383)|LUSC - Lung squamous cell carcinoma(224;0.00825)|Lung(119;0.0101)														---	---	---	---
Unknown	0	broad.mit.edu	37	2	233555809	233555816	+	IGR	DEL	TTTTTTTT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:233555809_233555816delTTTTTTTT								EFHD1 (8319 upstream) : GIGYF2 (6199 downstream)																																			---	---	---	---
GIGYF2	26058	broad.mit.edu	37	2	233633543	233633543	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:233633543delT	uc002vti.3	+						GIGYF2_uc010zmj.1_Intron|GIGYF2_uc002vtg.2_Intron|GIGYF2_uc002vtj.3_Intron|GIGYF2_uc002vtk.3_Intron|GIGYF2_uc002vth.3_Intron|GIGYF2_uc010zmk.1_Intron|GIGYF2_uc010zml.1_Intron|KCNJ13_uc002vtn.2_Intron|KCNJ13_uc002vto.2_Intron|KCNJ13_uc002vtp.2_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)														---	---	---	---
INPP5D	3635	broad.mit.edu	37	2	233943850	233943850	+	Intron	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:233943850delG	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)														---	---	---	---
INPP5D	3635	broad.mit.edu	37	2	234097218	234097218	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:234097218delT	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	234215899	234215899	+	5'Flank	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:234215899delA	uc002vuh.2	+						SAG_uc002vug.2_5'Flank|SAG_uc010zmq.1_5'Flank	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	234270444	234270444	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:234270444delT	uc002vui.1	+							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	234342027	234342027	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:234342027delA	uc002vui.1	+						DGKD_uc002vuj.1_Intron|DGKD_uc010fyh.1_Intron|DGKD_uc002vuk.1_5'Flank	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	234512065	234512065	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:234512065delT								USP40 (36637 upstream) : UGT1A8 (14226 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	234700962	234700962	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:234700962delT								UGT1A10 (19013 upstream) : HJURP (44525 downstream)																																			---	---	---	---
SPP2	6694	broad.mit.edu	37	2	234975061	234975061	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:234975061delA	uc002vvk.1	+						SPP2_uc010fyl.1_Intron	NM_006944	NP_008875			secreted phosphoprotein 2, 24kDa precursor						bone remodeling|skeletal system development	extracellular region	endopeptidase inhibitor activity				0		Breast(86;0.0109)|Renal(207;0.019)|all_lung(227;0.13)|all_hematologic(139;0.182)		Epithelial(121;5.73e-18)|BRCA - Breast invasive adenocarcinoma(100;0.000166)|Lung(119;0.00539)|LUSC - Lung squamous cell carcinoma(224;0.00846)														---	---	---	---
Unknown	0	broad.mit.edu	37	2	235271750	235271750	+	IGR	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:235271750delC								SPP2 (285974 upstream) : ARL4C (129938 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	235379115	235379115	+	IGR	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:235379115delC								SPP2 (393339 upstream) : ARL4C (22573 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	235430259	235430259	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:235430259delA								ARL4C (24566 upstream) : SH3BP4 (430369 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	235437109	235437109	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:235437109delT								ARL4C (31416 upstream) : SH3BP4 (423519 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	235840729	235840732	+	IGR	DEL	TGTT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:235840729_235840732delTGTT								ARL4C (435036 upstream) : SH3BP4 (19896 downstream)																																			---	---	---	---
AGAP1	116987	broad.mit.edu	37	2	236524075	236524075	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:236524075delT	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	236649867	236649868	+	Intron	INS	-	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:236649867_236649868insT	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	236681616	236681617	+	Intron	DEL	TG	-	-	rs72371484		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:236681616_236681617delTG	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	236691887	236691888	+	Intron	INS	-	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:236691887_236691888insA	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	237059718	237059721	+	IGR	DEL	TTTT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:237059718_237059721delTTTT								AGAP1 (25604 upstream) : GBX2 (14586 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	237084179	237084179	+	IGR	DEL	T	-	-	rs71875214		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:237084179delT								GBX2 (7527 upstream) : ASB18 (19337 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	237091779	237091779	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:237091779delT								GBX2 (15127 upstream) : ASB18 (11737 downstream)																																			---	---	---	---
ASB18	401036	broad.mit.edu	37	2	237146644	237146646	+	Intron	DEL	GTG	-	-	rs72060634		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:237146644_237146646delGTG	uc010znh.1	-						ASB18_uc010fyp.1_Intron	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	237209221	237209222	+	IGR	INS	-	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:237209221_237209222insT								ASB18 (36233 upstream) : IQCA1 (23572 downstream)																																			---	---	---	---
IQCA1	79781	broad.mit.edu	37	2	237256499	237256500	+	Intron	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:237256499_237256500delAA	uc002vvz.1	-						IQCA1_uc002vwb.2_Intron|IQCA1_uc002vwa.1_Intron|IQCA1_uc010zni.1_Intron	NM_024726	NP_079002			IQ motif containing with AAA domain 1								ATP binding			ovary(1)	1																		---	---	---	---
IQCA1	79781	broad.mit.edu	37	2	237396152	237396152	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:237396152delA	uc002vvz.1	-						IQCA1_uc002vwb.2_Intron|IQCA1_uc002vwa.1_Intron|IQCA1_uc010zni.1_Intron	NM_024726	NP_079002			IQ motif containing with AAA domain 1								ATP binding			ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	238101197	238101197	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:238101197delA								COPS8 (93710 upstream) : COL6A3 (131458 downstream)																																			---	---	---	---
COL6A3	1293	broad.mit.edu	37	2	238241981	238241982	+	Intron	INS	-	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:238241981_238241982insC	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)														---	---	---	---
Unknown	0	broad.mit.edu	37	2	238362249	238362250	+	IGR	DEL	TC	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:238362249_238362250delTC								COL6A3 (39399 upstream) : MLPH (32803 downstream)																																			---	---	---	---
MLPH	79083	broad.mit.edu	37	2	238459935	238459935	+	Intron	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:238459935delG	uc002vwt.2	+						MLPH_uc002vws.2_Intron|MLPH_uc002vwu.2_Intron|MLPH_uc002vwv.2_Intron|MLPH_uc002vww.2_Intron|MLPH_uc002vwx.2_Intron|MLPH_uc010fyu.2_Intron	NM_024101	NP_077006			melanophilin isoform 1								metal ion binding			ovary(1)	1		Breast(86;0.000381)|Renal(207;0.000966)|Ovarian(221;0.0695)|all_hematologic(139;0.095)|all_lung(227;0.17)|Melanoma(123;0.203)		Epithelial(121;1.17e-21)|OV - Ovarian serous cystadenocarcinoma(60;1.02e-10)|Kidney(56;4.23e-09)|KIRC - Kidney renal clear cell carcinoma(57;1.15e-07)|BRCA - Breast invasive adenocarcinoma(100;0.000439)|Lung(119;0.0132)|LUSC - Lung squamous cell carcinoma(224;0.0316)														---	---	---	---
Unknown	0	broad.mit.edu	37	2	238506923	238506923	+	IGR	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:238506923delC								RAB17 (7187 upstream) : LRRFIP1 (29301 downstream)																																			---	---	---	---
RBM44	375316	broad.mit.edu	37	2	238732146	238732146	+	Frame_Shift_Del	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:238732146delA	uc002vxi.3	+	9	2404	c.2272delA	c.(2272-2274)AAAfs	p.K758fs		NM_001080504	NP_001073973	Q6ZP01	RBM44_HUMAN	RNA binding motif protein 44	757							nucleotide binding|RNA binding			ovary(4)	4		Breast(86;0.0042)|Renal(207;0.00571)|Ovarian(221;0.17)|all_hematologic(139;0.182)		Epithelial(121;3.74e-22)|OV - Ovarian serous cystadenocarcinoma(60;5.3e-11)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;6.5e-08)|BRCA - Breast invasive adenocarcinoma(100;0.000118)|Lung(119;0.0112)|LUSC - Lung squamous cell carcinoma(224;0.0266)														---	---	---	---
SCLY	51540	broad.mit.edu	37	2	238984742	238984745	+	Intron	DEL	TTTT	-	-	rs71402761		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:238984742_238984745delTTTT	uc010fyv.2	+						SCLY_uc002vxm.3_Intron|SCLY_uc002vxn.2_Intron|SCLY_uc010znq.1_Intron|SCLY_uc010znr.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)														---	---	---	---
Unknown	0	broad.mit.edu	37	2	239404935	239404936	+	IGR	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:239404935_239404936delTT								ASB1 (44045 upstream) : TWIST2 (351737 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	240340858	240340858	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:240340858delT								HDAC4 (17512 upstream) : NDUFA10 (559300 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	240863931	240863931	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:240863931delA								HDAC4 (540585 upstream) : NDUFA10 (36227 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	241248401	241248402	+	IGR	DEL	TG	-	-	rs151325053		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:241248401_241248402delTG								OTOS (168328 upstream) : GPC1 (126713 downstream)																																			---	---	---	---
GPC1	2817	broad.mit.edu	37	2	241380805	241380806	+	Intron	INS	-	G	G	rs144341066	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:241380805_241380806insG	uc002vyw.3	+							NM_002081	NP_002072			glypican 1 precursor						axon guidance	anchored to membrane|extracellular space|integral to plasma membrane|proteinaceous extracellular matrix	heparan sulfate proteoglycan binding			breast(1)	1		all_epithelial(40;2.79e-15)|Breast(86;2.41e-05)|Renal(207;0.00183)|Ovarian(221;0.0228)|all_lung(227;0.0335)|Lung NSC(271;0.106)|all_hematologic(139;0.158)|Melanoma(123;0.16)|Hepatocellular(293;0.244)		Epithelial(32;4.51e-33)|all cancers(36;1.74e-30)|OV - Ovarian serous cystadenocarcinoma(60;4.73e-15)|Kidney(56;2.99e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.23e-08)|BRCA - Breast invasive adenocarcinoma(100;9.1e-06)|Colorectal(34;0.000487)|Lung(119;0.0013)|LUSC - Lung squamous cell carcinoma(224;0.0154)|COAD - Colon adenocarcinoma(134;0.0194)|READ - Rectum adenocarcinoma(96;0.0949)														---	---	---	---
ANKMY1	51281	broad.mit.edu	37	2	241426942	241426942	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:241426942delT	uc002vyz.1	-						ANKMY1_uc002vza.1_Intron|ANKMY1_uc010fzd.1_Intron|ANKMY1_uc002vzb.1_Intron|ANKMY1_uc002vzc.1_Intron|ANKMY1_uc002vzd.1_Intron	NM_016552	NP_057636			ankyrin repeat and MYND domain containing 1								zinc ion binding			central_nervous_system(1)	1		all_epithelial(40;2.79e-15)|Breast(86;2.41e-05)|Renal(207;0.00183)|Ovarian(221;0.0228)|all_lung(227;0.0335)|Lung NSC(271;0.106)|all_hematologic(139;0.158)|Melanoma(123;0.16)|Hepatocellular(293;0.244)		Epithelial(32;1.03e-30)|all cancers(36;4.78e-28)|OV - Ovarian serous cystadenocarcinoma(60;1.45e-14)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.23e-08)|BRCA - Breast invasive adenocarcinoma(100;7.8e-06)|Lung(119;0.00271)|LUSC - Lung squamous cell carcinoma(224;0.01)|Colorectal(34;0.0101)|COAD - Colon adenocarcinoma(134;0.0476)														---	---	---	---
ANKMY1	51281	broad.mit.edu	37	2	241437604	241437604	+	Intron	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:241437604delG	uc002vyz.1	-						ANKMY1_uc002vza.1_Intron|ANKMY1_uc010fzd.1_Intron|ANKMY1_uc002vzb.1_Intron|ANKMY1_uc002vzc.1_Intron|ANKMY1_uc002vzd.1_Intron	NM_016552	NP_057636			ankyrin repeat and MYND domain containing 1								zinc ion binding			central_nervous_system(1)	1		all_epithelial(40;2.79e-15)|Breast(86;2.41e-05)|Renal(207;0.00183)|Ovarian(221;0.0228)|all_lung(227;0.0335)|Lung NSC(271;0.106)|all_hematologic(139;0.158)|Melanoma(123;0.16)|Hepatocellular(293;0.244)		Epithelial(32;1.03e-30)|all cancers(36;4.78e-28)|OV - Ovarian serous cystadenocarcinoma(60;1.45e-14)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.23e-08)|BRCA - Breast invasive adenocarcinoma(100;7.8e-06)|Lung(119;0.00271)|LUSC - Lung squamous cell carcinoma(224;0.01)|Colorectal(34;0.0101)|COAD - Colon adenocarcinoma(134;0.0476)														---	---	---	---
KIF1A	547	broad.mit.edu	37	2	241679671	241679671	+	Intron	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:241679671delG	uc002vzy.2	-						KIF1A_uc010fzk.2_Intron|KIF1A_uc002vzz.1_Intron	NM_004321	NP_004312			axonal transport of synaptic vesicles						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	241701953	241701953	+	Intron	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:241701953delC	uc002vzy.2	-						KIF1A_uc010fzk.2_Intron|KIF1A_uc002vzz.1_Intron	NM_004321	NP_004312			axonal transport of synaptic vesicles						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)														---	---	---	---
HDLBP	3069	broad.mit.edu	37	2	242179467	242179467	+	Frame_Shift_Del	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:242179467delC	uc002waz.2	-	18	2468	c.2240delG	c.(2239-2241)GGCfs	p.G747fs	HDLBP_uc002wba.2_Frame_Shift_Del_p.G747fs|HDLBP_uc002wbb.2_Frame_Shift_Del_p.G699fs	NM_203346	NP_976221	Q00341	VIGLN_HUMAN	high density lipoprotein binding protein	747	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)														---	---	---	---
THAP4	51078	broad.mit.edu	37	2	242535578	242535579	+	Intron	INS	-	TT	TT			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:242535578_242535579insTT	uc002wbt.2	-						THAP4_uc002wbs.2_Intron	NM_015963	NP_057047			THAP domain containing 4 isoform 1								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)														---	---	---	---
THAP4	51078	broad.mit.edu	37	2	242551672	242551672	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:242551672delA	uc002wbt.2	-						THAP4_uc002wbs.2_Intron	NM_015963	NP_057047			THAP domain containing 4 isoform 1								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)														---	---	---	---
Unknown	0	broad.mit.edu	37	3	636023	636024	+	Intron	INS	-	T	T	rs60766772		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:636023_636024insT	uc003boy.1	+											Homo sapiens cDNA FLJ44328 fis, clone TRACH3002871.																														---	---	---	---
Unknown	0	broad.mit.edu	37	3	688509	688510	+	Intron	DEL	CA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:688509_688510delCA	uc003boy.1	+											Homo sapiens cDNA FLJ44328 fis, clone TRACH3002871.																														---	---	---	---
Unknown	0	broad.mit.edu	37	3	996188	996188	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:996188delT								CHL1 (545093 upstream) : CNTN6 (138432 downstream)																																			---	---	---	---
CNTN4	152330	broad.mit.edu	37	3	2533659	2533659	+	Intron	DEL	T	-	-	rs77085795		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:2533659delT	uc003bpc.2	+						CNTN4_uc003bpb.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)														---	---	---	---
CNTN4	152330	broad.mit.edu	37	3	2693563	2693563	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:2693563delT	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)														---	---	---	---
CNTN4	152330	broad.mit.edu	37	3	2725330	2725330	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:2725330delA	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)														---	---	---	---
CNTN4	152330	broad.mit.edu	37	3	3040333	3040333	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:3040333delA	uc003bpc.2	+						CNTN4_uc003bpb.1_Intron|CNTN4_uc003bpd.1_Intron|CNTN4_uc003bpe.2_Intron|CNTN4_uc003bpf.2_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)														---	---	---	---
CNTN4	152330	broad.mit.edu	37	3	3074624	3074624	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:3074624delA	uc003bpc.2	+						CNTN4_uc003bpb.1_Intron|CNTN4_uc003bpd.1_Intron|CNTN4_uc003bpe.2_Intron|CNTN4_uc003bpf.2_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)														---	---	---	---
Unknown	0	broad.mit.edu	37	3	3496346	3496348	+	IGR	DEL	TTT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:3496346_3496348delTTT								CRBN (274956 upstream) : SUMF1 (326688 downstream)																																			---	---	---	---
ITPR1	3708	broad.mit.edu	37	3	4567138	4567138	+	Intron	DEL	G	-	-	rs11711397	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:4567138delG	uc003bqa.2	+						ITPR1_uc010hbz.2_Intron|ITPR1_uc010hca.1_Intron|ITPR1_uc011asu.1_Intron|ITPR1_uc010hcb.1_Intron	NM_001099952	NP_001093422			inositol 1,4,5-triphosphate receptor, type 1						activation of phospholipase C activity|cell death|energy reserve metabolic process|nerve growth factor receptor signaling pathway|platelet activation|regulation of insulin secretion|response to hypoxia	endoplasmic reticulum membrane|integral to membrane|platelet dense granule membrane|platelet dense tubular network membrane	calcium ion transmembrane transporter activity|inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity|intracellular ligand-gated calcium channel activity|phosphatidylinositol binding|protein binding			lung(7)|breast(5)|ovary(4)|large_intestine(1)|liver(1)|skin(1)|kidney(1)|pancreas(1)	21				Epithelial(13;0.0199)|OV - Ovarian serous cystadenocarcinoma(96;0.0361)|all cancers(10;0.0982)														---	---	---	---
Unknown	0	broad.mit.edu	37	3	4923569	4923569	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:4923569delA								ITPR1 (34283 upstream) : BHLHE40 (97528 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	4939400	4939401	+	RNA	DEL	AA	-	-	rs77024844		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:4939400_4939401delAA	uc003bqe.1	-	4		c.1448_1449delTT								Homo sapiens cDNA FLJ32330 fis, clone PROST2004742.																														---	---	---	---
Unknown	0	broad.mit.edu	37	3	4997796	4997796	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:4997796delA	uc003bqe.1	-						uc010hce.1_Intron					Homo sapiens cDNA FLJ32330 fis, clone PROST2004742.																														---	---	---	---
Unknown	0	broad.mit.edu	37	3	5062949	5062949	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:5062949delA								BHLHE40 (36086 upstream) : ARL8B (100981 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	5153617	5153617	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:5153617delA								BHLHE40 (126754 upstream) : ARL8B (10313 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	5464303	5464303	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:5464303delA								EDEM1 (202654 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	5653857	5653857	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:5653857delT								EDEM1 (392208 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	5925091	5925091	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:5925091delA								EDEM1 (663442 upstream) : GRM7 (977711 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	5974851	5974851	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:5974851delT								EDEM1 (713202 upstream) : GRM7 (927951 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	6151195	6151196	+	IGR	DEL	TC	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:6151195_6151196delTC								EDEM1 (889546 upstream) : GRM7 (751606 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	6158842	6158842	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:6158842delA								EDEM1 (897193 upstream) : GRM7 (743960 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	6609395	6609395	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:6609395delT	uc003bqj.1	+											Homo sapiens clone P1 NTera2D1 teratocarcinoma mRNA.																														---	---	---	---
Unknown	0	broad.mit.edu	37	3	6650132	6650133	+	Intron	DEL	TT	-	-	rs145584263		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:6650132_6650133delTT	uc003bqj.1	+											Homo sapiens clone P1 NTera2D1 teratocarcinoma mRNA.																														---	---	---	---
GRM7	2917	broad.mit.edu	37	3	7599923	7599923	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:7599923delT	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	7877094	7877094	+	IGR	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:7877094delG								GRM7 (93876 upstream) : LMCD1 (666417 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	7885235	7885236	+	IGR	INS	-	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:7885235_7885236insG								GRM7 (102017 upstream) : LMCD1 (658275 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	8340912	8340912	+	Intron	DEL	A	-	-	rs35074408		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:8340912delA	uc003bqp.2	-											Homo sapiens cDNA FLJ42094 fis, clone TESOP2002489.																														---	---	---	---
Unknown	0	broad.mit.edu	37	3	8505273	8505273	+	Intron	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:8505273delC	uc003bqp.2	-											Homo sapiens cDNA FLJ42094 fis, clone TESOP2002489.																														---	---	---	---
Unknown	0	broad.mit.edu	37	3	9682460	9682461	+	IGR	INS	-	TGT	TGT	rs145233047	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:9682460_9682461insTGT								LHFPL4 (86974 upstream) : MTMR14 (8683 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	9816644	9816647	+	IGR	DEL	TTTT	-	-	rs79600085		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:9816644_9816647delTTTT								CAMK1 (4983 upstream) : TADA3 (5007 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	9905815	9905815	+	IGR	DEL	A	-	-	rs75251434		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:9905815delA								ARPC4 (8993 upstream) : CIDEC (2584 downstream)																																			---	---	---	---
TMEM111	55831	broad.mit.edu	37	3	10016252	10016252	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:10016252delT	uc003bun.2	-						CIDEC_uc003bto.2_Intron|TMEM111_uc003buo.2_Intron	NM_018447	NP_060917			transmembrane protein 111							integral to membrane					0																		---	---	---	---
IRAK2	3656	broad.mit.edu	37	3	10220145	10220145	+	Intron	DEL	A	-	-	rs75608252		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:10220145delA	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																		---	---	---	---
SEC13	6396	broad.mit.edu	37	3	10355524	10355524	+	Intron	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:10355524delG	uc003bvn.2	-						SEC13_uc003bvl.2_5'UTR|SEC13_uc003bvm.2_Intron|SEC13_uc003bvp.2_Intron|SEC13_uc003bvo.2_Intron|SEC13_uc003bvq.1_Intron|SEC13_uc003bvr.1_Intron|SEC13_uc011aul.1_Intron	NM_183352	NP_899195			SEC13 protein isoform 1						COPII vesicle coating|intracellular protein transport|mitotic prometaphase|mRNA transport|post-translational protein modification|protein N-linked glycosylation via asparagine|transmembrane transport	cytosol|endoplasmic reticulum membrane|ER to Golgi transport vesicle membrane|Nup107-160 complex	protein binding			ovary(1)	1																		---	---	---	---
SEC13	6396	broad.mit.edu	37	3	10363942	10363942	+	5'Flank	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:10363942delG	uc003bvn.2	-						SEC13_uc003bvm.2_5'Flank|SEC13_uc003bvp.2_5'Flank|SEC13_uc003bvo.2_5'Flank|SEC13_uc003bvq.1_5'Flank|SEC13_uc011aul.1_5'Flank	NM_183352	NP_899195			SEC13 protein isoform 1						COPII vesicle coating|intracellular protein transport|mitotic prometaphase|mRNA transport|post-translational protein modification|protein N-linked glycosylation via asparagine|transmembrane transport	cytosol|endoplasmic reticulum membrane|ER to Golgi transport vesicle membrane|Nup107-160 complex	protein binding			ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	3	10840831	10840835	+	IGR	DEL	GCCCT	-	-	rs142902016		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:10840831_10840835delGCCCT								LOC285370 (34954 upstream) : SLC6A11 (17082 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	11114273	11114273	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:11114273delT								SLC6A1 (33339 upstream) : HRH1 (64506 downstream)																																			---	---	---	---
HRH1	3269	broad.mit.edu	37	3	11179710	11179710	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:11179710delT	uc010hdr.2	+							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	11664956	11664956	+	Intron	DEL	A	-	-	rs146436215		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:11664956delA	uc003bwf.2	-						VGLL4_uc010hdx.1_Intron|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)														---	---	---	---
VGLL4	9686	broad.mit.edu	37	3	11725854	11725854	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:11725854delT	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)														---	---	---	---
Unknown	0	broad.mit.edu	37	3	12516203	12516203	+	IGR	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:12516203delG								PPARG (40349 upstream) : TSEN2 (9728 downstream)																																			---	---	---	---
TSEN2	80746	broad.mit.edu	37	3	12531748	12531748	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:12531748delT	uc003bxc.2	+						TSEN2_uc003bwy.2_Intron|TSEN2_uc003bwz.2_Intron|TSEN2_uc003bxa.2_Intron|TSEN2_uc011auq.1_Intron|TSEN2_uc003bxb.2_Intron|TSEN2_uc011aur.1_Intron	NM_025265	NP_079541			tRNA-intron nuclease 2 isoform 1						mRNA processing|tRNA splicing, via endonucleolytic cleavage and ligation	cytoplasm|nucleolus|tRNA-intron endonuclease complex	nucleic acid binding|tRNA-intron endonuclease activity			central_nervous_system(1)	1																		---	---	---	---
MKRN2	23609	broad.mit.edu	37	3	12598890	12598890	+	Intron	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:12598890delG	uc003bxd.2	+						MKRN2_uc003bxe.2_Intron|MKRN2_uc011aus.1_Intron	NM_014160	NP_054879			makorin ring finger protein 2							intracellular	ligase activity|nucleic acid binding|zinc ion binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	3	12714224	12714224	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:12714224delA								RAF1 (8524 upstream) : TMEM40 (61168 downstream)																																			---	---	---	---
IQSEC1	9922	broad.mit.edu	37	3	12991789	12991789	+	Intron	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:12991789delC	uc003bxt.2	-						IQSEC1_uc003bxu.3_Intron|IQSEC1_uc011auw.1_Intron	NM_014869	NP_055684			IQ motif and Sec7 domain 1 isoform b						regulation of ARF protein signal transduction	cytoplasm|nucleus	ARF guanyl-nucleotide exchange factor activity			ovary(1)	1																		---	---	---	---
NUP210	23225	broad.mit.edu	37	3	13451341	13451341	+	Intron	DEL	T	-	-	rs67505054		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:13451341delT	uc003bxv.1	-							NM_024923	NP_079199			nucleoporin 210 precursor						carbohydrate metabolic process|glucose transport|mRNA transport|protein transport|regulation of glucose transport|transmembrane transport|viral reproduction	endoplasmic reticulum membrane|nuclear membrane|nuclear pore				ovary(3)|large_intestine(3)|skin(3)|pancreas(1)|liver(1)	11	all_neural(104;0.187)																	---	---	---	---
Unknown	0	broad.mit.edu	37	3	13510073	13510074	+	IGR	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:13510073_13510074delAA								NUP210 (48264 upstream) : HDAC11 (11150 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	13513740	13513741	+	IGR	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:13513740_13513741delTT								NUP210 (51931 upstream) : HDAC11 (7483 downstream)																																			---	---	---	---
FBLN2	2199	broad.mit.edu	37	3	13590068	13590068	+	5'Flank	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:13590068delC	uc011avb.1	+						FBLN2_uc011auz.1_Intron|FBLN2_uc011ava.1_5'Flank	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)															---	---	---	---
TPRXL	348825	broad.mit.edu	37	3	13979816	13979816	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:13979816delT	uc011avd.1	+							NR_002223				RecName: Full=Putative protein TPRXL;												0																		---	---	---	---
TPRXL	348825	broad.mit.edu	37	3	14055331	14055331	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:14055331delT	uc011avd.1	+							NR_002223				RecName: Full=Putative protein TPRXL;												0																		---	---	---	---
GRIP2	80852	broad.mit.edu	37	3	14576034	14576035	+	Intron	DEL	TT	-	-	rs145572118		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:14576034_14576035delTT	uc011avi.1	-						GRIP2_uc011avh.1_Intron|GRIP2_uc003byv.1_Intron	NM_001080423	NP_001073892			glutamate receptor interacting protein 2						synaptic transmission	cytosol|plasma membrane	protein binding			pancreas(1)	1																		---	---	---	---
C3orf20	84077	broad.mit.edu	37	3	14761547	14761548	+	Intron	INS	-	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:14761547_14761548insT	uc003byy.2	+						C3orf20_uc003byz.2_Intron|C3orf20_uc003bza.2_Intron|C3orf20_uc003bzb.1_Intron	NM_032137	NP_115513			hypothetical protein LOC84077							cytoplasm|integral to membrane				ovary(3)|skin(1)	4																		---	---	---	---
COLQ	8292	broad.mit.edu	37	3	15505645	15505646	+	Intron	INS	-	G	G	rs138820065	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:15505645_15505646insG	uc003bzx.2	-						COLQ_uc003bzv.2_Intron|COLQ_uc003bzz.2_Intron|COLQ_uc010heo.2_Intron|COLQ_uc003cac.1_Intron|COLQ_uc003cae.1_Intron|COLQ_uc003cad.1_Intron	NM_005677	NP_005668			acetylcholinesterase collagen-like tail subunit						acetylcholine catabolic process in synaptic cleft|asymmetric protein localization	basal lamina|cell junction|collagen|extracellular space|synaptic cleft					0																		---	---	---	---
ANKRD28	23243	broad.mit.edu	37	3	15871447	15871450	+	Intron	DEL	AAAA	-	-	rs35459078		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:15871447_15871450delAAAA	uc003caj.1	-						ANKRD28_uc003cak.1_Intron	NM_015199	NP_056014			ankyrin repeat domain 28							nucleoplasm	protein binding			breast(1)	1																		---	---	---	---
OXNAD1	92106	broad.mit.edu	37	3	16336265	16336265	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:16336265delT	uc003caw.2	+						OXNAD1_uc010her.1_Intron|OXNAD1_uc003cax.2_Intron|OXNAD1_uc011awb.1_Intron	NM_138381	NP_612390			oxidoreductase NAD-binding domain containing 1								oxidoreductase activity			skin(1)	1																		---	---	---	---
RFTN1	23180	broad.mit.edu	37	3	16476153	16476153	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:16476153delA	uc003cay.2	-						RFTN1_uc010hes.2_Intron	NM_015150	NP_055965			raft-linking protein							plasma membrane				ovary(3)|central_nervous_system(1)	4																		---	---	---	---
RFTN1	23180	broad.mit.edu	37	3	16516114	16516114	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:16516114delA	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	16795603	16795603	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:16795603delT								DAZL (148597 upstream) : PLCL2 (48556 downstream)																																			---	---	---	---
PLCL2	23228	broad.mit.edu	37	3	17085199	17085200	+	Intron	INS	-	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:17085199_17085200insA	uc011awc.1	+						PLCL2_uc011awd.1_Intron	NM_001144382	NP_001137854			phospholipase C-like 2 isoform 1						intracellular signal transduction|lipid metabolic process	cytoplasm	calcium ion binding|phosphatidylinositol phospholipase C activity|signal transducer activity			skin(2)|ovary(1)|lung(1)	4																		---	---	---	---
Unknown	0	broad.mit.edu	37	3	17145053	17145053	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:17145053delA								PLCL2 (12956 upstream) : TBC1D5 (53602 downstream)																																			---	---	---	---
TBC1D5	9779	broad.mit.edu	37	3	17525948	17525951	+	Intron	DEL	GTGT	-	-	rs143352156		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:17525948_17525951delGTGT	uc003cbf.2	-						TBC1D5_uc010hev.2_Intron|TBC1D5_uc003cbe.2_Intron	NM_014744	NP_055559			TBC1 domain family, member 5 isoform b							intracellular	protein binding|Rab GTPase activator activity			ovary(1)	1																		---	---	---	---
TBC1D5	9779	broad.mit.edu	37	3	17538549	17538550	+	Intron	DEL	CT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:17538549_17538550delCT	uc003cbf.2	-						TBC1D5_uc010hev.2_Intron|TBC1D5_uc003cbe.2_Intron	NM_014744	NP_055559			TBC1 domain family, member 5 isoform b							intracellular	protein binding|Rab GTPase activator activity			ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	3	18026412	18026413	+	Intron	DEL	TC	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:18026412_18026413delTC	uc003cbg.2	+											Homo sapiens cDNA clone IMAGE:5584035.																														---	---	---	---
Unknown	0	broad.mit.edu	37	3	18169398	18169398	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:18169398delA	uc003cbg.2	+											Homo sapiens cDNA clone IMAGE:5584035.																												OREG0002777	type=REGULATORY REGION|Gene=TBC1D5-SATB1|Dataset=Vista Enhancers|EvidenceSubtype=In-vivo LacZ Expression Assay	---	---	---	---
SATB1	6304	broad.mit.edu	37	3	18465614	18465615	+	5'UTR	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:18465614_18465615delAA	uc003cbh.2	-	1					SATB1_uc003cbi.2_5'UTR|SATB1_uc003cbj.2_Intron	NM_002971	NP_002962			special AT-rich sequence binding protein 1						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																		---	---	---	---
Unknown	0	broad.mit.edu	37	3	18990009	18990011	+	IGR	DEL	TTC	-	-	rs67321300		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:18990009_18990011delTTC								SATB1 (509757 upstream) : KCNH8 (200006 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	19057867	19057867	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:19057867delT								SATB1 (577615 upstream) : KCNH8 (132150 downstream)																																			---	---	---	---
KCNH8	131096	broad.mit.edu	37	3	19518917	19518918	+	Intron	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:19518917_19518918delTT	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																		---	---	---	---
KAT2B	8850	broad.mit.edu	37	3	20169989	20169989	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:20169989delT	uc003cbq.2	+							NM_003884	NP_003875			K(lysine) acetyltransferase 2B						cell cycle arrest|cellular response to insulin stimulus|chromatin remodeling|histone H3 acetylation|interspecies interaction between organisms|N-terminal peptidyl-lysine acetylation|negative regulation of cell proliferation|transcription initiation from RNA polymerase I promoter	Ada2/Gcn5/Ada3 transcription activator complex|chromatin remodeling complex|PCAF complex	cyclin-dependent protein kinase inhibitor activity|histone acetyltransferase activity|histone deacetylase binding|protein kinase binding|transcription coactivator activity|transcription factor binding			ovary(1)|central_nervous_system(1)|pancreas(1)	3																		---	---	---	---
Unknown	0	broad.mit.edu	37	3	20672076	20672076	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:20672076delA								SGOL1 (444393 upstream) : VENTXP7 (775142 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	20883807	20883807	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:20883807delT								SGOL1 (656124 upstream) : VENTXP7 (563411 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	21436334	21436334	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:21436334delT								None (None upstream) : VENTXP7 (10884 downstream)																																			---	---	---	---
ZNF385D	79750	broad.mit.edu	37	3	21632524	21632524	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:21632524delA	uc003cce.2	-						ZNF385D_uc010hfb.1_Intron	NM_024697	NP_078973			zinc finger protein 385D							nucleus	nucleic acid binding|zinc ion binding			large_intestine(2)|skin(2)|ovary(1)	5																		---	---	---	---
ZNF385D	79750	broad.mit.edu	37	3	22107954	22107955	+	Intron	DEL	GT	-	-	rs111758630		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:22107954_22107955delGT	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	22286315	22286315	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:22286315delT	uc010hfb.1	-											Homo sapiens cDNA: FLJ22419 fis, clone HRC08593.							nucleus	nucleic acid binding|zinc ion binding			large_intestine(2)|skin(2)|ovary(1)	5																		---	---	---	---
UBE2E2	7325	broad.mit.edu	37	3	23442098	23442099	+	Intron	INS	-	AC	AC	rs144047017	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:23442098_23442099insAC	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																		---	---	---	---
UBE2E2	7325	broad.mit.edu	37	3	23562438	23562438	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:23562438delT	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	23771641	23771643	+	IGR	DEL	TTT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:23771641_23771643delTTT								UBE2E2 (139345 upstream) : UBE2E1 (75796 downstream)																																			---	---	---	---
UBE2E1	7324	broad.mit.edu	37	3	23863177	23863178	+	Intron	INS	-	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:23863177_23863178insT	uc003cch.2	+						UBE2E1_uc003cci.2_Intron|UBE2E1_uc011awh.1_Intron	NM_003341	NP_003332			ubiquitin-conjugating enzyme E2E 1 isoform 1						anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|histone H2B ubiquitination|histone monoubiquitination|ISG15-protein conjugation|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	cytosol|nucleoplasm|ubiquitin ligase complex	ATP binding|ISG15 ligase activity|protein binding|ubiquitin-protein ligase activity				0																		---	---	---	---
NKIRAS1	28512	broad.mit.edu	37	3	23968005	23968005	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:23968005delT	uc003cck.2	-							NM_020345	NP_065078			kappa B-ras 1						I-kappaB kinase/NF-kappaB cascade|small GTPase mediated signal transduction	cytoplasm	GTP binding|GTPase activity				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	3	25021058	25021059	+	IGR	INS	-	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:25021058_25021059insT								THRB (484605 upstream) : RARB (194764 downstream)																																			---	---	---	---
RARB	5915	broad.mit.edu	37	3	25254538	25254538	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:25254538delT	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	25554212	25554213	+	Intron	DEL	GT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:25554212_25554213delGT	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	25750803	25750803	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:25750803delA								TOP2B (44972 upstream) : NGLY1 (9633 downstream)																																			---	---	---	---
NGLY1	55768	broad.mit.edu	37	3	25820210	25820210	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:25820210delA	uc003cdl.2	-						NGLY1_uc010hfg.2_Intron|NGLY1_uc003cdm.2_Intron|NGLY1_uc011awo.1_Intron|NGLY1_uc003cdk.2_5'Flank	NM_018297	NP_060767			N-glycanase 1 isoform 1						glycoprotein catabolic process	cytoplasm	metal ion binding|peptide-N4-(N-acetyl-beta-glucosaminyl)asparagine amidase activity|protein binding			breast(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	3	26015090	26015090	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-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	26401986	26401986	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:26401986delT								OXSM (565962 upstream) : LRRC3B (262314 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	26558168	26558168	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:26558168delT								OXSM (722144 upstream) : LRRC3B (106132 downstream)																																			---	---	---	---
LRRC3B	116135	broad.mit.edu	37	3	26678106	26678106	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:26678106delA	uc003cdp.2	+						LRRC3B_uc003cdq.2_Intron	NM_052953	NP_443185			leucine rich repeat containing 3B precursor							integral to membrane				pancreas(2)|ovary(1)|skin(1)	4																		---	---	---	---
Unknown	0	broad.mit.edu	37	3	26841897	26841897	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:26841897delA								LRRC3B (89634 upstream) : NEK10 (310498 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	27047737	27047738	+	IGR	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:27047737_27047738delTT								LRRC3B (295474 upstream) : NEK10 (104657 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	27062890	27062890	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:27062890delA								LRRC3B (310627 upstream) : NEK10 (89505 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	27102233	27102234	+	IGR	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:27102233_27102234delAA								LRRC3B (349970 upstream) : NEK10 (50161 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	27658675	27658675	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:27658675delT								SLC4A7 (132837 upstream) : EOMES (99213 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	27692455	27692455	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:27692455delA								SLC4A7 (166617 upstream) : EOMES (65433 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	27744549	27744549	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:27744549delA								SLC4A7 (218711 upstream) : EOMES (13339 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	27826291	27826291	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:27826291delA								EOMES (62085 upstream) : CMC1 (456833 downstream)																																			---	---	---	---
CMC1	152100	broad.mit.edu	37	3	28342246	28342246	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:28342246delT	uc003cea.2	+							NM_182523	NP_872329			COX assembly mitochondrial protein homolog							mitochondrion	metal ion binding				0																		---	---	---	---
CMC1	152100	broad.mit.edu	37	3	28348863	28348863	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:28348863delA	uc003cea.2	+							NM_182523	NP_872329			COX assembly mitochondrial protein homolog							mitochondrion	metal ion binding				0																		---	---	---	---
ZCWPW2	152098	broad.mit.edu	37	3	28563298	28563298	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:28563298delA	uc003ceh.2	+						ZCWPW2_uc003cei.2_Intron|ZCWPW2_uc010hfo.2_Intron	NM_001040432	NP_001035522			zinc finger, CW type with PWWP domain 2								zinc ion binding			ovary(2)	2																		---	---	---	---
RBMS3	27303	broad.mit.edu	37	3	29660010	29660010	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:29660010delA	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)																---	---	---	---
RBMS3	27303	broad.mit.edu	37	3	29834722	29834722	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:29834722delA	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	30064366	30064366	+	IGR	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:30064366delG								RBMS3 (17747 upstream) : TGFBR2 (583628 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	30535904	30535911	+	IGR	DEL	TTTTTTTT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:30535904_30535911delTTTTTTTT								RBMS3 (489285 upstream) : TGFBR2 (112083 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	31131558	31131559	+	IGR	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:31131558_31131559delTT								GADL1 (195405 upstream) : STT3B (442932 downstream)																																			---	---	---	---
OSBPL10	114884	broad.mit.edu	37	3	31801664	31801666	+	Intron	DEL	GAG	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:31801664_31801666delGAG	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)														---	---	---	---
OSBPL10	114884	broad.mit.edu	37	3	31818812	31818812	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:31818812delT	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	32062525	32062525	+	IGR	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:32062525delG								ZNF860 (29405 upstream) : GPD1L (85619 downstream)																																			---	---	---	---
GPD1L	23171	broad.mit.edu	37	3	32176954	32176955	+	Intron	INS	-	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:32176954_32176955insT	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																		---	---	---	---
CMTM8	152189	broad.mit.edu	37	3	32411484	32411484	+	3'UTR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:32411484delA	uc003cex.2	+	4					CMTM8_uc010hfu.2_3'UTR	NM_178868	NP_849199			CKLF-like MARVEL transmembrane domain containing						chemotaxis	extracellular space|integral to membrane	cytokine activity				0																		---	---	---	---
CNOT10	25904	broad.mit.edu	37	3	32754704	32754704	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:32754704delT	uc003cfc.1	+						CNOT10_uc011axi.1_Intron|CNOT10_uc003cfd.1_Intron|CNOT10_uc003cfe.1_Intron|CNOT10_uc010hfv.1_Intron|CNOT10_uc011axj.1_Intron|CNOT10_uc010hfw.1_Intron	NM_015442	NP_056257			CCR4-NOT transcription complex, subunit 10						nuclear-transcribed mRNA poly(A) tail shortening	cytosol	protein binding			central_nervous_system(1)|skin(1)	2																		---	---	---	---
CNOT10	25904	broad.mit.edu	37	3	32778806	32778806	+	Intron	DEL	A	-	-	rs139514342		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:32778806delA	uc003cfc.1	+						CNOT10_uc011axi.1_Intron|CNOT10_uc003cfd.1_Intron|CNOT10_uc003cfe.1_Intron|CNOT10_uc010hfv.1_Intron|CNOT10_uc011axj.1_Intron|CNOT10_uc010hfw.1_Intron	NM_015442	NP_056257			CCR4-NOT transcription complex, subunit 10						nuclear-transcribed mRNA poly(A) tail shortening	cytosol	protein binding			central_nervous_system(1)|skin(1)	2																		---	---	---	---
CNOT10	25904	broad.mit.edu	37	3	32813841	32813843	+	Intron	DEL	AAA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:32813841_32813843delAAA	uc003cfc.1	+						CNOT10_uc003cfd.1_Intron|CNOT10_uc003cfe.1_Intron|CNOT10_uc010hfv.1_Intron|CNOT10_uc011axj.1_Intron|CNOT10_uc010hfw.1_Intron	NM_015442	NP_056257			CCR4-NOT transcription complex, subunit 10						nuclear-transcribed mRNA poly(A) tail shortening	cytosol	protein binding			central_nervous_system(1)|skin(1)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	3	32975244	32975244	+	IGR	DEL	A	-	-	rs78314440		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:32975244delA								TRIM71 (41474 upstream) : CCR4 (17822 downstream)																																			---	---	---	---
CRTAP	10491	broad.mit.edu	37	3	33174529	33174529	+	Intron	DEL	A	-	-	rs77744857		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:33174529delA	uc003cfl.3	+						CRTAP_uc010hfz.2_Intron|CRTAP_uc003cfm.2_Intron|CRTAP_uc003cfn.2_Intron	NM_006371	NP_006362			cartilage associated protein precursor							proteinaceous extracellular matrix	binding				0																		---	---	---	---
CRTAP	10491	broad.mit.edu	37	3	33179592	33179592	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:33179592delT	uc003cfl.3	+						CRTAP_uc010hfz.2_Intron|CRTAP_uc003cfm.2_Intron|CRTAP_uc003cfn.2_Intron	NM_006371	NP_006362			cartilage associated protein precursor							proteinaceous extracellular matrix	binding				0																		---	---	---	---
SUSD5	26032	broad.mit.edu	37	3	33193041	33193041	+	3'UTR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:33193041delT	uc003cfo.1	-	5						NM_015551	NP_056366			sushi domain containing 5 precursor						cell adhesion	integral to membrane	hyaluronic acid binding			ovary(1)|central_nervous_system(1)	2																		---	---	---	---
CLASP2	23122	broad.mit.edu	37	3	33663817	33663817	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:33663817delA	uc003cfu.2	-						CLASP2_uc003cft.2_Intron|CLASP2_uc010hgb.2_Intron|CLASP2_uc003cfv.2_Intron|CLASP2_uc011axu.1_Intron|CLASP2_uc003cfw.2_Intron|CLASP2_uc011axt.1_Intron	NM_015097	NP_055912			CLIP-associating protein 2											ovary(3)|central_nervous_system(1)	4																		---	---	---	---
Unknown	0	broad.mit.edu	37	3	33770530	33770532	+	IGR	DEL	AAA	-	-	rs5847788		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:33770530_33770532delAAA								CLASP2 (10682 upstream) : PDCD6IP (69534 downstream)																																			---	---	---	---
PDCD6IP	10015	broad.mit.edu	37	3	33889473	33889474	+	Intron	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:33889473_33889474delAA	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																		---	---	---	---
PDCD6IP	10015	broad.mit.edu	37	3	33893131	33893131	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:33893131delT	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	34258297	34258297	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:34258297delT								PDCD6IP (347103 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	34891089	34891089	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:34891089delT								PDCD6IP (979895 upstream) : ARPP21 (789992 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	35495537	35495537	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:35495537delA								None (None upstream) : ARPP21 (185544 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	35553358	35553358	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:35553358delA								None (None upstream) : ARPP21 (127723 downstream)																																			---	---	---	---
TRANK1	9881	broad.mit.edu	37	3	36904698	36904699	+	5'Flank	INS	-	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:36904698_36904699insA	uc003cgj.2	-							NM_014831	NP_055646			lupus brain antigen 1						DNA repair		ATP binding|ATP-dependent DNA helicase activity|DNA binding			ovary(1)|central_nervous_system(1)	2																		---	---	---	---
LRRFIP2	9209	broad.mit.edu	37	3	37172926	37172927	+	Intron	INS	-	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:37172926_37172927insA	uc003cgp.2	-						LRRFIP2_uc011ayf.1_Intron|LRRFIP2_uc003cgr.2_Intron|LRRFIP2_uc003cgs.3_Intron|LRRFIP2_uc003cgt.3_Intron	NM_006309	NP_006300			leucine rich repeat (in FLII) interacting						Wnt receptor signaling pathway		LRR domain binding			ovary(1)	1																		---	---	---	---
GOLGA4	2803	broad.mit.edu	37	3	37321050	37321050	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:37321050delT	uc003cgv.2	+						GOLGA4_uc010hgr.1_Intron|GOLGA4_uc003cgw.2_Intron|GOLGA4_uc010hgs.2_Intron|GOLGA4_uc003cgx.2_5'Flank|GOLGA4_uc003cgu.1_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																		---	---	---	---
GOLGA4	2803	broad.mit.edu	37	3	37332764	37332764	+	Intron	DEL	T	-	-	rs72002746		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:37332764delT	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																		---	---	---	---
GOLGA4	2803	broad.mit.edu	37	3	37376524	37376524	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:37376524delT	uc003cgv.2	+						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	37581045	37581045	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:37581045delT	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	37843715	37843715	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:37843715delA	uc003chd.2	+							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)														---	---	---	---
CTDSPL	10217	broad.mit.edu	37	3	37918848	37918848	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:37918848delT	uc003chg.2	+						CTDSPL_uc003chh.2_Intron	NM_001008392	NP_001008393			small CTD phosphatase 3 isoform 1							nucleus	metal ion binding|phosphoprotein phosphatase activity				0		Melanoma(1037;0.0122)		KIRC - Kidney renal clear cell carcinoma(284;0.0729)|Kidney(284;0.0902)														---	---	---	---
VILL	50853	broad.mit.edu	37	3	38039573	38039573	+	Intron	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:38039573delC	uc003chj.2	+						VILL_uc003chk.1_Intron|VILL_uc003chl.2_Intron|VILL_uc010hgu.2_Intron	NM_015873	NP_056957			villin-like protein						actin filament capping|cytoskeleton organization	actin cytoskeleton	actin binding|structural constituent of cytoskeleton				0				KIRC - Kidney renal clear cell carcinoma(284;0.0525)|Kidney(284;0.0661)														---	---	---	---
DLEC1	9940	broad.mit.edu	37	3	38137570	38137570	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:38137570delT	uc003cho.1	+						DLEC1_uc003chp.1_Intron|DLEC1_uc010hgv.1_Intron|DLEC1_uc003chr.1_Intron|DLEC1_uc010hgx.1_5'Flank	NM_007335	NP_031361			deleted in lung and esophageal cancer 1 isoform						negative regulation of cell proliferation	cytoplasm				ovary(2)|pancreas(2)|central_nervous_system(2)|skin(2)|breast(1)	9				KIRC - Kidney renal clear cell carcinoma(284;0.0664)|Kidney(284;0.0827)														---	---	---	---
OXSR1	9943	broad.mit.edu	37	3	38210794	38210798	+	Intron	DEL	TTTTG	-	-	rs76649293	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:38210794_38210798delTTTTG	uc003chy.2	+						OXSR1_uc010hhb.2_Intron|OXSR1_uc010hha.1_Intron	NM_005109	NP_005100			oxidative-stress responsive 1						intracellular protein kinase cascade|response to oxidative stress		ATP binding|identical protein binding|magnesium ion binding|protein serine/threonine kinase activity			skin(1)	1				KIRC - Kidney renal clear cell carcinoma(284;0.0588)|Kidney(284;0.0738)														---	---	---	---
EXOG	9941	broad.mit.edu	37	3	38539074	38539074	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:38539074delT	uc003cih.2	+						EXOG_uc010hhg.2_Intron|EXOG_uc011ayq.1_Intron|EXOG_uc003cij.2_Intron|EXOG_uc010hhd.2_Intron|EXOG_uc010hhe.2_Intron|EXOG_uc003cik.2_Intron|EXOG_uc010hhf.2_Intron|EXOG_uc003cii.2_Intron	NM_005107	NP_005098			endo/exonuclease (5'-3'), endonuclease G-like							mitochondrial inner membrane	endonuclease activity|metal ion binding|nucleic acid binding				0																		---	---	---	---
SCN11A	11280	broad.mit.edu	37	3	38949791	38949791	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:38949791delT	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)													---	---	---	---
Unknown	0	broad.mit.edu	37	3	39026007	39026007	+	IGR	DEL	T	-	-	rs11305181		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:39026007delT								SCN11A (33955 upstream) : WDR48 (67500 downstream)																																			---	---	---	---
CX3CR1	1524	broad.mit.edu	37	3	39305466	39305466	+	3'UTR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:39305466delA	uc003cjl.2	-	2						NM_001337	NP_001328			chemokine (C-X3-C motif) receptor 1						cell adhesion|cellular defense response|chemotaxis|interspecies interaction between organisms|response to wounding	integral to plasma membrane	chemokine receptor activity			lung(3)	3				KIRC - Kidney renal clear cell carcinoma(284;0.0557)|Kidney(284;0.0699)														---	---	---	---
Unknown	0	broad.mit.edu	37	3	39574379	39574379	+	IGR	DEL	A	-	-	rs72513006		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:39574379delA								MOBP (6524 upstream) : MYRIP (276924 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	39691194	39691197	+	IGR	DEL	TCTA	-	-	rs150707517		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:39691194_39691197delTCTA								MOBP (123339 upstream) : MYRIP (160106 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	39713762	39713762	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:39713762delT								MOBP (145907 upstream) : MYRIP (137541 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	39826509	39826509	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:39826509delA								MOBP (258654 upstream) : MYRIP (24794 downstream)																																			---	---	---	---
MYRIP	25924	broad.mit.edu	37	3	39931662	39931662	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:39931662delT	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)														---	---	---	---
Unknown	0	broad.mit.edu	37	3	40536937	40536938	+	IGR	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:40536937_40536938delTT								ZNF619 (6823 upstream) : ZNF620 (10592 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	40740450	40740450	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:40740450delA								ZNF621 (159407 upstream) : CTNNB1 (495951 downstream)																																			---	---	---	---
CTNNB1	1499	broad.mit.edu	37	3	41253199	41253199	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:41253199delT	uc010hia.1	+						CTNNB1_uc003ckp.2_Intron|CTNNB1_uc003ckq.2_Intron|CTNNB1_uc003ckr.2_Intron|CTNNB1_uc011azf.1_Intron|CTNNB1_uc011azg.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		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	41794819	41794820	+	Intron	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:41794819_41794820delAA	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)														---	---	---	---
Unknown	0	broad.mit.edu	37	3	42022857	42022858	+	IGR	DEL	TC	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:42022857_42022858delTC								ULK4 (19197 upstream) : TRAK1 (109888 downstream)																																			---	---	---	---
TRAK1	22906	broad.mit.edu	37	3	42159744	42159744	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:42159744delT	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	42176371	42176371	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:42176371delT	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	42202059	42202061	+	Intron	DEL	TTG	-	-	rs59260540		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:42202059_42202061delTTG	uc003cky.2	+						TRAK1_uc011azh.1_Intron|TRAK1_uc011azi.1_Intron|TRAK1_uc003ckz.3_Intron|TRAK1_uc011azj.1_Intron|TRAK1_uc003cla.2_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	42251305	42251306	+	Frame_Shift_Ins	INS	-	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:42251305_42251306insG	uc003cky.2	+	14	2007_2008	c.1791_1792insG	c.(1789-1794)CTTGGGfs	p.L597fs	TRAK1_uc011azh.1_Frame_Shift_Ins_p.L597fs|TRAK1_uc011azi.1_Frame_Shift_Ins_p.L597fs|TRAK1_uc011azj.1_Frame_Shift_Ins_p.L523fs|TRAK1_uc003cla.2_Frame_Shift_Ins_p.L539fs	NM_001042646	NP_001036111	Q9UPV9	TRAK1_HUMAN	OGT(O-Glc-NAc transferase)-interacting protein	597_598					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	42252862	42252862	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:42252862delT	uc003cky.2	+						TRAK1_uc011azh.1_3'UTR|TRAK1_uc011azi.1_Intron|TRAK1_uc011azj.1_3'UTR|TRAK1_uc003cla.2_3'UTR	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																		---	---	---	---
Unknown	0	broad.mit.edu	37	3	42279047	42279049	+	IGR	DEL	AAC	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:42279047_42279049delAAC								TRAK1 (11780 upstream) : CCK (20269 downstream)																																			---	---	---	---
LYZL4	131375	broad.mit.edu	37	3	42442878	42442879	+	Intron	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:42442878_42442879delTT	uc003cle.2	-							NM_144634	NP_653235			lysozyme-like 4 precursor						cell wall macromolecule catabolic process	extracellular region	lysozyme activity			central_nervous_system(1)	1				KIRC - Kidney renal clear cell carcinoma(284;0.222)														---	---	---	---
Unknown	0	broad.mit.edu	37	3	42509198	42509205	+	IGR	DEL	AGAAATAC	-	-	rs139196298		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:42509198_42509205delAGAAATAC								LYZL4 (57133 upstream) : VIPR1 (34899 downstream)																																			---	---	---	---
FAM198A	729085	broad.mit.edu	37	3	43078186	43078186	+	Intron	DEL	A	-	-	rs34104901		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:43078186delA	uc003cmp.3	+						FAM198A_uc010hii.2_Intron|FAM198A_uc003cmo.3_Intron|FAM198A_uc010hih.2_Intron	NM_001129908	NP_001123380			hypothetical protein LOC729085							extracellular region					0																		---	---	---	---
Unknown	0	broad.mit.edu	37	3	43260650	43260650	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:43260650delA								C3orf39 (113085 upstream) : SNRK (67354 downstream)																																			---	---	---	---
SNRK	54861	broad.mit.edu	37	3	43377619	43377619	+	Intron	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:43377619delC	uc003cms.3	+						SNRK_uc003cmt.3_Intron|SNRK_uc010hik.2_Intron|SNRK_uc011azr.1_Intron	NM_017719	NP_060189			SNF related 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)														---	---	---	---
ANO10	55129	broad.mit.edu	37	3	43646459	43646460	+	Intron	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:43646459_43646460delTT	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	43956213	43956213	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:43956213delT								ABHD5 (191997 upstream) : MIR138-1 (199491 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	44082799	44082800	+	IGR	DEL	AA	-	-	rs78388535		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:44082799_44082800delAA								ABHD5 (318583 upstream) : MIR138-1 (72904 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	44581331	44581331	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:44581331delT								ZNF445 (20105 upstream) : ZNF167 (15373 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	44653323	44653323	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:44653323delT								ZNF660 (15766 upstream) : ZNF197 (13188 downstream)																																			---	---	---	---
KIF15	56992	broad.mit.edu	37	3	44816593	44816593	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:44816593delA	uc003cnx.3	+						KIF15_uc010hiq.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)														---	---	---	---
KIF15	56992	broad.mit.edu	37	3	44882740	44882740	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:44882740delT	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)														---	---	---	---
LIMD1	8994	broad.mit.edu	37	3	45714525	45714525	+	Intron	DEL	A	-	-	rs72004554		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:45714525delA	uc003coq.2	+							NM_014240	NP_055055			LIM domains containing 1						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)														---	---	---	---
LZTFL1	54585	broad.mit.edu	37	3	45913167	45913167	+	Intron	DEL	T	-	-	rs34195376		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:45913167delT	uc003coy.1	-						LZTFL1_uc011bak.1_Intron	NM_020347	NP_065080			leucine zipper transcription factor-like 1												0				BRCA - Breast invasive adenocarcinoma(193;0.00867)|KIRC - Kidney renal clear cell carcinoma(197;0.0177)|Kidney(197;0.0208)														---	---	---	---
FYCO1	79443	broad.mit.edu	37	3	46028895	46028895	+	Intron	DEL	A	-	-	rs75357697		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:46028895delA	uc003cpb.3	-						FYCO1_uc011bal.1_5'Flank	NM_024513	NP_078789			FYVE and coiled-coil domain containing 1						transport	integral to membrane	metal ion binding|protein binding			central_nervous_system(1)	1				BRCA - Breast invasive adenocarcinoma(193;0.00147)|KIRC - Kidney renal clear cell carcinoma(197;0.0272)|Kidney(197;0.0323)														---	---	---	---
XCR1	2829	broad.mit.edu	37	3	46065707	46065713	+	Intron	DEL	AAAAAAA	-	-	rs35174940		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:46065707_46065713delAAAAAAA	uc003cpe.2	-						XCR1_uc003cpf.2_Intron	NM_005283	NP_005274			XC chemokine receptor 1						chemotaxis|G-protein signaling, coupled to cyclic nucleotide second messenger|inflammatory response	integral to plasma membrane	chemokine receptor activity			ovary(1)	1				BRCA - Breast invasive adenocarcinoma(193;0.00113)|KIRC - Kidney renal clear cell carcinoma(197;0.0172)|Kidney(197;0.0203)														---	---	---	---
Unknown	0	broad.mit.edu	37	3	46174168	46174168	+	IGR	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:46174168delG								XCR1 (105189 upstream) : CCR3 (30928 downstream)																																			---	---	---	---
LTF	4057	broad.mit.edu	37	3	46478937	46478937	+	Intron	DEL	A	-	-	rs34455820		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:46478937delA	uc003cpq.2	-						LTF_uc003fzr.2_Intron|LTF_uc010hjh.2_Intron|LTF_uc003cpr.2_Intron	NM_002343	NP_002334			lactotransferrin precursor						cellular iron ion homeostasis|defense response to bacterium|humoral immune response|iron ion transport	extracellular region|stored secretory granule	ferric iron binding|heparin binding|protein binding|serine-type endopeptidase activity			central_nervous_system(2)|ovary(1)|lung(1)	4				all cancers(1;7.55e-14)|GBM - Glioblastoma multiforme(1;2.1e-09)|Epithelial(1;9.25e-07)|Colorectal(1;3.81e-05)|BRCA - Breast invasive adenocarcinoma(193;0.00129)|COAD - Colon adenocarcinoma(1;0.00308)|KIRC - Kidney renal clear cell carcinoma(197;0.0205)|Kidney(197;0.0242)|OV - Ovarian serous cystadenocarcinoma(275;0.089)	Pefloxacin(DB00487)													---	---	---	---
LRRC2	79442	broad.mit.edu	37	3	46596132	46596135	+	Intron	DEL	AAAA	-	-	rs34382739		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:46596132_46596135delAAAA	uc010hji.2	-						LRRC2_uc003cpu.3_Intron	NM_024512	NP_078788			leucine rich repeat containing 2											ovary(1)	1		Ovarian(412;0.0563)		OV - Ovarian serous cystadenocarcinoma(275;6.37e-05)|BRCA - Breast invasive adenocarcinoma(193;0.00133)|KIRC - Kidney renal clear cell carcinoma(197;0.0214)|Kidney(197;0.0254)														---	---	---	---
Unknown	0	broad.mit.edu	37	3	47563209	47563210	+	IGR	INS	-	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:47563209_47563210insT								C3orf75 (8010 upstream) : CSPG5 (40519 downstream)																																			---	---	---	---
SMARCC1	6599	broad.mit.edu	37	3	47779603	47779603	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:47779603delA	uc003crq.2	-						SMARCC1_uc011bbd.1_Intron	NM_003074	NP_003065			SWI/SNF-related matrix-associated						chromatin remodeling|nervous system development|transcription, DNA-dependent	nBAF complex|npBAF complex|nucleoplasm|SWI/SNF complex|WINAC complex	DNA binding|protein N-terminus binding|transcription coactivator activity			skin(2)|lung(1)	3				BRCA - Breast invasive adenocarcinoma(193;7.47e-05)|KIRC - Kidney renal clear cell carcinoma(197;0.00862)|Kidney(197;0.01)														---	---	---	---
MAP4	4134	broad.mit.edu	37	3	47947575	47947575	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:47947575delA	uc003csb.2	-						MAP4_uc003csc.3_Intron|MAP4_uc011bbf.1_Intron|MAP4_uc003cry.2_Intron|MAP4_uc003csa.3_Intron|MAP4_uc003crz.3_Intron|MAP4_uc003csd.2_Intron	NM_002375	NP_002366			microtubule-associated protein 4 isoform 1						negative regulation of microtubule depolymerization	cytoplasm|microtubule|microtubule associated complex	protein binding|structural molecule activity			ovary(2)|pancreas(1)	3				BRCA - Breast invasive adenocarcinoma(193;0.000721)|KIRC - Kidney renal clear cell carcinoma(197;0.00641)|Kidney(197;0.00736)														---	---	---	---
Unknown	0	broad.mit.edu	37	3	48173675	48173675	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:48173675delT								MAP4 (42906 upstream) : CDC25A (24993 downstream)																																			---	---	---	---
CDC25A	993	broad.mit.edu	37	3	48226746	48226746	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:48226746delA	uc003csh.1	-						CDC25A_uc003csi.1_Intron	NM_001789	NP_001780			cell division cycle 25A isoform a						cell cycle checkpoint|cell division|cell proliferation|cellular response to UV|DNA replication|G1/S transition of mitotic cell cycle|G2/M transition of mitotic cell cycle|mitosis|regulation of cyclin-dependent protein kinase activity|S phase of mitotic cell cycle	cytosol|nucleoplasm	protein binding|protein tyrosine phosphatase activity			lung(3)|kidney(1)|skin(1)	5				BRCA - Breast invasive adenocarcinoma(193;0.000685)|KIRC - Kidney renal clear cell carcinoma(197;0.00596)|Kidney(197;0.00684)														---	---	---	---
PLXNB1	5364	broad.mit.edu	37	3	48459775	48459775	+	Intron	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:48459775delG	uc003csw.2	-						PLXNB1_uc003csu.2_Intron|PLXNB1_uc003csx.2_Intron|PLXNB1_uc010hjx.1_Intron|PLXNB1_uc003csy.1_5'Flank	NM_002673	NP_002664			plexin B1 precursor						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)														---	---	---	---
COL7A1	1294	broad.mit.edu	37	3	48611298	48611298	+	Frame_Shift_Del	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:48611298delG	uc003ctz.2	-	80	6528	c.6527delC	c.(6526-6528)CCTfs	p.P2176fs		NM_000094	NP_000085	Q02388	CO7A1_HUMAN	alpha 1 type VII collagen precursor	2176	Triple-helical region.				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)														---	---	---	---
IP6K2	51447	broad.mit.edu	37	3	48742219	48742219	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:48742219delT	uc003cup.2	-						IP6K2_uc003cuq.2_Intron|IP6K2_uc011bbq.1_Intron|IP6K2_uc011bbr.1_Intron|IP6K2_uc003cur.2_Intron|IP6K2_uc003cus.2_Intron|IP6K2_uc003cut.2_Intron|IP6K2_uc011bbs.1_Intron|IP6K2_uc011bbt.1_Intron|IP6K2_uc003cuv.1_Intron|IP6K2_uc011bbu.1_Intron|IP6K2_uc011bbv.1_Intron|IP6K2_uc003cuw.1_Intron	NM_001005909	NP_001005909			inositol hexaphosphate kinase 2 isoform a						negative regulation of cell growth|phosphatidylinositol phosphorylation|positive regulation of apoptosis|type I interferon-mediated signaling pathway	intermediate filament cytoskeleton|nucleus	ATP binding|inositol hexakisphosphate 5-kinase activity|inositol trisphosphate 3-kinase activity				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	3	48782317	48782317	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:48782317delT								IP6K2 (27397 upstream) : PRKAR2A (2901 downstream)																																			---	---	---	---
PRKAR2A	5576	broad.mit.edu	37	3	48860875	48860875	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:48860875delA	uc010hki.1	-						PRKAR2A_uc003cux.1_Intron|PRKAR2A_uc003cuy.1_Intron	NM_004157	NP_004148			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|transmembrane transport|water transport	centrosome|cytosol|membrane fraction	cAMP binding|cAMP-dependent protein kinase regulator activity			ovary(1)	1				BRCA - Breast invasive adenocarcinoma(193;0.000176)|Kidney(197;0.00246)|KIRC - Kidney renal clear cell carcinoma(197;0.00261)														---	---	---	---
ARIH2	10425	broad.mit.edu	37	3	48973634	48973634	+	Intron	DEL	T	-	-	rs79755326		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:48973634delT	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	49002793	49002793	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:49002793delA	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)														---	---	---	---
P4HTM	54681	broad.mit.edu	37	3	49043643	49043643	+	Intron	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:49043643delG	uc003cvg.2	+						P4HTM_uc003cvh.2_Intron|WDR6_uc011bbx.1_5'Flank|WDR6_uc003cvj.2_5'Flank|WDR6_uc011bby.1_5'Flank|WDR6_uc010hkn.2_5'Flank|WDR6_uc011bbz.1_5'Flank	NM_177939	NP_808808			hypoxia-inducible factor prolyl 4-hydroxylase							endoplasmic reticulum membrane|integral to membrane	calcium ion binding|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			skin(1)|pancreas(1)	2					Vitamin C(DB00126)													---	---	---	---
CCDC36	339834	broad.mit.edu	37	3	49272285	49272285	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:49272285delT	uc003cwk.2	+						CCDC36_uc003cwl.3_Intron|CCDC36_uc011bck.1_Intron|CCDC36_uc010hkt.2_Intron	NM_178173	NP_835467			coiled-coil domain containing 36											ovary(1)|kidney(1)	2				BRCA - Breast invasive adenocarcinoma(193;9.11e-05)|Kidney(197;0.00248)|KIRC - Kidney renal clear cell carcinoma(197;0.00262)														---	---	---	---
IP6K1	9807	broad.mit.edu	37	3	49788898	49788898	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:49788898delT	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																		---	---	---	---
CDHR4	389118	broad.mit.edu	37	3	49833796	49833798	+	Intron	DEL	TTT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:49833796_49833798delTTT	uc010hkz.2	-							NM_001007540	NP_001007541			cadherin-like 29 precursor						homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding				0																		---	---	---	---
RBM6	10180	broad.mit.edu	37	3	50103612	50103612	+	Intron	DEL	A	-	-	rs77592512	byFrequency;by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:50103612delA	uc003cyc.2	+						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)														---	---	---	---
GNAI2	2771	broad.mit.edu	37	3	50296330	50296331	+	3'UTR	DEL	GA	-	-	rs76340684		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:50296330_50296331delGA	uc003cyq.1	+	9					GNAI2_uc003cyo.1_3'UTR|GNAI2_uc003cyp.1_3'UTR|GNAI2_uc010hlg.1_3'UTR|GNAI2_uc011bdn.1_3'UTR|GNAI2_uc003cyr.1_3'UTR|uc003cys.1_5'Flank	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	50399696	50399696	+	5'Flank	DEL	T	-	-	rs34588082		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:50399696delT	uc003dan.1	-							NM_007024	NP_008955			PL6 protein						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)														---	---	---	---
CACNA2D2	9254	broad.mit.edu	37	3	50405148	50405148	+	Intron	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:50405148delG	uc003daq.2	-						CACNA2D2_uc003dap.2_Intron|CACNA2D2_uc003dao.2_5'Flank	NM_006030	NP_006021			calcium channel, voltage-dependent, alpha						energy reserve metabolic process|regulation of insulin secretion	integral to membrane|plasma membrane	calcium channel activity|metal ion binding|voltage-gated ion channel activity			lung(1)	1				BRCA - Breast invasive adenocarcinoma(193;0.000365)|KIRC - Kidney renal clear cell carcinoma(197;0.00862)|Kidney(197;0.01)	Gabapentin(DB00996)													---	---	---	---
CACNA2D2	9254	broad.mit.edu	37	3	50526123	50526123	+	Intron	DEL	T	-	-	rs78268339		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:50526123delT	uc003daq.2	-						CACNA2D2_uc003dap.2_Intron	NM_006030	NP_006021			calcium channel, voltage-dependent, alpha						energy reserve metabolic process|regulation of insulin secretion	integral to membrane|plasma membrane	calcium channel activity|metal ion binding|voltage-gated ion channel activity			lung(1)	1				BRCA - Breast invasive adenocarcinoma(193;0.000365)|KIRC - Kidney renal clear cell carcinoma(197;0.00862)|Kidney(197;0.01)	Gabapentin(DB00996)													---	---	---	---
MAPKAPK3	7867	broad.mit.edu	37	3	50661710	50661711	+	Intron	DEL	GT	-	-	rs67821486		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:50661710_50661711delGT	uc003day.1	+						MAPKAPK3_uc003daz.1_Intron|MAPKAPK3_uc003dba.1_Intron|MAPKAPK3_uc010hlr.1_Intron	NM_004635	NP_004626			mitogen-activated protein kinase-activated						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			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)														---	---	---	---
Unknown	0	broad.mit.edu	37	3	50688427	50688427	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:50688427delA								MAPKAPK3 (1708 upstream) : DOCK3 (24245 downstream)																																			---	---	---	---
DOCK3	1795	broad.mit.edu	37	3	51267151	51267153	+	Intron	DEL	TTG	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:51267151_51267153delTTG	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)														---	---	---	---
VPRBP	9730	broad.mit.edu	37	3	51472145	51472145	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:51472145delT	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)														---	---	---	---
Unknown	0	broad.mit.edu	37	3	51562565	51562565	+	IGR	DEL	T	-	-	rs74378144		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:51562565delT								VPRBP (28564 upstream) : RAD54L2 (13031 downstream)																																			---	---	---	---
RAD54L2	23132	broad.mit.edu	37	3	51616604	51616607	+	Intron	DEL	TTTT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:51616604_51616607delTTTT	uc011bdt.1	+						RAD54L2_uc003dbh.2_Intron	NM_015106	NP_055921			RAD54-like 2							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)														---	---	---	---
RAD54L2	23132	broad.mit.edu	37	3	51695289	51695289	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:51695289delT	uc011bdt.1	+						RAD54L2_uc003dbh.2_Intron|RAD54L2_uc011bdu.1_Intron|RAD54L2_uc003dbj.2_Intron	NM_015106	NP_055921			RAD54-like 2							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)														---	---	---	---
IQCF1	132141	broad.mit.edu	37	3	51925917	51925917	+	Intron	DEL	T	-	-	rs78367887		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:51925917delT	uc003dbq.3	-											Homo sapiens cDNA FLJ27508 fis, clone TST08061.											ovary(1)	1				BRCA - Breast invasive adenocarcinoma(193;8.01e-05)|Kidney(197;0.000541)|KIRC - Kidney renal clear cell carcinoma(197;0.000716)														---	---	---	---
RPL29	6159	broad.mit.edu	37	3	52030786	52030786	+	5'Flank	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:52030786delA	uc003dcs.2	-							NM_000992	NP_000983			ribosomal protein L29						embryo implantation|endocrine pancreas development|translational elongation|translational termination|viral transcription	cytosolic large ribosomal subunit	heparin binding|protein binding|RNA binding|structural constituent of ribosome				0				BRCA - Breast invasive adenocarcinoma(193;8.01e-05)|Kidney(197;0.000537)|KIRC - Kidney renal clear cell carcinoma(197;0.000716)														---	---	---	---
POC1A	25886	broad.mit.edu	37	3	52137840	52137840	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:52137840delA	uc003dcu.2	-						POC1A_uc003dcv.2_Intron|POC1A_uc003dcw.2_Intron	NM_015426	NP_056241			WD repeat domain 51A isoform 1							centriole|microtubule basal body					0																		---	---	---	---
DNAH1	25981	broad.mit.edu	37	3	52407464	52407464	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:52407464delA	uc011bef.1	+							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)														---	---	---	---
DNAH1	25981	broad.mit.edu	37	3	52418347	52418347	+	Intron	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:52418347delG	uc011bef.1	+						DNAH1_uc003ddv.2_5'Flank	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)														---	---	---	---
SEMA3G	56920	broad.mit.edu	37	3	52470567	52470568	+	Intron	DEL	CA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:52470567_52470568delCA	uc003dea.1	-							NM_020163	NP_064548			semaphorin sem2 precursor						multicellular organismal development	extracellular region|membrane	receptor activity			ovary(2)	2				BRCA - Breast invasive adenocarcinoma(193;1.69e-05)|Kidney(197;0.00173)|KIRC - Kidney renal clear cell carcinoma(197;0.00196)|OV - Ovarian serous cystadenocarcinoma(275;0.0333)														---	---	---	---
PBRM1	55193	broad.mit.edu	37	3	52621910	52621911	+	Intron	DEL	AT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:52621910_52621911delAT	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|PBRM1_uc003dfa.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	52662815	52662815	+	Intron	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:52662815delG	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								---	---	---	---
GNL3	26354	broad.mit.edu	37	3	52722571	52722571	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:52722571delA	uc003dfd.2	+						PBRM1_uc003dey.2_5'Flank|GNL3_uc011beh.1_Intron|GNL3_uc003dfe.2_Intron|GNL3_uc003dff.2_Intron|SNORD19_uc003dfg.1_5'Flank|SNORD19B_uc010hml.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)														---	---	---	---
MUSTN1	389125	broad.mit.edu	37	3	52866685	52866685	+	Intron	DEL	T	-	-	rs11313924		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:52866685delT	uc010hmq.1	-						ITIH4_uc011bem.1_5'Flank|ITIH4_uc011ben.1_5'Flank|ITIH4_uc003dfz.2_5'Flank|ITIH4_uc010hmp.1_5'Flank					Homo sapiens mRNA for hypothetical protein (ORF1), clone 03708.												0				BRCA - Breast invasive adenocarcinoma(193;6.56e-05)|Kidney(197;0.000586)|KIRC - Kidney renal clear cell carcinoma(197;0.000755)|OV - Ovarian serous cystadenocarcinoma(275;0.0471)														---	---	---	---
CACNA1D	776	broad.mit.edu	37	3	53526788	53526789	+	5'Flank	DEL	AA	-	-	rs35260748		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:53526788_53526789delAA	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	53694710	53694710	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:53694710delT	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	54089540	54089543	+	IGR	DEL	TTGT	-	-	rs71617210	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:54089540_54089543delTTGT								SELK (163551 upstream) : CACNA2D3 (67150 downstream)																																			---	---	---	---
CACNA2D3	55799	broad.mit.edu	37	3	54277618	54277618	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:54277618delA	uc003dhf.2	+						CACNA2D3_uc011beu.1_Intron|CACNA2D3_uc003dhg.1_Intron|CACNA2D3_uc003dhh.1_Intron|CACNA2D3_uc010hmv.1_Intron	NM_018398	NP_060868			calcium channel, voltage-dependent, alpha							integral to membrane	calcium channel activity|metal ion binding|voltage-gated ion channel activity			large_intestine(3)|ovary(1)|breast(1)|central_nervous_system(1)|skin(1)	7				KIRC - Kidney renal clear cell carcinoma(284;0.00287)|Kidney(284;0.00327)														---	---	---	---
CACNA2D3	55799	broad.mit.edu	37	3	54537778	54537779	+	Intron	INS	-	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:54537778_54537779insT	uc003dhf.2	+						CACNA2D3_uc011beu.1_Intron|CACNA2D3_uc003dhg.1_Intron|CACNA2D3_uc003dhh.1_Intron|CACNA2D3_uc010hmv.1_Intron	NM_018398	NP_060868			calcium channel, voltage-dependent, alpha							integral to membrane	calcium channel activity|metal ion binding|voltage-gated ion channel activity			large_intestine(3)|ovary(1)|breast(1)|central_nervous_system(1)|skin(1)	7				KIRC - Kidney renal clear cell carcinoma(284;0.00287)|Kidney(284;0.00327)														---	---	---	---
ERC2	26059	broad.mit.edu	37	3	55736569	55736569	+	Intron	DEL	T	-	-	rs111792037		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:55736569delT	uc003dhr.1	-						ERC2_uc003dhq.1_Intron	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)														---	---	---	---
ERC2	26059	broad.mit.edu	37	3	55990556	55990556	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:55990556delT	uc003dhr.1	-						ERC2_uc003dht.1_Intron	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)														---	---	---	---
ERC2	26059	broad.mit.edu	37	3	56018320	56018320	+	Intron	DEL	A	-	-	rs113812148		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:56018320delA	uc003dhr.1	-						ERC2_uc003dht.1_Intron	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)														---	---	---	---
ERC2	26059	broad.mit.edu	37	3	56162716	56162716	+	Intron	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:56162716delC	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)														---	---	---	---
ERC2	26059	broad.mit.edu	37	3	56208600	56208600	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:56208600delA	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)														---	---	---	---
ERC2	26059	broad.mit.edu	37	3	56344230	56344230	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:56344230delA	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)														---	---	---	---
ERC2	26059	broad.mit.edu	37	3	56401293	56401294	+	Intron	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:56401293_56401294delTT	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)														---	---	---	---
Unknown	0	broad.mit.edu	37	3	56580984	56580984	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:56580984delT								ERC2 (78593 upstream) : CCDC66 (10200 downstream)																																			---	---	---	---
CCDC66	285331	broad.mit.edu	37	3	56653283	56653283	+	Intron	DEL	T	-	-	rs113282062		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:56653283delT	uc003dhz.2	+						CCDC66_uc003dhy.2_Intron|CCDC66_uc003dhu.2_Intron|CCDC66_uc003dhx.2_Intron|CCDC66_uc003dia.2_Intron	NM_001141947	NP_001135419			coiled-coil domain containing 66 isoform 1											breast(1)	1				KIRC - Kidney renal clear cell carcinoma(284;0.0478)|Kidney(284;0.0597)|OV - Ovarian serous cystadenocarcinoma(275;0.233)														---	---	---	---
ARHGEF3	50650	broad.mit.edu	37	3	57096731	57096732	+	Intron	DEL	CA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:57096731_57096732delCA	uc003dih.2	-						SPATA12_uc003dij.1_Intron	NM_001128615	NP_001122087			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)														---	---	---	---
APPL1	26060	broad.mit.edu	37	3	57263355	57263355	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:57263355delT	uc003dio.2	+						APPL1_uc010hnb.2_Intron|APPL1_uc011bey.1_Intron	NM_012096	NP_036228			adaptor protein, phosphotyrosine interaction, PH						apoptosis|cell cycle|cell proliferation|insulin receptor signaling pathway|regulation of apoptosis|regulation of establishment of protein localization in plasma membrane|regulation of glucose import	cytosol|early endosome membrane|microsome|nucleus|vesicle membrane	protein kinase B binding			breast(1)	1				KIRC - Kidney renal clear cell carcinoma(284;0.0124)|Kidney(284;0.0144)														---	---	---	---
DNAH12	201625	broad.mit.edu	37	3	57424518	57424518	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:57424518delA	uc003dit.2	-							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	57439140	57439140	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:57439140delA	uc003dit.2	-							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																		---	---	---	---
Unknown	0	broad.mit.edu	37	3	57728342	57728343	+	IGR	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:57728342_57728343delAA								FAM116A (49526 upstream) : SLMAP (14831 downstream)																																			---	---	---	---
SLMAP	7871	broad.mit.edu	37	3	57898511	57898511	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:57898511delT	uc003dje.1	+						SLMAP_uc003djd.1_Intron|SLMAP_uc003djf.1_Intron|SLMAP_uc003djg.1_Intron|SLMAP_uc011bez.1_Intron|SLMAP_uc011bfa.1_Intron|SLMAP_uc003djh.2_Intron|SLMAP_uc003dji.1_Intron|SLMAP_uc011bfb.1_Intron|SLMAP_uc011bfc.1_Intron	NM_007159	NP_009090			sarcolemma associated protein						muscle contraction|protein folding	integral to plasma membrane|microtubule organizing center|prefoldin complex|sarcolemma|smooth endoplasmic reticulum	unfolded protein binding				0				BRCA - Breast invasive adenocarcinoma(55;0.000271)|KIRC - Kidney renal clear cell carcinoma(284;0.0602)|Kidney(284;0.0754)|OV - Ovarian serous cystadenocarcinoma(275;0.182)														---	---	---	---
SLMAP	7871	broad.mit.edu	37	3	57909952	57909952	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:57909952delT	uc003dje.1	+						SLMAP_uc003djd.1_Intron|SLMAP_uc003djf.1_Intron|SLMAP_uc003djg.1_Intron|SLMAP_uc011bez.1_Intron|SLMAP_uc011bfa.1_Intron|SLMAP_uc003dji.1_Intron|SLMAP_uc011bfb.1_Intron|SLMAP_uc011bfc.1_Intron	NM_007159	NP_009090			sarcolemma associated protein						muscle contraction|protein folding	integral to plasma membrane|microtubule organizing center|prefoldin complex|sarcolemma|smooth endoplasmic reticulum	unfolded protein binding				0				BRCA - Breast invasive adenocarcinoma(55;0.000271)|KIRC - Kidney renal clear cell carcinoma(284;0.0602)|Kidney(284;0.0754)|OV - Ovarian serous cystadenocarcinoma(275;0.182)														---	---	---	---
FLNB	2317	broad.mit.edu	37	3	58098519	58098519	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:58098519delT	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)														---	---	---	---
FAM3D	131177	broad.mit.edu	37	3	58638704	58638705	+	Intron	INS	-	ATCT	ATCT	rs75650938		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:58638704_58638705insATCT	uc003dkq.2	-							NM_138805	NP_620160			family with sequence similarity 3, member D						negative regulation of insulin secretion	extracellular region	cytokine activity				0				BRCA - Breast invasive adenocarcinoma(55;0.000225)|Kidney(10;0.000667)|KIRC - Kidney renal clear cell carcinoma(10;0.000802)|OV - Ovarian serous cystadenocarcinoma(275;0.169)														---	---	---	---
Unknown	0	broad.mit.edu	37	3	59169686	59169686	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:59169686delT								C3orf67 (133928 upstream) : FHIT (565352 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	59265347	59265348	+	IGR	DEL	TG	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:59265347_59265348delTG								C3orf67 (229589 upstream) : FHIT (469690 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	59309946	59309947	+	IGR	INS	-	TGTG	TGTG	rs72135008		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:59309946_59309947insTGTG								C3orf67 (274188 upstream) : FHIT (425091 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	59524004	59524015	+	IGR	DEL	CCCTCCCTCCCT	-	-	rs144518572		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:59524004_59524015delCCCTCCCTCCCT								C3orf67 (488246 upstream) : FHIT (211023 downstream)																																			---	---	---	---
FHIT	2272	broad.mit.edu	37	3	60675059	60675059	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:60675059delA	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	61358163	61358164	+	IGR	DEL	CA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:61358163_61358164delCA								FHIT (121030 upstream) : PTPRG (189079 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	61423443	61423444	+	IGR	DEL	AC	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:61423443_61423444delAC								FHIT (186310 upstream) : PTPRG (123799 downstream)																																			---	---	---	---
PTPRG	5793	broad.mit.edu	37	3	61638996	61638996	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:61638996delT	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)														---	---	---	---
LOC285401	285401	broad.mit.edu	37	3	62969435	62969435	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:62969435delA	uc003dlo.2	+						LOC285401_uc010hnr.1_Intron					Homo sapiens, clone IMAGE:5557531, mRNA.												0																		---	---	---	---
SYNPR	132204	broad.mit.edu	37	3	63417424	63417424	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:63417424delA	uc003dlp.2	+						SYNPR_uc011bfk.1_Intron|SYNPR_uc011bfl.1_Intron	NM_001130003	NP_001123475			synaptoporin isoform 1							cell junction|integral to membrane|synaptic vesicle membrane|synaptosome	transporter activity				0				BRCA - Breast invasive adenocarcinoma(55;0.000918)|KIRC - Kidney renal clear cell carcinoma(15;0.0658)|Kidney(15;0.0904)														---	---	---	---
SYNPR	132204	broad.mit.edu	37	3	63452131	63452131	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:63452131delT	uc003dlq.2	+						SYNPR_uc003dlp.2_Intron|SYNPR_uc011bfk.1_Intron|SYNPR_uc011bfl.1_Intron|SYNPR_uc010hnt.2_Intron|SYNPR_uc011bfm.1_Intron	NM_144642	NP_653243			synaptoporin isoform 2							cell junction|integral to membrane|synaptic vesicle membrane|synaptosome	transporter activity				0				BRCA - Breast invasive adenocarcinoma(55;0.000918)|KIRC - Kidney renal clear cell carcinoma(15;0.0658)|Kidney(15;0.0904)														---	---	---	---
Unknown	0	broad.mit.edu	37	3	63779849	63779850	+	IGR	DEL	AC	-	-	rs34728435		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:63779849_63779850delAC								SNTN (128968 upstream) : C3orf49 (25191 downstream)																																			---	---	---	---
C3orf49	132200	broad.mit.edu	37	3	63816850	63816850	+	Frame_Shift_Del	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:63816850delA	uc003dls.3	+	4	742	c.635delA	c.(634-636)GAAfs	p.E212fs		NR_026866				RecName: Full=Putative uncharacterized protein C3orf49;												0																		---	---	---	---
C3orf49	132200	broad.mit.edu	37	3	63820037	63820039	+	Intron	DEL	AAA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:63820037_63820039delAAA	uc003dls.3	+						THOC7_uc003dlt.3_Intron|THOC7_uc003dlu.3_Intron	NR_026866				RecName: Full=Putative uncharacterized protein C3orf49;												0																		---	---	---	---
PRICKLE2	166336	broad.mit.edu	37	3	64211562	64211562	+	5'Flank	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:64211562delT	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	64248301	64248301	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:64248301delA								PRICKLE2 (37170 upstream) : ADAMTS9 (253032 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	64284425	64284425	+	IGR	DEL	T	-	-	rs1102917	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:64284425delT								PRICKLE2 (73294 upstream) : ADAMTS9 (216908 downstream)																																			---	---	---	---
ADAMTS9	56999	broad.mit.edu	37	3	64534272	64534273	+	Intron	INS	-	G	G	rs144235877	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:64534272_64534273insG	uc003dmg.2	-						ADAMTS9_uc011bfo.1_Intron|ADAMTS9_uc011bfp.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	65273780	65273780	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:65273780delA								ADAMTS9 (600415 upstream) : MAGI1 (66127 downstream)																																			---	---	---	---
MAGI1	9223	broad.mit.edu	37	3	65690418	65690418	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:65690418delA	uc003dmn.2	-						MAGI1_uc003dmm.2_Intron|MAGI1_uc003dmo.2_Intron|MAGI1_uc003dmp.2_Intron|MAGI1_uc010hny.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)														---	---	---	---
LRIG1	26018	broad.mit.edu	37	3	66516465	66516465	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:66516465delT	uc003dmx.2	-						LRIG1_uc010hoa.2_Intron	NM_015541	NP_056356			leucine-rich repeats and immunoglobulin-like							integral to membrane				skin(3)|ovary(2)	5		Lung NSC(201;0.0101)		BRCA - Breast invasive adenocarcinoma(55;0.00047)														---	---	---	---
Unknown	0	broad.mit.edu	37	3	66687519	66687519	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:66687519delA								LRIG1 (136674 upstream) : KBTBD8 (361208 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	67270234	67270234	+	IGR	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:67270234delG								KBTBD8 (208604 upstream) : SUCLG2 (154911 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	67991754	67991754	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:67991754delT	uc003dnc.2	+											Homo sapiens mRNA; cDNA DKFZp686F1220 (from clone DKFZp686F1220).																														---	---	---	---
FAM19A1	407738	broad.mit.edu	37	3	68067118	68067119	+	Intron	INS	-	G	G	rs142151322	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:68067118_68067119insG	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)														---	---	---	---
FAM19A1	407738	broad.mit.edu	37	3	68079417	68079417	+	Intron	DEL	T	-	-	rs75332448		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:68079417delT	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)														---	---	---	---
FAM19A1	407738	broad.mit.edu	37	3	68257851	68257851	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:68257851delA	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)														---	---	---	---
FAM19A1	407738	broad.mit.edu	37	3	68584039	68584039	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:68584039delA	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)														---	---	---	---
FAM19A4	151647	broad.mit.edu	37	3	68821120	68821120	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:68821120delA	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)														---	---	---	---
Unknown	0	broad.mit.edu	37	3	69003271	69003271	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:69003271delT								FAM19A4 (21560 upstream) : C3orf64 (21098 downstream)																																			---	---	---	---
ARL6IP5	10550	broad.mit.edu	37	3	69153415	69153415	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:69153415delA	uc003dnr.2	+							NM_006407	NP_006398			ADP-ribosylation-like factor 6 interacting						L-glutamate transport	endoplasmic reticulum membrane|integral to membrane				ovary(1)	1		Lung NSC(201;0.0193)|Prostate(884;0.174)		BRCA - Breast invasive adenocarcinoma(55;7.78e-05)|Epithelial(33;0.000818)|LUSC - Lung squamous cell carcinoma(21;0.0118)|Lung(16;0.0189)|KIRC - Kidney renal clear cell carcinoma(39;0.203)|Kidney(39;0.238)														---	---	---	---
Unknown	0	broad.mit.edu	37	3	69177361	69177361	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:69177361delT								LMOD3 (5615 upstream) : FRMD4B (41785 downstream)																																			---	---	---	---
FRMD4B	23150	broad.mit.edu	37	3	69419264	69419265	+	Intron	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:69419264_69419265delTT	uc003dnv.2	-						FRMD4B_uc003dnw.2_Intron|FRMD4B_uc003dny.2_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	69719107	69719109	+	IGR	DEL	TTT	-	-	rs36118037		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:69719107_69719109delTTT								FRMD4B (127374 upstream) : MITF (69524 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	69772851	69772852	+	IGR	DEL	TC	-	-	rs139909901		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:69772851_69772852delTC								FRMD4B (181118 upstream) : MITF (15781 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	70617542	70617542	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:70617542delT								MITF (600056 upstream) : FOXP1 (387195 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	70826752	70826752	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:70826752delA								MITF (809266 upstream) : FOXP1 (177985 downstream)																																			---	---	---	---
FOXP1	27086	broad.mit.edu	37	3	71066009	71066009	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:71066009delA	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_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	71098711	71098711	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:71098711delA	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	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	71188061	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:71188061delA	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	71331767	71331767	+	Intron	DEL	A	-	-	rs34981481		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:71331767delA	uc003dop.2	-						FOXP1_uc003dom.2_Intron|FOXP1_uc003don.2_Intron|FOXP1_uc003doo.2_Intron|FOXP1_uc003doq.1_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								---	---	---	---
FOXP1	27086	broad.mit.edu	37	3	71482186	71482186	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:71482186delA	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								---	---	---	---
FOXP1	27086	broad.mit.edu	37	3	71632578	71632579	+	Intron	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:71632578_71632579delTT	uc003dop.2	-						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								---	---	---	---
RYBP	23429	broad.mit.edu	37	3	72479014	72479014	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:72479014delA	uc003dpe.2	-							NM_012234	NP_036366			RING1 and YY1 binding protein						apoptosis|histone H2A monoubiquitination|multicellular organismal development|negative regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	cytoplasm|nucleoplasm	DNA binding|protein binding|transcription corepressor activity|zinc ion binding				0		Prostate(10;0.00174)|Lung NSC(201;0.0659)|Myeloproliferative disorder(1037;0.204)		BRCA - Breast invasive adenocarcinoma(55;0.000197)|Epithelial(33;0.00068)|LUSC - Lung squamous cell carcinoma(21;0.00228)|Lung(16;0.00677)|KIRC - Kidney renal clear cell carcinoma(39;0.198)|Kidney(39;0.232)														---	---	---	---
Unknown	0	broad.mit.edu	37	3	72901396	72901396	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:72901396delT								SHQ1 (3798 upstream) : GXYLT2 (35989 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	73183953	73183953	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:73183953delT								PPP4R2 (68942 upstream) : PDZRN3 (247699 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	73238035	73238043	+	IGR	DEL	CTTCTCCTG	-	-	rs67077794		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:73238035_73238043delCTTCTCCTG								PPP4R2 (123024 upstream) : PDZRN3 (193609 downstream)																																			---	---	---	---
PDZRN3	23024	broad.mit.edu	37	3	73447008	73447009	+	Intron	INS	-	TACT	TACT			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:73447008_73447009insTACT	uc003dpl.1	-						PDZRN3_uc011bgh.1_Intron|PDZRN3_uc010hoe.1_Intron|PDZRN3_uc011bgf.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	73668010	73668010	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:73668010delT	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	73760954	73760954	+	IGR	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:73760954delC								PDZRN3 (86882 upstream) : CNTN3 (550768 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	73854987	73854987	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:73854987delA								PDZRN3 (180915 upstream) : CNTN3 (456735 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	74034294	74034296	+	IGR	DEL	AAA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:74034294_74034296delAAA								PDZRN3 (360222 upstream) : CNTN3 (277426 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	74113405	74113405	+	IGR	DEL	T	-	-	rs67762308		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:74113405delT								PDZRN3 (439333 upstream) : CNTN3 (198317 downstream)																																			---	---	---	---
CNTN3	5067	broad.mit.edu	37	3	74394020	74394021	+	Intron	DEL	AC	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:74394020_74394021delAC	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	74679290	74679290	+	IGR	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:74679290delG								CNTN3 (108947 upstream) : FAM86D (791415 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	74938131	74938132	+	IGR	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:74938131_74938132delAA								CNTN3 (367788 upstream) : FAM86D (532573 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	75114945	75114945	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:75114945delT								CNTN3 (544602 upstream) : FAM86D (355760 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	75278607	75278608	+	IGR	DEL	AG	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:75278607_75278608delAG								CNTN3 (708264 upstream) : FAM86D (192097 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	75347592	75347592	+	IGR	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:75347592delG								CNTN3 (777249 upstream) : FAM86D (123113 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	75469368	75469368	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:75469368delA								CNTN3 (899025 upstream) : FAM86D (1337 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	75687314	75687314	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:75687314delT								MIR1324 (7305 upstream) : ZNF717 (71480 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	75839243	75839243	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:75839243delA								ZNF717 (4573 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	76031023	76031023	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:76031023delT								ZNF717 (196353 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	76238066	76238066	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:76238066delA								ZNF717 (403396 upstream) : ROBO2 (851228 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	76292081	76292084	+	IGR	DEL	AAAC	-	-	rs140231081		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:76292081_76292084delAAAC								ZNF717 (457411 upstream) : ROBO2 (797210 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	76341044	76341044	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:76341044delT								ZNF717 (506374 upstream) : ROBO2 (748250 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	76482043	76482043	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:76482043delA								ZNF717 (647373 upstream) : ROBO2 (607251 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	76595941	76595941	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:76595941delT								ZNF717 (761271 upstream) : ROBO2 (493353 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	76990315	76990315	+	IGR	DEL	T	-	-	rs67622452		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:76990315delT								None (None upstream) : ROBO2 (98979 downstream)																																			---	---	---	---
ROBO2	6092	broad.mit.edu	37	3	77097198	77097199	+	Intron	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:77097198_77097199delAA	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	77385666	77385666	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:77385666delT	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	77679942	77679942	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:77679942delT	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	78409740	78409740	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:78409740delA								ROBO2 (713079 upstream) : ROBO1 (236648 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	78489008	78489008	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:78489008delT								ROBO2 (792347 upstream) : ROBO1 (157380 downstream)																																			---	---	---	---
ROBO1	6091	broad.mit.edu	37	3	78808418	78808418	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:78808418delA	uc003dqe.2	-						ROBO1_uc003dqb.2_Intron|ROBO1_uc003dqc.2_Intron|ROBO1_uc003dqd.2_Intron	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	79223857	79223858	+	Intron	INS	-	A	A	rs11323133		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:79223857_79223858insA	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	79849574	79849575	+	IGR	INS	-	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:79849574_79849575insG								ROBO1 (32515 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	80077449	80077449	+	IGR	DEL	T	-	-	rs138251606		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:80077449delT								ROBO1 (260390 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	80786748	80786748	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:80786748delT								ROBO1 (969689 upstream) : GBE1 (752102 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	80826169	80826169	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:80826169delT								None (None upstream) : GBE1 (712681 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	81083306	81083306	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:81083306delT								None (None upstream) : GBE1 (455544 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	81189725	81189725	+	IGR	DEL	C	-	-	rs75490511		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:81189725delC								None (None upstream) : GBE1 (349125 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	81867545	81867545	+	IGR	DEL	T	-	-	rs72049206		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:81867545delT								GBE1 (56595 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	82042155	82042155	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:82042155delA	uc003dqh.1	+											Homo sapiens cDNA clone IMAGE:5271111.																														---	---	---	---
Unknown	0	broad.mit.edu	37	3	83379325	83379326	+	IGR	DEL	CA	-	-	rs80266392		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:83379325_83379326delCA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	83809986	83809987	+	IGR	INS	-	A	A	rs151037811	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:83809986_83809987insA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	83878133	83878133	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:83878133delA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	83936581	83936581	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:83936581delT								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	84264721	84264721	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:84264721delT								None (None upstream) : CADM2 (743412 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	84842239	84842240	+	Intron	INS	-	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:84842239_84842240insA	uc003dqi.2	-											Homo sapiens cDNA clone IMAGE:4824471.																														---	---	---	---
CADM2	253559	broad.mit.edu	37	3	85043235	85043235	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:85043235delT	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	85197418	85197418	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:85197418delA	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	85307651	85307651	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:85307651delA	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	85512025	85512026	+	Intron	INS	-	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:85512025_85512026insA	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	85521930	85521931	+	Intron	DEL	TC	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:85521930_85521931delTC	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)														---	---	---	---
Unknown	0	broad.mit.edu	37	3	86787465	86787465	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:86787465delT								CADM2 (669517 upstream) : VGLL3 (199660 downstream)																																			---	---	---	---
CHMP2B	25978	broad.mit.edu	37	3	87294578	87294580	+	Intron	DEL	TTT	-	-	rs77725272		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:87294578_87294580delTTT	uc003dqp.3	+						CHMP2B_uc011bgn.1_Intron	NM_014043	NP_054762			chromatin modifying protein 2B						cellular membrane organization|endosome transport|protein transport	cytosol|late endosome membrane|mitochondrion|nucleus	protein domain specific binding			skin(2)|ovary(1)	3	all_cancers(8;0.104)|Lung SC(3;0.184)	Lung NSC(201;0.0777)		LUSC - Lung squamous cell carcinoma(29;0.00241)|Lung(72;0.00712)														---	---	---	---
POU1F1	5449	broad.mit.edu	37	3	87310534	87310534	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:87310534delA	uc003dqq.1	-						POU1F1_uc010hoj.1_Intron	NM_000306	NP_000297			pituitary specific transcription factor 1						negative regulation of cell proliferation|positive regulation of transcription, DNA-dependent|transcription from RNA polymerase II promoter	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			central_nervous_system(1)|skin(1)	2	all_cancers(8;0.104)|Lung SC(3;0.184)	Lung NSC(201;0.0777)		LUSC - Lung squamous cell carcinoma(29;0.00229)|Lung(72;0.00677)														---	---	---	---
Unknown	0	broad.mit.edu	37	3	87625286	87625288	+	IGR	DEL	TTT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:87625286_87625288delTTT								POU1F1 (299549 upstream) : HTR1F (406438 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	88512607	88512607	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:88512607delA								C3orf38 (305494 upstream) : EPHA3 (644067 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	88851122	88851122	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:88851122delT								C3orf38 (644009 upstream) : EPHA3 (305552 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	88862094	88862095	+	IGR	INS	-	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:88862094_88862095insG								C3orf38 (654981 upstream) : EPHA3 (294579 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	88866180	88866180	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:88866180delT								C3orf38 (659067 upstream) : EPHA3 (290494 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	89021424	89021425	+	IGR	INS	-	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:89021424_89021425insA								C3orf38 (814311 upstream) : EPHA3 (135249 downstream)																																			---	---	---	---
EPHA3	2042	broad.mit.edu	37	3	89207014	89207015	+	Intron	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:89207014_89207015delAA	uc003dqy.2	+						EPHA3_uc003dqx.1_Intron|EPHA3_uc010hon.1_Intron	NM_005233	NP_005224			ephrin receptor EphA3 isoform a precursor							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)			---	---	---	---
EPHA3	2042	broad.mit.edu	37	3	89528536	89528536	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:89528536delT	uc003dqy.2	+						EPHA3_uc010hon.1_Intron	NM_005233	NP_005224			ephrin receptor EphA3 isoform a precursor							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)			---	---	---	---
Unknown	0	broad.mit.edu	37	3	89842082	89842083	+	IGR	INS	-	AT	AT			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:89842082_89842083insAT								EPHA3 (310800 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	90001259	90001260	+	IGR	DEL	CA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:90001259_90001260delCA								EPHA3 (469977 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	90257675	90257675	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:90257675delT								EPHA3 (726393 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	90333153	90333154	+	IGR	INS	-	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:90333153_90333154insT								EPHA3 (801871 upstream) : None (None downstream)																																			---	---	---	---
ARL13B	200894	broad.mit.edu	37	3	93753075	93753075	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:93753075delA	uc003drc.2	+						ARL13B_uc010hop.2_Intron|ARL13B_uc003drd.2_Intron|ARL13B_uc003dre.2_Intron|ARL13B_uc003drf.2_Intron|ARL13B_uc003drg.2_Intron	NM_182896	NP_878899			ADP-ribosylation factor-like 2-like 1 isoform 1								GTP binding				0																		---	---	---	---
NSUN3	63899	broad.mit.edu	37	3	93810933	93810933	+	Intron	DEL	T	-	-	rs76620092		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:93810933delT	uc003drl.1	+							NM_022072	NP_071355			NOL1/NOP2/Sun domain family, member 3								methyltransferase activity			skin(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	3	93895795	93895795	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:93895795delA								NSUN3 (50165 upstream) : LOC255025 (761312 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	94331495	94331496	+	IGR	DEL	TG	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:94331495_94331496delTG								NSUN3 (485865 upstream) : LOC255025 (325611 downstream)																																			---	---	---	---
LOC255025	255025	broad.mit.edu	37	3	94880947	94880947	+	Intron	DEL	G	-	-	rs11321843		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:94880947delG	uc003drn.2	+											Homo sapiens hypothetical protein LOC255025, mRNA (cDNA clone IMAGE:5267157).												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	3	95460236	95460237	+	IGR	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:95460236_95460237delAA								LOC255025 (565157 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	95789741	95789741	+	IGR	DEL	T	-	-	rs67471225		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:95789741delT								LOC255025 (894662 upstream) : EPHA6 (743684 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	96177736	96177736	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:96177736delA								None (None upstream) : EPHA6 (355689 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	96212031	96212032	+	IGR	INS	-	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:96212031_96212032insT								None (None upstream) : EPHA6 (321393 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	96232417	96232417	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:96232417delA								None (None upstream) : EPHA6 (301008 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	96270951	96270952	+	IGR	INS	-	AGAT	AGAT	rs145046568	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:96270951_96270952insAGAT								None (None upstream) : EPHA6 (262473 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	96519353	96519353	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:96519353delT								None (None upstream) : EPHA6 (14072 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	96522484	96522485	+	IGR	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:96522484_96522485delAA								None (None upstream) : EPHA6 (10940 downstream)																																			---	---	---	---
EPHA6	285220	broad.mit.edu	37	3	96736828	96736830	+	Intron	DEL	TTT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:96736828_96736830delTTT	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	96847717	96847719	+	Intron	DEL	TTT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:96847717_96847719delTTT	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	96922838	96922839	+	Intron	INS	-	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:96922838_96922839insA	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	97019678	97019679	+	Intron	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:97019678_97019679delAA	uc010how.1	+							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	97319650	97319650	+	Intron	DEL	A	-	-	rs111876263		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:97319650delA	uc010how.1	+						EPHA6_uc011bgo.1_Intron|EPHA6_uc011bgp.1_Intron|EPHA6_uc003drs.3_Intron|EPHA6_uc003drr.3_Intron|EPHA6_uc003drt.2_Intron|EPHA6_uc010hox.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	97426686	97426687	+	Intron	DEL	CT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:97426686_97426687delCT	uc010how.1	+						EPHA6_uc003drt.2_Intron|EPHA6_uc010hox.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																		---	---	---	---
Unknown	0	broad.mit.edu	37	3	97532023	97532023	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:97532023delT								ARL6 (12072 upstream) : CRYBG3 (63796 downstream)																																			---	---	---	---
CRYBG3	131544	broad.mit.edu	37	3	97605313	97605313	+	Intron	DEL	A	-	-	rs9862347	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:97605313delA	uc003drx.2	+							NM_153605	NP_705833			beta-gamma crystallin domain containing 3												0																		---	---	---	---
MINA	84864	broad.mit.edu	37	3	97669754	97669754	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:97669754delA	uc003drz.1	-						MINA_uc003dry.1_5'Flank|MINA_uc003dsa.1_Intron|MINA_uc003dsb.1_Intron|MINA_uc003dsc.1_Intron|MINA_uc010hpa.1_Intron	NM_001042533	NP_001035998			MYC induced nuclear antigen isoform a						ribosome biogenesis	cytoplasm|nucleolus				ovary(1)	1																		---	---	---	---
MINA	84864	broad.mit.edu	37	3	97677471	97677472	+	Intron	INS	-	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:97677471_97677472insA	uc003drz.1	-						MINA_uc003dsa.1_Intron|MINA_uc003dsb.1_Intron|MINA_uc003dsc.1_Intron|MINA_uc010hpa.1_Intron|MINA_uc010hpb.1_Intron	NM_001042533	NP_001035998			MYC induced nuclear antigen isoform a						ribosome biogenesis	cytoplasm|nucleolus				ovary(1)	1																		---	---	---	---
OR5AC2	81050	broad.mit.edu	37	3	97805567	97805567	+	5'Flank	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:97805567delT	uc011bgs.1	+							NM_054106	NP_473447			olfactory receptor, family 5, subfamily AC,						sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			skin(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	3	98018447	98018447	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:98018447delA								OR5H2 (15771 upstream) : OR5K4 (54251 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	98056985	98056985	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:98056985delA								OR5H2 (54309 upstream) : OR5K4 (15713 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	98066005	98066005	+	IGR	DEL	G	-	-	rs9877169	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:98066005delG								OR5H2 (63329 upstream) : OR5K4 (6693 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	98379917	98379917	+	IGR	DEL	A	-	-	rs147721470		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:98379917delA								CPOX (67476 upstream) : ST3GAL6 (71235 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	98428397	98428399	+	IGR	DEL	AAA	-	-	rs63730160		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:98428397_98428399delAAA								CPOX (115956 upstream) : ST3GAL6 (22753 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	98442053	98442053	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:98442053delT								CPOX (129612 upstream) : ST3GAL6 (9099 downstream)																																			---	---	---	---
ST3GAL6	10402	broad.mit.edu	37	3	98490510	98490510	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:98490510delT	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	98600369	98600369	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:98600369delA	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	98697789	98697792	+	IGR	DEL	CAGT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:98697789_98697792delCAGT								DCBLD2 (77256 upstream) : COL8A1 (659662 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	98822168	98822168	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:98822168delT								DCBLD2 (201635 upstream) : COL8A1 (535286 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	99037348	99037348	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:99037348delA								DCBLD2 (416815 upstream) : COL8A1 (320106 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	99258603	99258603	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:99258603delA								DCBLD2 (638070 upstream) : COL8A1 (98851 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	99295612	99295612	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:99295612delA								DCBLD2 (675079 upstream) : COL8A1 (61842 downstream)																																			---	---	---	---
FILIP1L	11259	broad.mit.edu	37	3	99742397	99742397	+	Intron	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:99742397delG	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	99778310	99778310	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:99778310delT	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																		---	---	---	---
TBC1D23	55773	broad.mit.edu	37	3	100039736	100039736	+	Frame_Shift_Del	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:100039736delA	uc003dtt.2	+	18	2116	c.1939delA	c.(1939-1941)AAAfs	p.K647fs	TBC1D23_uc003dts.2_Frame_Shift_Del_p.K632fs|TBC1D23_uc003dtu.2_Frame_Shift_Del_p.K78fs	NM_018309	NP_060779	Q9NUY8	TBC23_HUMAN	TBC1 domain family, member 23	647						intracellular	Rab GTPase activator activity			ovary(1)|liver(1)	2																		---	---	---	---
TOMM70A	9868	broad.mit.edu	37	3	100108883	100108883	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:100108883delA	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	100378513	100378513	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:100378513delT	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																		---	---	---	---
ABI3BP	25890	broad.mit.edu	37	3	100666626	100666626	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:100666626delA	uc003dun.2	-						ABI3BP_uc003duo.2_Intron|ABI3BP_uc003dup.3_Intron	NM_015429	NP_056244			ABI gene family, member 3 (NESH) binding protein							extracellular space				ovary(2)|large_intestine(1)|haematopoietic_and_lymphoid_tissue(1)	4																		---	---	---	---
Unknown	0	broad.mit.edu	37	3	100811167	100811167	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:100811167delA								ABI3BP (98833 upstream) : IMPG2 (134121 downstream)																																			---	---	---	---
SENP7	57337	broad.mit.edu	37	3	101119510	101119511	+	Intron	DEL	TC	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:101119510_101119511delTC	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																		---	---	---	---
CEP97	79598	broad.mit.edu	37	3	101445761	101445761	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:101445761delA	uc003dvk.1	+						CEP97_uc010hpm.1_Intron|CEP97_uc011bhf.1_Intron|CEP97_uc003dvl.1_5'Flank	NM_024548	NP_078824			centrosomal protein 97kDa							centrosome|nucleus	protein binding			ovary(2)	2																		---	---	---	---
NFKBIZ	64332	broad.mit.edu	37	3	101574899	101574899	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:101574899delT	uc003dvp.2	+						NFKBIZ_uc003dvo.2_Intron|NFKBIZ_uc010hpo.2_Intron|NFKBIZ_uc003dvq.2_Intron	NM_031419	NP_113607			nuclear factor of kappa light polypeptide gene						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus				ovary(2)	2																		---	---	---	---
LOC152225	152225	broad.mit.edu	37	3	101658543	101658543	+	5'Flank	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:101658543delT	uc003dvr.1	+							NR_026934				Homo sapiens cDNA FLJ33269 fis, clone ASTRO2007578.												0																		---	---	---	---
ZPLD1	131368	broad.mit.edu	37	3	102077224	102077224	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:102077224delT	uc003dvs.1	+							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	102302035	102302035	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:102302035delA								ZPLD1 (103350 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	102522537	102522537	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:102522537delT								ZPLD1 (323852 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	102784108	102784109	+	IGR	DEL	TT	-	-	rs113985847		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:102784108_102784109delTT								ZPLD1 (585423 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	103071620	103071620	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:103071620delT								ZPLD1 (872935 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	103084962	103084962	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:103084962delA								ZPLD1 (886277 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	103240408	103240408	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:103240408delA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	103253217	103253218	+	IGR	INS	-	AT	AT			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:103253217_103253218insAT								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	103395803	103395803	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:103395803delA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	103449798	103449798	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:103449798delT								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	103582663	103582664	+	IGR	DEL	TC	-	-	rs4856088	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:103582663_103582664delTC								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	104046109	104046109	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:104046109delA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	104329533	104329533	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:104329533delA								None (None upstream) : ALCAM (756180 downstream)																																			---	---	---	---
ALCAM	214	broad.mit.edu	37	3	105286277	105286277	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:105286277delT	uc003dvx.2	+						ALCAM_uc003dvy.2_Intron|ALCAM_uc010hpp.2_Intron|ALCAM_uc003dvz.2_Intron	NM_001627	NP_001618			activated leukocyte cell adhesion molecule						cell adhesion|signal transduction	integral to membrane	receptor binding			ovary(2)|breast(1)	3																		---	---	---	---
Unknown	0	broad.mit.edu	37	3	105319948	105319953	+	IGR	DEL	ATACAC	-	-	rs2399050		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:105319948_105319953delATACAC								ALCAM (24205 upstream) : CBLB (57157 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	105375986	105375986	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:105375986delA								ALCAM (80243 upstream) : CBLB (1124 downstream)																																			---	---	---	---
CBLB	868	broad.mit.edu	37	3	105507284	105507284	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:105507284delA	uc003dwc.2	-						CBLB_uc011bhi.1_Intron|CBLB_uc003dwd.1_Intron|CBLB_uc003dwe.1_Intron|CBLB_uc011bhj.1_Intron	NM_170662	NP_733762			Cas-Br-M (murine) ecotropic retroviral						cell surface receptor linked signaling pathway|NLS-bearing substrate import into nucleus	cytoplasm|nucleus	calcium ion binding|ligase activity|signal transducer activity|zinc ion binding			lung(4)|ovary(3)|breast(1)|skin(1)	9								Mis S		AML								---	---	---	---
Unknown	0	broad.mit.edu	37	3	105820362	105820362	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:105820362delT								CBLB (232096 upstream) : LOC100302640 (735298 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	105854170	105854171	+	IGR	DEL	AG	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:105854170_105854171delAG								CBLB (265904 upstream) : LOC100302640 (701489 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	106204128	106204128	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:106204128delA								CBLB (615862 upstream) : LOC100302640 (351532 downstream)																																			---	---	---	---
LOC100302640	100302640	broad.mit.edu	37	3	106856229	106856229	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:106856229delT	uc003dwf.3	-						LOC100302640_uc011bhk.1_Intron					Homo sapiens cDNA clone IMAGE:5284861.												0																		---	---	---	---
LOC100302640	100302640	broad.mit.edu	37	3	106876689	106876689	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:106876689delT	uc003dwf.3	-						LOC100302640_uc011bhk.1_Intron					Homo sapiens cDNA clone IMAGE:5284861.												0																		---	---	---	---
LOC344595	344595	broad.mit.edu	37	3	106974094	106974098	+	Intron	DEL	GTTTT	-	-	rs57422550		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:106974094_106974098delGTTTT	uc010hpq.2	+							NR_028302				Homo sapiens cDNA FLJ31372 fis, clone NB9N42000281.												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	3	107115793	107115793	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:107115793delA								CCDC54 (18312 upstream) : BBX (125990 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	107173486	107173487	+	Intron	INS	-	AT	AT			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:107173486_107173487insAT	uc003dwj.2	+											Homo sapiens cDNA clone IMAGE:5312582.																														---	---	---	---
BBX	56987	broad.mit.edu	37	3	107242833	107242833	+	Intron	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:107242833delG	uc010hpr.2	+						BBX_uc003dwk.3_Intron|BBX_uc003dwl.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)															---	---	---	---
BBX	56987	broad.mit.edu	37	3	107331028	107331028	+	Intron	DEL	A	-	-	rs150153495		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:107331028delA	uc010hpr.2	+						BBX_uc003dwk.3_Intron|BBX_uc003dwl.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)															---	---	---	---
BBX	56987	broad.mit.edu	37	3	107336721	107336721	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:107336721delT	uc010hpr.2	+						BBX_uc003dwk.3_Intron|BBX_uc003dwl.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)															---	---	---	---
LOC151658	151658	broad.mit.edu	37	3	107587074	107587074	+	Intron	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:107587074delC	uc003dwp.3	-						LOC151658_uc003dwq.3_Intron	NR_015414				Homo sapiens hypothetical protein LOC151658, mRNA (cDNA clone IMAGE:5270728).												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	3	107728866	107728866	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:107728866delT								LOC285205 (81115 upstream) : CD47 (33075 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	107845425	107845426	+	IGR	DEL	AC	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:107845425_107845426delAC								CD47 (35490 upstream) : IFT57 (34234 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	107851381	107851382	+	IGR	DEL	CA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:107851381_107851382delCA								CD47 (41446 upstream) : IFT57 (28278 downstream)																																			---	---	---	---
HHLA2	11148	broad.mit.edu	37	3	108087095	108087095	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:108087095delA	uc003dwy.3	+						HHLA2_uc011bhl.1_Intron|HHLA2_uc010hpu.2_Intron|HHLA2_uc003dwz.2_Intron	NM_007072	NP_009003			HERV-H LTR-associating 2 precursor							integral to membrane				ovary(1)	1																		---	---	---	---
MYH15	22989	broad.mit.edu	37	3	108133346	108133347	+	Intron	DEL	TT	-	-	rs79578015		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:108133346_108133347delTT	uc003dxa.1	-							NM_014981	NP_055796			myosin, heavy polypeptide 15							myofibril|myosin filament	actin binding|ATP binding|calmodulin binding|motor activity			ovary(5)|central_nervous_system(2)	7																		---	---	---	---
TRAT1	50852	broad.mit.edu	37	3	108570476	108570479	+	Intron	DEL	AAAA	-	-	rs33945029		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:108570476_108570479delAAAA	uc003dxi.1	+						TRAT1_uc010hpx.1_Intron	NM_016388	NP_057472			T-cell receptor interacting molecule						cellular defense response|negative regulation of receptor recycling|negative regulation of transport|positive regulation of calcium-mediated signaling|positive regulation of T cell receptor signaling pathway|T cell receptor signaling pathway	integral to plasma membrane|T cell receptor complex	phosphatidylinositol-4,5-bisphosphate 3-kinase activity|transmembrane receptor protein tyrosine kinase adaptor activity			skin(1)	1																		---	---	---	---
MORC1	27136	broad.mit.edu	37	3	108690704	108690704	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:108690704delA	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	108813922	108813922	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:108813922delA	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																		---	---	---	---
C3orf66	677779	broad.mit.edu	37	3	108897650	108897652	+	Intron	DEL	AAG	-	-	rs66819422		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:108897650_108897652delAAG	uc003dxn.2	+							NR_026767				Homo sapiens cDNA FLJ41232 fis, clone BRAMY2030799.												0																		---	---	---	---
DPPA2	151871	broad.mit.edu	37	3	109027216	109027216	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:109027216delT	uc003dxo.2	-							NM_138815	NP_620170			developmental pluripotency associated 2							nucleus	nucleic acid binding			ovary(2)|upper_aerodigestive_tract(1)	3																		---	---	---	---
FLJ25363	401082	broad.mit.edu	37	3	109206592	109206592	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:109206592delT	uc003dxr.1	+							NM_001145553	NP_001139025			hypothetical protein LOC401082												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	3	109235361	109235361	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:109235361delA								FLJ25363 (21347 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	109296721	109296721	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:109296721delA								FLJ25363 (82707 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	109326684	109326684	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:109326684delT								FLJ25363 (112670 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	109331536	109331537	+	IGR	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:109331536_109331537delTT								FLJ25363 (117522 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	109526698	109526698	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:109526698delA								FLJ25363 (312684 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	109666553	109666554	+	IGR	DEL	AA	-	-	rs72232492		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:109666553_109666554delAA								FLJ25363 (452539 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	109703724	109703724	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:109703724delT								FLJ25363 (489710 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	109821213	109821213	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:109821213delT								FLJ25363 (607199 upstream) : PVRL3 (969652 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	109979486	109979486	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:109979486delA								FLJ25363 (765472 upstream) : PVRL3 (811379 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	110070868	110070868	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:110070868delT								FLJ25363 (856854 upstream) : PVRL3 (719997 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	110144154	110144154	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:110144154delT								FLJ25363 (930140 upstream) : PVRL3 (646711 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	110498043	110498043	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:110498043delA								None (None upstream) : PVRL3 (292822 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	110604344	110604344	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:110604344delT								None (None upstream) : PVRL3 (186521 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	110767239	110767239	+	IGR	DEL	A	-	-	rs11296571		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:110767239delA								None (None upstream) : PVRL3 (23626 downstream)																																			---	---	---	---
CD96	10225	broad.mit.edu	37	3	111299413	111299414	+	Intron	INS	-	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:111299413_111299414insA	uc003dxw.2	+						CD96_uc003dxv.2_Intron|CD96_uc003dxx.2_Intron|CD96_uc010hpy.1_Intron	NM_198196	NP_937839			CD96 antigen isoform 1 precursor						cell adhesion|immune response|regulation of immune response	integral to plasma membrane				skin(2)|central_nervous_system(1)	3														Opitz_Trigonocephaly_syndrome				---	---	---	---
PLCXD2	257068	broad.mit.edu	37	3	111449216	111449216	+	Intron	DEL	A	-	-	rs67891852		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:111449216delA	uc003dya.2	+						PLCXD2_uc003dxz.2_Intron|PHLDB2_uc003dyc.2_5'Flank	NM_001134478	NP_001127950			phosphatidylinositol-specific phospholipase C, X						intracellular signal transduction|lipid catabolic process		phospholipase C activity|signal transducer activity			skin(1)	1																		---	---	---	---
PHLDB2	90102	broad.mit.edu	37	3	111671328	111671328	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-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																		---	---	---	---
SLC9A10	285335	broad.mit.edu	37	3	111874037	111874037	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:111874037delA	uc003dyu.2	-						SLC9A10_uc011bhu.1_Intron|SLC9A10_uc010hqc.2_Intron	NM_183061	NP_898884			sperm-specific sodium proton exchanger						cell differentiation|multicellular organismal development|sodium ion transport|spermatogenesis	cilium|flagellar membrane|integral to membrane	solute:hydrogen antiporter activity			ovary(3)|breast(2)	5																		---	---	---	---
SLC9A10	285335	broad.mit.edu	37	3	111900634	111900634	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:111900634delA	uc003dyu.2	-						SLC9A10_uc011bhu.1_Intron|SLC9A10_uc010hqc.2_Intron	NM_183061	NP_898884			sperm-specific sodium proton exchanger						cell differentiation|multicellular organismal development|sodium ion transport|spermatogenesis	cilium|flagellar membrane|integral to membrane	solute:hydrogen antiporter activity			ovary(3)|breast(2)	5																		---	---	---	---
SLC9A10	285335	broad.mit.edu	37	3	112009662	112009664	+	Intron	DEL	TTT	-	-	rs111956603		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:112009662_112009664delTTT	uc003dyu.2	-						SLC9A10_uc010hqc.2_Intron	NM_183061	NP_898884			sperm-specific sodium proton exchanger						cell differentiation|multicellular organismal development|sodium ion transport|spermatogenesis	cilium|flagellar membrane|integral to membrane	solute:hydrogen antiporter activity			ovary(3)|breast(2)	5																		---	---	---	---
CD200	4345	broad.mit.edu	37	3	112062704	112062704	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:112062704delT	uc003dyw.2	+						CD200_uc010hqd.1_Intron|CD200_uc003dyx.2_Intron|CD200_uc003dyy.2_Intron|CD200_uc003dyz.2_Intron	NM_001004196	NP_001004196			CD200 antigen isoform b						regulation of immune response	integral to plasma membrane					0		Acute lymphoblastic leukemia(4;1.7e-08)|all_hematologic(4;8.82e-05)																---	---	---	---
CD200	4345	broad.mit.edu	37	3	112063697	112063697	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:112063697delT	uc003dyw.2	+						CD200_uc010hqd.1_Intron|CD200_uc003dyx.2_Intron|CD200_uc003dyy.2_Intron|CD200_uc003dyz.2_Intron	NM_001004196	NP_001004196			CD200 antigen isoform b						regulation of immune response	integral to plasma membrane					0		Acute lymphoblastic leukemia(4;1.7e-08)|all_hematologic(4;8.82e-05)																---	---	---	---
SLC35A5	55032	broad.mit.edu	37	3	112294970	112294971	+	Intron	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:112294970_112294971delTT	uc003dze.2	+							NM_017945	NP_060415			solute carrier family 35, member A5							Golgi membrane|integral to membrane	nucleotide-sugar transmembrane transporter activity|sugar:hydrogen symporter activity			ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	3	112320533	112320533	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:112320533delA								SLC35A5 (17531 upstream) : CCDC80 (2878 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	112424260	112424260	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:112424260delA								CCDC80 (64283 upstream) : CD200R1L (110296 downstream)																																			---	---	---	---
CD200R1	131450	broad.mit.edu	37	3	112645620	112645620	+	Intron	DEL	T	-	-	rs112012052		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:112645620delT	uc003dzk.1	-						CD200R1_uc003dzj.1_Intron|CD200R1_uc011bhx.1_Intron	NM_170780	NP_740750			CD200 receptor 1 isoform d						interspecies interaction between organisms|regulation of immune response	extracellular region|integral to membrane|plasma membrane	receptor activity			ovary(2)|pancreas(1)	3																		---	---	---	---
Unknown	0	broad.mit.edu	37	3	112834033	112834033	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:112834033delA								C3orf17 (95478 upstream) : BOC (96379 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	112879401	112879403	+	IGR	DEL	TTT	-	-	rs112495145		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:112879401_112879403delTTT								C3orf17 (140846 upstream) : BOC (51009 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	112898246	112898247	+	IGR	INS	-	AC	AC	rs141641454	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:112898246_112898247insAC								C3orf17 (159691 upstream) : BOC (32165 downstream)																																			---	---	---	---
BOC	91653	broad.mit.edu	37	3	112950047	112950047	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:112950047delT	uc003dzx.2	+						BOC_uc010hqi.2_Intron|BOC_uc003dzy.2_Intron|BOC_uc003dzz.2_Intron|BOC_uc003dzw.1_Intron|BOC_uc003eaa.1_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	113101499	113101499	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:113101499delA	uc003eae.1	-							NM_018338	NP_060808			WD repeat domain 52 isoform 2											central_nervous_system(1)	1																		---	---	---	---
SIDT1	54847	broad.mit.edu	37	3	113325706	113325707	+	Intron	INS	-	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:113325706_113325707insA	uc003eak.2	+						SIDT1_uc011bif.1_Intron|SIDT1_uc003eaj.1_Intron|SIDT1_uc011big.1_Intron|SIDT1_uc011bih.1_Intron|SIDT1_uc011bii.1_Intron	NM_017699	NP_060169			SID1 transmembrane family, member 1 precursor							integral to membrane				ovary(3)|pancreas(1)|skin(1)	5																		---	---	---	---
GRAMD1C	54762	broad.mit.edu	37	3	113619443	113619444	+	Intron	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:113619443_113619444delTT	uc003eaq.3	+						GRAMD1C_uc011bil.1_Intron|GRAMD1C_uc011bim.1_Intron|GRAMD1C_uc003ear.2_Intron|GRAMD1C_uc003eas.2_Intron	NM_017577	NP_060047			GRAM domain containing 1C							integral to membrane				ovary(2)|skin(1)	3																		---	---	---	---
DRD3	1814	broad.mit.edu	37	3	113878321	113878321	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:113878321delA	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)													---	---	---	---
DRD3	1814	broad.mit.edu	37	3	113904531	113904531	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:113904531delT	uc010hqn.1	-							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)													---	---	---	---
Unknown	0	broad.mit.edu	37	3	113972944	113972945	+	IGR	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:113972944_113972945delTT								ZNF80 (16519 upstream) : TIGIT (39930 downstream)																																			---	---	---	---
ZBTB20	26137	broad.mit.edu	37	3	114167128	114167128	+	Intron	DEL	A	-	-	rs111894767		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:114167128delA	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	114173566	114173566	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:114173566delA	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	114332635	114332635	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:114332635delT	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	114420600	114420600	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:114420600delA	uc003ebk.2	-						ZBTB20_uc003ebl.2_Intron|ZBTB20_uc003ebm.2_Intron|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	114783989	114783989	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:114783989delT	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	114900717	114900719	+	IGR	DEL	AAA	-	-	rs112788399		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:114900717_114900719delAAA								ZBTB20 (34590 upstream) : GAP43 (441432 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	115103936	115103938	+	IGR	DEL	AAG	-	-	rs144798591		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:115103936_115103938delAAG								ZBTB20 (237809 upstream) : GAP43 (238213 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	115529069	115529070	+	IGR	DEL	TC	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:115529069_115529070delTC								LSAMP (5051 upstream) : LOC285194 (899565 downstream)																																			---	---	---	---
LSAMP	4045	broad.mit.edu	37	3	115726510	115726511	+	Intron	INS	-	AC	AC	rs138649308	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:115726510_115726511insAC	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)														---	---	---	---
LSAMP	4045	broad.mit.edu	37	3	115844239	115844239	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:115844239delT	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)														---	---	---	---
LSAMP	4045	broad.mit.edu	37	3	116017276	116017276	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:116017276delA	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	116184465	116184465	+	IGR	DEL	T	-	-	rs63611261		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:116184465delT								LSAMP (660447 upstream) : LOC285194 (244170 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	116411726	116411726	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:116411726delA								LSAMP (887708 upstream) : LOC285194 (16909 downstream)																																			---	---	---	---
LOC285194	285194	broad.mit.edu	37	3	116425981	116425982	+	5'Flank	DEL	AT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:116425981_116425982delAT	uc010hqr.2	+						LOC285194_uc003ebu.3_5'Flank|LOC285194_uc011bit.1_5'Flank	NR_015391				Homo sapiens cDNA clone IMAGE:5266409.												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	3	116648736	116648736	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:116648736delA	uc003ebv.2	+											Homo sapiens cDNA clone IMAGE:5269228.																														---	---	---	---
Unknown	0	broad.mit.edu	37	3	116838871	116838872	+	IGR	DEL	TG	-	-	rs145485578	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:116838871_116838872delTG								LOC285194 (402986 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	117062680	117062680	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:117062680delA								LOC285194 (626795 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	117066079	117066079	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:117066079delT								LOC285194 (630194 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	117146990	117146991	+	IGR	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:117146990_117146991delTT								LOC285194 (711105 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	117449736	117449736	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:117449736delA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	118433136	118433137	+	Intron	INS	-	AT	AT			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:118433136_118433137insAT	uc011biu.1	-											Homo sapiens clone HA_003061 mRNA sequence.																														---	---	---	---
Unknown	0	broad.mit.edu	37	3	118484008	118484009	+	Intron	DEL	AG	-	-	rs71705116		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:118484008_118484009delAG	uc011biu.1	-											Homo sapiens clone HA_003061 mRNA sequence.																														---	---	---	---
IGSF11	152404	broad.mit.edu	37	3	118648582	118648582	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:118648582delA	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																		---	---	---	---
B4GALT4	8702	broad.mit.edu	37	3	118960773	118960773	+	5'Flank	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:118960773delC	uc003ecg.2	-						B4GALT4_uc003ece.1_5'Flank|B4GALT4_uc003ech.2_5'Flank|B4GALT4_uc003eci.2_5'Flank|B4GALT4_uc011biy.1_5'Flank	NM_212543	NP_997708			UDP-Gal:betaGlcNAc beta 1,4-						membrane lipid metabolic process|post-translational protein modification|protein N-linked glycosylation via asparagine	Golgi cisterna membrane|integral to membrane	metal ion binding|N-acetyllactosamine synthase activity				0				GBM - Glioblastoma multiforme(114;0.222)	N-Acetyl-D-glucosamine(DB00141)													---	---	---	---
ARHGAP31	57514	broad.mit.edu	37	3	119042351	119042351	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:119042351delT	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	119054866	119054866	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:119054866delA	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	119083111	119083111	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:119083111delA	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																		---	---	---	---
PLA1A	51365	broad.mit.edu	37	3	119334672	119334672	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:119334672delA	uc003ecu.2	+						PLA1A_uc003ecv.2_Intron|PLA1A_uc003ecw.2_Intron|PLA1A_uc011bjc.1_Intron	NM_015900	NP_056984			phospholipase A1 member A precursor						lipid catabolic process|phosphatidylserine metabolic process	extracellular region	phospholipase A1 activity			upper_aerodigestive_tract(1)|ovary(1)|central_nervous_system(1)	3																		---	---	---	---
Unknown	0	broad.mit.edu	37	3	119360004	119360004	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:119360004delA								PLA1A (11348 upstream) : POPDC2 (904 downstream)																																			---	---	---	---
NR1I2	8856	broad.mit.edu	37	3	119498512	119498513	+	5'Flank	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:119498512_119498513delAA	uc003edj.2	+						NR1I2_uc003edi.2_5'Flank	NM_003889	NP_003880			nuclear receptor subfamily 1, group I, member 2						drug export|exogenous drug catabolic process|negative regulation of transcription, DNA-dependent|positive regulation of transcription, DNA-dependent|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor|steroid metabolic process|xenobiotic metabolic process|xenobiotic transport	nucleoplasm	drug binding|protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|steroid hormone receptor activity|transcription coactivator activity|zinc ion binding			ovary(2)	2				GBM - Glioblastoma multiforme(114;0.175)	Estradiol(DB00783)|Ethinyl Estradiol(DB00977)|Rifampin(DB01045)|Vitamin E(DB00163)													---	---	---	---
NR1I2	8856	broad.mit.edu	37	3	119509091	119509091	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:119509091delT	uc003edj.2	+						NR1I2_uc003edi.2_Intron|NR1I2_uc003edk.2_Intron	NM_003889	NP_003880			nuclear receptor subfamily 1, group I, member 2						drug export|exogenous drug catabolic process|negative regulation of transcription, DNA-dependent|positive regulation of transcription, DNA-dependent|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor|steroid metabolic process|xenobiotic metabolic process|xenobiotic transport	nucleoplasm	drug binding|protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|steroid hormone receptor activity|transcription coactivator activity|zinc ion binding			ovary(2)	2				GBM - Glioblastoma multiforme(114;0.175)	Estradiol(DB00783)|Ethinyl Estradiol(DB00977)|Rifampin(DB01045)|Vitamin E(DB00163)													---	---	---	---
GSK3B	2932	broad.mit.edu	37	3	119724951	119724951	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:119724951delA	uc003edo.2	-						GSK3B_uc003edn.2_Intron	NM_001146156	NP_001139628			glycogen synthase kinase 3 beta isoform 2						axon guidance|epithelial to mesenchymal transition|ER overload response|glycogen metabolic process|hippocampus development|negative regulation of apoptosis|negative regulation of protein binding|negative regulation of protein complex assembly|nerve growth factor receptor signaling pathway|peptidyl-serine phosphorylation|phosphatidylinositol-mediated signaling|positive regulation of cell-matrix adhesion|positive regulation of protein complex assembly|positive regulation of protein export from nucleus|positive regulation of Rac GTPase activity|regulation of microtubule-based process|superior temporal gyrus development	Axin-APC-beta-catenin-GSK3B complex|beta-catenin destruction complex|centrosome|cytosol|nucleus|plasma membrane	ATP binding|beta-catenin binding|NF-kappaB binding|p53 binding|protein kinase A catalytic subunit binding|protein serine/threonine kinase activity|RNA polymerase II transcription factor binding|tau-protein kinase activity|ubiquitin protein ligase binding			lung(2)	2				GBM - Glioblastoma multiforme(114;0.24)	Lithium(DB01356)													---	---	---	---
GSK3B	2932	broad.mit.edu	37	3	119733514	119733514	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:119733514delT	uc003edo.2	-						GSK3B_uc003edn.2_Intron	NM_001146156	NP_001139628			glycogen synthase kinase 3 beta isoform 2						axon guidance|epithelial to mesenchymal transition|ER overload response|glycogen metabolic process|hippocampus development|negative regulation of apoptosis|negative regulation of protein binding|negative regulation of protein complex assembly|nerve growth factor receptor signaling pathway|peptidyl-serine phosphorylation|phosphatidylinositol-mediated signaling|positive regulation of cell-matrix adhesion|positive regulation of protein complex assembly|positive regulation of protein export from nucleus|positive regulation of Rac GTPase activity|regulation of microtubule-based process|superior temporal gyrus development	Axin-APC-beta-catenin-GSK3B complex|beta-catenin destruction complex|centrosome|cytosol|nucleus|plasma membrane	ATP binding|beta-catenin binding|NF-kappaB binding|p53 binding|protein kinase A catalytic subunit binding|protein serine/threonine kinase activity|RNA polymerase II transcription factor binding|tau-protein kinase activity|ubiquitin protein ligase binding			lung(2)	2				GBM - Glioblastoma multiforme(114;0.24)	Lithium(DB01356)													---	---	---	---
GPR156	165829	broad.mit.edu	37	3	119896648	119896650	+	Intron	DEL	AAA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:119896648_119896650delAAA	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)														---	---	---	---
Unknown	0	broad.mit.edu	37	3	120036926	120036926	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:120036926delA								GPR156 (73601 upstream) : LRRC58 (6650 downstream)																																			---	---	---	---
LRRC58	116064	broad.mit.edu	37	3	120062916	120062916	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:120062916delA	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	120219027	120219029	+	IGR	DEL	AAA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:120219027_120219029delAAA								FSTL1 (49109 upstream) : NDUFB4 (96099 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	120307968	120307969	+	IGR	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:120307968_120307969delTT								FSTL1 (138050 upstream) : NDUFB4 (7159 downstream)																																			---	---	---	---
HGD	3081	broad.mit.edu	37	3	120359047	120359049	+	Intron	DEL	AAA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:120359047_120359049delAAA	uc003edw.2	-						HGD_uc003edv.2_Intron	NM_000187	NP_000178			homogentisate 1,2-dioxygenase						L-phenylalanine catabolic process|tyrosine catabolic process	cytosol	homogentisate 1,2-dioxygenase activity|metal ion binding				0				GBM - Glioblastoma multiforme(114;0.158)														---	---	---	---
RABL3	285282	broad.mit.edu	37	3	120445915	120445915	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:120445915delA	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)														---	---	---	---
RABL3	285282	broad.mit.edu	37	3	120456814	120456814	+	Intron	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:120456814delG	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)														---	---	---	---
Unknown	0	broad.mit.edu	37	3	120526627	120526641	+	IGR	DEL	GAGGAAGAAGAAGAA	-	-	rs6791734	by1000genomes;by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:120526627_120526641delGAGGAAGAAGAAGAA								GTF2E1 (24712 upstream) : STXBP5L (100409 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	120553815	120553818	+	Intron	DEL	TGTT	-	-	rs10573161		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:120553815_120553818delTGTT	uc003eeb.1	-											Homo sapiens cDNA clone IMAGE:5266489.																														---	---	---	---
STXBP5L	9515	broad.mit.edu	37	3	120900258	120900258	+	Intron	DEL	A	-	-	rs80346827		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:120900258delA	uc003eec.3	+						STXBP5L_uc011bji.1_Intron	NM_014980	NP_055795			syntaxin binding protein 5-like						exocytosis|protein transport	cytoplasm|integral to membrane|plasma membrane				ovary(7)|skin(2)	9				GBM - Glioblastoma multiforme(114;0.0694)														---	---	---	---
STXBP5L	9515	broad.mit.edu	37	3	120968735	120968735	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:120968735delT	uc003eec.3	+						STXBP5L_uc011bji.1_Intron	NM_014980	NP_055795			syntaxin binding protein 5-like						exocytosis|protein transport	cytoplasm|integral to membrane|plasma membrane				ovary(7)|skin(2)	9				GBM - Glioblastoma multiforme(114;0.0694)														---	---	---	---
POLQ	10721	broad.mit.edu	37	3	121214119	121214120	+	Intron	DEL	AA	-	-	rs79330623		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:121214119_121214120delAA	uc003eee.3	-							NM_199420	NP_955452			DNA polymerase theta						DNA repair|DNA replication	nucleoplasm	ATP binding|ATP-dependent helicase activity|damaged DNA binding|DNA-directed DNA polymerase activity|single-stranded DNA-dependent ATPase activity			ovary(4)|breast(3)|lung(2)|upper_aerodigestive_tract(1)|skin(1)	11				GBM - Glioblastoma multiforme(114;0.0915)									DNA_polymerases_(catalytic_subunits)					---	---	---	---
Unknown	0	broad.mit.edu	37	3	121472010	121472010	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:121472010delA								GOLGB1 (3408 upstream) : IQCB1 (16600 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	121674375	121674375	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:121674375delT								SLC15A2 (11341 upstream) : ILDR1 (31796 downstream)																																			---	---	---	---
CD86	942	broad.mit.edu	37	3	121798374	121798374	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:121798374delT	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)													---	---	---	---
CD86	942	broad.mit.edu	37	3	121815968	121815968	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:121815968delT	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)													---	---	---	---
Unknown	0	broad.mit.edu	37	3	121849980	121849981	+	IGR	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:121849980_121849981delAA								CD86 (9998 upstream) : CASR (52549 downstream)																																			---	---	---	---
CCDC58	131076	broad.mit.edu	37	3	122081882	122081882	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:122081882delA	uc003eey.2	-							NM_001017928	NP_001017928			coiled-coil domain containing 58												0				GBM - Glioblastoma multiforme(114;0.148)														---	---	---	---
CCDC58	131076	broad.mit.edu	37	3	122082116	122082116	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:122082116delA	uc003eey.2	-							NM_001017928	NP_001017928			coiled-coil domain containing 58												0				GBM - Glioblastoma multiforme(114;0.148)														---	---	---	---
CCDC58	131076	broad.mit.edu	37	3	122095014	122095025	+	Intron	DEL	AAAAAAAAAAAA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:122095014_122095025delAAAAAAAAAAAA	uc003eey.2	-							NM_001017928	NP_001017928			coiled-coil domain containing 58												0				GBM - Glioblastoma multiforme(114;0.148)														---	---	---	---
PARP15	165631	broad.mit.edu	37	3	122343856	122343856	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:122343856delT	uc003efm.2	+						PARP15_uc003efn.2_Intron|PARP15_uc003efo.1_Intron|PARP15_uc003efp.1_Intron|PARP15_uc011bjt.1_Intron	NM_001113523	NP_001106995			poly (ADP-ribose) polymerase family, member 15						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	122403458	122403458	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:122403458delT	uc003efq.3	+							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	122411978	122411979	+	Intron	INS	-	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:122411978_122411979insC	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)														---	---	---	---
DIRC2	84925	broad.mit.edu	37	3	122554412	122554412	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:122554412delA	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)														---	---	---	---
SEMA5B	54437	broad.mit.edu	37	3	122631464	122631465	+	Intron	DEL	AA	-	-	rs150722244		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:122631464_122631465delAA	uc003efz.1	-						SEMA5B_uc011bju.1_Intron|SEMA5B_uc003ega.1_Intron|SEMA5B_uc003egb.1_Intron|SEMA5B_uc003efy.1_5'Flank	NM_001031702	NP_001026872			semaphorin 5B isoform 1						cell differentiation|nervous system development	integral to membrane	receptor activity			ovary(2)|breast(2)|pancreas(2)|central_nervous_system(1)	7				GBM - Glioblastoma multiforme(114;0.0367)														---	---	---	---
PDIA5	10954	broad.mit.edu	37	3	122806318	122806318	+	Intron	DEL	T	-	-	rs145616985		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:122806318delT	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)														---	---	---	---
PDIA5	10954	broad.mit.edu	37	3	122841127	122841127	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:122841127delA	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)														---	---	---	---
SEC22A	26984	broad.mit.edu	37	3	122975297	122975297	+	Intron	DEL	A	-	-	rs63205861		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:122975297delA	uc003ege.2	+						SEC22A_uc003egf.2_Intron	NM_012430	NP_036562			SEC22 vesicle trafficking protein homolog A						ER to Golgi vesicle-mediated transport|protein transport	endoplasmic reticulum membrane|integral to membrane	transporter activity			ovary(1)	1				GBM - Glioblastoma multiforme(114;0.0548)														---	---	---	---
Unknown	0	broad.mit.edu	37	3	123211586	123211586	+	RNA	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:123211586delT	uc010hrq.1	-	1		c.95delA								Homo sapiens clone 24416 mRNA sequence.																														---	---	---	---
PTPLB	201562	broad.mit.edu	37	3	123260117	123260117	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:123260117delA	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	123302050	123302050	+	Intron	DEL	A	-	-	rs142197091		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:123302050delA	uc003egj.2	-						uc003egk.2_5'Flank	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)														---	---	---	---
CCDC14	64770	broad.mit.edu	37	3	123674880	123674880	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:123674880delA	uc011bjx.1	-						CCDC14_uc003egv.3_5'Flank|CCDC14_uc003egx.3_5'UTR|CCDC14_uc010hrt.2_Intron|CCDC14_uc003egy.3_Intron|CCDC14_uc003egz.2_5'UTR	NM_022757	NP_073594			coiled-coil domain containing 14							centrosome					0		Lung NSC(201;0.0371)|Prostate(884;0.0405)|Myeloproliferative disorder(1037;0.205)		Lung(219;0.00942)|GBM - Glioblastoma multiforme(114;0.159)														---	---	---	---
KALRN	8997	broad.mit.edu	37	3	123788863	123788863	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:123788863delA	uc003ehd.2	+											Homo sapiens cDNA FLJ41073 fis, clone 3NB692008178.						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	123967102	123967102	+	Intron	DEL	C	-	-	rs78690628		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:123967102delC	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	124110906	124110906	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:124110906delT	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																		---	---	---	---
KALRN	8997	broad.mit.edu	37	3	124306747	124306748	+	Intron	INS	-	C	C	rs148268232	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:124306747_124306748insC	uc003ehg.2	+						KALRN_uc003ehi.2_Intron|KALRN_uc003ehk.2_Intron|KALRN_uc003ehj.2_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	124414587	124414588	+	Intron	DEL	TT	-	-	rs10677867		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:124414587_124414588delTT	uc003ehg.2	+						KALRN_uc003ehk.2_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	124433863	124433865	+	Intron	DEL	AAA	-	-	rs145634428		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:124433863_124433865delAAA	uc003ehg.2	+						KALRN_uc003ehk.2_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																		---	---	---	---
ITGB5	3693	broad.mit.edu	37	3	124551037	124551038	+	Intron	INS	-	A	A	rs144884707	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:124551037_124551038insA	uc003eho.2	-							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)														---	---	---	---
ITGB5	3693	broad.mit.edu	37	3	124558399	124558399	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:124558399delA	uc003eho.2	-							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)														---	---	---	---
Unknown	0	broad.mit.edu	37	3	124665561	124665561	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:124665561delA								MUC13 (11981 upstream) : HEG1 (18994 downstream)																																			---	---	---	---
SLC12A8	84561	broad.mit.edu	37	3	124830636	124830636	+	Intron	DEL	A	-	-	rs111739487		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:124830636delA	uc003ehv.3	-						SLC12A8_uc003ehw.3_Intron|SLC12A8_uc003eht.3_Intron|SLC12A8_uc003ehu.3_Intron|SLC12A8_uc010hry.2_Intron	NM_024628	NP_078904			solute carrier family 12, member 8						potassium ion transport	integral to membrane	symporter activity				0																		---	---	---	---
ZNF148	7707	broad.mit.edu	37	3	124959610	124959613	+	Intron	DEL	AAAA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:124959610_124959613delAAAA	uc003ehx.3	-						SLC12A8_uc003ehw.3_Intron|ZNF148_uc003ehz.3_Intron|ZNF148_uc010hsa.2_Intron|ZNF148_uc003eia.3_Intron|ZNF148_uc003ehy.2_Intron	NM_021964	NP_068799			zinc finger protein 148						cellular defense response|negative regulation of transcription from RNA polymerase II promoter|transcription from RNA polymerase II promoter	Golgi apparatus|nucleus	protein binding|sequence-specific DNA binding|zinc ion binding			skin(2)|ovary(1)|pancreas(1)	4																		---	---	---	---
ZNF148	7707	broad.mit.edu	37	3	125004399	125004401	+	Intron	DEL	AAA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:125004399_125004401delAAA	uc003ehx.3	-						ZNF148_uc003ehz.3_Intron|ZNF148_uc010hsa.2_Intron|ZNF148_uc003eia.3_Intron|ZNF148_uc003ehy.2_Intron	NM_021964	NP_068799			zinc finger protein 148						cellular defense response|negative regulation of transcription from RNA polymerase II promoter|transcription from RNA polymerase II promoter	Golgi apparatus|nucleus	protein binding|sequence-specific DNA binding|zinc ion binding			skin(2)|ovary(1)|pancreas(1)	4																		---	---	---	---
SNX4	8723	broad.mit.edu	37	3	125211269	125211269	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:125211269delT	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	125238434	125238434	+	Intron	DEL	C	-	-	rs146530138	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:125238434delC	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																		---	---	---	---
OSBPL11	114885	broad.mit.edu	37	3	125292053	125292054	+	Intron	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:125292053_125292054delAA	uc003eic.2	-							NM_022776	NP_073613			oxysterol binding protein-like 11						lipid transport		lipid binding			ovary(3)|breast(1)|kidney(1)	5																		---	---	---	---
Unknown	0	broad.mit.edu	37	3	125469071	125469071	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:125469071delT								OSBPL11 (154690 upstream) : MIR548I1 (40176 downstream)																																			---	---	---	---
ALDH1L1	10840	broad.mit.edu	37	3	125882974	125882974	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:125882974delA	uc003eim.1	-						ALDH1L1_uc010hse.1_Intron|ALDH1L1_uc011bki.1_Intron|ALDH1L1_uc010hsf.1_Intron|ALDH1L1_uc011bkj.1_Intron	NM_012190	NP_036322			aldehyde dehydrogenase 1 family, member L1						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)													---	---	---	---
Unknown	0	broad.mit.edu	37	3	126008983	126008983	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:126008983delT								ALDH1L1 (109498 upstream) : KLF15 (52495 downstream)																																			---	---	---	---
TXNRD3IT1	645840	broad.mit.edu	37	3	126363061	126363061	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:126363061delT	uc003ejd.1	-						TXNRD3IT1_uc011bkl.1_Intron					RecName: Full=Thioredoxin reductase 3;          EC=1.8.1.9; AltName: Full=Thioredoxin reductase TR2; AltName: Full=Thioredoxin and glutathione reductase;												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	3	126403275	126403276	+	IGR	DEL	CA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:126403275_126403276delCA								TXNRD3IT1 (29330 upstream) : CHCHD6 (19842 downstream)																																			---	---	---	---
CHCHD6	84303	broad.mit.edu	37	3	126482060	126482060	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:126482060delT	uc003ejf.1	+						CHCHD6_uc010hsj.1_Intron	NM_032343	NP_115719			coiled-coil-helix-coiled-coil-helix domain												0																		---	---	---	---
CHCHD6	84303	broad.mit.edu	37	3	126545647	126545647	+	Intron	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:126545647delC	uc003ejf.1	+						CHCHD6_uc010hsj.1_Intron	NM_032343	NP_115719			coiled-coil-helix-coiled-coil-helix domain												0																		---	---	---	---
CHCHD6	84303	broad.mit.edu	37	3	126553307	126553307	+	Intron	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:126553307delG	uc003ejf.1	+						CHCHD6_uc010hsj.1_Intron	NM_032343	NP_115719			coiled-coil-helix-coiled-coil-helix domain												0																		---	---	---	---
CHCHD6	84303	broad.mit.edu	37	3	126592150	126592150	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:126592150delT	uc003ejf.1	+						CHCHD6_uc010hsj.1_Intron	NM_032343	NP_115719			coiled-coil-helix-coiled-coil-helix domain												0																		---	---	---	---
CHCHD6	84303	broad.mit.edu	37	3	126664586	126664586	+	Intron	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:126664586delG	uc003ejf.1	+						CHCHD6_uc010hsj.1_Intron	NM_032343	NP_115719			coiled-coil-helix-coiled-coil-helix domain												0																		---	---	---	---
PLXNA1	5361	broad.mit.edu	37	3	126735762	126735762	+	Intron	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:126735762delC	uc003ejg.2	+							NM_032242	NP_115618			plexin A1						axon guidance	integral to membrane|intracellular|plasma membrane	semaphorin receptor activity			ovary(1)|pancreas(1)|skin(1)	3				GBM - Glioblastoma multiforme(114;0.155)														---	---	---	---
Unknown	0	broad.mit.edu	37	3	126865295	126865298	+	IGR	DEL	TGGA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:126865295_126865298delTGGA								PLXNA1 (109067 upstream) : TPRA1 (426610 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	127044033	127044033	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:127044033delA	uc003ejj.2	-											Homo sapiens, clone IMAGE:4618125, mRNA.																														---	---	---	---
Unknown	0	broad.mit.edu	37	3	127285419	127285419	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:127285419delT								PLXNA1 (529191 upstream) : TPRA1 (6489 downstream)																																			---	---	---	---
MCM2	4171	broad.mit.edu	37	3	127314927	127314927	+	5'Flank	DEL	T	-	-	rs112013218		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:127314927delT	uc003ejp.2	+						MCM2_uc011bkm.1_5'Flank	NM_004526	NP_004517			minichromosome maintenance complex component 2						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																		---	---	---	---
MGLL	11343	broad.mit.edu	37	3	127537222	127537224	+	Intron	DEL	TTT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:127537222_127537224delTTT	uc003ejx.2	-						MGLL_uc003ejw.2_Intron|MGLL_uc011bko.1_Intron|MGLL_uc010hsp.1_Intron	NM_001003794	NP_001003794			monoglyceride lipase isoform 2						arachidonic acid metabolic process|fatty acid biosynthetic process|inflammatory response|platelet activation|regulation of endocannabinoid signaling pathway|regulation of inflammatory response|regulation of sensory perception of pain|triglyceride catabolic process	plasma membrane	acylglycerol lipase activity|carboxylesterase activity|lysophospholipase activity|protein homodimerization activity				0																		---	---	---	---
GATA2	2624	broad.mit.edu	37	3	128202631	128202631	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:128202631delT	uc003ekm.3	-						GATA2_uc003ekn.3_Intron|GATA2_uc003eko.2_Intron	NM_001145661	NP_001139133			GATA binding protein 2 isoform 1						blood coagulation|negative regulation of fat cell differentiation|negative regulation of fat cell proliferation|negative regulation of neural precursor cell proliferation|negative regulation of Notch signaling pathway|phagocytosis|positive regulation of angiogenesis|positive regulation of phagocytosis|positive regulation of transcription from RNA polymerase II promoter	nucleoplasm	C2H2 zinc finger domain binding|chromatin binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription factor binding|zinc ion binding			haematopoietic_and_lymphoid_tissue(13)|lung(1)|skin(1)	15				GBM - Glioblastoma multiforme(114;0.173)				Mis		AML(CML blast transformation)								---	---	---	---
RAB7A	7879	broad.mit.edu	37	3	128532447	128532448	+	3'UTR	DEL	CA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:128532447_128532448delCA	uc003eks.1	+	6					RAB7A_uc010hsv.1_3'UTR|RAB7A_uc003ekt.2_Frame_Shift_Del_p.H194fs	NM_004637	NP_004628			RAB7, member RAS oncogene family						endocytosis|endosome to lysosome transport|epidermal growth factor catabolic process|protein transport|small GTPase mediated signal transduction	Golgi apparatus|late endosome|lysosome|melanosome|phagocytic vesicle	GDP binding|GTP binding|GTPase activity|protein binding				0				GBM - Glioblastoma multiforme(114;0.231)														---	---	---	---
ACAD9	28976	broad.mit.edu	37	3	128605726	128605727	+	Intron	DEL	TT	-	-	rs78504700		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:128605726_128605727delTT	uc003ela.3	+						ACAD9_uc010hsw.1_Intron|ACAD9_uc011bks.1_Intron|ACAD9_uc003elb.2_Intron	NM_014049	NP_054768			acyl-Coenzyme A dehydrogenase family, member 9							mitochondrion	acyl-CoA dehydrogenase activity|flavin adenine dinucleotide binding			ovary(2)|central_nervous_system(1)	3																		---	---	---	---
KIAA1257	57501	broad.mit.edu	37	3	128638091	128638091	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:128638091delT	uc003elg.1	-							NM_020741	NP_065792			hypothetical protein LOC57501												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	3	128761605	128761605	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:128761605delA								CCDC48 (2022 upstream) : GP9 (18040 downstream)																																			---	---	---	---
RAB43	339122	broad.mit.edu	37	3	128822413	128822417	+	Intron	DEL	TTTTT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:128822413_128822417delTTTTT	uc003eln.1	-						RAB43_uc003elo.1_Intron|RAB43_uc010hsy.1_Intron	NM_198490	NP_940892			RAB43 protein						protein transport|small GTPase mediated signal transduction	plasma membrane	GTP binding			lung(1)	1																		---	---	---	---
CNBP	7555	broad.mit.edu	37	3	128901783	128901786	+	Intron	DEL	TTGT	-	-	rs113840705		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:128901783_128901786delTTGT	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	128973139	128973139	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:128973139delA	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	128986463	128986463	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:128986463delA	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	128994815	128994816	+	Intron	DEL	AC	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:128994815_128994816delAC	uc003els.2	+						COPG_uc010htb.2_Intron|C3orf37_uc003elt.2_5'Flank|C3orf37_uc003elu.2_5'Flank	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																		---	---	---	---
IFT122	55764	broad.mit.edu	37	3	129183764	129183764	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:129183764delT	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_uc011bkx.1_Intron|IFT122_uc011bkz.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																		---	---	---	---
Unknown	0	broad.mit.edu	37	3	129254582	129254585	+	IGR	DEL	AAAC	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:129254582_129254585delAAAC								RHO (396 upstream) : H1FOO (7472 downstream)																																			---	---	---	---
TMCC1	23023	broad.mit.edu	37	3	129388279	129388280	+	Intron	INS	-	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:129388279_129388280insT	uc003emz.3	-						TMCC1_uc003emy.3_Intron|TMCC1_uc011blc.1_Intron|TMCC1_uc010htg.2_Intron	NM_001017395	NP_001017395			transmembrane and coiled-coil domain family 1							integral to membrane				skin(1)	1																		---	---	---	---
TMCC1	23023	broad.mit.edu	37	3	129419329	129419329	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:129419329delT	uc003emz.3	-						TMCC1_uc011blc.1_Intron|TMCC1_uc010htg.2_Intron	NM_001017395	NP_001017395			transmembrane and coiled-coil domain family 1							integral to membrane				skin(1)	1																		---	---	---	---
TMCC1	23023	broad.mit.edu	37	3	129465018	129465018	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:129465018delT	uc003emz.3	-						TMCC1_uc011blc.1_Intron|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	129635231	129635231	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:129635231delA								TMCC1 (22828 upstream) : TRH (57883 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	129642013	129642014	+	IGR	INS	-	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:129642013_129642014insC								TMCC1 (29610 upstream) : TRH (51100 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	130015598	130015599	+	IGR	INS	-	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:130015598_130015599insT								COL6A4P2 (22950 upstream) : COL29A1 (48760 downstream)																																			---	---	---	---
COL29A1	256076	broad.mit.edu	37	3	130074893	130074893	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:130074893delT	uc010htj.1	+						COL29A1_uc010hti.1_Intron	NM_153264	NP_694996			collagen, type XXIX, alpha 1						axon guidance|cell adhesion	collagen					0																		---	---	---	---
Unknown	0	broad.mit.edu	37	3	130244393	130244393	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:130244393delT								COL29A1 (40705 upstream) : COL6A6 (34785 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	130245658	130245659	+	IGR	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:130245658_130245659delAA								COL29A1 (41970 upstream) : COL6A6 (33519 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	130271920	130271920	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:130271920delT								COL29A1 (68232 upstream) : COL6A6 (7258 downstream)																																			---	---	---	---
COL6A6	131873	broad.mit.edu	37	3	130367861	130367861	+	Intron	DEL	T	-	-	rs72391450		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-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																		---	---	---	---
PIK3R4	30849	broad.mit.edu	37	3	130457902	130457902	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:130457902delT	uc003enj.2	-							NM_014602	NP_055417			phosphoinositide-3-kinase, regulatory subunit 4						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																		---	---	---	---
NEK11	79858	broad.mit.edu	37	3	130951976	130951977	+	Intron	DEL	GA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:130951976_130951977delGA	uc003eny.2	+						NEK11_uc003eoa.2_Intron|NEK11_uc003enz.2_Intron|NEK11_uc010htn.2_Intron|NEK11_uc011blk.1_Intron|NEK11_uc011bll.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	130978929	130978931	+	Intron	DEL	ATA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:130978929_130978931delATA	uc003eny.2	+						NEK11_uc003eoa.2_Intron|NEK11_uc003enz.2_Intron|NEK11_uc010htn.2_Intron|NEK11_uc011blk.1_Intron|NEK11_uc011bll.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	131117744	131117745	+	IGR	DEL	TG	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:131117744_131117745delTG								NUDT16 (12815 upstream) : MRPL3 (63301 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	131147240	131147241	+	IGR	DEL	AA	-	-	rs139630404		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:131147240_131147241delAA								NUDT16 (42311 upstream) : MRPL3 (33805 downstream)																																			---	---	---	---
CPNE4	131034	broad.mit.edu	37	3	131655809	131655809	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:131655809delA	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																		---	---	---	---
CPNE4	131034	broad.mit.edu	37	3	131767034	131767034	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:131767034delT	uc003eom.2	-							NM_130808	NP_570720			copine IV											upper_aerodigestive_tract(1)|central_nervous_system(1)|skin(1)	3																		---	---	---	---
DNAJC13	23317	broad.mit.edu	37	3	132193667	132193675	+	Intron	DEL	CCCCTTTTT	-	-	rs35380727		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:132193667_132193675delCCCCTTTTT	uc003eor.2	+							NM_015268	NP_056083			DnaJ (Hsp40) homolog, subfamily C, member 13								heat shock protein binding			ovary(1)|breast(1)	2																		---	---	---	---
DNAJC13	23317	broad.mit.edu	37	3	132242713	132242713	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:132242713delT	uc003eor.2	+							NM_015268	NP_056083			DnaJ (Hsp40) homolog, subfamily C, member 13								heat shock protein binding			ovary(1)|breast(1)	2																		---	---	---	---
ACAD11	84129	broad.mit.edu	37	3	132282612	132282612	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:132282612delT	uc003eov.3	-							NM_032169	NP_115545			putative acyl-CoA dehydrogenase							peroxisome	acyl-CoA dehydrogenase activity|flavin adenine dinucleotide binding|transferase activity, transferring phosphorus-containing groups			ovary(1)	1																		---	---	---	---
ACAD11	84129	broad.mit.edu	37	3	132366012	132366012	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:132366012delA	uc003eov.3	-						NPHP3_uc003eoz.1_Intron|ACAD11_uc003eoy.2_Intron	NM_032169	NP_115545			putative acyl-CoA dehydrogenase							peroxisome	acyl-CoA dehydrogenase activity|flavin adenine dinucleotide binding|transferase activity, transferring phosphorus-containing groups			ovary(1)	1																		---	---	---	---
NCRNA00119	348808	broad.mit.edu	37	3	132567778	132567779	+	Intron	DEL	GA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:132567778_132567779delGA	uc003epg.1	+							NR_002811				Homo sapiens cDNA clone IMAGE:4826885.												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	3	132596468	132596469	+	IGR	INS	-	AG	AG			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:132596468_132596469insAG								NCRNA00119 (3418 upstream) : TMEM108 (160702 downstream)																																			---	---	---	---
TMEM108	66000	broad.mit.edu	37	3	132784129	132784130	+	Intron	DEL	CA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:132784129_132784130delCA	uc003eph.2	+						TMEM108_uc003epi.2_Intron	NM_023943	NP_076432			transmembrane protein 108 precursor							integral to membrane				ovary(2)|skin(2)	4																		---	---	---	---
TMEM108	66000	broad.mit.edu	37	3	133114515	133114516	+	Intron	DEL	AC	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:133114515_133114516delAC	uc003eph.2	+						TMEM108_uc003epi.2_Intron|TMEM108_uc003epk.2_Intron|TMEM108_uc003epm.2_Intron	NM_023943	NP_076432			transmembrane protein 108 precursor							integral to membrane				ovary(2)|skin(2)	4																		---	---	---	---
BFSP2	8419	broad.mit.edu	37	3	133124373	133124373	+	Intron	DEL	A	-	-	rs151149633		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:133124373delA	uc003epn.1	+							NM_003571	NP_003562			phakinin						response to stimulus|visual perception	cytoplasm|intermediate filament|membrane	structural constituent of cytoskeleton|structural constituent of eye lens				0																		---	---	---	---
BFSP2	8419	broad.mit.edu	37	3	133185522	133185529	+	Intron	DEL	AAAAAAAA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:133185522_133185529delAAAAAAAA	uc003epn.1	+							NM_003571	NP_003562			phakinin						response to stimulus|visual perception	cytoplasm|intermediate filament|membrane	structural constituent of cytoskeleton|structural constituent of eye lens				0																		---	---	---	---
TOPBP1	11073	broad.mit.edu	37	3	133337435	133337435	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:133337435delT	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					---	---	---	---
Unknown	0	broad.mit.edu	37	3	133412309	133412309	+	IGR	DEL	T	-	-	rs7633129		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:133412309delT								TOPBP1 (31572 upstream) : TF (6902 downstream)																																			---	---	---	---
SRPRB	58477	broad.mit.edu	37	3	133526578	133526578	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:133526578delT	uc003epx.1	+							NM_021203	NP_067026			signal recognition particle receptor, beta							endoplasmic reticulum membrane|integral to membrane	GTP binding|protein binding|receptor activity			ovary(1)	1																		---	---	---	---
SRPRB	58477	broad.mit.edu	37	3	133530252	133530252	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:133530252delT	uc003epx.1	+							NM_021203	NP_067026			signal recognition particle receptor, beta							endoplasmic reticulum membrane|integral to membrane	GTP binding|protein binding|receptor activity			ovary(1)	1																		---	---	---	---
SLCO2A1	6578	broad.mit.edu	37	3	133711764	133711765	+	Intron	INS	-	GT	GT	rs35105748	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:133711764_133711765insGT	uc003eqa.3	-						SLCO2A1_uc003eqb.3_Intron|SLCO2A1_uc011blv.1_Intron|SLCO2A1_uc010htw.1_Intron	NM_005630	NP_005621			solute carrier organic anion transporter family,						sodium-independent organic anion transport	integral to plasma membrane|membrane fraction	prostaglandin transmembrane transporter activity|protein binding			central_nervous_system(1)	1																		---	---	---	---
SLCO2A1	6578	broad.mit.edu	37	3	133713355	133713356	+	Intron	DEL	CT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:133713355_133713356delCT	uc003eqa.3	-						SLCO2A1_uc003eqb.3_Intron|SLCO2A1_uc011blv.1_Intron|SLCO2A1_uc010htw.1_Intron	NM_005630	NP_005621			solute carrier organic anion transporter family,						sodium-independent organic anion transport	integral to plasma membrane|membrane fraction	prostaglandin transmembrane transporter activity|protein binding			central_nervous_system(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	3	133840389	133840389	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:133840389delT								SLCO2A1 (91469 upstream) : RYK (35589 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	133934199	133934201	+	IGR	DEL	GAG	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:133934199_133934201delGAG								RYK (-35387 upstream) : RYK (-58223 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	133950038	133950039	+	IGR	DEL	AA	-	-	rs72452774		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:133950038_133950039delAA								RYK (-19548 upstream) : RYK (-74061 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	133964219	133964220	+	IGR	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:133964219_133964220delAA								RYK (-5367 upstream) : RYK (-88242 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	134480576	134480577	+	IGR	DEL	TC	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:134480576_134480577delTC								KY (110098 upstream) : EPHB1 (33683 downstream)																																			---	---	---	---
EPHB1	2047	broad.mit.edu	37	3	134674865	134674866	+	Intron	DEL	CT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:134674865_134674866delCT	uc003eqt.2	+						EPHB1_uc010htz.1_Intron|EPHB1_uc011bly.1_Intron	NM_004441	NP_004432			ephrin receptor EphB1 precursor							integral to plasma membrane	ATP binding|ephrin receptor activity|protein binding			lung(11)|ovary(6)|stomach(4)|breast(3)|central_nervous_system(2)|skin(2)|large_intestine(1)|pancreas(1)	30																		---	---	---	---
EPHB1	2047	broad.mit.edu	37	3	134695580	134695580	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:134695580delA	uc003eqt.2	+						EPHB1_uc010htz.1_Intron|EPHB1_uc011bly.1_Intron	NM_004441	NP_004432			ephrin receptor EphB1 precursor							integral to plasma membrane	ATP binding|ephrin receptor activity|protein binding			lung(11)|ovary(6)|stomach(4)|breast(3)|central_nervous_system(2)|skin(2)|large_intestine(1)|pancreas(1)	30																		---	---	---	---
EPHB1	2047	broad.mit.edu	37	3	134698751	134698751	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:134698751delT	uc003eqt.2	+						EPHB1_uc010htz.1_Intron|EPHB1_uc011bly.1_Intron	NM_004441	NP_004432			ephrin receptor EphB1 precursor							integral to plasma membrane	ATP binding|ephrin receptor activity|protein binding			lung(11)|ovary(6)|stomach(4)|breast(3)|central_nervous_system(2)|skin(2)|large_intestine(1)|pancreas(1)	30																		---	---	---	---
EPHB1	2047	broad.mit.edu	37	3	134769755	134769760	+	Intron	DEL	TGTGTG	-	-	rs140912452		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:134769755_134769760delTGTGTG	uc003eqt.2	+						EPHB1_uc010htz.1_Intron|EPHB1_uc011bly.1_Intron	NM_004441	NP_004432			ephrin receptor EphB1 precursor							integral to plasma membrane	ATP binding|ephrin receptor activity|protein binding			lung(11)|ovary(6)|stomach(4)|breast(3)|central_nervous_system(2)|skin(2)|large_intestine(1)|pancreas(1)	30																		---	---	---	---
EPHB1	2047	broad.mit.edu	37	3	134902090	134902093	+	Intron	DEL	CTTC	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:134902090_134902093delCTTC	uc003eqt.2	+						EPHB1_uc003equ.2_Intron	NM_004441	NP_004432			ephrin receptor EphB1 precursor							integral to plasma membrane	ATP binding|ephrin receptor activity|protein binding			lung(11)|ovary(6)|stomach(4)|breast(3)|central_nervous_system(2)|skin(2)|large_intestine(1)|pancreas(1)	30																		---	---	---	---
EPHB1	2047	broad.mit.edu	37	3	134909929	134909929	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:134909929delA	uc003eqt.2	+						EPHB1_uc003equ.2_Intron	NM_004441	NP_004432			ephrin receptor EphB1 precursor							integral to plasma membrane	ATP binding|ephrin receptor activity|protein binding			lung(11)|ovary(6)|stomach(4)|breast(3)|central_nervous_system(2)|skin(2)|large_intestine(1)|pancreas(1)	30																		---	---	---	---
EPHB1	2047	broad.mit.edu	37	3	134913173	134913173	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:134913173delT	uc003eqt.2	+						EPHB1_uc003equ.2_Intron	NM_004441	NP_004432			ephrin receptor EphB1 precursor							integral to plasma membrane	ATP binding|ephrin receptor activity|protein binding			lung(11)|ovary(6)|stomach(4)|breast(3)|central_nervous_system(2)|skin(2)|large_intestine(1)|pancreas(1)	30																		---	---	---	---
Unknown	0	broad.mit.edu	37	3	135373301	135373301	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:135373301delA								EPHB1 (393996 upstream) : PPP2R3A (311266 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	135520560	135520560	+	IGR	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:135520560delG								EPHB1 (541255 upstream) : PPP2R3A (164007 downstream)																																			---	---	---	---
PPP2R3A	5523	broad.mit.edu	37	3	135685837	135685838	+	Intron	DEL	TG	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:135685837_135685838delTG	uc003eqv.1	+						PPP2R3A_uc011blz.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																		---	---	---	---
PPP2R3A	5523	broad.mit.edu	37	3	135730063	135730063	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:135730063delT	uc003eqv.1	+						PPP2R3A_uc011blz.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																		---	---	---	---
PPP2R3A	5523	broad.mit.edu	37	3	135839762	135839762	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:135839762delA	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																		---	---	---	---
PPP2R3A	5523	broad.mit.edu	37	3	135863503	135863505	+	Intron	DEL	AAA	-	-	rs111855021		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:135863503_135863505delAAA	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																		---	---	---	---
MSL2	55167	broad.mit.edu	37	3	135901558	135901558	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:135901558delA	uc003eqx.1	-						MSL2_uc011bmb.1_Intron	NM_018133	NP_060603			ring finger protein 184 isoform 1						histone H4-K16 acetylation	MSL complex	zinc ion binding			central_nervous_system(1)	1																		---	---	---	---
PCCB	5096	broad.mit.edu	37	3	135971856	135971856	+	Intron	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:135971856delG	uc003eqy.1	+						PCCB_uc003eqz.1_Intron|PCCB_uc011bmc.1_Intron|PCCB_uc011bmd.1_5'Flank	NM_000532	NP_000523			propionyl Coenzyme A carboxylase, beta						fatty acid beta-oxidation	mitochondrial matrix	ATP binding|propionyl-CoA carboxylase activity				0					Biotin(DB00121)|L-Valine(DB00161)													---	---	---	---
STAG1	10274	broad.mit.edu	37	3	136162921	136162924	+	Intron	DEL	TTTT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:136162921_136162924delTTTT	uc003era.1	-						STAG1_uc003erb.1_Intron|STAG1_uc003erc.1_Intron|STAG1_uc010hua.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	136483385	136483385	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:136483385delA								STAG1 (12140 upstream) : TMEM22 (54476 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	136525297	136525298	+	IGR	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:136525297_136525298delAA								STAG1 (54052 upstream) : TMEM22 (12563 downstream)																																			---	---	---	---
TMEM22	80723	broad.mit.edu	37	3	136534924	136534924	+	5'Flank	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:136534924delT	uc003erf.3	+						TMEM22_uc003erg.3_5'Flank|TMEM22_uc010hub.2_5'Flank	NM_001097600	NP_001091069			transmembrane protein 22							Golgi apparatus|integral to membrane				ovary(1)	1																		---	---	---	---
NCK1	4690	broad.mit.edu	37	3	136612021	136612026	+	Intron	DEL	TATATA	-	-	rs140904246	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:136612021_136612026delTATATA	uc003erh.2	+							NM_006153	NP_006144			NCK adaptor protein 1						axon guidance|positive regulation of actin filament polymerization|positive regulation of T cell proliferation|regulation of translation|signal complex assembly|T cell activation|T cell receptor signaling pathway	cytosol|endoplasmic reticulum|nucleus	cytoskeletal adaptor activity|receptor binding|receptor signaling complex scaffold activity			pancreas(1)	1																		---	---	---	---
IL20RB	53833	broad.mit.edu	37	3	136725304	136725304	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:136725304delT	uc003eri.1	+						IL20RB_uc003erj.1_Intron|IL20RB_uc010hud.1_Intron	NM_144717	NP_653318			interleukin 20 receptor beta precursor							integral to membrane	receptor activity			ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	3	136780167	136780168	+	IGR	DEL	GT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:136780167_136780168delGT								IL20RB (50247 upstream) : SOX14 (703411 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	137186603	137186603	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:137186603delA								IL20RB (456683 upstream) : SOX14 (296976 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	137261237	137261237	+	IGR	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:137261237delG								IL20RB (531317 upstream) : SOX14 (222342 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	137371363	137371364	+	IGR	INS	-	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:137371363_137371364insA								IL20RB (641443 upstream) : SOX14 (112215 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	137373517	137373517	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:137373517delA								IL20RB (643597 upstream) : SOX14 (110062 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	137561994	137561994	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:137561994delA								SOX14 (77598 upstream) : CLDN18 (155664 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	137588397	137588397	+	IGR	DEL	C	-	-	rs140623544	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:137588397delC								SOX14 (104001 upstream) : CLDN18 (129261 downstream)																																			---	---	---	---
ARMC8	25852	broad.mit.edu	37	3	137964256	137964256	+	Intron	DEL	T	-	-	rs77101605		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:137964256delT	uc003esa.1	+						ARMC8_uc003erw.2_3'UTR|ARMC8_uc003erx.2_3'UTR|ARMC8_uc003ery.2_3'UTR|ARMC8_uc003erz.2_3'UTR|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																		---	---	---	---
Unknown	0	broad.mit.edu	37	3	138357556	138357557	+	IGR	DEL	AA	-	-	rs75357840		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:138357556_138357557delAA								FAIM (5345 upstream) : PIK3CB (15303 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	138362975	138362975	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:138362975delT								FAIM (10764 upstream) : PIK3CB (9885 downstream)																																			---	---	---	---
PIK3CB	5291	broad.mit.edu	37	3	138377379	138377379	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:138377379delT	uc011bmq.1	-						PIK3CB_uc011bmn.1_Intron|PIK3CB_uc011bmo.1_Intron|PIK3CB_uc011bmp.1_Intron|PIK3CB_uc003est.1_5'Flank	NM_006219	NP_006210			catalytic phosphatidylinositol 3-kinase beta						activation of MAPK activity|chemotaxis|fibroblast growth factor receptor signaling pathway|G-protein coupled receptor protein signaling pathway|insulin receptor signaling pathway|leukocyte migration|nerve growth factor receptor signaling pathway|phosphatidylinositol-mediated signaling|platelet activation|T cell receptor signaling pathway	phosphatidylinositol 3-kinase complex	1-phosphatidylinositol-3-kinase activity|ATP binding|phosphatidylinositol-4,5-bisphosphate 3-kinase activity			breast(2)|ovary(1)|lung(1)|skin(1)	5																		---	---	---	---
PIK3CB	5291	broad.mit.edu	37	3	138402351	138402352	+	Intron	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:138402351_138402352delAA	uc011bmq.1	-						PIK3CB_uc011bmn.1_Intron|PIK3CB_uc011bmo.1_Intron|PIK3CB_uc011bmp.1_Intron	NM_006219	NP_006210			catalytic phosphatidylinositol 3-kinase beta						activation of MAPK activity|chemotaxis|fibroblast growth factor receptor signaling pathway|G-protein coupled receptor protein signaling pathway|insulin receptor signaling pathway|leukocyte migration|nerve growth factor receptor signaling pathway|phosphatidylinositol-mediated signaling|platelet activation|T cell receptor signaling pathway	phosphatidylinositol 3-kinase complex	1-phosphatidylinositol-3-kinase activity|ATP binding|phosphatidylinositol-4,5-bisphosphate 3-kinase activity			breast(2)|ovary(1)|lung(1)|skin(1)	5																		---	---	---	---
PIK3CB	5291	broad.mit.edu	37	3	138474573	138474573	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:138474573delT	uc011bmq.1	-							NM_006219	NP_006210			catalytic phosphatidylinositol 3-kinase beta						activation of MAPK activity|chemotaxis|fibroblast growth factor receptor signaling pathway|G-protein coupled receptor protein signaling pathway|insulin receptor signaling pathway|leukocyte migration|nerve growth factor receptor signaling pathway|phosphatidylinositol-mediated signaling|platelet activation|T cell receptor signaling pathway	phosphatidylinositol 3-kinase complex	1-phosphatidylinositol-3-kinase activity|ATP binding|phosphatidylinositol-4,5-bisphosphate 3-kinase activity			breast(2)|ovary(1)|lung(1)|skin(1)	5																		---	---	---	---
Unknown	0	broad.mit.edu	37	3	138698108	138698109	+	IGR	DEL	TT	-	-	rs111685939		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:138698108_138698109delTT								C3orf72 (25278 upstream) : PRR23A (24696 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	138855315	138855316	+	IGR	DEL	GA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:138855315_138855316delGA								BPESC1 (11312 upstream) : PISRT1 (96519 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	138903402	138903402	+	IGR	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:138903402delG								BPESC1 (59399 upstream) : PISRT1 (48433 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	139274346	139274346	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:139274346delA								RBP1 (15675 upstream) : NMNAT3 (4695 downstream)																																			---	---	---	---
NMNAT3	349565	broad.mit.edu	37	3	139339563	139339563	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:139339563delT	uc003etj.2	-						NMNAT3_uc003etk.2_Intron|NMNAT3_uc003etl.2_Intron|NMNAT3_uc010hul.2_Intron	NM_178177	NP_835471			nicotinamide mononucleotide adenylyltransferase						water-soluble vitamin metabolic process	cytosol|mitochondrion	ATP binding|nicotinamide-nucleotide adenylyltransferase activity|nicotinate-nucleotide adenylyltransferase activity				0																		---	---	---	---
NMNAT3	349565	broad.mit.edu	37	3	139392635	139392636	+	Intron	DEL	AG	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:139392635_139392636delAG	uc003etk.2	-						NMNAT3_uc003etl.2_Intron|NMNAT3_uc010hul.2_Intron	NM_178177	NP_835471			nicotinamide mononucleotide adenylyltransferase						water-soluble vitamin metabolic process	cytosol|mitochondrion	ATP binding|nicotinamide-nucleotide adenylyltransferase activity|nicotinate-nucleotide adenylyltransferase activity				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	3	139558042	139558043	+	IGR	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:139558042_139558043delTT								NMNAT3 (161202 upstream) : CLSTN2 (95984 downstream)																																			---	---	---	---
CLSTN2	64084	broad.mit.edu	37	3	139781441	139781442	+	Intron	INS	-	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:139781441_139781442insT	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	139851110	139851110	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:139851110delT	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	139879465	139879465	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:139879465delT	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	140425034	140425034	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:140425034delT								TRIM42 (5043 upstream) : SLC25A36 (235628 downstream)																																			---	---	---	---
SLC25A36	55186	broad.mit.edu	37	3	140689382	140689382	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:140689382delT	uc003etr.2	+						SLC25A36_uc003ets.2_Intron|SLC25A36_uc003etq.2_Intron|SLC25A36_uc011bmz.1_Intron	NM_001104647	NP_001098117			solute carrier family 25, member 36 isoform a						response to estradiol stimulus|transmembrane transport	integral to membrane|mitochondrial inner membrane	binding				0																		---	---	---	---
ZBTB38	253461	broad.mit.edu	37	3	141091329	141091329	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:141091329delA	uc003etw.2	+							NM_001080412	NP_001073881			zinc finger and BTB domain containing 38						positive regulation of transcription from RNA polymerase II promoter	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(3)	3																		---	---	---	---
RASA2	5922	broad.mit.edu	37	3	141281497	141281497	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:141281497delA	uc003etz.1	+						RASA2_uc010huq.1_Intron|RASA2_uc003eua.1_Intron|RASA2_uc011bnc.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																		---	---	---	---
RASA2	5922	broad.mit.edu	37	3	141289060	141289060	+	Intron	DEL	T	-	-	rs68189201		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:141289060delT	uc003etz.1	+						RASA2_uc010huq.1_Intron|RASA2_uc003eua.1_Intron|RASA2_uc011bnc.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																		---	---	---	---
Unknown	0	broad.mit.edu	37	3	141428265	141428265	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:141428265delT								RASA2 (97068 upstream) : RNF7 (28786 downstream)																																			---	---	---	---
ATP1B3	483	broad.mit.edu	37	3	141618713	141618713	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:141618713delA	uc003eug.1	+						ATP1B3_uc011bne.1_Intron|ATP1B3_uc003euh.1_Intron	NM_001679	NP_001670			Na+/K+ -ATPase beta 3 subunit						ATP biosynthetic process|blood coagulation|leukocyte migration	melanosome|sodium:potassium-exchanging ATPase complex	protein binding|sodium:potassium-exchanging ATPase activity				0																		---	---	---	---
ATP1B3	483	broad.mit.edu	37	3	141637292	141637295	+	Intron	DEL	TTTT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:141637292_141637295delTTTT	uc003eug.1	+						ATP1B3_uc011bne.1_Intron|ATP1B3_uc003euh.1_Intron	NM_001679	NP_001670			Na+/K+ -ATPase beta 3 subunit						ATP biosynthetic process|blood coagulation|leukocyte migration	melanosome|sodium:potassium-exchanging ATPase complex	protein binding|sodium:potassium-exchanging ATPase activity				0																		---	---	---	---
TFDP2	7029	broad.mit.edu	37	3	141672056	141672056	+	Intron	DEL	A	-	-	rs140575104		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:141672056delA	uc003eun.3	-						TFDP2_uc003euk.3_Intron|TFDP2_uc010hur.2_Intron|TFDP2_uc003eul.3_Intron|TFDP2_uc011bnf.1_Intron|TFDP2_uc011bng.1_Intron|TFDP2_uc003eum.3_Intron	NM_006286	NP_006277			transcription factor Dp-2 (E2F dimerization						cell cycle	transcription factor complex	DNA binding|protein domain specific binding|sequence-specific DNA binding transcription factor activity|transcription cofactor activity|transcription factor binding			kidney(1)	1																		---	---	---	---
TFDP2	7029	broad.mit.edu	37	3	141860668	141860668	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:141860668delA	uc003eun.3	-						TFDP2_uc003eum.3_Intron|TFDP2_uc003euo.2_Intron	NM_006286	NP_006277			transcription factor Dp-2 (E2F dimerization						cell cycle	transcription factor complex	DNA binding|protein domain specific binding|sequence-specific DNA binding transcription factor activity|transcription cofactor activity|transcription factor binding			kidney(1)	1																		---	---	---	---
GK5	256356	broad.mit.edu	37	3	141924151	141924151	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:141924151delA	uc003euq.1	-						GK5_uc010hus.1_Intron|GK5_uc010hut.1_Intron	NM_001039547	NP_001034636			glycerol kinase 5 (putative)						glycerol metabolic process		ATP binding|glycerol kinase activity				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	3	141962298	141962299	+	IGR	DEL	TT	-	-	rs112114903		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:141962298_141962299delTT								GK5 (17870 upstream) : XRN1 (63152 downstream)																																			---	---	---	---
XRN1	54464	broad.mit.edu	37	3	142051517	142051517	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:142051517delA	uc003eus.2	-						XRN1_uc010huu.2_Intron|XRN1_uc003eut.2_Intron|XRN1_uc003euu.2_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	142378515	142378517	+	Intron	DEL	TTT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:142378515_142378517delTTT	uc010huv.2	+						PLS1_uc003euz.2_Intron|PLS1_uc003eva.2_Intron	NM_001145319	NP_001138791			plastin 1							cytoplasm	actin filament binding|calcium ion binding|structural constituent of cytoskeleton			ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	3	142433188	142433188	+	IGR	DEL	T	-	-	rs78978640		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:142433188delT								PLS1 (685 upstream) : TRPC1 (10078 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	142438749	142438749	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:142438749delA								PLS1 (6246 upstream) : TRPC1 (4517 downstream)																																			---	---	---	---
PCOLCE2	26577	broad.mit.edu	37	3	142540749	142540749	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:142540749delT	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																		---	---	---	---
PCOLCE2	26577	broad.mit.edu	37	3	142557907	142557907	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:142557907delA	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																		---	---	---	---
Unknown	0	broad.mit.edu	37	3	142935420	142935420	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:142935420delT								CHST2 (93610 upstream) : SLC9A9 (48645 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	142958962	142958965	+	IGR	DEL	TTTT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:142958962_142958965delTTTT								CHST2 (117152 upstream) : SLC9A9 (25100 downstream)																																			---	---	---	---
SLC9A9	285195	broad.mit.edu	37	3	143316950	143316950	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:143316950delT	uc003evn.2	-						SLC9A9_uc011bnk.1_Intron	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	143591137	143591138	+	IGR	INS	-	TGTGTG	TGTGTG	rs142146670	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:143591137_143591138insTGTGTG								SLC9A9 (23791 upstream) : C3orf58 (99502 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	143591765	143591765	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:143591765delA								SLC9A9 (24419 upstream) : C3orf58 (98875 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	143616959	143616959	+	IGR	DEL	T	-	-	rs78496305		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:143616959delT								SLC9A9 (49613 upstream) : C3orf58 (73681 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	143726989	143726989	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:143726989delT								C3orf58 (15780 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	143852460	143852461	+	IGR	INS	-	T	T	rs77026808		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:143852460_143852461insT								C3orf58 (141251 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	144041816	144041817	+	IGR	INS	-	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:144041816_144041817insC								C3orf58 (330607 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	144304628	144304628	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:144304628delA								C3orf58 (593419 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	144383452	144383452	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:144383452delT								C3orf58 (672243 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	144589231	144589231	+	IGR	DEL	G	-	-	rs35154200		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:144589231delG								C3orf58 (878022 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	144962974	144962974	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:144962974delA								None (None upstream) : PLOD2 (824254 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	144964347	144964347	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:144964347delT								None (None upstream) : PLOD2 (822881 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	145382805	145382806	+	IGR	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:145382805_145382806delAA								None (None upstream) : PLOD2 (404422 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	146456896	146456896	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:146456896delT								PLSCR5 (132893 upstream) : ZIC4 (646941 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	146601557	146601557	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:146601557delA								PLSCR5 (277554 upstream) : ZIC4 (502280 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	146656505	146656505	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:146656505delA								PLSCR5 (332502 upstream) : ZIC4 (447332 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	146923442	146923442	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:146923442delT								PLSCR5 (599439 upstream) : ZIC4 (180395 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	146974562	146974562	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:146974562delT								PLSCR5 (650559 upstream) : ZIC4 (129275 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	147096663	147096663	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:147096663delA								PLSCR5 (772660 upstream) : ZIC4 (7174 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	147550617	147550617	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:147550617delT								ZIC1 (416113 upstream) : AGTR1 (865041 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	147602395	147602395	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:147602395delA								ZIC1 (467891 upstream) : AGTR1 (813263 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	148204467	148204469	+	IGR	DEL	CTT	-	-	rs146674166		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:148204467_148204469delCTT								None (None upstream) : AGTR1 (211189 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	148375219	148375220	+	IGR	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:148375219_148375220delAA								None (None upstream) : AGTR1 (40438 downstream)																																			---	---	---	---
CPA3	1359	broad.mit.edu	37	3	148591981	148591981	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:148591981delT	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)															---	---	---	---
CPA3	1359	broad.mit.edu	37	3	148614215	148614215	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:148614215delT	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)															---	---	---	---
HLTF	6596	broad.mit.edu	37	3	148786945	148786946	+	Intron	INS	-	A	A	rs140071037	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:148786945_148786946insA	uc003ewq.1	-						HLTF_uc003ewr.1_Intron|HLTF_uc003ews.1_Intron|HLTF_uc010hve.1_Intron	NM_139048	NP_620636			helicase-like transcription factor						chromatin modification|transcription, DNA-dependent	nucleus	ATP binding|DNA binding|helicase activity|ligase activity|zinc ion binding			ovary(1)	1			LUSC - Lung squamous cell carcinoma(72;0.0473)|Lung(72;0.0607)															---	---	---	---
TM4SF18	116441	broad.mit.edu	37	3	149042947	149042947	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:149042947delA	uc003exa.2	-							NM_138786	NP_620141			transmembrane 4 L six family member 18							integral to membrane				ovary(1)	1			LUSC - Lung squamous cell carcinoma(72;0.0378)|Lung(72;0.048)															---	---	---	---
TM4SF1	4071	broad.mit.edu	37	3	149087439	149087439	+	3'UTR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:149087439delA	uc003exb.1	-	5					TM4SF1_uc003exc.1_3'UTR	NM_014220	NP_055035			transmembrane 4 superfamily member 1							integral to plasma membrane					0			LUSC - Lung squamous cell carcinoma(72;0.0378)|Lung(72;0.048)															---	---	---	---
WWTR1	25937	broad.mit.edu	37	3	149251548	149251548	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:149251548delA	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)															---	---	---	---
Unknown	0	broad.mit.edu	37	3	149448289	149448290	+	IGR	INS	-	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:149448289_149448290insA								WWTR1 (27174 upstream) : COMMD2 (7970 downstream)																																			---	---	---	---
RNF13	11342	broad.mit.edu	37	3	149608176	149608176	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:149608176delT	uc003exn.3	+						RNF13_uc003exp.3_Intron|RNF13_uc010hvh.2_Intron	NM_007282	NP_009213			ring finger protein 13						protein autoubiquitination	endoplasmic reticulum membrane|Golgi membrane|integral to membrane|late endosome membrane|lysosomal membrane|nuclear inner membrane	ubiquitin-protein ligase activity|zinc ion binding			ovary(1)	1		all_neural(597;0.0138)|Myeloproliferative disorder(1037;0.0255)	LUSC - Lung squamous cell carcinoma(72;0.0538)|Lung(72;0.066)															---	---	---	---
RNF13	11342	broad.mit.edu	37	3	149614271	149614271	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:149614271delT	uc003exn.3	+						RNF13_uc003exp.3_Intron|RNF13_uc010hvh.2_Intron	NM_007282	NP_009213			ring finger protein 13						protein autoubiquitination	endoplasmic reticulum membrane|Golgi membrane|integral to membrane|late endosome membrane|lysosomal membrane|nuclear inner membrane	ubiquitin-protein ligase activity|zinc ion binding			ovary(1)	1		all_neural(597;0.0138)|Myeloproliferative disorder(1037;0.0255)	LUSC - Lung squamous cell carcinoma(72;0.0538)|Lung(72;0.066)															---	---	---	---
Unknown	0	broad.mit.edu	37	3	149759442	149759445	+	IGR	DEL	AGAC	-	-	rs35740476		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:149759442_149759445delAGAC								PFN2 (70701 upstream) : TSC22D2 (367343 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	150011402	150011403	+	IGR	DEL	TC	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:150011402_150011403delTC								PFN2 (322661 upstream) : TSC22D2 (115385 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	150034217	150034217	+	IGR	DEL	A	-	-	rs78253351	byFrequency;by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:150034217delA								PFN2 (345476 upstream) : TSC22D2 (92571 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	150056166	150056166	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:150056166delA								PFN2 (367425 upstream) : TSC22D2 (70622 downstream)																																			---	---	---	---
EIF2A	83939	broad.mit.edu	37	3	150270631	150270631	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:150270631delT	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_Intron	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)															---	---	---	---
EIF2A	83939	broad.mit.edu	37	3	150293876	150293876	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:150293876delA	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_Intron|uc003eye.1_Intron	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)															---	---	---	---
Unknown	0	broad.mit.edu	37	3	150527246	150527247	+	IGR	INS	-	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:150527246_150527247insT								SIAH2 (45983 upstream) : CLRN1OS (43024 downstream)																																			---	---	---	---
CLRN1OS	116933	broad.mit.edu	37	3	150727307	150727308	+	Intron	DEL	TC	-	-	rs76555967	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:150727307_150727308delTC	uc011bny.1	+						CLRN1OS_uc003eyl.2_Intron					Homo sapiens usher critical region protein (UCRP) pseudogene mRNA, complete sequence.												0																		---	---	---	---
MED12L	116931	broad.mit.edu	37	3	150851391	150851392	+	Intron	DEL	AA	-	-	rs112153520		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:150851391_150851392delAA	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	151057431	151057431	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:151057431delA	uc003eyp.2	+						MED12L_uc011bnz.1_Intron|P2RY12_uc011boa.1_Intron|P2RY12_uc003eyw.1_Intron|P2RY12_uc003eyx.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	151103034	151103034	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:151103034delT	uc003eyp.2	+						MED12L_uc011bnz.1_Intron|P2RY12_uc011boa.1_5'Flank|P2RY12_uc003eyx.1_5'Flank|MED12L_uc003eyy.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)															---	---	---	---
Unknown	0	broad.mit.edu	37	3	151846546	151846547	+	IGR	DEL	TC	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:151846546_151846547delTC								SUCNR1 (246896 upstream) : LOC401093 (133866 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	151864024	151864024	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:151864024delT								SUCNR1 (264374 upstream) : LOC401093 (116389 downstream)																																			---	---	---	---
MBNL1	4154	broad.mit.edu	37	3	152124440	152124440	+	Intron	DEL	A	-	-	rs34227599		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:152124440delA	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)															---	---	---	---
MBNL1	4154	broad.mit.edu	37	3	152177176	152177176	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:152177176delT	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|MBNL1_uc010hvp.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	152200239	152200239	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:152200239delT								MBNL1 (16671 upstream) : P2RY1 (352497 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	152439639	152439639	+	IGR	DEL	A	-	-	rs66680197		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:152439639delA								MBNL1 (256071 upstream) : P2RY1 (113097 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	152799777	152799778	+	IGR	INS	-	CA	CA			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:152799777_152799778insCA								P2RY1 (243936 upstream) : RAP2B (80251 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	152831231	152831231	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:152831231delA								P2RY1 (275390 upstream) : RAP2B (48798 downstream)																																			---	---	---	---
GPR149	344758	broad.mit.edu	37	3	154072360	154072360	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:154072360delT	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	154168346	154168347	+	IGR	DEL	CT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:154168346_154168347delCT								GPR149 (20842 upstream) : MME (573566 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	154261138	154261138	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:154261138delA								GPR149 (113634 upstream) : MME (480775 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	154684411	154684414	+	IGR	DEL	TTTG	-	-	rs111344601		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:154684411_154684414delTTTG								GPR149 (536907 upstream) : MME (57499 downstream)																																			---	---	---	---
GMPS	8833	broad.mit.edu	37	3	155595293	155595293	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:155595293delA	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								---	---	---	---
GMPS	8833	broad.mit.edu	37	3	155632554	155632554	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-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								---	---	---	---
Unknown	0	broad.mit.edu	37	3	155829897	155829897	+	IGR	DEL	T	-	-	rs28406457		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:155829897delT								GMPS (174379 upstream) : KCNAB1 (8440 downstream)																																			---	---	---	---
KCNAB1	7881	broad.mit.edu	37	3	156055173	156055173	+	Intron	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:156055173delC	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)															---	---	---	---
KCNAB1	7881	broad.mit.edu	37	3	156169372	156169374	+	Intron	DEL	TTC	-	-	rs66488636		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:156169372_156169374delTTC	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)															---	---	---	---
KCNAB1	7881	broad.mit.edu	37	3	156245435	156245435	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:156245435delT	uc003far.2	+						KCNAB1_uc011bon.1_Intron|KCNAB1_uc003fas.2_Intron|KCNAB1_uc003fat.2_Intron|KCNAB1_uc010hvt.1_Intron|KCNAB1_uc011boo.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	156504009	156504009	+	Intron	DEL	T	-	-	rs67838290		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:156504009delT	uc003fax.1	-											Homo sapiens cDNA FLJ31839 fis, clone NT2RP7000086.																														---	---	---	---
LEKR1	389170	broad.mit.edu	37	3	156572513	156572513	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:156572513delT	uc003fbb.2	+						LEKR1_uc003fba.1_Intron					Homo sapiens cDNA FLJ16641 fis, clone TESTI4028958.												0			LUSC - Lung squamous cell carcinoma(72;0.0461)|Lung(72;0.0465)															---	---	---	---
Unknown	0	broad.mit.edu	37	3	157596688	157596688	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:157596688delT								C3orf55 (277669 upstream) : SHOX2 (217113 downstream)																																			---	---	---	---
RSRC1	51319	broad.mit.edu	37	3	157836266	157836266	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:157836266delT	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	158050761	158050762	+	Intron	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:158050761_158050762delTT	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	158214713	158214713	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:158214713delA	uc003fbt.2	+						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	158226293	158226293	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:158226293delT	uc003fbt.2	+						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)															---	---	---	---
SCHIP1	29970	broad.mit.edu	37	3	159339461	159339462	+	Intron	INS	-	T	T	rs148319581	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:159339461_159339462insT	uc003fcs.1	+						SCHIP1_uc003fcq.1_Intron|SCHIP1_uc003fcr.1_Intron|SCHIP1_uc003fct.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)															---	---	---	---
SCHIP1	29970	broad.mit.edu	37	3	159348778	159348778	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:159348778delA	uc003fcs.1	+						SCHIP1_uc003fcq.1_Intron|SCHIP1_uc003fcr.1_Intron|SCHIP1_uc003fct.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)															---	---	---	---
SCHIP1	29970	broad.mit.edu	37	3	159537032	159537033	+	Intron	DEL	GA	-	-	rs77316168		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:159537032_159537033delGA	uc003fcs.1	+						SCHIP1_uc003fcq.1_Intron|SCHIP1_uc003fcr.1_Intron|SCHIP1_uc003fct.1_Intron|SCHIP1_uc010hvz.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)															---	---	---	---
SCHIP1	29970	broad.mit.edu	37	3	159597060	159597060	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:159597060delT	uc003fcs.1	+						SCHIP1_uc003fcq.1_Intron|SCHIP1_uc003fcr.1_Intron|SCHIP1_uc003fct.1_Intron|SCHIP1_uc010hvz.1_Intron|SCHIP1_uc003fcu.1_Intron|SCHIP1_uc003fcv.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)															---	---	---	---
SCHIP1	29970	broad.mit.edu	37	3	159609359	159609359	+	Intron	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:159609359delC	uc003fcs.1	+						SCHIP1_uc003fcq.1_Intron|SCHIP1_uc003fcr.1_Intron|SCHIP1_uc003fct.1_Intron|SCHIP1_uc010hvz.1_Intron|SCHIP1_uc003fcu.1_Intron|SCHIP1_uc003fcv.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)															---	---	---	---
Unknown	0	broad.mit.edu	37	3	159764303	159764304	+	Intron	INS	-	TTGTTG	TTGTTG	rs141392051	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:159764303_159764304insTTGTTG	uc003fcw.1	-											Homo sapiens cDNA FLJ39842 fis, clone SPLEN2014293.																														---	---	---	---
Unknown	0	broad.mit.edu	37	3	159896001	159896001	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:159896001delT	uc003fcw.1	-											Homo sapiens cDNA FLJ39842 fis, clone SPLEN2014293.																														---	---	---	---
SMC4	10051	broad.mit.edu	37	3	160129696	160129696	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:160129696delT	uc003fdh.2	+						IFT80_uc003fda.2_Intron|SMC4_uc003fdf.1_Intron|SMC4_uc003fdg.1_Intron|SMC4_uc010hwc.1_Intron|SMC4_uc003fdi.2_Intron|SMC4_uc003fdj.2_Intron|SMC4_uc010hwd.2_Intron|SMC4_uc003fdl.2_5'Flank	NM_001002800	NP_001002800			SMC4 structural maintenance of chromosomes						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)															---	---	---	---
KPNA4	3840	broad.mit.edu	37	3	160261650	160261650	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:160261650delT	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)															---	---	---	---
PPM1L	151742	broad.mit.edu	37	3	160645395	160645396	+	Intron	DEL	TG	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:160645395_160645396delTG	uc003fdr.2	+						PPM1L_uc003fds.2_Intron|PPM1L_uc003fdt.2_Intron|PPM1L_uc010hwf.2_Intron	NM_139245	NP_640338			protein phosphatase 1 (formerly 2C)-like						protein dephosphorylation|sphingolipid metabolic process	endoplasmic reticulum membrane|integral to membrane|protein serine/threonine phosphatase complex	metal ion binding|protein serine/threonine phosphatase activity			breast(1)	1			Lung(72;0.00149)|LUSC - Lung squamous cell carcinoma(72;0.00216)															---	---	---	---
PPM1L	151742	broad.mit.edu	37	3	160710864	160710865	+	Intron	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:160710864_160710865delTT	uc003fdr.2	+						PPM1L_uc003fds.2_Intron|PPM1L_uc003fdt.2_Intron|PPM1L_uc010hwf.2_Intron	NM_139245	NP_640338			protein phosphatase 1 (formerly 2C)-like						protein dephosphorylation|sphingolipid metabolic process	endoplasmic reticulum membrane|integral to membrane|protein serine/threonine phosphatase complex	metal ion binding|protein serine/threonine phosphatase activity			breast(1)	1			Lung(72;0.00149)|LUSC - Lung squamous cell carcinoma(72;0.00216)															---	---	---	---
PPM1L	151742	broad.mit.edu	37	3	160778040	160778040	+	Intron	DEL	G	-	-	rs67346292		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:160778040delG	uc003fdr.2	+						PPM1L_uc003fds.2_Intron|PPM1L_uc003fdt.2_Intron|PPM1L_uc010hwf.2_Intron	NM_139245	NP_640338			protein phosphatase 1 (formerly 2C)-like						protein dephosphorylation|sphingolipid metabolic process	endoplasmic reticulum membrane|integral to membrane|protein serine/threonine phosphatase complex	metal ion binding|protein serine/threonine phosphatase activity			breast(1)	1			Lung(72;0.00149)|LUSC - Lung squamous cell carcinoma(72;0.00216)															---	---	---	---
Unknown	0	broad.mit.edu	37	3	160845258	160845259	+	IGR	INS	-	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:160845258_160845259insA								B3GALNT1 (22098 upstream) : NMD3 (93840 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	161132632	161132639	+	IGR	DEL	GTGTGTGT	-	-	rs113427775		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:161132632_161132639delGTGTGTGT								C3orf57 (42761 upstream) : OTOL1 (81957 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	161355954	161355954	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:161355954delT								OTOL1 (134226 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	161671560	161671560	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:161671560delT								OTOL1 (449832 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	161789694	161789694	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:161789694delT								OTOL1 (567966 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	161801157	161801157	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:161801157delT								OTOL1 (579429 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	162246572	162246572	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:162246572delT								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	162273198	162273198	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:162273198delT								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	162454954	162454954	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:162454954delT	uc003feg.2	+											Homo sapiens, clone IMAGE:2905387, mRNA.																														---	---	---	---
Unknown	0	broad.mit.edu	37	3	162478222	162478222	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:162478222delT	uc003feg.2	+											Homo sapiens, clone IMAGE:2905387, mRNA.																														---	---	---	---
Unknown	0	broad.mit.edu	37	3	162919811	162919811	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:162919811delT	uc003feg.2	+						uc003feh.2_Intron					Homo sapiens, clone IMAGE:2905387, mRNA.																														---	---	---	---
Unknown	0	broad.mit.edu	37	3	163033136	163033136	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:163033136delT								None (None upstream) : MIR1263 (856123 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	163393863	163393863	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:163393863delA								None (None upstream) : MIR1263 (495396 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	163709443	163709444	+	IGR	INS	-	T	T	rs148725789	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:163709443_163709444insT								None (None upstream) : MIR1263 (179815 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	163752780	163752780	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:163752780delA								None (None upstream) : MIR1263 (136479 downstream)																																			---	---	---	---
MIR1263	100302148	broad.mit.edu	37	3	163892095	163892095	+	5'Flank	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:163892095delT	hsa-mir-1263|MI0006398	-																							0																		---	---	---	---
MIR720	100302198	broad.mit.edu	37	3	164058696	164058697	+	5'Flank	DEL	AG	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:164058696_164058697delAG	hsa-mir-720|MI0006654	+																							0																		---	---	---	---
Unknown	0	broad.mit.edu	37	3	164201784	164201787	+	IGR	DEL	AGAT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:164201784_164201787delAGAT								MIR720 (142546 upstream) : SI (494900 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	164663996	164663997	+	IGR	INS	-	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:164663996_164663997insA								MIR720 (604758 upstream) : SI (32690 downstream)																																			---	---	---	---
SLITRK3	22865	broad.mit.edu	37	3	164917312	164917312	+	5'Flank	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:164917312delA	uc003fek.2	-							NM_014926	NP_055741			slit and trk like 3 protein precursor							integral to membrane				ovary(6)|skin(3)|pancreas(1)	10															HNSCC(40;0.11)			---	---	---	---
Unknown	0	broad.mit.edu	37	3	164933664	164933664	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:164933664delT								SLITRK3 (19195 upstream) : BCHE (557030 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	165463020	165463020	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:165463020delA								SLITRK3 (548551 upstream) : BCHE (27674 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	166644822	166644823	+	IGR	DEL	CT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:166644822_166644823delCT								None (None upstream) : ZBBX (313258 downstream)																																			---	---	---	---
ZBBX	79740	broad.mit.edu	37	3	167035559	167035559	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:167035559delA	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	167167197	167167197	+	Intron	DEL	A	-	-	rs78539252	byFrequency;by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:167167197delA	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																		---	---	---	---
WDR49	151790	broad.mit.edu	37	3	167337265	167337265	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:167337265delA	uc003fev.1	-						WDR49_uc011bpd.1_Intron|WDR49_uc003few.1_Intron	NM_178824	NP_849146			WD repeat domain 49											large_intestine(1)|ovary(1)|skin(1)	3																		---	---	---	---
PDCD10	11235	broad.mit.edu	37	3	167402273	167402274	+	Intron	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:167402273_167402274delAA	uc003fex.2	-						PDCD10_uc003fez.2_Intron|PDCD10_uc003fey.2_Intron	NM_007217	NP_009148			programmed cell death 10						angiogenesis|apoptosis|negative regulation of apoptosis|positive regulation of cell proliferation|positive regulation of MAP kinase activity	cytosol|Golgi membrane|plasma membrane	protein homodimerization activity|protein N-terminus binding			lung(1)|central_nervous_system(1)	2														Familial_Cerebral_Cavernous_Angioma				---	---	---	---
Unknown	0	broad.mit.edu	37	3	167630757	167630757	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:167630757delT	uc003ffc.2	+						uc003ffd.2_Intron					Homo sapiens cDNA FLJ36036 fis, clone TESTI2017125.																														---	---	---	---
Unknown	0	broad.mit.edu	37	3	168013812	168013814	+	IGR	DEL	TTT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:168013812_168013814delTTT								GOLIM4 (200395 upstream) : MIR551B (255828 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	168133108	168133108	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:168133108delT								GOLIM4 (319691 upstream) : MIR551B (136534 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	168189630	168189630	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:168189630delT								GOLIM4 (376213 upstream) : MIR551B (80012 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	168342900	168342901	+	IGR	DEL	GA	-	-	rs3863111		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:168342900_168342901delGA								MIR551B (73163 upstream) : C3orf50 (184683 downstream)																																			---	---	---	---
MECOM	2122	broad.mit.edu	37	3	168974132	168974134	+	Intron	DEL	AAA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:168974132_168974134delAAA	uc011bpj.1	-						MECOM_uc003ffl.2_Intron|MECOM_uc011bpk.1_Intron|MECOM_uc010hwn.2_Intron|MECOM_uc011bpl.1_Intron	NM_004991	NP_004982			MDS1 and EVI1 complex locus isoform c						apoptosis|cell differentiation|hemopoietic stem cell proliferation|negative regulation of JNK cascade|negative regulation of programmed cell death|negative regulation of transcription, DNA-dependent|regulation of cell cycle	nuclear speck	DNA binding|protein binding|protein homodimerization activity|sequence-specific DNA binding transcription factor activity|zinc ion binding			lung(5)|skin(5)|upper_aerodigestive_tract(1)|central_nervous_system(1)|ovary(1)|pancreas(1)	14																		---	---	---	---
MECOM	2122	broad.mit.edu	37	3	168985551	168985552	+	Intron	DEL	TT	-	-	rs111515471		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:168985551_168985552delTT	uc011bpj.1	-						MECOM_uc003ffl.2_Intron|MECOM_uc011bpk.1_Intron|MECOM_uc010hwn.2_Intron|MECOM_uc011bpl.1_Intron	NM_004991	NP_004982			MDS1 and EVI1 complex locus isoform c						apoptosis|cell differentiation|hemopoietic stem cell proliferation|negative regulation of JNK cascade|negative regulation of programmed cell death|negative regulation of transcription, DNA-dependent|regulation of cell cycle	nuclear speck	DNA binding|protein binding|protein homodimerization activity|sequence-specific DNA binding transcription factor activity|zinc ion binding			lung(5)|skin(5)|upper_aerodigestive_tract(1)|central_nervous_system(1)|ovary(1)|pancreas(1)	14																		---	---	---	---
MECOM	2122	broad.mit.edu	37	3	169092666	169092666	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:169092666delT	uc011bpj.1	-						MECOM_uc003ffl.2_Intron|MECOM_uc011bpk.1_Intron|MECOM_uc010hwn.2_Intron|MECOM_uc011bpl.1_Intron	NM_004991	NP_004982			MDS1 and EVI1 complex locus isoform c						apoptosis|cell differentiation|hemopoietic stem cell proliferation|negative regulation of JNK cascade|negative regulation of programmed cell death|negative regulation of transcription, DNA-dependent|regulation of cell cycle	nuclear speck	DNA binding|protein binding|protein homodimerization activity|sequence-specific DNA binding transcription factor activity|zinc ion binding			lung(5)|skin(5)|upper_aerodigestive_tract(1)|central_nervous_system(1)|ovary(1)|pancreas(1)	14																		---	---	---	---
MECOM	2122	broad.mit.edu	37	3	169269161	169269164	+	Intron	DEL	TAAA	-	-	rs76089058	byFrequency;by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:169269161_169269164delTAAA	uc011bpj.1	-						MECOM_uc011bpk.1_Intron|MECOM_uc010hwn.2_Intron|MECOM_uc011bpl.1_Intron	NM_004991	NP_004982			MDS1 and EVI1 complex locus isoform c						apoptosis|cell differentiation|hemopoietic stem cell proliferation|negative regulation of JNK cascade|negative regulation of programmed cell death|negative regulation of transcription, DNA-dependent|regulation of cell cycle	nuclear speck	DNA binding|protein binding|protein homodimerization activity|sequence-specific DNA binding transcription factor activity|zinc ion binding			lung(5)|skin(5)|upper_aerodigestive_tract(1)|central_nervous_system(1)|ovary(1)|pancreas(1)	14																		---	---	---	---
MECOM	2122	broad.mit.edu	37	3	169331903	169331903	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:169331903delT	uc011bpj.1	-						MECOM_uc011bpk.1_Intron|MECOM_uc010hwn.2_Intron|MECOM_uc011bpl.1_Intron	NM_004991	NP_004982			MDS1 and EVI1 complex locus isoform c						apoptosis|cell differentiation|hemopoietic stem cell proliferation|negative regulation of JNK cascade|negative regulation of programmed cell death|negative regulation of transcription, DNA-dependent|regulation of cell cycle	nuclear speck	DNA binding|protein binding|protein homodimerization activity|sequence-specific DNA binding transcription factor activity|zinc ion binding			lung(5)|skin(5)|upper_aerodigestive_tract(1)|central_nervous_system(1)|ovary(1)|pancreas(1)	14																		---	---	---	---
MYNN	55892	broad.mit.edu	37	3	169501506	169501506	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-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	169505874	169505874	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:169505874delT								MYNN (539 upstream) : LRRC34 (5392 downstream)																																			---	---	---	---
LRRC31	79782	broad.mit.edu	37	3	169563671	169563671	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:169563671delA	uc003fgc.1	-						LRRC31_uc010hwp.1_Intron	NM_024727	NP_079003			leucine rich repeat containing 31											ovary(2)|skin(1)	3	all_cancers(22;2.76e-22)|all_epithelial(15;4.73e-27)|all_lung(20;9.24e-17)|Lung NSC(18;3.85e-16)|Ovarian(172;0.000223)|Breast(254;0.197)		Lung(28;2.71e-13)|STAD - Stomach adenocarcinoma(35;0.00943)															---	---	---	---
LRRC31	79782	broad.mit.edu	37	3	169569213	169569213	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:169569213delA	uc003fgc.1	-						LRRC31_uc010hwp.1_Intron	NM_024727	NP_079003			leucine rich repeat containing 31											ovary(2)|skin(1)	3	all_cancers(22;2.76e-22)|all_epithelial(15;4.73e-27)|all_lung(20;9.24e-17)|Lung NSC(18;3.85e-16)|Ovarian(172;0.000223)|Breast(254;0.197)		Lung(28;2.71e-13)|STAD - Stomach adenocarcinoma(35;0.00943)															---	---	---	---
Unknown	0	broad.mit.edu	37	3	169615073	169615073	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:169615073delA								LRRC31 (27413 upstream) : SAMD7 (14409 downstream)																																			---	---	---	---
SEC62	7095	broad.mit.edu	37	3	169708057	169708057	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:169708057delT	uc003fgg.2	+						SEC62_uc003fgh.2_Intron	NM_003262	NP_003253			translocation protein 1						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																		---	---	---	---
GPR160	26996	broad.mit.edu	37	3	169777466	169777467	+	Intron	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:169777466_169777467delTT	uc003fgi.2	+						GPR160_uc010hwq.2_Intron	NM_014373	NP_055188			G protein-coupled receptor 160							integral to membrane|plasma membrane	G-protein coupled receptor activity				0	all_cancers(22;3.26e-22)|all_epithelial(15;5.71e-27)|all_lung(20;8.41e-17)|Lung NSC(18;3.49e-16)|Ovarian(172;0.000337)|Breast(254;0.169)		Lung(28;2.71e-13)|STAD - Stomach adenocarcinoma(35;0.0655)															---	---	---	---
GPR160	26996	broad.mit.edu	37	3	169791121	169791121	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:169791121delT	uc003fgi.2	+						GPR160_uc010hwq.2_Intron	NM_014373	NP_055188			G protein-coupled receptor 160							integral to membrane|plasma membrane	G-protein coupled receptor activity				0	all_cancers(22;3.26e-22)|all_epithelial(15;5.71e-27)|all_lung(20;8.41e-17)|Lung NSC(18;3.49e-16)|Ovarian(172;0.000337)|Breast(254;0.169)		Lung(28;2.71e-13)|STAD - Stomach adenocarcinoma(35;0.0655)															---	---	---	---
GPR160	26996	broad.mit.edu	37	3	169792606	169792606	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:169792606delT	uc003fgi.2	+						GPR160_uc010hwq.2_Intron	NM_014373	NP_055188			G protein-coupled receptor 160							integral to membrane|plasma membrane	G-protein coupled receptor activity				0	all_cancers(22;3.26e-22)|all_epithelial(15;5.71e-27)|all_lung(20;8.41e-17)|Lung NSC(18;3.49e-16)|Ovarian(172;0.000337)|Breast(254;0.169)		Lung(28;2.71e-13)|STAD - Stomach adenocarcinoma(35;0.0655)															---	---	---	---
GPR160	26996	broad.mit.edu	37	3	169795110	169795110	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:169795110delT	uc003fgi.2	+						GPR160_uc010hwq.2_5'UTR	NM_014373	NP_055188			G protein-coupled receptor 160							integral to membrane|plasma membrane	G-protein coupled receptor activity				0	all_cancers(22;3.26e-22)|all_epithelial(15;5.71e-27)|all_lung(20;8.41e-17)|Lung NSC(18;3.49e-16)|Ovarian(172;0.000337)|Breast(254;0.169)		Lung(28;2.71e-13)|STAD - Stomach adenocarcinoma(35;0.0655)															---	---	---	---
PHC3	80012	broad.mit.edu	37	3	169847492	169847494	+	Intron	DEL	AAT	-	-	rs79158343		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:169847492_169847494delAAT	uc010hws.1	-						PHC3_uc003fgl.2_Intron|PHC3_uc011bpq.1_Intron|PHC3_uc011bpr.1_Intron	NM_024947	NP_079223			polyhomeotic like 3						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)															---	---	---	---
PRKCI	5584	broad.mit.edu	37	3	169970394	169970394	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:169970394delT	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	169976104	169976104	+	Intron	DEL	T	-	-	rs112940759		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:169976104delT	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	169982020	169982021	+	Intron	DEL	TT	-	-	rs66760963		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:169982020_169982021delTT	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	170012488	170012488	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:170012488delT	uc003fgs.2	+						PRKCI_uc003fgt.2_Intron	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)															---	---	---	---
Unknown	0	broad.mit.edu	37	3	170071089	170071090	+	IGR	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:170071089_170071090delTT								PRKCI (47319 upstream) : SKIL (4383 downstream)																																			---	---	---	---
CLDN11	5010	broad.mit.edu	37	3	170399415	170399415	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:170399415delT	uc011bpt.1	+						uc003fha.1_Intron	NM_005602	NP_005593			claudin 11						calcium-independent cell-cell adhesion	integral to membrane|tight junction	identical protein binding|structural molecule activity			central_nervous_system(1)	1	all_cancers(22;5.62e-23)|all_epithelial(15;7.54e-28)|all_lung(20;2.51e-17)|Lung NSC(18;1.02e-16)|Ovarian(172;0.000567)|Breast(254;0.137)		Lung(28;2.71e-13)|STAD - Stomach adenocarcinoma(35;0.197)															---	---	---	---
CLDN11	5010	broad.mit.edu	37	3	170508646	170508646	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:170508646delT	uc011bpt.1	+							NM_005602	NP_005593			claudin 11						calcium-independent cell-cell adhesion	integral to membrane|tight junction	identical protein binding|structural molecule activity			central_nervous_system(1)	1	all_cancers(22;5.62e-23)|all_epithelial(15;7.54e-28)|all_lung(20;2.51e-17)|Lung NSC(18;1.02e-16)|Ovarian(172;0.000567)|Breast(254;0.137)		Lung(28;2.71e-13)|STAD - Stomach adenocarcinoma(35;0.197)															---	---	---	---
EIF5A2	56648	broad.mit.edu	37	3	170612505	170612505	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:170612505delT	uc003fhd.2	-							NM_020390	NP_065123			eIF-5A2 protein						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)															---	---	---	---
EIF5A2	56648	broad.mit.edu	37	3	170617523	170617523	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:170617523delA	uc003fhd.2	-							NM_020390	NP_065123			eIF-5A2 protein						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)															---	---	---	---
Unknown	0	broad.mit.edu	37	3	170707670	170707671	+	IGR	DEL	CA	-	-	rs58609626		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:170707670_170707671delCA								EIF5A2 (81244 upstream) : SLC2A2 (6466 downstream)																																			---	---	---	---
SLC2A2	6514	broad.mit.edu	37	3	170736123	170736123	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-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	170819514	170819514	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:170819514delA	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_uc003fhg.2_5'UTR	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	170998976	170998976	+	Intron	DEL	A	-	-	rs111816889		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:170998976delA	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	171051374	171051381	+	Intron	DEL	AAAAAAAA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:171051374_171051381delAAAAAAAA	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)															---	---	---	---
Unknown	0	broad.mit.edu	37	3	171309234	171309234	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:171309234delT								TNIK (131037 upstream) : PLD1 (9386 downstream)																																			---	---	---	---
PLD1	5337	broad.mit.edu	37	3	171323375	171323376	+	Intron	DEL	TA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:171323375_171323376delTA	uc003fhs.2	-						PLD1_uc003fht.2_Intron	NM_002662	NP_002653			phospholipase D1 isoform a						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	171841884	171841884	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:171841884delT	uc003fhy.2	+						FNDC3B_uc003fhz.3_Intron|FNDC3B_uc003fhx.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)														---	---	---	---
FNDC3B	64778	broad.mit.edu	37	3	171872016	171872016	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:171872016delT	uc003fhy.2	+						FNDC3B_uc003fhz.3_Intron|FNDC3B_uc003fia.2_Intron|FNDC3B_uc003fhx.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)														---	---	---	---
FNDC3B	64778	broad.mit.edu	37	3	172080402	172080402	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:172080402delT	uc003fhy.2	+						FNDC3B_uc003fhz.3_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	172181335	172181335	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:172181335delT								GHSR (15132 upstream) : TNFSF10 (42130 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	172191018	172191019	+	IGR	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:172191018_172191019delAA								GHSR (24815 upstream) : TNFSF10 (32446 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	172273634	172273634	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:172273634delA								TNFSF10 (32365 upstream) : NCEH1 (74802 downstream)																																			---	---	---	---
NCEH1	57552	broad.mit.edu	37	3	172427572	172427572	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:172427572delT	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																		---	---	---	---
Unknown	0	broad.mit.edu	37	3	172433654	172433654	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:172433654delT								NCEH1 (4646 upstream) : ECT2 (34878 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	172463980	172463981	+	IGR	INS	-	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:172463980_172463981insG								NCEH1 (34972 upstream) : ECT2 (4551 downstream)																																			---	---	---	---
ECT2	1894	broad.mit.edu	37	3	172500665	172500665	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:172500665delT	uc003fii.2	+						ECT2_uc010hwv.1_Intron|ECT2_uc003fih.2_Intron|ECT2_uc003fij.1_Intron|ECT2_uc003fik.1_Intron|ECT2_uc003fil.1_Intron	NM_018098	NP_060568			epithelial cell transforming sequence 2 oncogene						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	Rho guanyl-nucleotide exchange factor activity|signal transducer activity			breast(2)|ovary(1)|skin(1)	4	Ovarian(172;0.00197)|Breast(254;0.158)		Lung(28;1.33e-14)|LUSC - Lung squamous cell carcinoma(14;1.48e-14)															---	---	---	---
ECT2	1894	broad.mit.edu	37	3	172536642	172536642	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:172536642delA	uc003fii.2	+						ECT2_uc003fih.2_Intron|ECT2_uc003fij.1_Intron|ECT2_uc003fik.1_Intron|ECT2_uc003fil.1_Intron|ECT2_uc003fim.1_Intron	NM_018098	NP_060568			epithelial cell transforming sequence 2 oncogene						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	Rho guanyl-nucleotide exchange factor activity|signal transducer activity			breast(2)|ovary(1)|skin(1)	4	Ovarian(172;0.00197)|Breast(254;0.158)		Lung(28;1.33e-14)|LUSC - Lung squamous cell carcinoma(14;1.48e-14)															---	---	---	---
Unknown	0	broad.mit.edu	37	3	172578537	172578537	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:172578537delA								ECT2 (39274 upstream) : SPATA16 (28611 downstream)																																			---	---	---	---
SPATA16	83893	broad.mit.edu	37	3	172694862	172694862	+	Intron	DEL	A	-	-	rs74715497		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:172694862delA	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)															---	---	---	---
Unknown	0	broad.mit.edu	37	3	173077842	173077842	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:173077842delA								SPATA16 (218810 upstream) : NLGN1 (38402 downstream)																																			---	---	---	---
NLGN1	22871	broad.mit.edu	37	3	173141331	173141331	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-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	173220872	173220873	+	Intron	INS	-	TG	TG	rs144519410	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:173220872_173220873insTG	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	173254210	173254210	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:173254210delA	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	173385430	173385430	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:173385430delT	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	173415326	173415326	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:173415326delT	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	173526893	173526894	+	Intron	INS	-	T	T	rs150007446	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:173526893_173526894insT	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	173671934	173671934	+	Intron	DEL	A	-	-	rs66737252		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:173671934delA	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	173713456	173713457	+	Intron	DEL	TT	-	-	rs66538676		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:173713456_173713457delTT	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	173818488	173818488	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:173818488delT	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	173891482	173891483	+	Intron	INS	-	TG	TG			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:173891482_173891483insTG	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	173942489	173942489	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:173942489delA	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)															---	---	---	---
Unknown	0	broad.mit.edu	37	3	174006286	174006286	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:174006286delT								NLGN1 (5170 upstream) : NAALADL2 (570825 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	174425632	174425632	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:174425632delA	uc003fir.2	+						uc003fis.2_Intron|uc010hwx.1_Intron					Homo sapiens NAALADL2 gene, partial 5'UTR, variant 1.																														---	---	---	---
Unknown	0	broad.mit.edu	37	3	174512951	174512951	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:174512951delT								NLGN1 (511835 upstream) : NAALADL2 (64160 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	174539128	174539128	+	IGR	DEL	A	-	-	rs77055309		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:174539128delA								NLGN1 (538012 upstream) : NAALADL2 (37983 downstream)																																			---	---	---	---
NAALADL2	254827	broad.mit.edu	37	3	174598445	174598445	+	Intron	DEL	C	-	-	rs76089421		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:174598445delC	uc003fit.2	+						NAALADL2_uc003fiu.1_Intron	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)														---	---	---	---
NAALADL2	254827	broad.mit.edu	37	3	174701903	174701903	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:174701903delA	uc003fit.2	+						NAALADL2_uc003fiu.1_Intron	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)														---	---	---	---
NAALADL2	254827	broad.mit.edu	37	3	174744446	174744446	+	Intron	DEL	A	-	-	rs112697779		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:174744446delA	uc003fit.2	+						NAALADL2_uc003fiu.1_Intron	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)														---	---	---	---
NAALADL2	254827	broad.mit.edu	37	3	174792350	174792350	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:174792350delA	uc003fit.2	+						NAALADL2_uc003fiu.1_Intron	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)														---	---	---	---
NAALADL2	254827	broad.mit.edu	37	3	175027397	175027397	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:175027397delT	uc003fit.2	+						NAALADL2_uc003fiu.1_Intron|NAALADL2_uc010hwy.1_Intron|NAALADL2_uc010hwz.1_Intron	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)														---	---	---	---
NAALADL2	254827	broad.mit.edu	37	3	175171839	175171839	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:175171839delT	uc003fit.2	+						NAALADL2_uc003fiu.1_Intron|NAALADL2_uc010hwy.1_Intron|NAALADL2_uc010hwz.1_Intron	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)														---	---	---	---
NAALADL2	254827	broad.mit.edu	37	3	175371016	175371016	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:175371016delA	uc003fit.2	+						NAALADL2_uc010hwy.1_Intron	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)														---	---	---	---
NAALADL2	254827	broad.mit.edu	37	3	175412860	175412861	+	Intron	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:175412860_175412861delAA	uc003fit.2	+							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)														---	---	---	---
NAALADL2	254827	broad.mit.edu	37	3	175472857	175472857	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:175472857delA	uc003fit.2	+							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	175524644	175524644	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:175524644delA								NAALADL2 (1218 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	175558932	175558933	+	IGR	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:175558932_175558933delTT								NAALADL2 (35506 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	175660568	175660568	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:175660568delA								NAALADL2 (137142 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	175704079	175704079	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:175704079delT								NAALADL2 (180653 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	175794437	175794437	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:175794437delA								NAALADL2 (271011 upstream) : TBL1XR1 (944106 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	175871144	175871144	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:175871144delA								NAALADL2 (347718 upstream) : TBL1XR1 (867399 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	175876010	175876010	+	IGR	DEL	A	-	-	rs67976717		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:175876010delA								NAALADL2 (352584 upstream) : TBL1XR1 (862533 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	175906980	175906980	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:175906980delT								NAALADL2 (383554 upstream) : TBL1XR1 (831563 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	175923698	175923698	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:175923698delA								NAALADL2 (400272 upstream) : TBL1XR1 (814845 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	175937799	175937799	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:175937799delA								NAALADL2 (414373 upstream) : TBL1XR1 (800744 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	176157510	176157512	+	IGR	DEL	AAA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:176157510_176157512delAAA								NAALADL2 (634084 upstream) : TBL1XR1 (581031 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	176174788	176174788	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:176174788delA								NAALADL2 (651362 upstream) : TBL1XR1 (563755 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	176297342	176297342	+	IGR	DEL	G	-	-	rs111901680		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:176297342delG								NAALADL2 (773916 upstream) : TBL1XR1 (441201 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	176309030	176309030	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:176309030delT								NAALADL2 (785604 upstream) : TBL1XR1 (429513 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	176380685	176380686	+	IGR	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:176380685_176380686delTT								NAALADL2 (857259 upstream) : TBL1XR1 (357857 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	176485779	176485779	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:176485779delA								NAALADL2 (962353 upstream) : TBL1XR1 (252764 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	176625958	176625958	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:176625958delT								None (None upstream) : TBL1XR1 (112585 downstream)																																			---	---	---	---
TBL1XR1	79718	broad.mit.edu	37	3	176912915	176912915	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:176912915delA	uc003fiw.3	-						TBL1XR1_uc003fix.3_Intron|TBL1XR1_uc011bpz.1_Intron|TBL1XR1_uc003fiy.2_Intron	NM_024665	NP_078941			transducin (beta)-like 1 X-linked receptor 1						canonical Wnt receptor signaling pathway|cellular lipid metabolic process|chromatin modification|negative regulation of transcription from RNA polymerase II promoter|positive regulation of transcription from RNA polymerase II promoter|proteasomal ubiquitin-dependent protein catabolic process|transcription, DNA-dependent	spindle microtubule|transcriptional repressor complex	beta-catenin binding|histone binding|protein N-terminus binding|transcription corepressor activity|transcription regulatory region DNA binding			ovary(1)	1	all_cancers(143;1.44e-17)|Ovarian(172;0.00163)|Breast(254;0.214)	Acute lymphoblastic leukemia(1;0.00599)|all_hematologic(1;0.0632)|Prostate(884;0.215)	OV - Ovarian serous cystadenocarcinoma(80;9.83e-31)															---	---	---	---
Unknown	0	broad.mit.edu	37	3	177028545	177028546	+	IGR	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:177028545_177028546delTT								TBL1XR1 (113497 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	177235514	177235514	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:177235514delT								TBL1XR1 (320466 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	177321352	177321352	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:177321352delT								TBL1XR1 (406304 upstream) : KCNMB2 (932872 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	177330075	177330080	+	IGR	DEL	TTTTTT	-	-	rs10576547		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:177330075_177330080delTTTTTT								TBL1XR1 (415027 upstream) : KCNMB2 (924144 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	177331274	177331278	+	IGR	DEL	TTTTT	-	-	rs72400988		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:177331274_177331278delTTTTT								TBL1XR1 (416226 upstream) : KCNMB2 (922946 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	177592513	177592513	+	Intron	DEL	T	-	-	rs67420726		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:177592513delT	uc003fiz.1	+											Homo sapiens cDNA FLJ31690 fis, clone NT2RI2005621.																														---	---	---	---
Unknown	0	broad.mit.edu	37	3	177828460	177828460	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:177828460delT								TBL1XR1 (913412 upstream) : KCNMB2 (425764 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	178097355	178097355	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:178097355delT	uc003fja.1	-											Homo sapiens cDNA FLJ34436 fis, clone HLUNG2001013.																														---	---	---	---
KCNMB2	10242	broad.mit.edu	37	3	178267715	178267715	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:178267715delT	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)															---	---	---	---
KCNMB2	10242	broad.mit.edu	37	3	178317351	178317351	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:178317351delT	uc003fjd.2	+						uc003fjb.1_Intron|uc003fjc.1_Intron|KCNMB2_uc003fje.2_Intron|KCNMB2_uc003fjf.2_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	178601543	178601545	+	IGR	DEL	AAA	-	-	rs77455295		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:178601543_178601545delAAA								KCNMB2 (39327 upstream) : ZMAT3 (139982 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	178612411	178612412	+	IGR	DEL	AA	-	-	rs76886321		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:178612411_178612412delAA								KCNMB2 (50195 upstream) : ZMAT3 (129115 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	178820946	178820946	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:178820946delA	uc003fjj.2	-											Homo sapiens cDNA clone IMAGE:4821793.																														---	---	---	---
PIK3CA	5290	broad.mit.edu	37	3	178867258	178867258	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:178867258delT	uc003fjk.2	+						uc003fjj.2_5'Flank	NM_006218	NP_006209			phosphoinositide-3-kinase, catalytic, alpha						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)			---	---	---	---
PIK3CA	5290	broad.mit.edu	37	3	178867804	178867806	+	Intron	DEL	TTT	-	-	rs113847531		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:178867804_178867806delTTT	uc003fjk.2	+						uc003fjj.2_5'Flank	NM_006218	NP_006209			phosphoinositide-3-kinase, catalytic, alpha						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)			---	---	---	---
PIK3CA	5290	broad.mit.edu	37	3	178941854	178941854	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:178941854delT	uc003fjk.2	+							NM_006218	NP_006209			phosphoinositide-3-kinase, catalytic, alpha						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)			---	---	---	---
ZNF639	51193	broad.mit.edu	37	3	179052260	179052260	+	3'UTR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:179052260delT	uc003fjq.1	+	6					ZNF639_uc003fjr.1_3'UTR	NM_016331	NP_057415			zinc finger protein 639						initiation of viral infection|negative regulation by host of viral transcription|negative regulation of transcription, DNA-dependent|positive regulation by host of viral transcription|positive regulation of cell growth|positive regulation of transcription, DNA-dependent	nucleus	protein self-association|sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding|zinc ion binding				0	all_cancers(143;7.9e-17)|Ovarian(172;0.0172)|Breast(254;0.155)		OV - Ovarian serous cystadenocarcinoma(80;5.78e-26)|GBM - Glioblastoma multiforme(14;0.003)|BRCA - Breast invasive adenocarcinoma(182;0.0923)															---	---	---	---
MFN1	55669	broad.mit.edu	37	3	179094713	179094713	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:179094713delT	uc003fjs.2	+						MFN1_uc010hxb.2_Intron|MFN1_uc003fjt.2_Intron|MFN1_uc010hxc.2_Intron	NM_033540	NP_284941			mitofusin 1						mitochondrial fusion	integral to membrane|mitochondrial outer membrane	GTP binding|GTPase activity			ovary(2)|large_intestine(1)	3	all_cancers(143;1.67e-16)|Ovarian(172;0.0172)|Breast(254;0.155)		OV - Ovarian serous cystadenocarcinoma(80;5.78e-26)|GBM - Glioblastoma multiforme(14;0.00225)|BRCA - Breast invasive adenocarcinoma(182;0.0923)															---	---	---	---
Unknown	0	broad.mit.edu	37	3	179208010	179208010	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:179208010delT								GNB4 (38639 upstream) : ACTL6A (72698 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	179351823	179351823	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:179351823delA								NDUFB5 (9536 upstream) : USP13 (19110 downstream)																																			---	---	---	---
USP13	8975	broad.mit.edu	37	3	179369779	179369779	+	5'Flank	DEL	A	-	-	rs79318847		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:179369779delA	uc003fkh.2	+						USP13_uc003fkf.2_5'Flank	NM_003940	NP_003931			ubiquitin thiolesterase 13						ubiquitin-dependent protein catabolic process		cysteine-type endopeptidase activity|omega peptidase activity|protein binding|ubiquitin thiolesterase activity|ubiquitin-specific protease activity|zinc ion binding			ovary(1)	1	all_cancers(143;7.79e-15)|Ovarian(172;0.0338)|Breast(254;0.148)		OV - Ovarian serous cystadenocarcinoma(80;1e-25)|GBM - Glioblastoma multiforme(14;0.0169)															---	---	---	---
USP13	8975	broad.mit.edu	37	3	179437494	179437494	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:179437494delA	uc003fkh.2	+						USP13_uc003fkf.2_Intron	NM_003940	NP_003931			ubiquitin thiolesterase 13						ubiquitin-dependent protein catabolic process		cysteine-type endopeptidase activity|omega peptidase activity|protein binding|ubiquitin thiolesterase activity|ubiquitin-specific protease activity|zinc ion binding			ovary(1)	1	all_cancers(143;7.79e-15)|Ovarian(172;0.0338)|Breast(254;0.148)		OV - Ovarian serous cystadenocarcinoma(80;1e-25)|GBM - Glioblastoma multiforme(14;0.0169)															---	---	---	---
USP13	8975	broad.mit.edu	37	3	179438600	179438601	+	Intron	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:179438600_179438601delTT	uc003fkh.2	+						USP13_uc003fkf.2_Intron	NM_003940	NP_003931			ubiquitin thiolesterase 13						ubiquitin-dependent protein catabolic process		cysteine-type endopeptidase activity|omega peptidase activity|protein binding|ubiquitin thiolesterase activity|ubiquitin-specific protease activity|zinc ion binding			ovary(1)	1	all_cancers(143;7.79e-15)|Ovarian(172;0.0338)|Breast(254;0.148)		OV - Ovarian serous cystadenocarcinoma(80;1e-25)|GBM - Glioblastoma multiforme(14;0.0169)															---	---	---	---
USP13	8975	broad.mit.edu	37	3	179461522	179461522	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:179461522delT	uc003fkh.2	+						USP13_uc003fkf.2_Intron	NM_003940	NP_003931			ubiquitin thiolesterase 13						ubiquitin-dependent protein catabolic process		cysteine-type endopeptidase activity|omega peptidase activity|protein binding|ubiquitin thiolesterase activity|ubiquitin-specific protease activity|zinc ion binding			ovary(1)	1	all_cancers(143;7.79e-15)|Ovarian(172;0.0338)|Breast(254;0.148)		OV - Ovarian serous cystadenocarcinoma(80;1e-25)|GBM - Glioblastoma multiforme(14;0.0169)															---	---	---	---
USP13	8975	broad.mit.edu	37	3	179479203	179479203	+	Intron	DEL	T	-	-	rs74695249		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:179479203delT	uc003fkh.2	+							NM_003940	NP_003931			ubiquitin thiolesterase 13						ubiquitin-dependent protein catabolic process		cysteine-type endopeptidase activity|omega peptidase activity|protein binding|ubiquitin thiolesterase activity|ubiquitin-specific protease activity|zinc ion binding			ovary(1)	1	all_cancers(143;7.79e-15)|Ovarian(172;0.0338)|Breast(254;0.148)		OV - Ovarian serous cystadenocarcinoma(80;1e-25)|GBM - Glioblastoma multiforme(14;0.0169)															---	---	---	---
Unknown	0	broad.mit.edu	37	3	179801149	179801149	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:179801149delA								PEX5L (46632 upstream) : TTC14 (518769 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	179962346	179962346	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:179962346delT								PEX5L (207829 upstream) : TTC14 (357572 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	180280922	180280922	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:180280922delA								PEX5L (526405 upstream) : TTC14 (38996 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	180304892	180304892	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:180304892delT								PEX5L (550375 upstream) : TTC14 (15026 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	180475889	180475895	+	Intron	DEL	TTTTTTT	-	-	rs11357460		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:180475889_180475895delTTTTTTT	uc003fko.2	-											Homo sapiens mRNA; cDNA DKFZp434A128 (from clone DKFZp434A128).																														---	---	---	---
Unknown	0	broad.mit.edu	37	3	180514237	180514237	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:180514237delT	uc003fko.2	-											Homo sapiens mRNA; cDNA DKFZp434A128 (from clone DKFZp434A128).																														---	---	---	---
Unknown	0	broad.mit.edu	37	3	180578082	180578085	+	Intron	DEL	AGGA	-	-	rs113077171		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:180578082_180578085delAGGA	uc003fko.2	-											Homo sapiens mRNA; cDNA DKFZp434A128 (from clone DKFZp434A128).																														---	---	---	---
Unknown	0	broad.mit.edu	37	3	180612996	180612997	+	IGR	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:180612996_180612997delTT								CCDC39 (157334 upstream) : FXR1 (17455 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	180890744	180890744	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:180890744delA								DNAJC19 (183214 upstream) : SOX2OT (390765 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	181032101	181032102	+	IGR	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:181032101_181032102delAA								DNAJC19 (324571 upstream) : SOX2OT (249407 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	181136653	181136653	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:181136653delA								DNAJC19 (429123 upstream) : SOX2OT (144856 downstream)																																			---	---	---	---
SOX2OT	347689	broad.mit.edu	37	3	181279184	181279184	+	5'Flank	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:181279184delT	uc003fkv.2	+											Homo sapiens cDNA FLJ12764 fis, clone NT2RP2001506.												0																		---	---	---	---
SOX2OT	347689	broad.mit.edu	37	3	181359297	181359297	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:181359297delA	uc003fkv.2	+						SOX2OT_uc003fkw.3_Intron					Homo sapiens cDNA FLJ12764 fis, clone NT2RP2001506.												0																		---	---	---	---
SOX2OT	347689	broad.mit.edu	37	3	181364898	181364898	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:181364898delA	uc003fkv.2	+						SOX2OT_uc003fkw.3_Intron					Homo sapiens cDNA FLJ12764 fis, clone NT2RP2001506.												0																		---	---	---	---
SOX2OT	347689	broad.mit.edu	37	3	181370204	181370205	+	Intron	DEL	AC	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:181370204_181370205delAC	uc003fkv.2	+						SOX2OT_uc003fkw.3_Intron					Homo sapiens cDNA FLJ12764 fis, clone NT2RP2001506.												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	3	181459181	181459193	+	IGR	DEL	TTTTTTTTTTTTT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:181459181_181459193delTTTTTTTTTTTTT								SOX2OT (178 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	181480413	181480413	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:181480413delA								SOX2OT (21410 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	181483740	181483740	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:181483740delA								SOX2OT (24737 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	181703617	181703617	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:181703617delT	uc003fky.2	+											Homo sapiens cDNA clone IMAGE:5296886.																														---	---	---	---
Unknown	0	broad.mit.edu	37	3	181825122	181825122	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:181825122delT								SOX2OT (366119 upstream) : ATP11B (686169 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	181861092	181861092	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:181861092delT								SOX2OT (402089 upstream) : ATP11B (650199 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	182152858	182152858	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:182152858delA								SOX2OT (693855 upstream) : ATP11B (358433 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	182169695	182169695	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:182169695delT								SOX2OT (710692 upstream) : ATP11B (341596 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	182175849	182175849	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:182175849delT								SOX2OT (716846 upstream) : ATP11B (335442 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	182254089	182254090	+	IGR	DEL	TT	-	-	rs113237009		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:182254089_182254090delTT								SOX2OT (795086 upstream) : ATP11B (257201 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	182272551	182272551	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:182272551delT								SOX2OT (813548 upstream) : ATP11B (238740 downstream)																																			---	---	---	---
MCCC1	56922	broad.mit.edu	37	3	182779041	182779041	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:182779041delT	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)													---	---	---	---
MCF2L2	23101	broad.mit.edu	37	3	182997816	182997818	+	Intron	DEL	AAA	-	-	rs76530126		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:182997816_182997818delAAA	uc003fli.1	-						MCF2L2_uc003flj.1_Intron|MCF2L2_uc011bqr.1_Intron	NM_015078	NP_055893			Rho family guanine-nucleotide exchange factor						regulation of Rho protein signal transduction	intracellular	Rho guanyl-nucleotide exchange factor activity			ovary(2)|large_intestine(2)|breast(1)	5	all_cancers(143;1.26e-12)|Ovarian(172;0.0355)		all cancers(12;3.35e-44)|Epithelial(37;6.48e-38)|LUSC - Lung squamous cell carcinoma(7;7.12e-25)|Lung(8;6.39e-23)|OV - Ovarian serous cystadenocarcinoma(80;6.75e-21)															---	---	---	---
Unknown	0	broad.mit.edu	37	3	183343832	183343834	+	IGR	DEL	TTG	-	-	rs4859126		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:183343832_183343834delTTG								KLHL6 (70333 upstream) : KLHL24 (9577 downstream)																																			---	---	---	---
KLHL24	54800	broad.mit.edu	37	3	183396774	183396774	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:183396774delT	uc003flv.2	+						KLHL24_uc003flw.2_Intron	NM_017644	NP_060114			DRE1 protein							axon|cytoplasm|perikaryon				ovary(1)	1	all_cancers(143;2.88e-10)|Ovarian(172;0.0303)		all cancers(12;1.43e-42)|Epithelial(37;1.73e-36)|OV - Ovarian serous cystadenocarcinoma(80;8.75e-22)															---	---	---	---
YEATS2	55689	broad.mit.edu	37	3	183420622	183420623	+	Intron	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:183420622_183420623delAA	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)															---	---	---	---
YEATS2	55689	broad.mit.edu	37	3	183462636	183462636	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:183462636delT	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)															---	---	---	---
YEATS2	55689	broad.mit.edu	37	3	183466046	183466049	+	Intron	DEL	TTTT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:183466046_183466049delTTTT	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)															---	---	---	---
YEATS2	55689	broad.mit.edu	37	3	183472814	183472815	+	Intron	INS	-	A	A	rs71670606		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:183472814_183472815insA	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)															---	---	---	---
YEATS2	55689	broad.mit.edu	37	3	183521762	183521762	+	Intron	DEL	T	-	-	rs112874863		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:183521762delT	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)															---	---	---	---
ABCC5	10057	broad.mit.edu	37	3	183673210	183673210	+	Intron	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:183673210delC	uc003fmg.2	-						ABCC5_uc011bqt.1_Intron|ABCC5_uc010hxl.2_Intron	NM_005688	NP_005679			ATP-binding cassette, sub-family C, member 5							integral to plasma membrane|membrane fraction	ATP binding|ATPase activity, coupled to transmembrane movement of substances|organic anion transmembrane transporter activity			ovary(2)|large_intestine(1)|central_nervous_system(1)	4	all_cancers(143;1.85e-10)|Ovarian(172;0.0303)		Epithelial(37;1.74e-35)|OV - Ovarian serous cystadenocarcinoma(80;6.48e-22)															---	---	---	---
HTR3C	170572	broad.mit.edu	37	3	183768442	183768443	+	5'Flank	INS	-	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:183768442_183768443insT	uc003fmk.2	+							NM_130770	NP_570126			5-hydroxytryptamine receptor 3 subunit C							integral to membrane|plasma membrane|postsynaptic membrane	extracellular ligand-gated ion channel activity|receptor activity			large_intestine(1)|ovary(1)|central_nervous_system(1)	3	all_cancers(143;2.33e-10)|Ovarian(172;0.0303)		Epithelial(37;1.74e-35)|OV - Ovarian serous cystadenocarcinoma(80;3.11e-22)															---	---	---	---
HTR3C	170572	broad.mit.edu	37	3	183770453	183770454	+	5'Flank	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:183770453_183770454delAA	uc003fmk.2	+							NM_130770	NP_570126			5-hydroxytryptamine receptor 3 subunit C							integral to membrane|plasma membrane|postsynaptic membrane	extracellular ligand-gated ion channel activity|receptor activity			large_intestine(1)|ovary(1)|central_nervous_system(1)	3	all_cancers(143;2.33e-10)|Ovarian(172;0.0303)		Epithelial(37;1.74e-35)|OV - Ovarian serous cystadenocarcinoma(80;3.11e-22)															---	---	---	---
Unknown	0	broad.mit.edu	37	3	183792565	183792565	+	IGR	DEL	C	-	-	rs9881525	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:183792565delC								HTR3C (14106 upstream) : HTR3E (22287 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	183917855	183917855	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:183917855delA								ABCF3 (6060 upstream) : VWA5B2 (30462 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	183921764	183921764	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:183921764delT								ABCF3 (9969 upstream) : VWA5B2 (26553 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	183943845	183943845	+	IGR	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:183943845delC								ABCF3 (32050 upstream) : VWA5B2 (4472 downstream)																																			---	---	---	---
ECE2	9718	broad.mit.edu	37	3	183976948	183976948	+	Intron	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:183976948delC	uc003fni.3	+							NM_014693	NP_055508			endothelin converting enzyme 2 isoform A						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)															---	---	---	---
PSMD2	5708	broad.mit.edu	37	3	184014923	184014926	+	5'Flank	DEL	AAAA	-	-	rs34810769		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:184014923_184014926delAAAA	uc003fnn.1	+							NM_002808	NP_002799			proteasome 26S non-ATPase subunit 2						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)													---	---	---	---
CHRD	8646	broad.mit.edu	37	3	184098961	184098961	+	Intron	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:184098961delG	uc003fov.2	+						CHRD_uc003fow.2_Intron|CHRD_uc003fox.2_Intron|CHRD_uc003foy.2_Intron|CHRD_uc010hyc.2_5'Flank|CHRD_uc011brr.1_5'Flank	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)															---	---	---	---
Unknown	0	broad.mit.edu	37	3	184113496	184113496	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:184113496delA								CHRD (5877 upstream) : EPHB3 (166091 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	184375225	184375229	+	IGR	DEL	TTTTT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:184375225_184375229delTTTTT								EPHB3 (75030 upstream) : MAGEF1 (52927 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	184452573	184452573	+	IGR	DEL	T	-	-	rs4686690	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:184452573delT								MAGEF1 (22737 upstream) : VPS8 (77358 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	184516053	184516053	+	IGR	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:184516053delC								MAGEF1 (86217 upstream) : VPS8 (13878 downstream)																																			---	---	---	---
VPS8	23355	broad.mit.edu	37	3	184631713	184631713	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:184631713delT	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)															---	---	---	---
VPS8	23355	broad.mit.edu	37	3	184686337	184686338	+	Intron	INS	-	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:184686337_184686338insT	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)															---	---	---	---
VPS8	23355	broad.mit.edu	37	3	184750458	184750459	+	Intron	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:184750458_184750459delTT	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)															---	---	---	---
VPS8	23355	broad.mit.edu	37	3	184752473	184752473	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:184752473delT	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)															---	---	---	---
MAP3K13	9175	broad.mit.edu	37	3	185083028	185083029	+	Intron	INS	-	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:185083028_185083029insA	uc010hyf.2	+						MAP3K13_uc011brt.1_Intron|MAP3K13_uc003fph.3_Intron|MAP3K13_uc011bru.1_Intron|MAP3K13_uc003fpi.2_Intron|MAP3K13_uc010hyg.2_Intron	NM_004721	NP_004712			mitogen-activated protein kinase kinase kinase						activation of MAPKK activity|JNK cascade|positive regulation of NF-kappaB transcription factor activity|protein autophosphorylation	cytoplasm|membrane|membrane fraction	ATP binding|magnesium ion binding|MAP kinase kinase kinase activity|protein homodimerization activity|protein kinase binding			ovary(2)|skin(1)	3	all_cancers(143;7.21e-11)|Ovarian(172;0.0339)		OV - Ovarian serous cystadenocarcinoma(80;1.93e-20)															---	---	---	---
LIPH	200879	broad.mit.edu	37	3	185250229	185250230	+	Intron	DEL	GC	-	-	rs9856267	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:185250229_185250230delGC	uc003fpm.2	-						LIPH_uc010hyh.2_Intron	NM_139248	NP_640341			lipase, member H precursor						lipid catabolic process	extracellular space|plasma membrane	heparin binding|phospholipase activity			ovary(1)|pancreas(1)	2	all_cancers(143;8.87e-11)|Ovarian(172;0.0386)		OV - Ovarian serous cystadenocarcinoma(80;1.31e-21)															---	---	---	---
SENP2	59343	broad.mit.edu	37	3	185319428	185319434	+	Intron	DEL	TTTTTTT	-	-	rs62772661		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:185319428_185319434delTTTTTTT	uc003fpn.2	+						SENP2_uc011brv.1_Intron|SENP2_uc011brw.1_Intron	NM_021627	NP_067640			SUMO1/sentrin/SMT3 specific protease 2						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)															---	---	---	---
SENP2	59343	broad.mit.edu	37	3	185336667	185336668	+	Intron	DEL	AA	-	-	rs77707823		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:185336667_185336668delAA	uc003fpn.2	+						SENP2_uc011brv.1_Intron|SENP2_uc011brw.1_Intron	NM_021627	NP_067640			SUMO1/sentrin/SMT3 specific protease 2						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)															---	---	---	---
Unknown	0	broad.mit.edu	37	3	185568808	185568811	+	IGR	DEL	TTTT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:185568808_185568811delTTTT								IGF2BP2 (25981 upstream) : TRA2B (63549 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	185571694	185571694	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:185571694delT								IGF2BP2 (28867 upstream) : TRA2B (60666 downstream)																																			---	---	---	---
TRA2B	6434	broad.mit.edu	37	3	185654146	185654146	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:185654146delA	uc003fpv.2	-						TRA2B_uc003fpu.2_RNA|TRA2B_uc010hym.2_Intron|TRA2B_uc003fpw.2_Intron|TRA2B_uc003fpx.2_Intron	NM_004593	NP_004584			splicing factor, arginine/serine-rich 10						nuclear mRNA splicing, via spliceosome	nucleus	nucleotide binding|protein binding|RNA binding			ovary(2)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	3	185666848	185666848	+	IGR	DEL	A	-	-	rs63509361		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:185666848delA								TRA2B (10924 upstream) : ETV5 (97260 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	185672880	185672881	+	IGR	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:185672880_185672881delTT								TRA2B (16956 upstream) : ETV5 (91227 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	185735956	185735959	+	IGR	DEL	GAGA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:185735956_185735959delGAGA								TRA2B (80032 upstream) : ETV5 (28149 downstream)																																			---	---	---	---
ETV5	2119	broad.mit.edu	37	3	185802072	185802081	+	Intron	DEL	AAAAAAAAAA	-	-	rs35288935		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:185802072_185802081delAAAAAAAAAA	uc003fpz.2	-						ETV5_uc003fpy.2_Intron	NM_004454	NP_004445			ets variant gene 5 (ets-related molecule)						cellular response to oxidative stress	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding			ovary(2)|skin(2)|breast(1)	5	all_cancers(143;4.06e-12)|Ovarian(172;0.0386)|Breast(254;0.247)		OV - Ovarian serous cystadenocarcinoma(80;1.62e-24)					T	TMPRSS2|SCL45A3	Prostate 								---	---	---	---
DGKG	1608	broad.mit.edu	37	3	185916743	185916743	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:185916743delT	uc003fqa.2	-						DGKG_uc003fqb.2_Intron|DGKG_uc003fqc.2_Intron|DGKG_uc011brx.1_Intron	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)													---	---	---	---
DGKG	1608	broad.mit.edu	37	3	186030768	186030768	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:186030768delA	uc003fqa.2	-						DGKG_uc003fqb.2_Intron|DGKG_uc003fqc.2_Intron|DGKG_uc011brx.1_Intron	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)													---	---	---	---
DGKG	1608	broad.mit.edu	37	3	186045686	186045686	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:186045686delA	uc003fqa.2	-						DGKG_uc003fqb.2_Intron|DGKG_uc003fqc.2_Intron|DGKG_uc011brx.1_Intron	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)													---	---	---	---
Unknown	0	broad.mit.edu	37	3	186173679	186173682	+	Intron	DEL	ACAC	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:186173679_186173682delACAC	uc003fqd.1	-											Homo sapiens cDNA FLJ32735 fis, clone TESTI2001229.																														---	---	---	---
TBCCD1	55171	broad.mit.edu	37	3	186268857	186268857	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:186268857delT	uc003fqg.2	-						TBCCD1_uc011bry.1_Intron|TBCCD1_uc003fqh.2_Intron	NM_018138	NP_060608			TBCC domain containing 1						cell morphogenesis|maintenance of centrosome location|maintenance of Golgi location|regulation of cell migration|regulation of cell shape	spindle pole centrosome	binding			large_intestine(1)|ovary(1)	2	all_cancers(143;3.75e-12)|Ovarian(172;0.0339)		OV - Ovarian serous cystadenocarcinoma(80;4.3e-21)	GBM - Glioblastoma multiforme(93;0.0474)														---	---	---	---
TBCCD1	55171	broad.mit.edu	37	3	186285789	186285789	+	5'Flank	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:186285789delT	uc003fqg.2	-						TBCCD1_uc011bry.1_Intron|TBCCD1_uc003fqh.2_Intron|DNAJB11_uc003fqi.2_5'Flank	NM_018138	NP_060608			TBCC domain containing 1						cell morphogenesis|maintenance of centrosome location|maintenance of Golgi location|regulation of cell migration|regulation of cell shape	spindle pole centrosome	binding			large_intestine(1)|ovary(1)	2	all_cancers(143;3.75e-12)|Ovarian(172;0.0339)		OV - Ovarian serous cystadenocarcinoma(80;4.3e-21)	GBM - Glioblastoma multiforme(93;0.0474)														---	---	---	---
AHSG	197	broad.mit.edu	37	3	186330746	186330746	+	5'Flank	DEL	T	-	-	rs66939339		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:186330746delT	uc003fqk.3	+						AHSG_uc003fqj.2_5'Flank|AHSG_uc003fql.3_5'Flank|AHSG_uc003fqm.3_5'Flank|AHSG_uc010hyp.2_5'Flank	NM_001622	NP_001613			alpha-2-HS-glycoprotein						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)														---	---	---	---
Unknown	0	broad.mit.edu	37	3	186424365	186424366	+	IGR	DEL	AT	-	-	rs145143464	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:186424365_186424366delAT								HRG (28343 upstream) : KNG1 (10754 downstream)																																			---	---	---	---
RFC4	5984	broad.mit.edu	37	3	186520521	186520522	+	Intron	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:186520521_186520522delTT	uc003fqz.2	-						RFC4_uc011bsc.1_Intron|RFC4_uc011bsd.1_Intron	NM_002916	NP_002907			replication factor C 4						cell cycle checkpoint|DNA strand elongation involved in DNA replication|nucleotide-excision repair, DNA gap filling|phosphatidylinositol-mediated signaling|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			breast(2)|upper_aerodigestive_tract(1)|ovary(1)|large_intestine(1)	5	all_cancers(143;2.92e-12)|Ovarian(172;0.0339)		OV - Ovarian serous cystadenocarcinoma(80;7.41e-21)	GBM - Glioblastoma multiforme(93;0.0739)														---	---	---	---
Unknown	0	broad.mit.edu	37	3	186639768	186639768	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:186639768delT								ADIPOQ (63518 upstream) : ST6GAL1 (8748 downstream)																																			---	---	---	---
RPL39L	116832	broad.mit.edu	37	3	186846156	186846156	+	Intron	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:186846156delG	uc003fre.1	-						RPL39L_uc003frf.1_Intron	NM_052969	NP_443201			ribosomal protein L39-like protein						spermatogenesis|translation	cytosolic large ribosomal subunit	structural constituent of ribosome				0	all_cancers(143;2.61e-12)|Ovarian(172;0.0339)		OV - Ovarian serous cystadenocarcinoma(80;1.87e-18)	GBM - Glioblastoma multiforme(93;0.0745)														---	---	---	---
Unknown	0	broad.mit.edu	37	3	187468034	187468034	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:187468034delT								BCL6 (4559 upstream) : LPP (403685 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	187662916	187662916	+	IGR	DEL	G	-	-	rs67967027		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:187662916delG								BCL6 (199441 upstream) : LPP (208803 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	187694355	187694356	+	5'Flank	INS	-	T	T	rs139609281	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:187694355_187694356insT	uc003frr.1	-											full-length cDNA clone CS0DL012YA13 of B cells (Ramos cell line) Cot 25-normalized of Homo sapiens (human).																														---	---	---	---
Unknown	0	broad.mit.edu	37	3	187831953	187831955	+	IGR	DEL	TTT	-	-	rs34667567		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:187831953_187831955delTTT								BCL6 (368478 upstream) : LPP (39764 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	187837938	187837938	+	IGR	DEL	T	-	-	rs5855175		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:187837938delT								BCL6 (374463 upstream) : LPP (33781 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	187858844	187858844	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:187858844delT								BCL6 (395369 upstream) : LPP (12875 downstream)																																			---	---	---	---
LPP	4026	broad.mit.edu	37	3	187911535	187911535	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:187911535delT	uc011bsg.1	+							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	188121656	188121657	+	Intron	DEL	TG	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:188121656_188121657delTG	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	188232019	188232019	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:188232019delT	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	188242334	188242334	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:188242334delA	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	188464248	188464249	+	Intron	INS	-	T	T	rs142602930	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:188464248_188464249insT	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								---	---	---	---
LPP	4026	broad.mit.edu	37	3	188530686	188530686	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:188530686delT	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								---	---	---	---
LPP	4026	broad.mit.edu	37	3	188541274	188541274	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:188541274delA	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	188857722	188857722	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:188857722delA	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	188948224	188948224	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-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)														---	---	---	---
Unknown	0	broad.mit.edu	37	3	189083817	189083817	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:189083817delT								TPRG1 (42547 upstream) : TP63 (265399 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	189099334	189099334	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:189099334delT								TPRG1 (58064 upstream) : TP63 (249882 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	189306213	189306213	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:189306213delT								TPRG1 (264943 upstream) : TP63 (43003 downstream)																																			---	---	---	---
TP63	8626	broad.mit.edu	37	3	189497855	189497855	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:189497855delA	uc003fry.2	+						TP63_uc003frx.2_Intron|TP63_uc003frz.2_Intron|TP63_uc010hzc.1_Intron	NM_003722	NP_003713			tumor protein p63 isoform 1						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	189531385	189531386	+	Intron	DEL	TT	-	-	rs75257492		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:189531385_189531386delTT	uc003fry.2	+						TP63_uc003frx.2_Intron|TP63_uc003frz.2_Intron|TP63_uc010hzc.1_Intron|TP63_uc003fsa.2_Intron|TP63_uc003fsb.2_Intron|TP63_uc003fsc.2_Intron|TP63_uc003fsd.2_Intron|TP63_uc010hzd.1_Intron|TP63_uc003fse.1_Intron	NM_003722	NP_003713			tumor protein p63 isoform 1						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)			---	---	---	---
LEPREL1	55214	broad.mit.edu	37	3	189700671	189700671	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-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)													---	---	---	---
LEPREL1	55214	broad.mit.edu	37	3	189802740	189802741	+	Intron	DEL	AA	-	-	rs78659237		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:189802740_189802741delAA	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	189824335	189824336	+	Intron	DEL	TT	-	-	rs72402880		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:189824335_189824336delTT	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	190224744	190224745	+	IGR	INS	-	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:190224744_190224745insA								TMEM207 (57079 upstream) : IL1RAP (7146 downstream)																																			---	---	---	---
IL1RAP	3556	broad.mit.edu	37	3	190303602	190303602	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:190303602delA	uc003fsm.1	+						IL1RAP_uc003fsk.2_Intron|IL1RAP_uc003fsl.2_Intron|IL1RAP_uc010hzf.2_Intron|IL1RAP_uc010hzg.1_Intron|IL1RAP_uc003fsn.1_Intron|IL1RAP_uc003fso.1_Intron|IL1RAP_uc003fsp.1_Intron|IL1RAP_uc003fsq.2_Intron	NM_002182	NP_002173			interleukin 1 receptor accessory protein isoform						inflammatory response|innate immune response|protein complex assembly	extracellular region|integral to plasma membrane				ovary(1)	1	all_cancers(143;3.61e-10)|Ovarian(172;0.0733)|Breast(254;0.21)		Lung(62;1.95e-06)|LUSC - Lung squamous cell carcinoma(58;2.05e-06)	GBM - Glioblastoma multiforme(93;0.00851)														---	---	---	---
Unknown	0	broad.mit.edu	37	3	190412761	190412761	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:190412761delA								IL1RAP (36918 upstream) : LOC647309 (157765 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	190711544	190711544	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:190711544delT								SNAR-I (115705 upstream) : OSTN (218778 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	190855139	190855139	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:190855139delA								SNAR-I (259300 upstream) : OSTN (75183 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	190901720	190901720	+	IGR	DEL	A	-	-	rs111772074		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:190901720delA								SNAR-I (305881 upstream) : OSTN (28602 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	190912824	190912824	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:190912824delT								SNAR-I (316985 upstream) : OSTN (17498 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	191300287	191300287	+	IGR	DEL	A	-	-	rs35460929		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:191300287delA								PYDC2 (121044 upstream) : FGF12 (559397 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	191663536	191663537	+	IGR	INS	-	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:191663536_191663537insT								PYDC2 (484293 upstream) : FGF12 (196147 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	191665069	191665069	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:191665069delT								PYDC2 (485826 upstream) : FGF12 (194615 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	191716907	191716907	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:191716907delT								PYDC2 (537664 upstream) : FGF12 (142777 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	191782358	191782358	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:191782358delT								PYDC2 (603115 upstream) : FGF12 (77326 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	191831164	191831164	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:191831164delT								PYDC2 (651921 upstream) : FGF12 (28520 downstream)																																			---	---	---	---
FGF12	2257	broad.mit.edu	37	3	191991696	191991697	+	Intron	DEL	AA	-	-	rs67157460		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:191991696_191991697delAA	uc003fsx.2	-						FGF12_uc003fsy.2_Intron	NM_021032	NP_066360			fibroblast growth factor 12 isoform 1						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)														---	---	---	---
FGF12	2257	broad.mit.edu	37	3	192147983	192147984	+	Intron	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:192147983_192147984delAA	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)														---	---	---	---
FGF12	2257	broad.mit.edu	37	3	192385965	192385965	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:192385965delA	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	192486778	192486778	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:192486778delT								FGF12 (41390 upstream) : C3orf59 (27829 downstream)																																			---	---	---	---
C3orf59	151963	broad.mit.edu	37	3	192575433	192575433	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:192575433delA	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	192664309	192664310	+	IGR	DEL	TG	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:192664309_192664310delTG								C3orf59 (28359 upstream) : HRASLS (294608 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	192811279	192811279	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:192811279delA								C3orf59 (175329 upstream) : HRASLS (147639 downstream)																																			---	---	---	---
ATP13A5	344905	broad.mit.edu	37	3	192993594	192993594	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:192993594delT	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	193064667	193064667	+	Intron	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:193064667delG	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	193086872	193086872	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:193086872delT	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	193216130	193216130	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:193216130delA	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)														---	---	---	---
ATP13A4	84239	broad.mit.edu	37	3	193221653	193221653	+	Intron	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:193221653delC	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)														---	---	---	---
Unknown	0	broad.mit.edu	37	3	193278004	193278004	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:193278004delT								ATP13A4 (5308 upstream) : OPA1 (32929 downstream)																																			---	---	---	---
OPA1	4976	broad.mit.edu	37	3	193354644	193354644	+	Intron	DEL	T	-	-	rs11324182		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:193354644delT	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	193360958	193360958	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:193360958delA	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	193620695	193620695	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:193620695delT								OPA1 (205096 upstream) : LOC100128023 (90189 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	193748433	193748434	+	IGR	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:193748433_193748434delTT								LOC100128023 (36406 upstream) : HES1 (105500 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	193842659	193842659	+	IGR	DEL	T	-	-	rs79243999		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:193842659delT								LOC100128023 (130632 upstream) : HES1 (11275 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	193994348	193994348	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:193994348delA								HES1 (137952 upstream) : LOC100131551 (23076 downstream)																																			---	---	---	---
ATP13A3	79572	broad.mit.edu	37	3	194146918	194146918	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:194146918delT	uc003fty.3	-						ATP13A3_uc003ftx.3_5'Flank	NM_024524	NP_078800			ATPase type 13A3						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)														---	---	---	---
TMEM44	93109	broad.mit.edu	37	3	194322039	194322039	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:194322039delT	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)														---	---	---	---
Unknown	0	broad.mit.edu	37	3	194504776	194504776	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:194504776delA								FAM43A (95012 upstream) : C3orf21 (284239 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	194679308	194679308	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:194679308delT								FAM43A (269544 upstream) : C3orf21 (109707 downstream)																																			---	---	---	---
C3orf21	152002	broad.mit.edu	37	3	194822529	194822529	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:194822529delA	uc003fum.3	-						C3orf21_uc003ful.2_Intron|C3orf21_uc003fuk.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	194910862	194910862	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:194910862delA	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	194915808	194915808	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:194915808delT	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)														---	---	---	---
ACAP2	23527	broad.mit.edu	37	3	195049150	195049150	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:195049150delA	uc003fun.3	-							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	195082165	195082165	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:195082165delA	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																		---	---	---	---
PPP1R2	5504	broad.mit.edu	37	3	195269528	195269529	+	Intron	DEL	AA	-	-	rs72445004		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:195269528_195269529delAA	uc003fup.2	-						PPP1R2_uc003fuq.3_Intron	NM_006241	NP_006232			protein phosphatase 1, regulatory subunit 2						glycogen metabolic process|regulation of phosphoprotein phosphatase activity|regulation of signal transduction		protein binding|protein serine/threonine phosphatase inhibitor activity			urinary_tract(1)	1	all_cancers(143;1.8e-08)|Ovarian(172;0.0634)		Epithelial(36;2.64e-22)|all cancers(36;2.69e-20)|OV - Ovarian serous cystadenocarcinoma(49;3.52e-19)|Lung(62;0.000104)|LUSC - Lung squamous cell carcinoma(58;0.000128)	GBM - Glioblastoma multiforme(46;9.55e-05)														---	---	---	---
Unknown	0	broad.mit.edu	37	3	195354244	195354245	+	IGR	INS	-	A	A	rs148606126	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:195354244_195354245insA								APOD (43168 upstream) : SDHAP2 (30665 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	195430743	195430743	+	Intron	DEL	A	-	-	rs146496321		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:195430743delA	uc011btd.1	+						uc003fux.1_Intron					Homo sapiens cDNA FLJ46488 fis, clone THYMU3026869.																														---	---	---	---
MUC20	200958	broad.mit.edu	37	3	195447640	195447642	+	5'Flank	DEL	AAG	-	-	rs71725990		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:195447640_195447642delAAG	uc010hzo.2	+							NM_152673	NP_689886			mucin 20 isoform L						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)														---	---	---	---
MUC20	200958	broad.mit.edu	37	3	195454243	195454244	+	Intron	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:195454243_195454244delAA	uc010hzo.2	+						MUC20_uc010hzp.2_Intron	NM_152673	NP_689886			mucin 20 isoform L						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)														---	---	---	---
MUC20	200958	broad.mit.edu	37	3	195461607	195461607	+	3'UTR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:195461607delT	uc010hzo.2	+	5					MUC20_uc010hzp.2_3'UTR	NM_152673	NP_689886			mucin 20 isoform L						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)														---	---	---	---
MUC20	200958	broad.mit.edu	37	3	195464521	195464521	+	3'UTR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:195464521delA	uc010hzo.2	+	5					MUC20_uc010hzp.2_3'UTR	NM_152673	NP_689886			mucin 20 isoform L						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)														---	---	---	---
Unknown	0	broad.mit.edu	37	3	195470196	195470196	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:195470196delA								MUC20 (5657 upstream) : MUC4 (3444 downstream)																																			---	---	---	---
MUC4	4585	broad.mit.edu	37	3	195522716	195522717	+	Intron	DEL	GA	-	-	rs142683912	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:195522716_195522717delGA	uc011bto.1	-						MUC4_uc003fvo.2_Intron|MUC4_uc003fvp.2_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	195674731	195674731	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:195674731delT								TNK2 (35915 upstream) : SDHAP1 (12061 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	195885705	195885705	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:195885705delT	uc011bts.1	+						uc011btt.1_Intron					Homo sapiens cDNA FLJ25996 fis, clone DMC06615.																														---	---	---	---
Unknown	0	broad.mit.edu	37	3	195904179	195904181	+	IGR	DEL	AAA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:195904179_195904181delAAA								TFRC (95147 upstream) : ZDHHC19 (20143 downstream)																																			---	---	---	---
PCYT1A	5130	broad.mit.edu	37	3	195975231	195975231	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:195975231delT	uc003fwg.2	-						PCYT1A_uc003fwh.2_Intron	NM_005017	NP_005008			choline phosphate cytidylyltransferase 1 alpha							cytosol|soluble fraction	choline-phosphate cytidylyltransferase activity				0	all_cancers(143;1.19e-08)|Ovarian(172;0.0634)|Breast(254;0.206)		Epithelial(36;1.28e-24)|all cancers(36;1.01e-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;0.00259)	Choline(DB00122)													---	---	---	---
UBXN7	26043	broad.mit.edu	37	3	196086777	196086779	+	Intron	DEL	AAA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:196086777_196086779delAAA	uc003fwm.3	-						UBXN7_uc003fwn.3_Intron|UBXN7_uc010iae.2_Intron	NM_015562	NP_056377			UBX domain containing 7								protein binding			ovary(2)|pancreas(1)	3																		---	---	---	---
UBXN7	26043	broad.mit.edu	37	3	196088571	196088571	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:196088571delT	uc003fwm.3	-						UBXN7_uc003fwn.3_Intron|UBXN7_uc010iae.2_Intron	NM_015562	NP_056377			UBX domain containing 7								protein binding			ovary(2)|pancreas(1)	3																		---	---	---	---
RNF168	165918	broad.mit.edu	37	3	196213226	196213226	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:196213226delT	uc003fwq.2	-						RNF168_uc010iah.2_Intron	NM_152617	NP_689830			ring finger protein 168						double-strand break repair|histone H2A K63-linked ubiquitination|positive regulation of DNA repair|response to ionizing radiation	nucleus|ubiquitin ligase complex	chromatin binding|histone binding|ubiquitin binding|ubiquitin-protein ligase activity|zinc ion binding				0	all_cancers(143;1e-08)|Ovarian(172;0.0634)|Breast(254;0.206)		Epithelial(36;5.25e-24)|all cancers(36;5.47e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.76e-18)|LUSC - Lung squamous cell carcinoma(58;1.51e-06)|Lung(62;1.95e-06)	GBM - Glioblastoma multiforme(46;0.00348)														---	---	---	---
FBXO45	200933	broad.mit.edu	37	3	196307650	196307650	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:196307650delT	uc010iai.2	+							NM_001105573	NP_001099043			F-box protein 45						nervous system development|proteasomal ubiquitin-dependent protein catabolic process|protein ubiquitination involved in ubiquitin-dependent protein catabolic process|response to DNA damage stimulus	cell junction|postsynaptic membrane|presynaptic membrane	protein binding			skin(1)	1	all_cancers(143;8.88e-09)|Ovarian(172;0.0634)|Breast(254;0.135)		Epithelial(36;2.75e-23)|all cancers(36;2.47e-21)|OV - Ovarian serous cystadenocarcinoma(49;2.32e-18)|LUSC - Lung squamous cell carcinoma(58;1.51e-06)|Lung(62;1.95e-06)	GBM - Glioblastoma multiforme(46;0.00314)														---	---	---	---
Unknown	0	broad.mit.edu	37	3	196347942	196347942	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:196347942delA								FBXO45 (32014 upstream) : LRRC33 (18714 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	196356354	196356355	+	IGR	INS	-	TCTA	TCTA	rs137876704	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:196356354_196356355insTCTA								FBXO45 (40426 upstream) : LRRC33 (10301 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	196420496	196420496	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:196420496delT								LRRC33 (31624 upstream) : C3orf34 (12653 downstream)																																			---	---	---	---
SENP5	205564	broad.mit.edu	37	3	196645986	196645987	+	Intron	DEL	AG	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:196645986_196645987delAG	uc003fwz.3	+						SENP5_uc011bty.1_Intron	NM_152699	NP_689912			SUMO1/sentrin specific peptidase 5						cell cycle|cell division|proteolysis	nucleolus	cysteine-type peptidase activity			breast(2)|lung(1)	3	all_cancers(143;1.8e-08)|Ovarian(172;0.0634)|Breast(254;0.135)		Epithelial(36;3.14e-24)|all cancers(36;2.1e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.03e-18)|LUSC - Lung squamous cell carcinoma(58;1.51e-06)|Lung(62;1.95e-06)	GBM - Glioblastoma multiforme(46;0.004)														---	---	---	---
PIGZ	80235	broad.mit.edu	37	3	196681802	196681803	+	Intron	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:196681802_196681803delTT	uc003fxh.2	-							NM_025163	NP_079439			phosphatidylinositol glycan anchor biosynthesis,						GPI anchor biosynthetic process	integral to membrane|intrinsic to endoplasmic reticulum membrane	alpha-1,2-mannosyltransferase activity			ovary(3)	3	all_cancers(143;1.05e-08)|Ovarian(172;0.0634)|Breast(254;0.0838)		Epithelial(36;4.29e-24)|all cancers(36;2.79e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.03e-18)|LUSC - Lung squamous cell carcinoma(58;1.51e-06)|Lung(62;1.95e-06)	GBM - Glioblastoma multiforme(46;0.00603)														---	---	---	---
DLG1	1739	broad.mit.edu	37	3	196783955	196783955	+	Intron	DEL	T	-	-	rs33962901		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:196783955delT	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	196800675	196800675	+	Intron	DEL	T	-	-	rs79754382		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:196800675delT	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|DLG1_uc011buf.1_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	196934985	196934985	+	Intron	DEL	A	-	-	rs67453962		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:196934985delA	uc003fxo.3	-						DLG1_uc011bud.1_Intron|DLG1_uc003fxn.3_Intron|DLG1_uc011bue.1_Intron|DLG1_uc010ial.2_Intron|DLG1_uc011buf.1_Intron|DLG1_uc003fxp.2_Intron|DLG1_uc010iam.1_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	196983842	196983842	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:196983842delA	uc003fxo.3	-						DLG1_uc011bud.1_Intron|DLG1_uc003fxn.3_Intron|DLG1_uc011bue.1_Intron|DLG1_uc010ial.2_Intron|DLG1_uc011buf.1_Intron|DLG1_uc003fxp.2_Intron|DLG1_uc010iam.1_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	197307131	197307132	+	IGR	INS	-	GA	GA	rs139707362	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:197307131_197307132insGA								BDH1 (6937 upstream) : LOC220729 (12855 downstream)																																			---	---	---	---
LOC220729	220729	broad.mit.edu	37	3	197335926	197335928	+	Intron	DEL	TTT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:197335926_197335928delTTT	uc011bug.1	-											Homo sapiens cDNA FLJ60865 complete cds, highly similar to Succinate dehydrogenase (ubiquinone) flavoprotein subunit, mitochondrial precursor (EC 1.3.5.1).												0																		---	---	---	---
LOC220729	220729	broad.mit.edu	37	3	197346771	197346771	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:197346771delA	uc011bug.1	-						LOC220729_uc003fxw.2_Intron|LOC220729_uc003fxy.2_Intron|LOC220729_uc010iao.1_Intron					Homo sapiens cDNA FLJ60865 complete cds, highly similar to Succinate dehydrogenase (ubiquinone) flavoprotein subunit, mitochondrial precursor (EC 1.3.5.1).												0																		---	---	---	---
FYTTD1	84248	broad.mit.edu	37	3	197508915	197508915	+	3'UTR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:197508915delT	uc003fyi.2	+	9					FYTTD1_uc011bui.1_3'UTR|FYTTD1_uc011buj.1_RNA|FYTTD1_uc011buk.1_3'UTR	NM_032288	NP_115664			forty-two-three domain containing 1 isoform 1						mRNA export from nucleus	nuclear speck	mRNA binding|protein binding				0	all_cancers(143;1.15e-09)|Ovarian(172;0.0418)|Breast(254;0.0976)	Lung NSC(153;0.132)	Epithelial(36;2.19e-23)|all cancers(36;1.39e-21)|OV - Ovarian serous cystadenocarcinoma(49;1.21e-18)|LUSC - Lung squamous cell carcinoma(58;1.51e-06)|Lung(62;1.95e-06)	GBM - Glioblastoma multiforme(93;0.175)														---	---	---	---
IQCG	84223	broad.mit.edu	37	3	197644608	197644609	+	Intron	DEL	TT	-	-	rs11351894		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:197644608_197644609delTT	uc003fyo.2	-						IQCG_uc003fyn.2_Intron|IQCG_uc003fyp.2_Intron|IQCG_uc003fyq.3_Intron	NM_001134435	NP_001127907			IQ motif containing G												0	all_cancers(143;1.15e-09)|Ovarian(172;0.0418)|Breast(254;0.0976)		Epithelial(36;7.19e-24)|all cancers(36;3.34e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|LUSC - Lung squamous cell carcinoma(58;6.94e-07)|Lung(62;9.92e-07)	GBM - Glioblastoma multiforme(93;0.149)														---	---	---	---
IQCG	84223	broad.mit.edu	37	3	197670508	197670508	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:197670508delA	uc003fyo.2	-						IQCG_uc003fyp.2_Intron|IQCG_uc003fyq.3_Intron	NM_001134435	NP_001127907			IQ motif containing G												0	all_cancers(143;1.15e-09)|Ovarian(172;0.0418)|Breast(254;0.0976)		Epithelial(36;7.19e-24)|all cancers(36;3.34e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|LUSC - Lung squamous cell carcinoma(58;6.94e-07)|Lung(62;9.92e-07)	GBM - Glioblastoma multiforme(93;0.149)														---	---	---	---
IQCG	84223	broad.mit.edu	37	3	197671126	197671128	+	Intron	DEL	TTT	-	-	rs74574846		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:197671126_197671128delTTT	uc003fyo.2	-						IQCG_uc003fyp.2_Intron|IQCG_uc003fyq.3_Intron	NM_001134435	NP_001127907			IQ motif containing G												0	all_cancers(143;1.15e-09)|Ovarian(172;0.0418)|Breast(254;0.0976)		Epithelial(36;7.19e-24)|all cancers(36;3.34e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|LUSC - Lung squamous cell carcinoma(58;6.94e-07)|Lung(62;9.92e-07)	GBM - Glioblastoma multiforme(93;0.149)														---	---	---	---
LMLN	89782	broad.mit.edu	37	3	197752837	197752837	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:197752837delT	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)														---	---	---	---
Unknown	0	broad.mit.edu	37	4	29172	29172	+	IGR	DEL	A	-	-	rs145707628		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:29172delA								None (None upstream) : ZNF595 (24055 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	43797	43797	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:43797delA								None (None upstream) : ZNF595 (9430 downstream)																																			---	---	---	---
ZNF595	152687	broad.mit.edu	37	4	54783	54783	+	Intron	DEL	T	-	-	rs113477648		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:54783delT	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)														---	---	---	---
Unknown	0	broad.mit.edu	37	4	587228	587228	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:587228delT								PIGG (53909 upstream) : PDE6B (32135 downstream)																																			---	---	---	---
TMEM175	84286	broad.mit.edu	37	4	951539	951539	+	Intron	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:951539delC	uc003gbq.2	+						TMEM175_uc003gbr.2_Intron|TMEM175_uc003gbu.2_Intron|TMEM175_uc003gbs.2_Intron|TMEM175_uc003gbt.2_Intron|TMEM175_uc003gbv.2_Intron|TMEM175_uc010ibm.2_Intron	NM_032326	NP_115702			transmembrane protein 175							integral to membrane					0			OV - Ovarian serous cystadenocarcinoma(23;0.0158)															---	---	---	---
SLC26A1	10861	broad.mit.edu	37	4	978613	978613	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:978613delA	uc003gbx.2	-						IDUA_uc003gby.2_5'Flank|IDUA_uc003gbz.2_5'Flank|IDUA_uc003gca.2_5'Flank	NM_134425	NP_602297			solute carrier family 26, member 1 isoform b							integral to membrane|plasma membrane	secondary active sulfate transmembrane transporter activity			skin(1)	1			OV - Ovarian serous cystadenocarcinoma(23;0.0158)															---	---	---	---
C4orf42	92070	broad.mit.edu	37	4	1255334	1255334	+	Intron	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:1255334delC	uc003gcy.1	+											Homo sapiens cDNA FLJ31571 fis, clone NT2RI2001726.											ovary(1)	1			OV - Ovarian serous cystadenocarcinoma(23;0.0101)	Colorectal(103;0.188)														---	---	---	---
KIAA1530	57654	broad.mit.edu	37	4	1339663	1339664	+	5'Flank	INS	-	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:1339663_1339664insA	uc003gde.3	+							NM_020894	NP_065945			hypothetical protein LOC57654												0			OV - Ovarian serous cystadenocarcinoma(23;0.0138)															---	---	---	---
Unknown	0	broad.mit.edu	37	4	1397744	1397745	+	IGR	DEL	CT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:1397744_1397745delCT								CRIPAK (7962 upstream) : FAM53A (243864 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	1635576	1635576	+	IGR	DEL	A	-	-	rs144556169	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:1635576delA								CRIPAK (245794 upstream) : FAM53A (6033 downstream)																																			---	---	---	---
FAM53A	152877	broad.mit.edu	37	4	1678172	1678172	+	Intron	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:1678172delG	uc011bve.1	-						FAM53A_uc010ibw.2_Intron	NM_001013622	NP_001013644			dorsal neural-tube nuclear protein							nucleus					0		all_epithelial(65;0.206)|Breast(71;0.212)	OV - Ovarian serous cystadenocarcinoma(23;0.0145)															---	---	---	---
FAM53A	152877	broad.mit.edu	37	4	1682525	1682525	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:1682525delA	uc011bve.1	-						FAM53A_uc010ibw.2_Intron	NM_001013622	NP_001013644			dorsal neural-tube nuclear protein							nucleus					0		all_epithelial(65;0.206)|Breast(71;0.212)	OV - Ovarian serous cystadenocarcinoma(23;0.0145)															---	---	---	---
Unknown	0	broad.mit.edu	37	4	1786743	1786743	+	IGR	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:1786743delG								TACC3 (39848 upstream) : FGFR3 (8296 downstream)																																			---	---	---	---
FGFR3	2261	broad.mit.edu	37	4	1808177	1808177	+	Intron	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:1808177delG	uc003gdr.3	+						FGFR3_uc003gdu.2_Intron|FGFR3_uc003gds.3_Intron|FGFR3_uc003gdq.3_Intron	NM_000142	NP_000133			fibroblast growth factor receptor 3 isoform 1						bone maturation|cell growth|insulin receptor signaling pathway|JAK-STAT cascade|MAPKKK cascade|negative regulation of developmental growth|positive regulation of cell proliferation	integral to plasma membrane	ATP binding|fibroblast growth factor binding|fibroblast growth factor receptor activity|identical protein binding			urinary_tract(2177)|skin(314)|upper_aerodigestive_tract(57)|haematopoietic_and_lymphoid_tissue(24)|prostate(9)|cervix(6)|central_nervous_system(4)|large_intestine(3)|lung(3)|testis(2)|pancreas(1)	2600		Breast(71;0.212)|all_epithelial(65;0.241)	all cancers(2;0.000145)|OV - Ovarian serous cystadenocarcinoma(23;0.0019)|Epithelial(3;0.00221)|GBM - Glioblastoma multiforme(2;0.234)		Palifermin(DB00039)		1	Mis|T	IGH@|ETV6	bladder|MM|T-cell lymphoma		Hypochondroplasia|Thanatophoric dysplasia		Muenke_syndrome|Saethre-Chotzen_syndrome				---	---	---	---
WHSC1	7468	broad.mit.edu	37	4	1911961	1911962	+	Intron	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:1911961_1911962delTT	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								---	---	---	---
WHSC1	7468	broad.mit.edu	37	4	1961587	1961587	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:1961587delT	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	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	2090456	2090456	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:2090456delT	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					---	---	---	---
POLN	353497	broad.mit.edu	37	4	2240173	2240173	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:2240173delA	uc011bvi.1	-						HAUS3_uc011bvj.1_Intron|HAUS3_uc003ges.1_Intron|HAUS3_uc003get.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					---	---	---	---
ZFYVE28	57732	broad.mit.edu	37	4	2418534	2418535	+	Intron	INS	-	CCT	CCT	rs150116151	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:2418534_2418535insCCT	uc003gex.1	-						ZFYVE28_uc011bvl.1_Intron|ZFYVE28_uc003gez.2_Intron	NM_020972	NP_066023			zinc finger, FYVE domain containing 28						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																		---	---	---	---
RNF4	6047	broad.mit.edu	37	4	2482311	2482312	+	Intron	DEL	AA	-	-	rs113417443		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:2482311_2482312delAA	uc003gfb.2	+						RNF4_uc010ici.1_Intron|RNF4_uc010icj.2_Intron|RNF4_uc003gfc.2_Intron	NM_002938	NP_002929			ring finger protein 4						androgen receptor signaling pathway|positive regulation of transcription from RNA polymerase II promoter|proteasomal ubiquitin-dependent protein catabolic process|protein autoubiquitination|protein K11-linked ubiquitination|protein K48-linked ubiquitination|protein K6-linked ubiquitination|protein K63-linked ubiquitination|regulation of kinetochore assembly|regulation of spindle assembly|response to arsenic-containing substance	cytoplasm|PML body	androgen receptor binding|DNA binding|nucleosome binding|sequence-specific DNA binding transcription factor activity|SUMO polymer binding|transcription coactivator activity|ubiquitin-protein ligase activity|zinc ion binding				0		all_epithelial(65;0.241)																---	---	---	---
SH3BP2	6452	broad.mit.edu	37	4	2828302	2828303	+	Intron	DEL	TG	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:2828302_2828303delTG	uc003gfi.3	+						SH3BP2_uc011bvp.1_Intron|SH3BP2_uc003gfj.3_Intron|SH3BP2_uc003gfk.3_Intron|SH3BP2_uc003gfl.3_Intron|SH3BP2_uc003gfm.3_5'UTR	NM_001122681	NP_001116153			SH3-domain binding protein 2 isoform a						signal transduction		SH3 domain binding|SH3/SH2 adaptor activity			central_nervous_system(1)	1				UCEC - Uterine corpus endometrioid carcinoma (64;0.164)										Cherubism				---	---	---	---
ADD1	118	broad.mit.edu	37	4	2900321	2900321	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:2900321delT	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_Frame_Shift_Del_p.D134fs	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)														---	---	---	---
GRK4	2868	broad.mit.edu	37	4	3002459	3002459	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:3002459delT	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	3187929	3187929	+	Intron	DEL	A	-	-	rs113401608		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:3187929delA	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	3314644	3314644	+	5'Flank	DEL	A	-	-	rs71652768		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:3314644delA	uc003ggw.2	+						RGS12_uc003ggu.2_Intron|RGS12_uc010ics.1_Intron|RGS12_uc011bvr.1_Intron|RGS12_uc003ggv.2_5'Flank	NM_198229	NP_937872			regulator of G-protein signalling 12 isoform 1							condensed nuclear chromosome|cytoplasm|plasma membrane	GTPase activator activity|receptor signaling protein activity			skin(1)	1				UCEC - Uterine corpus endometrioid carcinoma (64;0.168)														---	---	---	---
Unknown	0	broad.mit.edu	37	4	3583719	3583725	+	Intron	DEL	GGAAGGA	-	-	rs66844729		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:3583719_3583725delGGAAGGA	uc003ghj.1	+						uc003ghk.1_Intron					Homo sapiens cDNA FLJ35424 fis, clone SMINT2001461.																														---	---	---	---
Unknown	0	broad.mit.edu	37	4	3610868	3610868	+	IGR	DEL	A	-	-	rs11321586		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:3610868delA								LRPAP1 (76644 upstream) : ADRA2C (157207 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	3619124	3619127	+	IGR	DEL	TCCT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:3619124_3619127delTCCT								LRPAP1 (84900 upstream) : ADRA2C (148948 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	3859868	3859869	+	IGR	INS	-	C	C	rs146326902	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:3859868_3859869insC								ADRA2C (89617 upstream) : LOC348926 (83801 downstream)																																			---	---	---	---
STX18	53407	broad.mit.edu	37	4	4501564	4501565	+	Intron	INS	-	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:4501564_4501565insG	uc003gic.2	-							NM_016930	NP_058626			syntaxin 18						ER to Golgi vesicle-mediated transport|intracellular protein transport	endoplasmic reticulum membrane|Golgi membrane|integral to membrane	SNAP receptor activity				0				UCEC - Uterine corpus endometrioid carcinoma (64;0.0534)														---	---	---	---
Unknown	0	broad.mit.edu	37	4	4548486	4548486	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:4548486delA	uc003gid.2	+											Homo sapiens, clone IMAGE:5204729, mRNA.																														---	---	---	---
EVC2	132884	broad.mit.edu	37	4	5678575	5678575	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:5678575delT	uc003gij.2	-						EVC2_uc011bwb.1_Intron|EVC2_uc003gik.2_Intron	NM_147127	NP_667338			limbin							integral to membrane				large_intestine(3)|ovary(2)	5																		---	---	---	---
JAKMIP1	152789	broad.mit.edu	37	4	6172803	6172803	+	Intron	DEL	C	-	-	rs149182941		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:6172803delC	uc003giu.3	-						JAKMIP1_uc010idb.1_Intron|JAKMIP1_uc010idc.1_Intron|JAKMIP1_uc010idd.1_Intron|JAKMIP1_uc011bwc.1_Intron|JAKMIP1_uc003giv.3_Intron|JAKMIP1_uc010ide.2_Intron	NM_144720	NP_653321			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																		---	---	---	---
PPP2R2C	5522	broad.mit.edu	37	4	6378179	6378179	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:6378179delT	uc003gjc.2	-						PPP2R2C_uc003gjb.2_Intron|PPP2R2C_uc011bwd.1_Intron|PPP2R2C_uc011bwe.1_Intron|PPP2R2C_uc003gja.2_Intron|PPP2R2C_uc003gjd.1_Intron	NM_020416	NP_065149			gamma isoform of regulatory subunit B55, protein						signal transduction	protein phosphatase type 2A complex	protein phosphatase type 2A regulator activity			ovary(1)|kidney(1)|central_nervous_system(1)|skin(1)	4																		---	---	---	---
MRFAP1L1	114932	broad.mit.edu	37	4	6711494	6711494	+	5'UTR	DEL	T	-	-	rs71695362		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:6711494delT	uc003gjn.2	-	1					MRFAP1L1_uc003gjo.2_5'UTR	NM_203462	NP_982287			Morf4 family associated protein 1-like 1												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	4	6895677	6895678	+	IGR	INS	-	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:6895677_6895678insA								KIAA0232 (9780 upstream) : TBC1D14 (15493 downstream)																																			---	---	---	---
TBC1D14	57533	broad.mit.edu	37	4	6954558	6954558	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:6954558delT	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																		---	---	---	---
Unknown	0	broad.mit.edu	37	4	7089205	7089205	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:7089205delT								GRPEL1 (19405 upstream) : FLJ36777 (9946 downstream)																																			---	---	---	---
SORCS2	57537	broad.mit.edu	37	4	7533808	7533808	+	Intron	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:7533808delG	uc003gkb.3	+						SORCS2_uc011bwi.1_Intron	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	7726032	7726034	+	Intron	DEL	TGG	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:7726032_7726034delTGG	uc003gkb.3	+						SORCS2_uc011bwi.1_Intron	NM_020777	NP_065828			VPS10 domain receptor protein SORCS 2 precursor							integral to membrane	neuropeptide receptor activity			ovary(1)|central_nervous_system(1)	2																		---	---	---	---
C4orf23	152992	broad.mit.edu	37	4	8478449	8478449	+	3'UTR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:8478449delA	uc003glg.1	+	11					C4orf23_uc003gli.1_RNA	NM_152544	NP_689757			hypothetical protein LOC152992 isoform 2						tRNA processing	cytoplasm	methyltransferase activity|nucleic acid binding|zinc ion binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	4	8823027	8823027	+	IGR	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:8823027delG								CPZ (201541 upstream) : HMX1 (45746 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	8842310	8842310	+	IGR	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:8842310delC								CPZ (220824 upstream) : HMX1 (26463 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	8928476	8928476	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:8928476delT								HMX1 (54933 upstream) : LOC650293 (23001 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	9541895	9541896	+	IGR	INS	-	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:9541895_9541896insA								DEFB131 (89656 upstream) : MIR548I2 (15893 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	9586101	9586102	+	IGR	INS	-	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:9586101_9586102insA								MIR548I2 (28164 upstream) : DRD5 (197156 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	9588381	9588381	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:9588381delT								MIR548I2 (30444 upstream) : DRD5 (194877 downstream)																																			---	---	---	---
WDR1	9948	broad.mit.edu	37	4	10090025	10090026	+	Intron	INS	-	TG	TG			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:10090025_10090026insTG	uc003gmf.2	-						WDR1_uc003gmg.2_Intron|WDR1_uc003gmh.1_Intron|WDR1_uc011bwu.1_Intron	NM_017491	NP_059830			WD repeat-containing protein 1 isoform 1						platelet activation|platelet degranulation|sensory perception of sound	cytoskeleton|cytosol|extracellular region	actin binding			ovary(2)|pancreas(1)	3				STAD - Stomach adenocarcinoma(129;0.000703)|Colorectal(103;0.0057)|LUSC - Lung squamous cell carcinoma(721;0.0232)														---	---	---	---
WDR1	9948	broad.mit.edu	37	4	10112736	10112738	+	Intron	DEL	CTC	-	-	rs77764131		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:10112736_10112738delCTC	uc003gmf.2	-						WDR1_uc003gmg.2_Intron	NM_017491	NP_059830			WD repeat-containing protein 1 isoform 1						platelet activation|platelet degranulation|sensory perception of sound	cytoskeleton|cytosol|extracellular region	actin binding			ovary(2)|pancreas(1)	3				STAD - Stomach adenocarcinoma(129;0.000703)|Colorectal(103;0.0057)|LUSC - Lung squamous cell carcinoma(721;0.0232)														---	---	---	---
Unknown	0	broad.mit.edu	37	4	10274886	10274886	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:10274886delT								WDR1 (156313 upstream) : ZNF518B (166619 downstream)																																			---	---	---	---
CLNK	116449	broad.mit.edu	37	4	10492397	10492398	+	Intron	INS	-	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:10492397_10492398insT	uc003gmo.3	-							NM_052964	NP_443196			mast cell immunoreceptor signal transducer						immune response|intracellular signal transduction	intracellular	SH3/SH2 adaptor activity			ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	4	14055489	14055500	+	IGR	DEL	ACACACACACAC	-	-	rs34608344		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:14055489_14055500delACACACACACAC								BOD1L (426161 upstream) : CPEB2 (950022 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	14670012	14670014	+	Intron	DEL	TTT	-	-	rs35845449		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:14670012_14670014delTTT	uc003gne.2	-						uc003gnf.2_Intron					Homo sapiens cDNA clone IMAGE:3604199, **** WARNING: chimeric clone ****.																														---	---	---	---
Unknown	0	broad.mit.edu	37	4	15288362	15288363	+	IGR	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:15288362_15288363delAA								CPEB2 (216588 upstream) : C1QTNF7 (53197 downstream)																																			---	---	---	---
FBXL5	26234	broad.mit.edu	37	4	15632545	15632545	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:15632545delT	uc003goc.1	-						FBXL5_uc010idw.1_Intron|FBXL5_uc003gob.1_Intron|FBXL5_uc010idx.1_Intron|FBXL5_uc003god.1_Intron|FBXL5_uc010idy.1_Intron	NM_012161	NP_036293			F-box and leucine-rich repeat protein 5 isoform						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																		---	---	---	---
FBXL5	26234	broad.mit.edu	37	4	15642249	15642249	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:15642249delT	uc003goc.1	-						FBXL5_uc010idw.1_Intron|FBXL5_uc003gob.1_Intron|FBXL5_uc010idx.1_Intron|FBXL5_uc003god.1_Intron|FBXL5_uc010idy.1_Intron	NM_012161	NP_036293			F-box and leucine-rich repeat protein 5 isoform						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																		---	---	---	---
Unknown	0	broad.mit.edu	37	4	15667647	15667647	+	IGR	DEL	A	-	-	rs13105439		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:15667647delA								FBXL5 (10634 upstream) : FAM200B (15705 downstream)																																			---	---	---	---
CD38	952	broad.mit.edu	37	4	15829814	15829814	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:15829814delT	uc011bxc.1	+						CD38_uc003gol.1_Intron	NM_001775	NP_001766			CD38 antigen						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																		---	---	---	---
Unknown	0	broad.mit.edu	37	4	15934301	15934301	+	IGR	DEL	A	-	-	rs79641709		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:15934301delA								CD38 (83595 upstream) : FGFBP1 (2894 downstream)																																			---	---	---	---
PROM1	8842	broad.mit.edu	37	4	15988033	15988033	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:15988033delT	uc003goo.2	-						PROM1_uc003gor.2_Intron|PROM1_uc003gos.2_Intron|PROM1_uc003got.2_Intron|PROM1_uc003gou.2_Intron|PROM1_uc003gop.2_Intron|PROM1_uc003goq.3_Intron	NM_006017	NP_006008			prominin 1 isoform 1						camera-type eye photoreceptor cell differentiation|photoreceptor cell maintenance|retina layer formation	apical plasma membrane|cell surface|integral to plasma membrane|microvillus membrane|photoreceptor outer segment membrane|plasma membrane	beta-actinin binding|cadherin binding			ovary(3)|upper_aerodigestive_tract(1)|lung(1)|kidney(1)|central_nervous_system(1)	7																		---	---	---	---
PROM1	8842	broad.mit.edu	37	4	16071986	16071986	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:16071986delT	uc003goo.2	-						PROM1_uc003gor.2_Intron|PROM1_uc003gos.2_Intron|PROM1_uc003got.2_Intron|PROM1_uc003gou.2_Intron|PROM1_uc003gop.2_Intron|PROM1_uc003goq.3_Intron|PROM1_uc010iec.1_Intron	NM_006017	NP_006008			prominin 1 isoform 1						camera-type eye photoreceptor cell differentiation|photoreceptor cell maintenance|retina layer formation	apical plasma membrane|cell surface|integral to plasma membrane|microvillus membrane|photoreceptor outer segment membrane|plasma membrane	beta-actinin binding|cadherin binding			ovary(3)|upper_aerodigestive_tract(1)|lung(1)|kidney(1)|central_nervous_system(1)	7																		---	---	---	---
LDB2	9079	broad.mit.edu	37	4	16508368	16508369	+	Intron	INS	-	TTG	TTG	rs143439163	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:16508368_16508369insTTG	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																		---	---	---	---
LDB2	9079	broad.mit.edu	37	4	16746091	16746091	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:16746091delT	uc003goz.2	-						LDB2_uc003gpa.2_Intron|LDB2_uc003gpb.2_Intron|LDB2_uc011bxh.1_Intron|LDB2_uc010iee.2_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	17019434	17019434	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:17019434delA								LDB2 (119010 upstream) : QDPR (468586 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	17320148	17320148	+	IGR	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:17320148delC								LDB2 (419724 upstream) : QDPR (167872 downstream)																																			---	---	---	---
LCORL	254251	broad.mit.edu	37	4	17982281	17982281	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:17982281delT	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	18688564	18688564	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:18688564delA								LCORL (665179 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	18879358	18879358	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:18879358delT								LCORL (855973 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	18985891	18985891	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:18985891delT								LCORL (962506 upstream) : None (None downstream)																																			---	---	---	---
KCNIP4	80333	broad.mit.edu	37	4	20844535	20844537	+	Intron	DEL	TTT	-	-	rs33931406		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:20844535_20844537delTTT	uc003gqe.2	-						KCNIP4_uc003gqf.1_Intron|KCNIP4_uc003gqg.1_Intron|KCNIP4_uc003gqh.1_Intron|KCNIP4_uc003gqi.1_Intron|KCNIP4_uc010iel.2_Intron|KCNIP4_uc003gqd.3_Intron	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	21100255	21100255	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:21100255delA	uc003gqf.1	-						KCNIP4_uc003gqg.1_Intron|KCNIP4_uc003gqh.1_Intron|KCNIP4_uc003gqi.1_Intron	NM_147183	NP_671712			Kv channel interacting protein 4 isoform 4							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	21265592	21265593	+	Intron	DEL	GT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:21265592_21265593delGT	uc003gqf.1	-						KCNIP4_uc003gqg.1_Intron|KCNIP4_uc003gqh.1_Intron|KCNIP4_uc003gqi.1_Intron	NM_147183	NP_671712			Kv channel interacting protein 4 isoform 4							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	21458675	21458675	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:21458675delA	uc003gqh.1	-						KCNIP4_uc003gqg.1_Intron|KCNIP4_uc003gqi.1_Intron	NM_001035003	NP_001030175			Kv channel interacting protein 4 isoform 5							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	21473975	21473976	+	Intron	INS	-	GA	GA			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:21473975_21473976insGA	uc003gqh.1	-						KCNIP4_uc003gqg.1_Intron|KCNIP4_uc003gqi.1_Intron	NM_001035003	NP_001030175			Kv channel interacting protein 4 isoform 5							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	22389156	22389156	+	3'UTR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:22389156delA	uc003gqm.1	-	19					GPR125_uc010ieo.1_3'UTR|GPR125_uc003gql.1_3'UTR	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)																---	---	---	---
GBA3	57733	broad.mit.edu	37	4	22750449	22750449	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:22750449delT	uc003gqp.3	+						GBA3_uc010iep.2_Intron|GBA3_uc011bxo.1_Intron	NM_020973	NP_066024			cytosolic beta-glucosidase isoform a						glycoside catabolic process|glycosylceramide catabolic process	cytosol	beta-galactosidase activity|beta-glucosidase activity|cation binding|glycosylceramidase activity				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	4	22951769	22951769	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:22951769delA								GBA3 (130578 upstream) : PPARGC1A (841876 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	23158576	23158576	+	IGR	DEL	T	-	-	rs67602447		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:23158576delT								GBA3 (337385 upstream) : PPARGC1A (635069 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	23288435	23288435	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:23288435delT								GBA3 (467244 upstream) : PPARGC1A (505210 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	23335781	23335782	+	IGR	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:23335781_23335782delTT								GBA3 (514590 upstream) : PPARGC1A (457863 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	23421474	23421474	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:23421474delT								GBA3 (600283 upstream) : PPARGC1A (372171 downstream)																																			---	---	---	---
PPARGC1A	10891	broad.mit.edu	37	4	23825732	23825732	+	Intron	DEL	T	-	-	rs56881226	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:23825732delT	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	23943699	23943699	+	IGR	DEL	A	-	-	rs4540032		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:23943699delA								PPARGC1A (51999 upstream) : MIR573 (578116 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	24235377	24235378	+	IGR	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:24235377_24235378delAA								PPARGC1A (343677 upstream) : MIR573 (286437 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	24250112	24250112	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:24250112delA								PPARGC1A (358412 upstream) : MIR573 (271703 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	24416811	24416811	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:24416811delA								PPARGC1A (525111 upstream) : MIR573 (105004 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	24418653	24418654	+	IGR	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:24418653_24418654delAA								PPARGC1A (526953 upstream) : MIR573 (103161 downstream)																																			---	---	---	---
DHX15	1665	broad.mit.edu	37	4	24544451	24544451	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:24544451delA	uc003gqx.2	-							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)																---	---	---	---
DHX15	1665	broad.mit.edu	37	4	24551252	24551254	+	Intron	DEL	TGT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:24551252_24551254delTGT	uc003gqx.2	-							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)																---	---	---	---
PI4K2B	55300	broad.mit.edu	37	4	25261983	25261985	+	Intron	DEL	TTT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:25261983_25261985delTTT	uc003grk.2	+						PI4K2B_uc011bxs.1_Intron	NM_018323	NP_060793			phosphatidylinositol 4-kinase type 2 beta							cytoplasm|membrane	1-phosphatidylinositol 4-kinase activity|ATP binding			ovary(2)|skin(2)	4		Breast(46;0.173)																---	---	---	---
ZCCHC4	29063	broad.mit.edu	37	4	25358179	25358179	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:25358179delT	uc003grl.3	+						ZCCHC4_uc003grn.3_Intron	NM_024936	NP_079212			zinc finger, CCHC domain containing 4								methyltransferase activity|nucleic acid binding|zinc ion binding			ovary(2)	2		Breast(46;0.0503)																---	---	---	---
SLC34A2	10568	broad.mit.edu	37	4	25663177	25663177	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:25663177delT	uc003grr.2	+						SLC34A2_uc003grs.2_Intron|SLC34A2_uc010iev.2_Intron	NM_006424	NP_006415			solute carrier family 34 (sodium phosphate),						cellular phosphate ion homeostasis	apical plasma membrane|brush border membrane|integral to plasma membrane	phosphate binding|sodium ion binding|sodium-dependent phosphate transmembrane transporter activity|sodium:phosphate symporter activity			skin(3)|ovary(1)|kidney(1)	5		Breast(46;0.0503)																---	---	---	---
Unknown	0	broad.mit.edu	37	4	25932389	25932389	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:25932389delT								C4orf52 (889 upstream) : RBPJ (388943 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	26148770	26148770	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:26148770delA								C4orf52 (217270 upstream) : RBPJ (172562 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	26262948	26262948	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:26262948delT								C4orf52 (331448 upstream) : RBPJ (58384 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	26568350	26568350	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:26568350delA								CCKAR (76308 upstream) : TBC1D19 (17196 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	26787318	26787319	+	IGR	DEL	TG	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:26787318_26787319delTG								TBC1D19 (30403 upstream) : STIM2 (75045 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	27101227	27101227	+	IGR	DEL	G	-	-	rs34317599		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:27101227delG								STIM2 (75419 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	27867969	27867969	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:27867969delT								STIM2 (842161 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	28264341	28264341	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:28264341delT								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	28366465	28366465	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:28366465delA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	28377822	28377822	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:28377822delA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	29239916	29239916	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:29239916delA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	29383530	29383530	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:29383530delT								None (None upstream) : None (None downstream)																																			---	---	---	---
PCDH7	5099	broad.mit.edu	37	4	31038616	31038616	+	Intron	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:31038616delC	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	31647588	31647588	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:31647588delT								PCDH7 (499167 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	31762022	31762022	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:31762022delA								PCDH7 (613601 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	32343525	32343525	+	IGR	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:32343525delG								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	32816016	32816016	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:32816016delT								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	33320388	33320388	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:33320388delA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	33798726	33798726	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:33798726delA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	33859146	33859146	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:33859146delA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	33860353	33860353	+	IGR	DEL	A	-	-	rs79573340		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:33860353delA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	33887652	33887652	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:33887652delA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	34067948	34067949	+	IGR	INS	-	T	T	rs139335366	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:34067948_34067949insT								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	34141019	34141020	+	IGR	INS	-	G	G	rs146194883	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:34141019_34141020insG								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	34197280	34197281	+	IGR	INS	-	A	A	rs138573925	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:34197280_34197281insA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	34425598	34425598	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:34425598delA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	34779468	34779468	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:34779468delA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	35061512	35061512	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:35061512delT								None (None upstream) : ARAP2 (888332 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	35553204	35553207	+	IGR	DEL	TCTA	-	-	rs35459673	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:35553204_35553207delTCTA								None (None upstream) : ARAP2 (396637 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	35775413	35775413	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:35775413delA								None (None upstream) : ARAP2 (174431 downstream)																																			---	---	---	---
ARAP2	116984	broad.mit.edu	37	4	35981008	35981008	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:35981008delT	uc003gso.2	-											Homo sapiens cDNA clone IMAGE:5296543.						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	36622117	36622117	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:36622117delA								MIR1255B-1 (194067 upstream) : KIAA1239 (624573 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	36982223	36982223	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:36982223delA								MIR1255B-1 (554173 upstream) : KIAA1239 (264467 downstream)																																			---	---	---	---
RELL1	768211	broad.mit.edu	37	4	37636845	37636845	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:37636845delA	uc003gsz.2	-						RELL1_uc010ifc.2_Intron	NM_001085399	NP_001078868			receptor expressed in lymphoid tissues like 1							cytoplasm|integral to membrane|microtubule cytoskeleton|plasma membrane					0																		---	---	---	---
TBC1D1	23216	broad.mit.edu	37	4	37951215	37951215	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:37951215delA	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																		---	---	---	---
TBC1D1	23216	broad.mit.edu	37	4	38061505	38061505	+	Intron	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:38061505delC	uc003gtb.2	+						TBC1D1_uc011byd.1_Intron|TBC1D1_uc010ifd.2_Intron|TBC1D1_uc011byf.1_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	38194069	38194070	+	IGR	INS	-	TAGC	TAGC	rs150024191	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:38194069_38194070insTAGC								TBC1D1 (53276 upstream) : FLJ13197 (420252 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	38252078	38252080	+	IGR	DEL	ATT	-	-	rs150788105		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:38252078_38252080delATT								TBC1D1 (111285 upstream) : FLJ13197 (362242 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	38301219	38301219	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:38301219delA								TBC1D1 (160426 upstream) : FLJ13197 (313103 downstream)																																			---	---	---	---
TLR10	81793	broad.mit.edu	37	4	38778916	38778917	+	5'Flank	INS	-	GA	GA			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:38778916_38778917insGA	uc003gti.2	-						TLR10_uc003gtj.2_Intron|TLR10_uc003gtk.2_Intron	NM_030956	NP_112218			toll-like receptor 10 precursor						inflammatory response|innate immune response|MyD88-dependent toll-like receptor signaling pathway	integral to membrane|plasma membrane	transmembrane receptor activity			lung(1)|breast(1)	2																		---	---	---	---
KLHL5	51088	broad.mit.edu	37	4	39104135	39104136	+	Intron	INS	-	C	C	rs148769950	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:39104135_39104136insC	uc003gts.2	+						KLHL5_uc003gtp.2_Intron|KLHL5_uc003gtq.2_Intron|KLHL5_uc003gtr.1_Intron|KLHL5_uc003gtt.2_Intron	NM_015990	NP_057074			kelch-like 5 isoform 1							cytoplasm|cytoskeleton	actin binding			ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	4	39133794	39133794	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:39133794delA								KLHL5 (9966 upstream) : WDR19 (50230 downstream)																																			---	---	---	---
WDR19	57728	broad.mit.edu	37	4	39245702	39245702	+	Intron	DEL	A	-	-	rs34311970		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:39245702delA	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																		---	---	---	---
LIAS	11019	broad.mit.edu	37	4	39468962	39468962	+	Intron	DEL	T	-	-	rs78228460		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:39468962delT	uc003guf.2	+						LIAS_uc003gug.2_Intron|LIAS_uc003guh.2_Intron	NM_006859	NP_006850			lipoic acid synthetase isoform 1 precursor						inflammatory response|response to lipopolysaccharide|response to oxidative stress	mitochondrion	4 iron, 4 sulfur cluster binding|lipoate synthase activity|metal ion binding				0					Lipoic Acid(DB00166)													---	---	---	---
UGDH	7358	broad.mit.edu	37	4	39507525	39507528	+	Intron	DEL	AAAA	-	-	rs35867925		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:39507525_39507528delAAAA	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	39651770	39651770	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:39651770delT	uc003gup.1	+											Homo sapiens cDNA clone IMAGE:4830514.																														---	---	---	---
Unknown	0	broad.mit.edu	37	4	39788816	39788818	+	IGR	DEL	TTT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:39788816_39788818delTTT								UBE2K (4408 upstream) : PDS5A (35666 downstream)																																			---	---	---	---
PDS5A	23244	broad.mit.edu	37	4	39882634	39882634	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:39882634delT	uc003guv.3	-						PDS5A_uc010ifo.2_Intron	NM_001100399	NP_001093869			PDS5, regulator of cohesion maintenance, homolog						cell division|mitosis|negative regulation of DNA replication	chromatin|nucleus	identical protein binding				0																		---	---	---	---
CHRNA9	55584	broad.mit.edu	37	4	40352711	40352716	+	Intron	DEL	ACACAC	-	-	rs71753029		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:40352711_40352716delACACAC	uc003gva.1	+							NM_017581	NP_060051			cholinergic receptor, nicotinic, alpha 9						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	40438960	40438961	+	Intron	INS	-	AA	AA			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:40438960_40438961insAA	uc003gvc.2	-						RBM47_uc003gvd.2_Intron|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																		---	---	---	---
APBB2	323	broad.mit.edu	37	4	40937779	40937780	+	Intron	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:40937779_40937780delTT	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																		---	---	---	---
APBB2	323	broad.mit.edu	37	4	41197135	41197135	+	Intron	DEL	C	-	-	rs6841208	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:41197135delC	uc003gvl.2	-						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																		---	---	---	---
LIMCH1	22998	broad.mit.edu	37	4	41386228	41386228	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:41386228delT	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_5'Flank	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	41714979	41714979	+	IGR	DEL	T	-	-	rs111321976		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:41714979delT								LIMCH1 (12920 upstream) : PHOX2B (31121 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	41726403	41726403	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:41726403delA								LIMCH1 (24344 upstream) : PHOX2B (19697 downstream)																																			---	---	---	---
BEND4	389206	broad.mit.edu	37	4	42119789	42119789	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:42119789delA	uc003gwn.2	-						BEND4_uc003gwm.2_Intron	NM_207406	NP_997289			BEN domain containing 4 isoform a												0																		---	---	---	---
ATP8A1	10396	broad.mit.edu	37	4	42644007	42644007	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-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	42882530	42882530	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:42882530delT								ATP8A1 (223408 upstream) : GRXCR1 (12754 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	43166840	43166841	+	IGR	INS	-	TAT	TAT	rs144484858	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:43166840_43166841insTAT								GRXCR1 (134167 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	43469629	43469629	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:43469629delT								GRXCR1 (436956 upstream) : KCTD8 (706293 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	44066615	44066616	+	IGR	DEL	CT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:44066615_44066616delCT								None (None upstream) : KCTD8 (109306 downstream)																																			---	---	---	---
KCTD8	386617	broad.mit.edu	37	4	44428039	44428039	+	Intron	DEL	A	-	-	rs75458375		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:44428039delA	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)			---	---	---	---
Unknown	0	broad.mit.edu	37	4	44554543	44554543	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:44554543delT								KCTD8 (103719 upstream) : YIPF7 (69811 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	45567153	45567156	+	IGR	DEL	AAAA	-	-	rs33919232		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:45567153_45567156delAAAA								GNPDA2 (838541 upstream) : GABRG1 (470633 downstream)																																			---	---	---	---
GABRG1	2565	broad.mit.edu	37	4	46060358	46060358	+	Frame_Shift_Del	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:46060358delA	uc003gxb.2	-	7	944	c.792delT	c.(790-792)TTTfs	p.F264fs		NM_173536	NP_775807	Q8N1C3	GBRG1_HUMAN	gamma-aminobutyric acid A receptor, gamma 1	264	Extracellular (Probable).				gamma-aminobutyric acid signaling pathway	cell junction|chloride channel complex|postsynaptic membrane	chloride channel activity|extracellular ligand-gated ion channel activity			ovary(2)	2				Lung(65;0.106)|LUSC - Lung squamous cell carcinoma(721;0.23)														---	---	---	---
COX7B2	170712	broad.mit.edu	37	4	46837407	46837407	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:46837407delA	uc003gxf.2	-						COX7B2_uc010ige.2_Intron	NM_130902	NP_570972			cytochrome c oxidase subunit VIIb2 precursor							integral to membrane|mitochondrial respiratory chain	cytochrome-c oxidase activity				0																		---	---	---	---
CORIN	10699	broad.mit.edu	37	4	47695103	47695103	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-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	47788964	47788964	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:47788964delA	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	47916234	47916236	+	Intron	DEL	AAA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:47916234_47916236delAAA	uc010igh.2	-						uc003gxr.1_5'Flank|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																		---	---	---	---
CNGA1	1259	broad.mit.edu	37	4	48014390	48014390	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:48014390delA	uc003gxt.3	-						CNGA1_uc003gxv.1_Intron	NM_000087	NP_000078			cyclic nucleotide gated channel alpha 1 isoform						response to stimulus|visual perception	integral to plasma membrane	cGMP binding|ion channel activity			ovary(2)	2																		---	---	---	---
TEC	7006	broad.mit.edu	37	4	48169637	48169640	+	Intron	DEL	AAGA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:48169637_48169640delAAGA	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																		---	---	---	---
Unknown	0	broad.mit.edu	37	4	48478442	48478443	+	IGR	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:48478442_48478443delTT								SLAIN2 (50229 upstream) : SLC10A4 (6917 downstream)																																			---	---	---	---
FRYL	285527	broad.mit.edu	37	4	48530450	48530450	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:48530450delA	uc003gyh.1	-						FRYL_uc003gyg.1_Intron|FRYL_uc003gyi.1_Intron|FRYL_uc003gyj.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	48707487	48707488	+	Intron	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:48707487_48707488delAA	uc003gyh.1	-						FRYL_uc003gyk.2_Intron|FRYL_uc003gym.1_Intron|FRYL_uc003gyn.3_Intron	NM_015030	NP_055845			furry-like						regulation of transcription, DNA-dependent|transcription, DNA-dependent		protein binding			skin(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	4	48969311	48969311	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:48969311delT								OCIAD2 (60496 upstream) : CWH43 (18954 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	49335406	49335408	+	IGR	DEL	TTT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:49335406_49335408delTTT								CWH43 (271313 upstream) : None (None downstream)																																			---	---	---	---
SPATA18	132671	broad.mit.edu	37	4	52926826	52926826	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-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)															---	---	---	---
KIAA0114	57291	broad.mit.edu	37	4	53579389	53579389	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:53579389delA	uc003gzo.2	+						KIAA0114_uc003gzp.2_Intron|SNORA26_uc003gzq.1_5'Flank	NR_024031				Homo sapiens, clone IMAGE:3885428, mRNA.												0																		---	---	---	---
SCFD2	152579	broad.mit.edu	37	4	53901517	53901517	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:53901517delA	uc003gzu.2	-						SCFD2_uc010igm.2_Intron	NM_152540	NP_689753			sec1 family domain containing 2						protein transport|vesicle docking involved in exocytosis					ovary(2)|pancreas(1)	3			GBM - Glioblastoma multiforme(3;1.07e-26)|LUSC - Lung squamous cell carcinoma(32;0.0134)															---	---	---	---
PDGFRA	5156	broad.mit.edu	37	4	54630763	54630763	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:54630763delT	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	54820452	54820452	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:54820452delT	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	55298415	55298415	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:55298415delA								PDGFRA (134004 upstream) : KIT (225680 downstream)																																			---	---	---	---
KIT	3815	broad.mit.edu	37	4	55522081	55522082	+	5'Flank	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:55522081_55522082delTT	uc010igr.2	+						KIT_uc010igs.2_5'Flank	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				---	---	---	---
Unknown	0	broad.mit.edu	37	4	55809504	55809504	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:55809504delT								KIT (202625 upstream) : KDR (134923 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	55836829	55836831	+	IGR	DEL	TTT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:55836829_55836831delTTT								KIT (229950 upstream) : KDR (107596 downstream)																																			---	---	---	---
KDR	3791	broad.mit.edu	37	4	55958996	55959001	+	Intron	DEL	AGAAGC	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:55958996_55959001delAGAAGC	uc003has.2	-						KDR_uc003hat.1_Intron	NM_002253	NP_002244			kinase insert domain receptor precursor						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)			---	---	---	---
Unknown	0	broad.mit.edu	37	4	56021397	56021398	+	IGR	DEL	AA	-	-	rs77636132		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:56021397_56021398delAA								KDR (29635 upstream) : SRD5A3 (191011 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	56179421	56179421	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:56179421delT								KDR (187659 upstream) : SRD5A3 (32988 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	56185652	56185652	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:56185652delA								KDR (193890 upstream) : SRD5A3 (26757 downstream)																																			---	---	---	---
SRD5A3	79644	broad.mit.edu	37	4	56217825	56217827	+	Intron	DEL	AAA	-	-	rs34820507		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:56217825_56217827delAAA	uc003hau.2	+							NM_024592	NP_078868			steroid 5 alpha-reductase 3						androgen biosynthetic process|dolichol metabolic process|dolichol-linked oligosaccharide biosynthetic process|polyprenol catabolic process	endoplasmic reticulum membrane|integral to membrane	3-oxo-5-alpha-steroid 4-dehydrogenase activity|oxidoreductase activity, acting on the CH-CH group of donors, NAD or NADP as acceptor				0	all_cancers(7;0.0308)|all_lung(4;0.00195)|Lung NSC(11;0.00431)|all_epithelial(27;0.0425)|Glioma(25;0.08)|all_neural(26;0.101)		Epithelial(7;0.0179)															---	---	---	---
TMEM165	55858	broad.mit.edu	37	4	56273361	56273362	+	Intron	INS	-	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:56273361_56273362insA	uc003hax.2	+						TMEM165_uc011bzy.1_Intron	NM_018475	NP_060945			transmembrane protein 165							integral to membrane					0	Lung NSC(11;0.00545)|Glioma(25;0.08)|all_neural(26;0.101)|all_epithelial(27;0.135)		LUSC - Lung squamous cell carcinoma(4;1.62e-07)|Lung(4;1.34e-06)|Epithelial(7;0.0103)															---	---	---	---
EXOC1	55763	broad.mit.edu	37	4	56719846	56719847	+	5'UTR	INS	-	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:56719846_56719847insG	uc003hbe.1	+	1					EXOC1_uc003hbf.1_5'UTR|EXOC1_uc003hbg.1_5'UTR	NM_018261	NP_060731			exocyst complex component 1 isoform 1						exocytosis|protein transport	exocyst	protein binding			ovary(2)|skin(2)|lung(1)|central_nervous_system(1)	6	Glioma(25;0.08)|all_neural(26;0.101)																	---	---	---	---
Unknown	0	broad.mit.edu	37	4	57402584	57402584	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:57402584delA								ARL9 (12526 upstream) : HOPX (111570 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	57701487	57701487	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:57701487delA								SPINK2 (13594 upstream) : REST (72555 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	58134361	58134361	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:58134361delA								IGFBP7 (157822 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	58242365	58242365	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:58242365delT								IGFBP7 (265826 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	58354864	58354865	+	IGR	INS	-	AAG	AAG	rs139562647	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:58354864_58354865insAAG								IGFBP7 (378325 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	59339966	59339967	+	IGR	INS	-	A	A	rs149234454	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:59339966_59339967insA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	61871683	61871683	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:61871683delA								None (None upstream) : LPHN3 (195291 downstream)																																			---	---	---	---
LPHN3	23284	broad.mit.edu	37	4	62302608	62302609	+	Intron	INS	-	A	A	rs144255110	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:62302608_62302609insA	uc003hcq.3	+						LPHN3_uc010ihg.1_Intron					RecName: Full=Latrophilin-3; AltName: Full=Calcium-independent alpha-latrotoxin receptor 3; AltName: Full=Lectomedin-3; Flags: 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																		---	---	---	---
LPHN3	23284	broad.mit.edu	37	4	62838924	62838924	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:62838924delA	uc010ihh.2	+						LPHN3_uc003hcq.3_Intron|LPHN3_uc003hct.2_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	63428217	63428218	+	IGR	INS	-	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:63428217_63428218insT								LPHN3 (490050 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	63499302	63499302	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:63499302delA								LPHN3 (561135 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	63826450	63826450	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:63826450delT								LPHN3 (888283 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	64833598	64833598	+	IGR	DEL	A	-	-	rs72149000		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:64833598delA								None (None upstream) : TECRL (310587 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	65648136	65648136	+	IGR	DEL	T	-	-	rs34410479		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:65648136delT								TECRL (372958 upstream) : EPHA5 (537146 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	65981992	65981992	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:65981992delA								TECRL (706814 upstream) : EPHA5 (203290 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	66564487	66564487	+	IGR	DEL	A	-	-	rs35968776		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:66564487delA								EPHA5 (28834 upstream) : MIR1269 (578055 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	66806832	66806832	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:66806832delA								EPHA5 (271179 upstream) : MIR1269 (335710 downstream)																																			---	---	---	---
MIR1269	100302177	broad.mit.edu	37	4	67142261	67142262	+	5'Flank	INS	-	G	G	rs7437072	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:67142261_67142262insG	hsa-mir-1269|MI0006406	+																							0																		---	---	---	---
Unknown	0	broad.mit.edu	37	4	67654775	67654775	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:67654775delT								MIR1269 (512129 upstream) : CENPC1 (683214 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	67867922	67867922	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:67867922delT								MIR1269 (725276 upstream) : CENPC1 (470067 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	68196369	68196369	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:68196369delA								None (None upstream) : CENPC1 (141620 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	68336722	68336723	+	5'Flank	DEL	AA	-	-	rs34391346		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:68336722_68336723delAA	uc003hdc.1	-											Homo sapiens cDNA FLJ35884 fis, clone TESTI2008960.																														---	---	---	---
LOC550112	550112	broad.mit.edu	37	4	68841366	68841366	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:68841366delA	uc003hdl.3	+											Homo sapiens chromosome 4 cDNA.												0																		---	---	---	---
LOC550112	550112	broad.mit.edu	37	4	68847312	68847312	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:68847312delT	uc003hdl.3	+											Homo sapiens chromosome 4 cDNA.												0																		---	---	---	---
LOC550112	550112	broad.mit.edu	37	4	68906030	68906031	+	Intron	INS	-	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:68906030_68906031insT	uc003hdl.3	+											Homo sapiens chromosome 4 cDNA.												0																		---	---	---	---
TMPRSS11F	389208	broad.mit.edu	37	4	68920031	68920031	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:68920031delT	uc003hdt.1	-						LOC550112_uc003hdl.3_Intron|uc011cak.1_Intron	NM_207407	NP_997290			transmembrane protease, serine 11F						proteolysis	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-4200-01A-01D-1126-08	TCGA-BR-4200-11A-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																		---	---	---	---
Unknown	0	broad.mit.edu	37	4	69141007	69141008	+	IGR	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:69141007_69141008delTT								TMPRSS11B (29595 upstream) : YTHDC1 (35098 downstream)																																			---	---	---	---
YTHDC1	91746	broad.mit.edu	37	4	69198815	69198815	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:69198815delA	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	70061884	70061885	+	IGR	INS	-	TA	TA			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:70061884_70061885insTA								UGT2B7 (83180 upstream) : UGT2B11 (4168 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	70267902	70267902	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:70267902delA								UGT2B28 (107135 upstream) : UGT2B4 (77982 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	70397715	70397716	+	IGR	DEL	TC	-	-	rs145365794		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:70397715_70397716delTC								UGT2B4 (5983 upstream) : UGT2A1 (56420 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	70773346	70773346	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:70773346delT								SULT1E1 (47476 upstream) : CSN1S1 (23453 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	71056646	71056647	+	IGR	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:71056646_71056647delAA								C4orf40 (24322 upstream) : ODAM (5597 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	71160003	71160003	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:71160003delT								CSN3 (42860 upstream) : C4orf35 (40668 downstream)																																			---	---	---	---
ENAM	10117	broad.mit.edu	37	4	71501493	71501494	+	Intron	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:71501493_71501494delTT	uc011caw.1	+							NM_031889	NP_114095			enamelin precursor						bone mineralization|odontogenesis	proteinaceous extracellular matrix	structural constituent of tooth enamel			ovary(3)	3			Lung(101;0.235)															---	---	---	---
IGJ	3512	broad.mit.edu	37	4	71529084	71529084	+	Intron	DEL	T	-	-	rs112374791		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:71529084delT	uc003hfn.3	-						IGJ_uc010ihz.2_Intron	NM_144646	NP_653247			immunoglobulin J chain						immune response	extracellular region	antigen binding				0			Lung(101;0.235)															---	---	---	---
RUFY3	22902	broad.mit.edu	37	4	71646802	71646803	+	Intron	DEL	AA	-	-	rs35495444		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:71646802_71646803delAA	uc003hfq.2	+						RUFY3_uc003hfp.3_Intron|RUFY3_uc011cax.1_Intron|RUFY3_uc003hfr.2_Intron|RUFY3_uc011cay.1_Intron	NM_014961	NP_055776			RUN and FYVE domain containing 3 isoform 2						negative regulation of axonogenesis	filopodium|growth cone					0		all_hematologic(202;0.248)	Lung(101;0.235)															---	---	---	---
Unknown	0	broad.mit.edu	37	4	71713093	71713094	+	IGR	DEL	AG	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:71713093_71713094delAG								GRSF1 (7466 upstream) : MOBKL1A (54970 downstream)																																			---	---	---	---
MOBKL1A	92597	broad.mit.edu	37	4	71837726	71837726	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:71837726delT	uc003hfw.2	+						MOBKL1A_uc003hfv.1_Intron|MOBKL1A_uc011cba.1_Intron	NM_173468	NP_775739			MOB1, Mps One Binder kinase activator-like 1A						hippo signaling cascade|protein autophosphorylation	cytoplasm|nucleus	kinase activator activity|kinase binding|metal ion binding				0		all_hematologic(202;0.21)	Lung(101;0.235)															---	---	---	---
Unknown	0	broad.mit.edu	37	4	73113842	73113842	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:73113842delA								NPFFR2 (95094 upstream) : ADAMTS3 (32845 downstream)																																			---	---	---	---
ADAMTS3	9508	broad.mit.edu	37	4	73174951	73174952	+	Intron	DEL	TT	-	-	rs76753805		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:73174951_73174952delTT	uc003hgk.1	-						ADAMTS3_uc003hgl.2_Intron	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)															---	---	---	---
ADAMTS3	9508	broad.mit.edu	37	4	73177069	73177069	+	Intron	DEL	T	-	-	rs34684425		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:73177069delT	uc003hgk.1	-						ADAMTS3_uc003hgl.2_Intron	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)															---	---	---	---
ADAMTS3	9508	broad.mit.edu	37	4	73186466	73186466	+	Frame_Shift_Del	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:73186466delA	uc003hgk.1	-	7	1104	c.1067delT	c.(1066-1068)TTAfs	p.L356fs		NM_014243	NP_055058	O15072	ATS3_HUMAN	ADAM metallopeptidase with thrombospondin type 1	356	Peptidase M12B.				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	73808827	73808829	+	IGR	DEL	AAA	-	-	rs78818763		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:73808827_73808829delAAA								ADAMTS3 (374311 upstream) : COX18 (111587 downstream)																																			---	---	---	---
MTHFD2L	441024	broad.mit.edu	37	4	75081686	75081686	+	Intron	DEL	A	-	-	rs76329015		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:75081686delA	uc011cbk.1	+						MTHFD2L_uc011cbj.1_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)															---	---	---	---
AREG	374	broad.mit.edu	37	4	75344170	75344170	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:75344170delA	uc011cbl.1	+							NM_001657	NP_001648			amphiregulin preproprotein						cell proliferation|cell-cell signaling|epidermal growth factor receptor signaling pathway|G-protein coupled receptor protein signaling pathway|positive regulation of DNA replication	cell surface|extracellular space|integral to membrane	cytokine activity|growth factor activity				0			Lung(101;0.196)															---	---	---	---
Unknown	0	broad.mit.edu	37	4	76276139	76276140	+	IGR	DEL	CT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:76276139_76276140delCT								PARM1 (300816 upstream) : RCHY1 (128215 downstream)																																			---	---	---	---
C4orf26	152816	broad.mit.edu	37	4	76489680	76489680	+	3'UTR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:76489680delA	uc003hip.1	+	2					C4orf26_uc011cbn.1_RNA|C4orf26_uc011cbo.1_Frame_Shift_Del_p.A156fs	NM_178497	NP_848592			hypothetical protein LOC152816 precursor							extracellular region					0			Lung(101;0.0973)|LUSC - Lung squamous cell carcinoma(112;0.122)															---	---	---	---
USO1	8615	broad.mit.edu	37	4	76734267	76734268	+	Intron	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:76734267_76734268delAA	uc003hiu.2	+						USO1_uc003hiv.2_Intron|USO1_uc003hiw.2_Intron	NM_003715	NP_003706			USO1 homolog, vesicle docking protein						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)															---	---	---	---
ART3	419	broad.mit.edu	37	4	76998096	76998096	+	Intron	DEL	T	-	-	rs79661366		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:76998096delT	uc003hjo.2	+						ART3_uc003hji.2_Intron|ART3_uc003hjj.2_Intron|ART3_uc003hjk.2_Intron|ART3_uc010ija.1_Intron|ART3_uc003hjn.2_Intron|ART3_uc003hjp.2_Intron|ART3_uc010ijb.2_Intron|ART3_uc003hjq.2_Intron	NM_001130016	NP_001123488			ADP-ribosyltransferase 3 isoform a						protein ADP-ribosylation	anchored to membrane|integral to plasma membrane	NAD(P)+-protein-arginine ADP-ribosyltransferase activity|NAD+ ADP-ribosyltransferase activity			ovary(2)	2			Lung(101;0.0809)|LUSC - Lung squamous cell carcinoma(112;0.0934)															---	---	---	---
ART3	419	broad.mit.edu	37	4	77022907	77022907	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:77022907delA	uc003hjo.2	+						ART3_uc003hjk.2_Intron|ART3_uc003hjn.2_Intron|ART3_uc003hjp.2_Intron|ART3_uc010ijb.2_Intron|ART3_uc003hjq.2_Intron|ART3_uc003hjr.2_Intron|ART3_uc010ijc.2_Intron|ART3_uc010ijd.2_Intron	NM_001130016	NP_001123488			ADP-ribosyltransferase 3 isoform a						protein ADP-ribosylation	anchored to membrane|integral to plasma membrane	NAD(P)+-protein-arginine ADP-ribosyltransferase activity|NAD+ ADP-ribosyltransferase activity			ovary(2)	2			Lung(101;0.0809)|LUSC - Lung squamous cell carcinoma(112;0.0934)															---	---	---	---
SEPT11	55752	broad.mit.edu	37	4	77879953	77879954	+	Intron	INS	-	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:77879953_77879954insA	uc003hkj.2	+						SEPT11_uc010ijh.1_Intron|SEPT11_uc011cca.1_Intron	NM_018243	NP_060713			septin 11						cell cycle|cell division|protein heterooligomerization	axon|cell junction|dendritic spine|septin complex|stress fiber|synapse	GTP binding|protein binding				0																		---	---	---	---
CCNG2	901	broad.mit.edu	37	4	78081696	78081697	+	Intron	DEL	GA	-	-	rs76116731		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:78081696_78081697delGA	uc003hkq.3	+						CCNG2_uc003hkn.3_Intron|CCNG2_uc011ccc.1_Intron|CCNG2_uc003hkp.3_Intron	NM_004354	NP_004345			cyclin G2						cell cycle checkpoint|cell division|mitosis	cytoplasm				ovary(2)|lung(1)	3																		---	---	---	---
Unknown	0	broad.mit.edu	37	4	78295573	78295576	+	IGR	DEL	CTGA	-	-	rs137968033		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:78295573_78295576delCTGA								CCNG2 (204363 upstream) : CXCL13 (137331 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	78311710	78311710	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:78311710delT								CCNG2 (220500 upstream) : CXCL13 (121197 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	78922987	78922987	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:78922987delT								MRPL1 (49043 upstream) : FRAS1 (55737 downstream)																																			---	---	---	---
FRAS1	80144	broad.mit.edu	37	4	79043135	79043135	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:79043135delT	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	79365014	79365014	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:79365014delT	uc003hlb.2	+						FRAS1_uc003hkw.2_Intron|FRAS1_uc010ijj.1_Intron	NM_025074	NP_079350			Fraser syndrome 1						cell communication	integral to membrane|plasma membrane	metal ion binding			large_intestine(5)	5																		---	---	---	---
Unknown	0	broad.mit.edu	37	4	79623457	79623458	+	IGR	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:79623457_79623458delAA								ANXA3 (91855 upstream) : BMP2K (74074 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	79971605	79971607	+	Intron	DEL	CTC	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:79971605_79971607delCTC	uc003hlr.1	+											Homo sapiens full length insert cDNA clone YY75G10.																														---	---	---	---
Unknown	0	broad.mit.edu	37	4	80432440	80432440	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:80432440delT	uc003hlv.2	+											Homo sapiens cDNA FLJ41919 fis, clone PERIC2002272.																														---	---	---	---
Unknown	0	broad.mit.edu	37	4	80443726	80443727	+	Intron	DEL	GT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:80443726_80443727delGT	uc003hlv.2	+											Homo sapiens cDNA FLJ41919 fis, clone PERIC2002272.																														---	---	---	---
Unknown	0	broad.mit.edu	37	4	81013780	81013780	+	IGR	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:81013780delC								ANTXR2 (19303 upstream) : PRDM8 (91659 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	81050828	81050828	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:81050828delT								ANTXR2 (56351 upstream) : PRDM8 (54611 downstream)																																			---	---	---	---
PRDM8	56978	broad.mit.edu	37	4	81124815	81124815	+	3'UTR	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:81124815delC	uc010ijo.2	+	8					PRDM8_uc003hmb.3_3'UTR|PRDM8_uc003hmc.3_3'UTR	NM_020226	NP_064611			PR domain containing 8						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			skin(1)	1																		---	---	---	---
C4orf22	255119	broad.mit.edu	37	4	81391619	81391620	+	Intron	INS	-	GTAA	GTAA	rs148957277	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:81391619_81391620insGTAA	uc003hmf.2	+						C4orf22_uc010ijp.2_Intron	NM_152770	NP_689983			hypothetical protein LOC255119											skin(2)	2																		---	---	---	---
C4orf22	255119	broad.mit.edu	37	4	81398216	81398216	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:81398216delT	uc003hmf.2	+						C4orf22_uc010ijp.2_Intron	NM_152770	NP_689983			hypothetical protein LOC255119											skin(2)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	4	81998289	81998290	+	IGR	DEL	AA	-	-	rs112962812		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:81998289_81998290delAA								BMP3 (19605 upstream) : PRKG2 (11547 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	82469872	82469872	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:82469872delT								RASGEF1B (76811 upstream) : HNRNPD (804595 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	82782613	82782613	+	IGR	DEL	A	-	-	rs510300		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:82782613delA								RASGEF1B (389552 upstream) : HNRNPD (491854 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	82795869	82795869	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:82795869delA								RASGEF1B (402808 upstream) : HNRNPD (478598 downstream)																																			---	---	---	---
TMEM150C	441027	broad.mit.edu	37	4	83483587	83483587	+	5'Flank	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:83483587delT	uc003hmy.1	-						TMEM150C_uc011ccj.1_5'Flank	NM_001080506	NP_001073975			transmembrane protein 150C							integral to membrane				ovary(1)	1																		---	---	---	---
SCD5	79966	broad.mit.edu	37	4	83702569	83702569	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:83702569delA	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)																---	---	---	---
THAP9	79725	broad.mit.edu	37	4	83838382	83838382	+	Frame_Shift_Del	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:83838382delT	uc003hnt.2	+	5	1136	c.1017delT	c.(1015-1017)TATfs	p.Y339fs	THAP9_uc003hns.1_Frame_Shift_Del_p.Y195fs|THAP9_uc003hnu.1_RNA|THAP9_uc003hnv.2_Frame_Shift_Del_p.Y56fs	NM_024672	NP_078948	Q9H5L6	THAP9_HUMAN	THAP domain containing 9	339							DNA binding|metal ion binding			ovary(2)|large_intestine(1)|central_nervous_system(1)|pancreas(1)	5		Hepatocellular(203;0.114)																---	---	---	---
COQ2	27235	broad.mit.edu	37	4	84193954	84193955	+	Intron	INS	-	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:84193954_84193955insA	uc003hog.2	-						COQ2_uc011ccp.1_Intron|COQ2_uc003hof.2_Intron|COQ2_uc003hoh.1_Intron	NM_015697	NP_056512			para-hydroxybenzoate-polyprenyltransferase,						glycerol metabolic process|isoprenoid biosynthetic process|ubiquinone biosynthetic process	mitochondrial membrane	4-hydroxybenzoate decaprenyltransferase activity|4-hydroxybenzoate nonaprenyltransferase activity			ovary(1)|central_nervous_system(1)	2		Hepatocellular(203;0.114)																---	---	---	---
COQ2	27235	broad.mit.edu	37	4	84197973	84197973	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:84197973delA	uc003hog.2	-						COQ2_uc011ccp.1_Intron|COQ2_uc003hof.2_Intron|COQ2_uc003hoh.1_Intron	NM_015697	NP_056512			para-hydroxybenzoate-polyprenyltransferase,						glycerol metabolic process|isoprenoid biosynthetic process|ubiquinone biosynthetic process	mitochondrial membrane	4-hydroxybenzoate decaprenyltransferase activity|4-hydroxybenzoate nonaprenyltransferase activity			ovary(1)|central_nervous_system(1)	2		Hepatocellular(203;0.114)																---	---	---	---
COQ2	27235	broad.mit.edu	37	4	84203115	84203118	+	Intron	DEL	TTTT	-	-	rs79644674		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:84203115_84203118delTTTT	uc003hog.2	-						COQ2_uc011ccp.1_Intron|COQ2_uc003hof.2_5'Flank|COQ2_uc003hoh.1_Intron	NM_015697	NP_056512			para-hydroxybenzoate-polyprenyltransferase,						glycerol metabolic process|isoprenoid biosynthetic process|ubiquinone biosynthetic process	mitochondrial membrane	4-hydroxybenzoate decaprenyltransferase activity|4-hydroxybenzoate nonaprenyltransferase activity			ovary(1)|central_nervous_system(1)	2		Hepatocellular(203;0.114)																---	---	---	---
Unknown	0	broad.mit.edu	37	4	84628680	84628681	+	IGR	INS	-	AC	AC	rs28585627	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:84628680_84628681insAC								AGPAT9 (101655 upstream) : NKX6-1 (785755 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	84657143	84657143	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:84657143delT								AGPAT9 (130118 upstream) : NKX6-1 (757293 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	85107461	85107461	+	Intron	DEL	A	-	-	rs72060175		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:85107461delA	uc010ikd.1	-						uc003hoz.1_Intron					Homo sapiens cDNA FLJ37966 fis, clone CTONG2009871.																														---	---	---	---
Unknown	0	broad.mit.edu	37	4	85265782	85265782	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:85265782delA								AGPAT9 (738757 upstream) : NKX6-1 (148654 downstream)																																			---	---	---	---
WDFY3	23001	broad.mit.edu	37	4	85732875	85732875	+	Intron	DEL	T	-	-	rs140627504		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:85732875delT	uc003hpd.2	-						WDFY3_uc003hpf.2_Intron	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)														---	---	---	---
Unknown	0	broad.mit.edu	37	4	85939917	85939918	+	IGR	DEL	TT	-	-	rs71672749		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:85939917_85939918delTT								C4orf12 (11749 upstream) : ARHGAP24 (456366 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	86099012	86099013	+	IGR	INS	-	TC	TC	rs141408247	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:86099012_86099013insTC								C4orf12 (170844 upstream) : ARHGAP24 (297271 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	86218434	86218434	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:86218434delA								C4orf12 (290266 upstream) : ARHGAP24 (177850 downstream)																																			---	---	---	---
MAPK10	5602	broad.mit.edu	37	4	87275256	87275257	+	Intron	DEL	TG	-	-	rs4693144	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:87275256_87275257delTG	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	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)														---	---	---	---
PTPN13	5783	broad.mit.edu	37	4	87664631	87664632	+	Intron	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:87664631_87664632delAA	uc003hpz.2	+						PTPN13_uc003hpy.2_Intron|PTPN13_uc003hqa.2_Intron|PTPN13_uc003hqb.2_Intron	NM_080683	NP_542414			protein tyrosine phosphatase, non-receptor type							cytoplasm|cytoskeleton|plasma membrane	protein binding|protein binding|protein tyrosine phosphatase activity			ovary(4)|breast(1)|kidney(1)	6		Hepatocellular(203;0.114)|all_hematologic(202;0.21)|Acute lymphoblastic leukemia(40;0.242)		OV - Ovarian serous cystadenocarcinoma(123;0.00082)														---	---	---	---
PTPN13	5783	broad.mit.edu	37	4	87705769	87705770	+	Intron	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:87705769_87705770delAA	uc003hpz.2	+						PTPN13_uc003hpy.2_Intron|PTPN13_uc003hqa.2_Intron|PTPN13_uc003hqb.2_Intron|PTPN13_uc003hqc.1_Intron	NM_080683	NP_542414			protein tyrosine phosphatase, non-receptor type							cytoplasm|cytoskeleton|plasma membrane	protein binding|protein binding|protein tyrosine phosphatase activity			ovary(4)|breast(1)|kidney(1)	6		Hepatocellular(203;0.114)|all_hematologic(202;0.21)|Acute lymphoblastic leukemia(40;0.242)		OV - Ovarian serous cystadenocarcinoma(123;0.00082)														---	---	---	---
AFF1	4299	broad.mit.edu	37	4	87994654	87994655	+	Intron	INS	-	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:87994654_87994655insT	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)														---	---	---	---
Unknown	0	broad.mit.edu	37	4	88199164	88199164	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:88199164delA								KLHL8 (57490 upstream) : HSD17B13 (25777 downstream)																																			---	---	---	---
HSD17B13	345275	broad.mit.edu	37	4	88240452	88240453	+	Intron	INS	-	AAACA	AAACA	rs150296745	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:88240452_88240453insAAACA	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)														---	---	---	---
Unknown	0	broad.mit.edu	37	4	88815267	88815267	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:88815267delT								MEPE (47325 upstream) : SPP1 (81535 downstream)																																			---	---	---	---
FAM13A	10144	broad.mit.edu	37	4	89796618	89796618	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:89796618delA	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																		---	---	---	---
FAM13A	10144	broad.mit.edu	37	4	89830645	89830645	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:89830645delT	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	90258471	90258471	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:90258471delA								GPRIN3 (29310 upstream) : SNCA (386780 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	90328129	90328130	+	IGR	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:90328129_90328130delAA								GPRIN3 (98968 upstream) : SNCA (317121 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	90478058	90478058	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:90478058delT								GPRIN3 (248897 upstream) : SNCA (167193 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	90541583	90541583	+	IGR	DEL	T	-	-	rs66920606		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:90541583delT								GPRIN3 (312422 upstream) : SNCA (103668 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	90623648	90623648	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:90623648delT								GPRIN3 (394487 upstream) : SNCA (21603 downstream)																																			---	---	---	---
FAM190A	401145	broad.mit.edu	37	4	91496131	91496132	+	Intron	INS	-	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:91496131_91496132insT	uc003hsv.3	+						FAM190A_uc010ikv.2_Intron|FAM190A_uc003hsw.2_Intron	NM_001145065	NP_001138537			KIAA1680 protein isoform 1											large_intestine(1)|ovary(1)	2																		---	---	---	---
FAM190A	401145	broad.mit.edu	37	4	91768394	91768394	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:91768394delA	uc003hsv.3	+						FAM190A_uc010ikv.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	92065816	92065816	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:92065816delT	uc003hsv.3	+							NM_001145065	NP_001138537			KIAA1680 protein isoform 1											large_intestine(1)|ovary(1)	2																		---	---	---	---
FAM190A	401145	broad.mit.edu	37	4	92144522	92144522	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:92144522delA	uc003hsv.3	+							NM_001145065	NP_001138537			KIAA1680 protein isoform 1											large_intestine(1)|ovary(1)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	4	93104031	93104031	+	IGR	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:93104031delC								FAM190A (580662 upstream) : GRID2 (121519 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	93170047	93170047	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:93170047delT								FAM190A (646678 upstream) : GRID2 (55503 downstream)																																			---	---	---	---
GRID2	2895	broad.mit.edu	37	4	93548480	93548480	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:93548480delT	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	93710624	93710625	+	Intron	DEL	CT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:93710624_93710625delCT	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	93756925	93756925	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:93756925delA	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	93874140	93874140	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:93874140delT	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	94120774	94120774	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:94120774delA	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	94123071	94123071	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:94123071delT	uc011cdt.1	+						GRID2_uc010ikx.2_Intron|GRID2_uc011cdu.1_Intron|GRID2_uc011cdv.1_Intron|GRID2_uc010ikz.1_5'Flank	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	94356114	94356114	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:94356114delT	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	94551958	94551958	+	Intron	DEL	A	-	-	rs35728659		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:94551958delA	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)													---	---	---	---
Unknown	0	broad.mit.edu	37	4	94964083	94964084	+	IGR	INS	-	GT	GT	rs142017922	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:94964083_94964084insGT								ATOH1 (212941 upstream) : SMARCAD1 (164675 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	95057908	95057908	+	IGR	DEL	G	-	-	rs112227666		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:95057908delG								ATOH1 (306766 upstream) : SMARCAD1 (70851 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	95059960	95059960	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:95059960delA								ATOH1 (308818 upstream) : SMARCAD1 (68799 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	95278404	95278404	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:95278404delT								HPGDS (14377 upstream) : PDLIM5 (94634 downstream)																																			---	---	---	---
PDLIM5	10611	broad.mit.edu	37	4	95578859	95578859	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:95578859delT	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	95630929	95630929	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:95630929delA								PDLIM5 (41553 upstream) : BMPR1B (48199 downstream)																																			---	---	---	---
BMPR1B	658	broad.mit.edu	37	4	96039469	96039471	+	Intron	DEL	TTT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:96039469_96039471delTTT	uc003htm.3	+						BMPR1B_uc010ilb.2_Intron|BMPR1B_uc003htn.3_Intron	NM_001203	NP_001194			bone morphogenetic protein receptor, type IB						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)														---	---	---	---
UNC5C	8633	broad.mit.edu	37	4	96199633	96199634	+	Intron	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:96199633_96199634delTT	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	97010580	97010580	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:97010580delA								PDHA2 (247956 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	97252249	97252249	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:97252249delA	uc003hts.1	+											full-length cDNA clone CS0DI013YE21 of Placenta Cot 25-normalized of Homo sapiens (human).																														---	---	---	---
Unknown	0	broad.mit.edu	37	4	97303504	97303505	+	IGR	INS	-	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:97303504_97303505insT								PDHA2 (540880 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	97360807	97360807	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:97360807delT								PDHA2 (598183 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	97665335	97665335	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:97665335delT								PDHA2 (902711 upstream) : C4orf37 (814699 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	98152667	98152667	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:98152667delA								None (None upstream) : C4orf37 (327367 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	98166790	98166791	+	IGR	DEL	GT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:98166790_98166791delGT								None (None upstream) : C4orf37 (313243 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	98423841	98423841	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:98423841delA								None (None upstream) : C4orf37 (56193 downstream)																																			---	---	---	---
RAP1GDS1	5910	broad.mit.edu	37	4	99191874	99191874	+	Intron	DEL	T	-	-	rs35945066		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:99191874delT	uc003htx.3	+						RAP1GDS1_uc003htu.2_Intron|RAP1GDS1_uc003htw.3_Intron|RAP1GDS1_uc003htv.3_Intron|RAP1GDS1_uc003htz.3_Intron|RAP1GDS1_uc003hty.3_Intron|RAP1GDS1_uc003hua.3_Intron	NM_001100427	NP_001093897			RAP1, GTP-GDP dissociation stimulator 1 isoform								binding|GTPase activator activity			ovary(1)|lung(1)|breast(1)	3				OV - Ovarian serous cystadenocarcinoma(123;2.9e-07)|LUSC - Lung squamous cell carcinoma(1;0.0253)|Lung(1;0.0576)				T	NUP98	T-ALL								---	---	---	---
RAP1GDS1	5910	broad.mit.edu	37	4	99270988	99270989	+	Intron	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:99270988_99270989delTT	uc003htx.3	+						RAP1GDS1_uc003htu.2_Intron|RAP1GDS1_uc003htw.3_Intron|RAP1GDS1_uc003htv.3_Intron|RAP1GDS1_uc003htz.3_Intron|RAP1GDS1_uc003hty.3_Intron|RAP1GDS1_uc003hua.3_Intron	NM_001100427	NP_001093897			RAP1, GTP-GDP dissociation stimulator 1 isoform								binding|GTPase activator activity			ovary(1)|lung(1)|breast(1)	3				OV - Ovarian serous cystadenocarcinoma(123;2.9e-07)|LUSC - Lung squamous cell carcinoma(1;0.0253)|Lung(1;0.0576)				T	NUP98	T-ALL								---	---	---	---
TSPAN5	10098	broad.mit.edu	37	4	99477146	99477147	+	Intron	INS	-	CA	CA			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:99477146_99477147insCA	uc003hub.2	-						TSPAN5_uc011cdz.1_Intron	NM_005723	NP_005714			transmembrane 4 superfamily member 9							integral to membrane					0				OV - Ovarian serous cystadenocarcinoma(123;1.89e-07)														---	---	---	---
TSPAN5	10098	broad.mit.edu	37	4	99574402	99574402	+	Intron	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:99574402delC	uc003hub.2	-						TSPAN5_uc011cdz.1_Intron	NM_005723	NP_005714			transmembrane 4 superfamily member 9							integral to membrane					0				OV - Ovarian serous cystadenocarcinoma(123;1.89e-07)														---	---	---	---
METAP1	23173	broad.mit.edu	37	4	99976239	99976239	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:99976239delT	uc003huf.3	+						METAP1_uc003hug.2_Intron|METAP1_uc010ild.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)														---	---	---	---
ADH1C	126	broad.mit.edu	37	4	100267775	100267775	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:100267775delT	uc003huu.2	-							NM_000669	NP_000660			class I alcohol dehydrogenase, gamma subunit						ethanol oxidation|xenobiotic metabolic process	cytosol	alcohol dehydrogenase (NAD) activity|zinc ion binding				0				OV - Ovarian serous cystadenocarcinoma(123;1.08e-07)	Fomepizole(DB01213)|NADH(DB00157)									Naso-/Oropharyngeal/Laryngeal_Cancer_Familial_Clustering_of				---	---	---	---
Unknown	0	broad.mit.edu	37	4	100552850	100552850	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:100552850delA								MTTP (7697 upstream) : DAPP1 (185131 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	100604898	100604898	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:100604898delA								MTTP (59745 upstream) : DAPP1 (133083 downstream)																																			---	---	---	---
BANK1	55024	broad.mit.edu	37	4	102965187	102965187	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-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	103361429	103361429	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:103361429delA								SLC39A8 (94774 upstream) : NFKB1 (61057 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	103545221	103545221	+	IGR	DEL	T	-	-	rs76526716		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:103545221delT								NFKB1 (6763 upstream) : MANBA (7423 downstream)																																	OREG0016278	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
MANBA	4126	broad.mit.edu	37	4	103653071	103653071	+	Intron	DEL	T	-	-	rs11445346		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:103653071delT	uc003hwg.2	-						MANBA_uc011ces.1_Intron	NM_005908	NP_005899			mannosidase, beta A, lysosomal precursor						carbohydrate metabolic process|protein modification process	lysosome	beta-mannosidase activity|cation binding			ovary(1)	1		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;4.44e-08)														---	---	---	---
MANBA	4126	broad.mit.edu	37	4	103673002	103673002	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:103673002delA	uc003hwg.2	-						MANBA_uc011ces.1_Intron	NM_005908	NP_005899			mannosidase, beta A, lysosomal precursor						carbohydrate metabolic process|protein modification process	lysosome	beta-mannosidase activity|cation binding			ovary(1)	1		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;4.44e-08)														---	---	---	---
MANBA	4126	broad.mit.edu	37	4	103681246	103681247	+	Intron	INS	-	AC	AC	rs142161964	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:103681246_103681247insAC	uc003hwg.2	-						MANBA_uc011ces.1_Intron	NM_005908	NP_005899			mannosidase, beta A, lysosomal precursor						carbohydrate metabolic process|protein modification process	lysosome	beta-mannosidase activity|cation binding			ovary(1)	1		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;4.44e-08)														---	---	---	---
NHEDC1	150159	broad.mit.edu	37	4	103830760	103830761	+	Intron	INS	-	AA	AA			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:103830760_103830761insAA	uc003hww.2	-						NHEDC1_uc003hwu.2_Intron|NHEDC1_uc010ilm.2_Intron|NHEDC1_uc003hwv.2_Intron|NHEDC1_uc011cev.1_Intron	NM_139173	NP_631912			Na+/H+ exchanger domain containing 1 isoform 1							integral to membrane	solute:hydrogen antiporter activity			ovary(1)|skin(1)	2		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;1.5e-08)														---	---	---	---
NHEDC2	133308	broad.mit.edu	37	4	103954418	103954418	+	Intron	DEL	A	-	-	rs74531859	byFrequency;by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:103954418delA	uc003hwx.3	-						NHEDC2_uc010iln.1_Intron|NHEDC2_uc003hwy.2_Intron|NHEDC2_uc011cew.1_Intron|NHEDC2_uc011cex.1_Intron	NM_178833	NP_849155			Na+/H+ exchanger domain containing 2						sodium ion transport	integral to membrane|mitochondrial membrane	solute:hydrogen antiporter activity				0				OV - Ovarian serous cystadenocarcinoma(123;2.3e-08)														---	---	---	---
Unknown	0	broad.mit.edu	37	4	104479491	104479491	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:104479491delA								CENPE (359925 upstream) : TACR3 (31134 downstream)																																			---	---	---	---
TACR3	6870	broad.mit.edu	37	4	104512849	104512849	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:104512849delA	uc003hxe.1	-							NM_001059	NP_001050			tachykinin receptor 3							integral to plasma membrane	tachykinin receptor activity			ovary(3)|lung(2)|breast(1)|skin(1)	7		Hepatocellular(203;0.217)		UCEC - Uterine corpus endometrioid carcinoma (10;0.22)|OV - Ovarian serous cystadenocarcinoma(123;3.4e-08)														---	---	---	---
Unknown	0	broad.mit.edu	37	4	105125424	105125424	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:105125424delA								TACR3 (484451 upstream) : CXXC4 (267921 downstream)																																			---	---	---	---
TET2	54790	broad.mit.edu	37	4	106187505	106187505	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:106187505delA	uc003hxk.2	+						TET2_uc011cez.1_Intron|TET2_uc003hxj.2_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								---	---	---	---
Unknown	0	broad.mit.edu	37	4	106220990	106220990	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:106220990delA								TET2 (20032 upstream) : PPA2 (69245 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	106260760	106260761	+	IGR	DEL	TC	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:106260760_106260761delTC								TET2 (59802 upstream) : PPA2 (29474 downstream)																																			---	---	---	---
ARHGEF38	54848	broad.mit.edu	37	4	106502349	106502349	+	Intron	DEL	C	-	-	rs79004299		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:106502349delC	uc003hxu.2	+							NM_017700	NP_060170			hypothetical protein LOC54848						regulation of Rho protein signal transduction	intracellular	Rho guanyl-nucleotide exchange factor activity			ovary(2)|breast(1)	3																		---	---	---	---
ARHGEF38	54848	broad.mit.edu	37	4	106511195	106511196	+	Intron	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:106511195_106511196delAA	uc003hxu.2	+							NM_017700	NP_060170			hypothetical protein LOC54848						regulation of Rho protein signal transduction	intracellular	Rho guanyl-nucleotide exchange factor activity			ovary(2)|breast(1)	3																		---	---	---	---
ARHGEF38	54848	broad.mit.edu	37	4	106551819	106551820	+	Intron	INS	-	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:106551819_106551820insA	uc003hxu.2	+							NM_017700	NP_060170			hypothetical protein LOC54848						regulation of Rho protein signal transduction	intracellular	Rho guanyl-nucleotide exchange factor activity			ovary(2)|breast(1)	3																		---	---	---	---
ARHGEF38	54848	broad.mit.edu	37	4	106551895	106551895	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:106551895delA	uc003hxu.2	+							NM_017700	NP_060170			hypothetical protein LOC54848						regulation of Rho protein signal transduction	intracellular	Rho guanyl-nucleotide exchange factor activity			ovary(2)|breast(1)	3																		---	---	---	---
GSTCD	79807	broad.mit.edu	37	4	106724857	106724857	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:106724857delA	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)														---	---	---	---
NPNT	255743	broad.mit.edu	37	4	106859952	106859952	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:106859952delT	uc003hya.2	+						NPNT_uc011cfc.1_Intron|NPNT_uc011cfd.1_Intron|NPNT_uc011cfe.1_Intron|NPNT_uc010ilt.1_Intron|NPNT_uc011cff.1_Intron|NPNT_uc010ilu.1_Intron	NM_001033047	NP_001028219			nephronectin precursor						cell differentiation	membrane	calcium ion binding			skin(1)	1		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;5.41e-07)														---	---	---	---
Unknown	0	broad.mit.edu	37	4	107681391	107681391	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:107681391delA								AIMP1 (411012 upstream) : DKK2 (161569 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	108242119	108242119	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:108242119delA								DKK2 (37273 upstream) : PAPSS1 (292704 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	108254633	108254633	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:108254633delA								DKK2 (49787 upstream) : PAPSS1 (280190 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	108327120	108327120	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:108327120delT								DKK2 (122274 upstream) : PAPSS1 (207703 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	108508091	108508092	+	IGR	INS	-	T	T	rs137893008	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:108508091_108508092insT								DKK2 (303245 upstream) : PAPSS1 (26731 downstream)																																			---	---	---	---
HADH	3033	broad.mit.edu	37	4	108939586	108939586	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:108939586delT	uc003hyq.2	+						HADH_uc010ilx.2_Intron|HADH_uc010ily.2_Intron|HADH_uc003hyr.2_Intron	NM_005327	NP_005318			L-3-hydroxyacyl-Coenzyme A dehydrogenase						fatty acid beta-oxidation	mitochondrial matrix	3-hydroxyacyl-CoA dehydrogenase activity|NAD+ binding			ovary(1)	1		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;0.000168)	NADH(DB00157)											OREG0016285	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	109141245	109141248	+	IGR	DEL	AAAA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:109141245_109141248delAAAA								LEF1 (51667 upstream) : LOC285456 (318098 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	109624075	109624076	+	IGR	DEL	AC	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:109624075_109624076delAC								OSTC (35095 upstream) : AGXT2L1 (39128 downstream)																																			---	---	---	---
SEC24B	10427	broad.mit.edu	37	4	110453489	110453490	+	Intron	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:110453489_110453490delAA	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)														---	---	---	---
Unknown	0	broad.mit.edu	37	4	111196614	111196615	+	IGR	DEL	AG	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:111196614_111196615delAG								ELOVL6 (76794 upstream) : ENPEP (200614 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	111232063	111232063	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:111232063delA								ELOVL6 (112243 upstream) : ENPEP (165166 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	111689176	111689176	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:111689176delT								PITX2 (126059 upstream) : MIR297 (92562 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	112754389	112754390	+	IGR	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:112754389_112754390delAA								MIR297 (972586 upstream) : C4orf32 (312163 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	112940108	112940108	+	IGR	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:112940108delC								None (None upstream) : C4orf32 (126445 downstream)																																			---	---	---	---
AP1AR	55435	broad.mit.edu	37	4	113186056	113186057	+	Intron	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:113186056_113186057delTT	uc003iaj.3	+						AP1AR_uc010imm.1_Intron|AP1AR_uc003iak.3_Intron	NM_018569	NP_061039			adaptor-related protein complex 1 associated						protein transport	early endosome|Golgi apparatus|late endosome|transport vesicle					0																		---	---	---	---
LARP7	51574	broad.mit.edu	37	4	113574479	113574480	+	Intron	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:113574479_113574480delTT	uc003iay.2	+						LARP7_uc003iaz.2_Intron|LARP7_uc003iba.2_Intron|LARP7_uc003ibb.2_Intron	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)														---	---	---	---
Unknown	0	broad.mit.edu	37	4	113652295	113652296	+	IGR	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:113652295_113652296delAA								LARP7 (73554 upstream) : ANK2 (86943 downstream)																																			---	---	---	---
ANK2	287	broad.mit.edu	37	4	114289147	114289147	+	Intron	DEL	A	-	-	rs55966162	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:114289147delA	uc003ibe.3	+						ANK2_uc003ibd.3_Intron|ANK2_uc003ibf.3_Intron|ANK2_uc011cgc.1_Intron|ANK2_uc003ibg.3_Intron|ANK2_uc003ibh.3_Intron|ANK2_uc011cgd.1_Intron	NM_001148	NP_001139			ankyrin 2 isoform 1						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)														---	---	---	---
CAMK2D	817	broad.mit.edu	37	4	114377066	114377066	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:114377066delA	uc003ibi.2	-						CAMK2D_uc003ibj.2_Intron|CAMK2D_uc003ibk.2_Intron|CAMK2D_uc003ibo.3_Intron	NM_001221	NP_001212			calcium/calmodulin-dependent protein kinase II						interferon-gamma-mediated signaling pathway|regulation of cell growth|synaptic transmission	calcium- and calmodulin-dependent protein kinase complex|cytosol|endocytic vesicle membrane|nucleoplasm|plasma membrane	ATP binding|calmodulin binding|calmodulin-dependent protein kinase activity			ovary(1)	1		Ovarian(17;0.00369)|Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;0.000271)														---	---	---	---
Unknown	0	broad.mit.edu	37	4	114747040	114747041	+	IGR	INS	-	CAAACT	CAAACT	rs140119034	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:114747040_114747041insCAAACT								CAMK2D (63957 upstream) : ARSJ (74399 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	115415761	115415762	+	IGR	DEL	AA	-	-	rs72197634		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:115415761_115415762delAA								ARSJ (514883 upstream) : UGT8 (103849 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	115727798	115727798	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:115727798delT								UGT8 (129596 upstream) : NDST4 (21133 downstream)																																			---	---	---	---
NDST4	64579	broad.mit.edu	37	4	115775633	115775633	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:115775633delT	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	116192853	116192853	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:116192853delA								NDST4 (157821 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	116657563	116657563	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:116657563delA								NDST4 (622531 upstream) : MIR1973 (563318 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	117589651	117589656	+	IGR	DEL	TTATCC	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:117589651_117589656delTTATCC								MIR1973 (368727 upstream) : TRAM1L1 (415060 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	118188564	118188564	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:118188564delA								TRAM1L1 (181828 upstream) : NDST3 (766209 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	118283987	118283987	+	IGR	DEL	A	-	-	rs76844463		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:118283987delA								TRAM1L1 (277251 upstream) : NDST3 (670786 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	119569747	119569748	+	IGR	INS	-	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:119569747_119569748insG								CEP170L (94390 upstream) : METTL14 (36826 downstream)																																			---	---	---	---
SYNPO2	171024	broad.mit.edu	37	4	119879716	119879717	+	Intron	INS	-	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:119879716_119879717insG	uc003icm.3	+						SYNPO2_uc010ina.2_Intron|SYNPO2_uc010inb.2_Intron|SYNPO2_uc011cgh.1_Intron	NM_001128933	NP_001122405			synaptopodin 2 isoform b							nucleus|Z disc	14-3-3 protein binding|actin binding|muscle alpha-actinin binding			ovary(2)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	4	120316095	120316096	+	Intron	INS	-	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:120316095_120316096insT	uc003icx.1	+											Homo sapiens cDNA FLJ40382 fis, clone TESTI2035775.																														---	---	---	---
MAD2L1	4085	broad.mit.edu	37	4	120986038	120986039	+	Intron	INS	-	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:120986038_120986039insA	uc003idl.2	-						MAD2L1_uc003idm.2_Intron	NM_002358	NP_002349			MAD2-like 1						anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|cell division|mitotic cell cycle spindle assembly checkpoint|mitotic prometaphase|negative regulation of apoptosis|negative regulation of mitotic anaphase-promoting complex activity|positive regulation of mitotic cell cycle spindle assembly checkpoint	condensed chromosome kinetochore|cytosol|nucleus|perinuclear region of cytoplasm	protein homodimerization activity				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	4	121003243	121003244	+	IGR	DEL	TG	-	-	rs112400167		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:121003243_121003244delTG								MAD2L1 (15230 upstream) : PRDM5 (612686 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	121213052	121213052	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:121213052delT								MAD2L1 (225039 upstream) : PRDM5 (402878 downstream)																																			---	---	---	---
EXOSC9	5393	broad.mit.edu	37	4	122734369	122734369	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:122734369delA	uc003iea.2	+						EXOSC9_uc003idz.2_Intron|EXOSC9_uc003ieb.2_Intron|EXOSC9_uc010inp.1_Intron	NM_005033	NP_005024			exosome component 9 isoform 2						exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay|immune response|nuclear mRNA surveillance|nuclear polyadenylation-dependent rRNA catabolic process|positive regulation of cell growth|rRNA processing	cytosol|nuclear exosome (RNase complex)|nucleolus|nucleolus|nucleus	3'-5'-exoribonuclease activity|AU-rich element binding|protein binding				0																		---	---	---	---
BBS7	55212	broad.mit.edu	37	4	122765171	122765171	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:122765171delA	uc003ied.2	-						BBS7_uc003iee.1_Intron	NM_176824	NP_789794			Bardet-Biedl syndrome 7 protein isoform a						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	123144401	123144401	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:123144401delA	uc003ieh.2	+						KIAA1109_uc003iei.1_Intron|KIAA1109_uc010ins.1_Intron|KIAA1109_uc003iej.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																		---	---	---	---
KIAA1109	84162	broad.mit.edu	37	4	123234945	123234945	+	Intron	DEL	A	-	-	rs72925991	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-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																		---	---	---	---
SPATA5	166378	broad.mit.edu	37	4	123908683	123908683	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:123908683delT	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	124217072	124217072	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:124217072delA	uc003iez.3	+							NM_145207	NP_660208			spermatogenesis associated 5						cell differentiation|multicellular organismal development|spermatogenesis	mitochondrion	ATP binding|nucleoside-triphosphatase activity				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	4	125253777	125253777	+	IGR	DEL	A	-	-	rs77213880		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:125253777delA								LOC285419 (402259 upstream) : ANKRD50 (331691 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	126079677	126079678	+	IGR	DEL	AA	-	-	rs111658453		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:126079677_126079678delAA								ANKRD50 (445790 upstream) : FAT4 (157889 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	126121302	126121302	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:126121302delA								ANKRD50 (487415 upstream) : FAT4 (116265 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	126837607	126837609	+	IGR	DEL	TTT	-	-	rs35785150		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:126837607_126837609delTTT								MIR2054 (409145 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	126949062	126949063	+	IGR	INS	-	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:126949062_126949063insA								MIR2054 (520600 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	128076737	128076737	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:128076737delT								None (None upstream) : INTU (477383 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	128305527	128305528	+	IGR	DEL	TG	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:128305527_128305528delTG								None (None upstream) : INTU (248592 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	128645128	128645128	+	IGR	DEL	A	-	-	rs67626277		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:128645128delA								INTU (7198 upstream) : SLC25A31 (6427 downstream)																																			---	---	---	---
SLC25A31	83447	broad.mit.edu	37	4	128652528	128652529	+	Intron	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:128652528_128652529delAA	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																		---	---	---	---
LARP1B	55132	broad.mit.edu	37	4	129075256	129075256	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:129075256delT	uc003iga.2	+						LARP1B_uc003igc.2_Intron|LARP1B_uc003igb.1_Intron	NM_018078	NP_060548			La ribonucleoprotein domain family member 2								RNA binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	4	129244788	129244789	+	IGR	INS	-	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:129244788_129244789insT								PGRMC2 (35840 upstream) : PHF17 (485990 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	129261730	129261731	+	IGR	INS	-	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:129261730_129261731insA								PGRMC2 (52782 upstream) : PHF17 (469048 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	129468178	129468178	+	IGR	DEL	T	-	-	rs68038643		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:129468178delT								PGRMC2 (259230 upstream) : PHF17 (262601 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	129561953	129561953	+	IGR	DEL	A	-	-	rs71865918		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:129561953delA								PGRMC2 (353005 upstream) : PHF17 (168826 downstream)																																			---	---	---	---
PHF17	79960	broad.mit.edu	37	4	129743878	129743879	+	Intron	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:129743878_129743879delAA	uc003igk.2	+						PHF17_uc003igj.2_Intron|PHF17_uc003igl.2_Intron|PHF17_uc011cgy.1_Intron|PHF17_uc003igm.2_Intron	NM_199320	NP_955352			PHD finger protein 17 long isoform						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																		---	---	---	---
Unknown	0	broad.mit.edu	37	4	130165973	130165973	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:130165973delA								C4orf33 (132131 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	130722687	130722687	+	Intron	DEL	T	-	-	rs75815425		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:130722687delT	uc003igw.1	+											Homo sapiens cDNA clone IMAGE:5170949, partial cds.																														---	---	---	---
Unknown	0	broad.mit.edu	37	4	131102614	131102614	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:131102614delA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	131225836	131225836	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:131225836delT								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	131710173	131710173	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:131710173delA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	132522008	132522008	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:132522008delA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	132974173	132974173	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:132974173delA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	133136910	133136911	+	IGR	DEL	AC	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:133136910_133136911delAC								None (None upstream) : PCDH10 (933559 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	133283583	133283583	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:133283583delA								None (None upstream) : PCDH10 (786887 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	133395300	133395301	+	IGR	DEL	GT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:133395300_133395301delGT								None (None upstream) : PCDH10 (675169 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	133507607	133507607	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:133507607delT								None (None upstream) : PCDH10 (562863 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	133840740	133840740	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:133840740delT								None (None upstream) : PCDH10 (229730 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	134168433	134168433	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:134168433delA								PCDH10 (55702 upstream) : PABPC4L (949058 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	135087063	135087063	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:135087063delA								PCDH10 (974332 upstream) : PABPC4L (30428 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	135135358	135135359	+	IGR	INS	-	A	A	rs34054645		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:135135358_135135359insA								PABPC4L (12455 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	135732458	135732458	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:135732458delA								PABPC4L (609555 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	135800933	135800938	+	IGR	DEL	AAAAAA	-	-	rs113435274		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:135800933_135800938delAAAAAA								PABPC4L (678030 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	136597551	136597552	+	IGR	INS	-	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:136597551_136597552insA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	136902437	136902438	+	IGR	INS	-	T	T	rs140833354	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:136902437_136902438insT								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	137164369	137164370	+	IGR	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:137164369_137164370delAA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	138544976	138544976	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:138544976delA								PCDH18 (91328 upstream) : SLC7A11 (540272 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	138755531	138755531	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:138755531delA								PCDH18 (301883 upstream) : SLC7A11 (329717 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	138821648	138821648	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:138821648delT								PCDH18 (368000 upstream) : SLC7A11 (263600 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	138898653	138898654	+	IGR	INS	-	TG	TG	rs144029956	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:138898653_138898654insTG								PCDH18 (445005 upstream) : SLC7A11 (186594 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	139493618	139493619	+	IGR	INS	-	ACAA	ACAA	rs75719317		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:139493618_139493619insACAA								SLC7A11 (330115 upstream) : CCRN4L (443324 downstream)																																			---	---	---	---
ELF2	1998	broad.mit.edu	37	4	140024042	140024043	+	Intron	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:140024042_140024043delTT	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)																	---	---	---	---
ELF2	1998	broad.mit.edu	37	4	140035904	140035904	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:140035904delA	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)																	---	---	---	---
NAA15	80155	broad.mit.edu	37	4	140270590	140270592	+	Intron	DEL	TTT	-	-	rs112955393		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:140270590_140270592delTTT	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	140307821	140307821	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:140307821delA	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																		---	---	---	---
RAB33B	83452	broad.mit.edu	37	4	140379438	140379438	+	Intron	DEL	T	-	-	rs75626919		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:140379438delT	uc003ihv.2	+							NM_031296	NP_112586			RAB33B, member RAS oncogene family						protein transport|small GTPase mediated signal transduction	Golgi membrane	GTP binding				0	all_hematologic(180;0.162)																	---	---	---	---
SETD7	80854	broad.mit.edu	37	4	140445977	140445977	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:140445977delT	uc003ihw.2	-							NM_030648	NP_085151			SET domain-containing protein 7						peptidyl-lysine dimethylation|peptidyl-lysine monomethylation|regulation of transcription, DNA-dependent|transcription, DNA-dependent	chromosome|nucleus	histone-lysine N-methyltransferase activity|p53 binding			ovary(1)|central_nervous_system(1)	2	all_hematologic(180;0.156)																	---	---	---	---
MAML3	55534	broad.mit.edu	37	4	140929506	140929506	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:140929506delA	uc003ihz.1	-						MAML3_uc011chd.1_Intron	NM_018717	NP_061187			mastermind-like 3						Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	nuclear speck	transcription coactivator activity			ovary(1)	1	all_hematologic(180;0.162)																	---	---	---	---
Unknown	0	broad.mit.edu	37	4	141147865	141147865	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:141147865delA								MAML3 (72632 upstream) : SCOC (30575 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	141377825	141377825	+	RNA	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:141377825delA	uc003iij.1	-	6		c.3581delT								Homo sapiens similar to RIKEN cDNA 4933434I20, mRNA (cDNA clone IMAGE:5267198).																														---	---	---	---
Unknown	0	broad.mit.edu	37	4	141698964	141698964	+	IGR	DEL	A	-	-	rs146912992	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:141698964delA								TBC1D9 (21493 upstream) : RNF150 (87761 downstream)																																			---	---	---	---
RNF150	57484	broad.mit.edu	37	4	141877770	141877770	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:141877770delA	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	142123513	142123513	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:142123513delA								RNF150 (68897 upstream) : ZNF330 (18536 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	142823962	142823962	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:142823962delA								IL15 (169351 upstream) : INPP4B (125222 downstream)																																			---	---	---	---
INPP4B	8821	broad.mit.edu	37	4	143126032	143126032	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:143126032delA	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)																	---	---	---	---
Unknown	0	broad.mit.edu	37	4	144172503	144172503	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:144172503delA								USP38 (29363 upstream) : GAB1 (85480 downstream)																																			---	---	---	---
SMARCA5	8467	broad.mit.edu	37	4	144471021	144471021	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-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	144476723	144476725	+	IGR	DEL	TTT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:144476723_144476725delTTT								SMARCA5 (2157 upstream) : LOC441046 (3900 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	144498742	144498742	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:144498742delT								LOC441046 (9429 upstream) : GYPE (293278 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	145388934	145388935	+	IGR	DEL	AT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:145388934_145388935delAT								GYPA (327030 upstream) : HHIP (178238 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	145394927	145394927	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:145394927delA								GYPA (333023 upstream) : HHIP (172246 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	145450875	145450875	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:145450875delA								GYPA (388971 upstream) : HHIP (116298 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	145744813	145744814	+	IGR	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:145744813_145744814delTT								HHIP (84932 upstream) : ANAPC10 (171500 downstream)																																			---	---	---	---
SMAD1	4086	broad.mit.edu	37	4	146400292	146400292	+	5'Flank	DEL	A	-	-	rs77436741		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:146400292delA	uc003ikc.2	+							NM_005900	NP_005891			Sma- and Mad-related protein 1						BMP signaling pathway|embryonic pattern specification|primary miRNA processing|SMAD protein complex assembly|transforming growth factor beta receptor signaling pathway	cytosol|integral to membrane|nuclear inner membrane	co-SMAD binding|I-SMAD binding|identical protein binding|protein kinase binding|sequence-specific DNA binding transcription factor activity|transforming growth factor beta receptor, pathway-specific cytoplasmic mediator activity			ovary(1)	1	all_hematologic(180;0.151)																	---	---	---	---
MMAA	166785	broad.mit.edu	37	4	146559521	146559522	+	Intron	DEL	AA	-	-	rs78469116		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:146559521_146559522delAA	uc003ikh.3	+						MMAA_uc003ikg.2_Intron|MMAA_uc003iki.1_5'Flank|MMAA_uc010iow.2_5'Flank	NM_172250	NP_758454			methylmalonic aciduria type A precursor							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	146770908	146770908	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:146770908delT	uc003ikn.2	-						ZNF827_uc003ikm.2_Intron|ZNF827_uc010iox.2_Intron	NM_178835	NP_849157			zinc finger protein 827						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0	all_hematologic(180;0.151)																	---	---	---	---
Unknown	0	broad.mit.edu	37	4	147035640	147035640	+	Intron	DEL	A	-	-	rs113944792		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:147035640delA	uc003iko.1	-						uc010ioy.1_Intron					Homo sapiens cDNA FLJ32671 fis, clone TESTI1000128.																														---	---	---	---
SLC10A7	84068	broad.mit.edu	37	4	147412706	147412706	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:147412706delA	uc010ioz.2	-						SLC10A7_uc003ikr.2_Intron|SLC10A7_uc010ipa.2_Intron|SLC10A7_uc003iks.2_Intron|SLC10A7_uc003ikt.2_Intron	NM_001029998	NP_001025169			solute carrier family 10 (sodium/bile acid							integral to membrane	bile acid:sodium symporter activity				0	all_hematologic(180;0.151)																	---	---	---	---
TMEM184C	55751	broad.mit.edu	37	4	148549705	148549705	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:148549705delA	uc003ila.3	+							NM_018241	NP_060711			transmembrane protein 184C							integral to membrane					0																		---	---	---	---
ARHGAP10	79658	broad.mit.edu	37	4	148830794	148830794	+	Intron	DEL	T	-	-	rs77063685		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:148830794delT	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)														---	---	---	---
ARHGAP10	79658	broad.mit.edu	37	4	148840727	148840728	+	Intron	DEL	TC	-	-	rs67509221		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:148840727_148840728delTC	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)														---	---	---	---
NR3C2	4306	broad.mit.edu	37	4	149042185	149042185	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:149042185delT	uc003ilj.3	-						NR3C2_uc003ilk.3_Intron|NR3C2_uc010iph.2_Intron	NM_000901	NP_000892			nuclear receptor subfamily 3, group C, member 2						regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor	endoplasmic reticulum membrane|nucleoplasm	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|steroid binding|steroid hormone receptor activity|zinc ion binding			large_intestine(1)	1	all_hematologic(180;0.151)			GBM - Glioblastoma multiforme(119;0.0614)	Desoxycorticosterone Pivalate(DB01134)|Eplerenone(DB00700)|Fludrocortisone(DB00687)|Spironolactone(DB00421)													---	---	---	---
NR3C2	4306	broad.mit.edu	37	4	149340248	149340248	+	Intron	DEL	T	-	-	rs33928091		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:149340248delT	uc003ilj.3	-						NR3C2_uc003ilk.3_Intron|NR3C2_uc010iph.2_Intron	NM_000901	NP_000892			nuclear receptor subfamily 3, group C, member 2						regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor	endoplasmic reticulum membrane|nucleoplasm	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|steroid binding|steroid hormone receptor activity|zinc ion binding			large_intestine(1)	1	all_hematologic(180;0.151)			GBM - Glioblastoma multiforme(119;0.0614)	Desoxycorticosterone Pivalate(DB01134)|Eplerenone(DB00700)|Fludrocortisone(DB00687)|Spironolactone(DB00421)													---	---	---	---
Unknown	0	broad.mit.edu	37	4	149676384	149676385	+	IGR	INS	-	TC	TC	rs144863566	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:149676384_149676385insTC								NR3C2 (312741 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	150800992	150800992	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:150800992delA								None (None upstream) : DCLK2 (199088 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	150911556	150911557	+	IGR	INS	-	A	A	rs145932013	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:150911556_150911557insA								None (None upstream) : DCLK2 (88523 downstream)																																			---	---	---	---
LRBA	987	broad.mit.edu	37	4	151842494	151842494	+	Intron	DEL	A	-	-	rs145809894	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:151842494delA	uc010ipj.2	-						LRBA_uc003ilu.3_Intron|LRBA_uc010ipk.1_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)																	---	---	---	---
SH3D19	152503	broad.mit.edu	37	4	152049145	152049145	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:152049145delT	uc010ipl.1	-						SH3D19_uc003imb.2_Intron|SH3D19_uc003imc.2_Intron|SH3D19_uc003ime.2_Intron|SH3D19_uc010ipm.2_Intron	NM_001009555	NP_001009555			SH3 domain containing 19 isoform a						cellular membrane organization|positive regulation of membrane protein ectodomain proteolysis|post-Golgi vesicle-mediated transport	cytosol|Golgi apparatus|nucleus|plasma membrane	proline-rich region binding			ovary(1)|skin(1)	2	all_hematologic(180;0.093)	Acute lymphoblastic leukemia(8;0.138)																---	---	---	---
Unknown	0	broad.mit.edu	37	4	152213452	152213452	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:152213452delA								PRSS48 (849 upstream) : FAM160A1 (116946 downstream)																																			---	---	---	---
PET112L	5188	broad.mit.edu	37	4	152642390	152642390	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:152642390delA	uc003iml.2	-						PET112L_uc003imm.3_Intron	NM_004564	NP_004555			PET112-like precursor							mitochondrion	ATP binding|carbon-nitrogen ligase activity, with glutamine as amido-N-donor|translation factor activity, nucleic acid binding				0	all_hematologic(180;0.093)	Acute lymphoblastic leukemia(8;0.138)			L-Glutamic Acid(DB00142)|L-Glutamine(DB00130)													---	---	---	---
Unknown	0	broad.mit.edu	37	4	152923831	152923831	+	IGR	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:152923831delG								PET112L (241685 upstream) : FBXW7 (318580 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	152954709	152954709	+	IGR	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:152954709delG								PET112L (272563 upstream) : FBXW7 (287702 downstream)																																			---	---	---	---
ARFIP1	27236	broad.mit.edu	37	4	153763980	153763981	+	Intron	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:153763980_153763981delTT	uc003imz.2	+						ARFIP1_uc003inb.2_Intron|ARFIP1_uc003ina.2_Intron|ARFIP1_uc003inc.2_Intron|ARFIP1_uc011cij.1_Intron	NM_001025595	NP_001020766			ADP-ribosylation factor interacting protein 1						intracellular protein transport|regulation of protein secretion	cytosol|Golgi membrane				ovary(1)	1	all_hematologic(180;0.093)																	---	---	---	---
ARFIP1	27236	broad.mit.edu	37	4	153820318	153820318	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:153820318delT	uc003imz.2	+						ARFIP1_uc003inb.2_Intron|ARFIP1_uc003ina.2_Intron|ARFIP1_uc003inc.2_Intron|ARFIP1_uc011cij.1_Intron	NM_001025595	NP_001020766			ADP-ribosylation factor interacting protein 1						intracellular protein transport|regulation of protein secretion	cytosol|Golgi membrane				ovary(1)	1	all_hematologic(180;0.093)																	---	---	---	---
Unknown	0	broad.mit.edu	37	4	153834152	153834152	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:153834152delT								ARFIP1 (1091 upstream) : FHDC1 (29983 downstream)																																			---	---	---	---
MND1	84057	broad.mit.edu	37	4	154301455	154301455	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:154301455delT	uc003ink.1	+							NM_032117	NP_115493			GAJ protein						DNA recombination|meiosis	nucleus	DNA binding				0	all_hematologic(180;0.093)																	---	---	---	---
MND1	84057	broad.mit.edu	37	4	154336198	154336198	+	3'UTR	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:154336198delC	uc003ink.1	+	8						NM_032117	NP_115493			GAJ protein						DNA recombination|meiosis	nucleus	DNA binding				0	all_hematologic(180;0.093)																	---	---	---	---
Unknown	0	broad.mit.edu	37	4	154998189	154998189	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:154998189delA								SFRP2 (287961 upstream) : DCHS2 (157338 downstream)																																			---	---	---	---
FGA	2243	broad.mit.edu	37	4	155505988	155505988	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:155505988delA	uc003iod.1	-							NM_000508	NP_000499			fibrinogen, alpha polypeptide isoform alpha-E						platelet activation|platelet degranulation|protein polymerization|response to calcium ion|signal transduction	external side of plasma membrane|fibrinogen complex|platelet alpha granule lumen	eukaryotic cell surface binding|protein binding, bridging|receptor binding			ovary(2)|breast(1)	3	all_hematologic(180;0.215)	Renal(120;0.0458)			Alteplase(DB00009)|Anistreplase(DB00029)|Reteplase(DB00015)|Sucralfate(DB00364)|Tenecteplase(DB00031)													---	---	---	---
Unknown	0	broad.mit.edu	37	4	155574838	155574841	+	Intron	DEL	TTTT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:155574838_155574841delTTTT	uc003iol.2	+											Homo sapiens cDNA FLJ31672 fis, clone NT2RI2005048.																														---	---	---	---
Unknown	0	broad.mit.edu	37	4	156216341	156216341	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:156216341delT								NPY2R (78115 upstream) : MAP9 (47473 downstream)																																			---	---	---	---
MAP9	79884	broad.mit.edu	37	4	156271742	156271742	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:156271742delT	uc003ios.2	-						MAP9_uc011cin.1_Intron	NM_001039580	NP_001034669			aster-associated protein						cell division|mitosis	cytoplasm|microtubule|spindle				ovary(1)|central_nervous_system(1)	2	all_hematologic(180;0.24)	Renal(120;0.0458)		COAD - Colon adenocarcinoma(41;0.143)														---	---	---	---
ACCN5	51802	broad.mit.edu	37	4	156773541	156773541	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-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)														---	---	---	---
CTSO	1519	broad.mit.edu	37	4	156858762	156858762	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:156858762delT	uc003ipg.2	-							NM_001334	NP_001325			cathepsin O preproprotein						proteolysis	lysosome	cysteine-type endopeptidase activity				0	all_hematologic(180;0.24)	Renal(120;0.0458)		KIRC - Kidney renal clear cell carcinoma(143;0.05)|Kidney(143;0.0627)|COAD - Colon adenocarcinoma(41;0.148)														---	---	---	---
Unknown	0	broad.mit.edu	37	4	156882480	156882480	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:156882480delT								CTSO (7432 upstream) : PDGFC (800284 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	157099425	157099425	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:157099425delT								CTSO (224377 upstream) : PDGFC (583339 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	157117924	157117924	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:157117924delA								CTSO (242876 upstream) : PDGFC (564840 downstream)																																			---	---	---	---
PDGFC	56034	broad.mit.edu	37	4	157845569	157845569	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:157845569delA	uc003iph.1	-						PDGFC_uc003ipi.1_Intron|PDGFC_uc011cis.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	158067177	158067178	+	Intron	DEL	TT	-	-	rs79575709		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:158067177_158067178delTT	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	158233695	158233695	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:158233695delT	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	158476031	158476031	+	IGR	DEL	T	-	-	rs34057044		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:158476031delT								GRIA2 (188807 upstream) : LOC340017 (17611 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	159018434	159018434	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:159018434delT								LOC340017 (521139 upstream) : FAM198B (27299 downstream)																																			---	---	---	---
FAM198B	51313	broad.mit.edu	37	4	159083250	159083250	+	Intron	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:159083250delC	uc003ipp.3	-						FAM198B_uc003ipq.3_Intron|FAM198B_uc003ipr.3_Intron	NM_016613	NP_057697			hypothetical protein LOC51313 isoform 2							Golgi membrane|integral to membrane					0																		---	---	---	---
RXFP1	59350	broad.mit.edu	37	4	159458127	159458127	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:159458127delA	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)														---	---	---	---
C4orf45	152940	broad.mit.edu	37	4	159925158	159925158	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:159925158delT	uc003iqf.1	-						C4orf45_uc010iqt.1_Intron	NM_152543	NP_689756			hypothetical protein LOC152940												0																		---	---	---	---
C4orf45	152940	broad.mit.edu	37	4	159973168	159973168	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:159973168delA	uc010iqt.1	-											Homo sapiens cDNA FLJ25371 fis, clone TST01885.												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	4	160139909	160139909	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:160139909delA								C4orf45 (115804 upstream) : RAPGEF2 (49089 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	160157004	160157004	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:160157004delT								C4orf45 (132899 upstream) : RAPGEF2 (31994 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	160803590	160803591	+	IGR	INS	-	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:160803590_160803591insT								RAPGEF2 (522291 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	161353110	161353110	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:161353110delT								None (None upstream) : FSTL5 (951941 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	161802868	161802868	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:161802868delT								None (None upstream) : FSTL5 (502183 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	161994531	161994531	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:161994531delA								None (None upstream) : FSTL5 (310520 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	162169775	162169775	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:162169775delA								None (None upstream) : FSTL5 (135276 downstream)																																			---	---	---	---
FSTL5	56884	broad.mit.edu	37	4	162764557	162764558	+	Intron	INS	-	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:162764557_162764558insT	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)														---	---	---	---
Unknown	0	broad.mit.edu	37	4	163124281	163124282	+	IGR	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:163124281_163124282delTT								FSTL5 (39095 upstream) : NAF1 (923578 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	163206502	163206503	+	IGR	DEL	TG	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:163206502_163206503delTG								FSTL5 (121316 upstream) : NAF1 (841357 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	163671606	163671606	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:163671606delT								FSTL5 (586420 upstream) : NAF1 (376254 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	163757774	163757774	+	IGR	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:163757774delC								FSTL5 (672588 upstream) : NAF1 (290086 downstream)																																			---	---	---	---
C4orf43	55319	broad.mit.edu	37	4	164436769	164436769	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:164436769delT	uc003iqq.3	+							NM_018352	NP_060822			hypothetical protein LOC55319												0																		---	---	---	---
MARCH1	55016	broad.mit.edu	37	4	164764939	164764940	+	Intron	INS	-	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:164764939_164764940insT	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	164794218	164794219	+	Intron	INS	-	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:164794218_164794219insA	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	164925855	164925855	+	Intron	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:164925855delC	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	165334357	165334358	+	IGR	DEL	AG	-	-	rs76323656		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:165334357_165334358delAG								MARCH1 (29155 upstream) : TRIM61 (541242 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	165865192	165865192	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:165865192delA								MARCH1 (559990 upstream) : TRIM61 (10408 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	165869423	165869424	+	IGR	INS	-	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:165869423_165869424insA								MARCH1 (564221 upstream) : TRIM61 (6176 downstream)																																			---	---	---	---
CPE	1363	broad.mit.edu	37	4	166418824	166418824	+	3'UTR	DEL	T	-	-	rs71754350		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:166418824delT	uc003irg.3	+	9						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	166498306	166498307	+	IGR	DEL	GA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:166498306_166498307delGA								CPE (78825 upstream) : TLL1 (296103 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	166768378	166768378	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:166768378delA								CPE (348897 upstream) : TLL1 (26032 downstream)																																			---	---	---	---
TLL1	7092	broad.mit.edu	37	4	166929955	166929957	+	Intron	DEL	TTT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:166929955_166929957delTTT	uc003irh.1	+						TLL1_uc011cjn.1_Intron|TLL1_uc011cjo.1_Intron	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)														---	---	---	---
TLL1	7092	broad.mit.edu	37	4	166964732	166964732	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:166964732delT	uc003irh.1	+						TLL1_uc011cjn.1_Intron|TLL1_uc011cjo.1_Intron	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	167119439	167119439	+	IGR	DEL	C	-	-	rs74659556		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:167119439delC								TLL1 (94446 upstream) : SPOCK3 (535097 downstream)																																			---	---	---	---
SPOCK3	50859	broad.mit.edu	37	4	168023156	168023156	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:168023156delT	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|SPOCK3_uc011cjw.1_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	168741254	168741255	+	IGR	INS	-	TG	TG	rs147143552	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:168741254_168741255insTG								SPOCK3 (585513 upstream) : ANXA10 (272452 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	168864771	168864771	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:168864771delA								SPOCK3 (709030 upstream) : ANXA10 (148936 downstream)																																			---	---	---	---
ANXA10	11199	broad.mit.edu	37	4	169105961	169105961	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:169105961delT	uc003irm.2	+						ANXA10_uc003irn.2_Intron	NM_007193	NP_009124			annexin A10								calcium ion binding|calcium-dependent phospholipid binding				0		Prostate(90;0.00876)|Renal(120;0.0183)|all_neural(102;0.0837)|Melanoma(52;0.132)		GBM - Glioblastoma multiforme(119;0.0325)														---	---	---	---
DDX60	55601	broad.mit.edu	37	4	169232271	169232271	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:169232271delT	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)														---	---	---	---
PALLD	23022	broad.mit.edu	37	4	169502155	169502156	+	Intron	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:169502155_169502156delAA	uc011cjx.1	+						PALLD_uc003iru.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	170000118	170000120	+	IGR	DEL	TTT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:170000118_170000120delTTT								CBR4 (68696 upstream) : SH3RF1 (15287 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	170008380	170008380	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:170008380delA								CBR4 (76958 upstream) : SH3RF1 (7027 downstream)																																			---	---	---	---
SH3RF1	57630	broad.mit.edu	37	4	170043448	170043448	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:170043448delA	uc003isa.1	-						SH3RF1_uc010irc.1_Intron	NM_020870	NP_065921			SH3 domain containing ring finger 1							Golgi apparatus|lamellipodium|perinuclear region of cytoplasm	ligase activity|zinc ion binding			breast(2)|lung(1)	3		Prostate(90;0.00267)|Renal(120;0.0183)		GBM - Glioblastoma multiforme(119;0.0287)														---	---	---	---
SH3RF1	57630	broad.mit.edu	37	4	170176919	170176919	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:170176919delT	uc003isa.1	-							NM_020870	NP_065921			SH3 domain containing ring finger 1							Golgi apparatus|lamellipodium|perinuclear region of cytoplasm	ligase activity|zinc ion binding			breast(2)|lung(1)	3		Prostate(90;0.00267)|Renal(120;0.0183)		GBM - Glioblastoma multiforme(119;0.0287)														---	---	---	---
Unknown	0	broad.mit.edu	37	4	170897943	170897945	+	5'Flank	DEL	AAG	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:170897943_170897945delAAG	uc003ism.1	-											Homo sapiens cDNA FLJ43052 fis, clone BRTHA3006318.																														---	---	---	---
Unknown	0	broad.mit.edu	37	4	170970688	170970688	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:170970688delA								MFAP3L (23259 upstream) : AADAT (10686 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	171101432	171101433	+	IGR	DEL	AC	-	-	rs35518549	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:171101432_171101433delAC								AADAT (90060 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	171562611	171562611	+	IGR	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:171562611delG								AADAT (551239 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	171668546	171668547	+	IGR	INS	-	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:171668546_171668547insA								AADAT (657174 upstream) : None (None downstream)																																			---	---	---	---
GALNTL6	442117	broad.mit.edu	37	4	172770077	172770077	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:172770077delT	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	173376041	173376041	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:173376041delT	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	173599181	173599182	+	Intron	DEL	TA	-	-	rs151155982		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:173599181_173599182delTA	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	173961139	173961141	+	In_Frame_Del	DEL	AGA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:173961139_173961141delAGA	uc003isv.2	+	13	2430_2432	c.1694_1696delAGA	c.(1693-1698)GAGAAG>GAG	p.K567del		NM_001034845	NP_001030017	Q49A17	GLTL6_HUMAN	N-acetylgalactosaminyltransferase-like 6	567	Ricin B-type lectin.|Lumenal (Potential).					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	174070716	174070716	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:174070716delT	uc003isy.1	-											Homo sapiens cDNA clone IMAGE:5267797.																														---	---	---	---
Unknown	0	broad.mit.edu	37	4	174267291	174267291	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:174267291delT								HMGB2 (11696 upstream) : SAP30 (24802 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	174679875	174679875	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:174679875delA								MORF4 (142081 upstream) : FBXO8 (477937 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	174778829	174778829	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:174778829delA								MORF4 (241035 upstream) : FBXO8 (378983 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	175052709	175052709	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:175052709delA	uc003ito.1	-											Homo sapiens cDNA FLJ43267 fis, clone IMR322007704.																														---	---	---	---
KIAA1712	80817	broad.mit.edu	37	4	175222102	175222102	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:175222102delT	uc003itr.2	+						KIAA1712_uc010iro.2_Intron|KIAA1712_uc003its.2_Intron	NM_001040157	NP_001035247			HBV PreS1-transactivated protein 3 isoform a							centrosome|midbody|spindle pole					0		Prostate(90;0.00276)|Melanoma(52;0.0179)|Renal(120;0.0376)|Breast(14;0.0991)|all_hematologic(60;0.124)|all_neural(102;0.196)		all cancers(43;4.06e-18)|Epithelial(43;1.18e-15)|OV - Ovarian serous cystadenocarcinoma(60;4.65e-09)|GBM - Glioblastoma multiforme(59;0.00098)|STAD - Stomach adenocarcinoma(60;0.0029)|LUSC - Lung squamous cell carcinoma(193;0.0949)														---	---	---	---
HPGD	3248	broad.mit.edu	37	4	175416588	175416588	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:175416588delT	uc003itu.2	-						HPGD_uc003itt.2_Intron|HPGD_uc003itv.2_Intron|HPGD_uc011ckf.1_Intron|HPGD_uc010irp.2_Intron|HPGD_uc010irq.2_Intron|HPGD_uc011ckg.1_Intron|HPGD_uc011ckh.1_Intron|HPGD_uc003itw.2_3'UTR	NM_000860	NP_000851			hydroxyprostaglandin dehydrogenase 15-(NAD)						female pregnancy|lipoxygenase pathway|negative regulation of cell cycle|parturition|prostaglandin metabolic process|transforming growth factor beta receptor signaling pathway	cytosol|nucleus	15-hydroxyprostaglandin dehydrogenase (NAD+) activity|NAD+ binding|prostaglandin E receptor activity|protein homodimerization activity				0		Prostate(90;0.00763)|Melanoma(52;0.0179)|Renal(120;0.0376)|Breast(14;0.0991)|all_hematologic(60;0.124)|all_neural(102;0.196)		all cancers(43;2.6e-18)|Epithelial(43;4.19e-16)|OV - Ovarian serous cystadenocarcinoma(60;5.23e-09)|GBM - Glioblastoma multiforme(59;0.00176)|STAD - Stomach adenocarcinoma(60;0.00299)|LUSC - Lung squamous cell carcinoma(193;0.0253)	NADH(DB00157)													---	---	---	---
Unknown	0	broad.mit.edu	37	4	176479835	176479835	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:176479835delA								ADAM29 (580505 upstream) : GPM6A (74254 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	176546311	176546311	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:176546311delT								ADAM29 (646981 upstream) : GPM6A (7778 downstream)																																			---	---	---	---
SPATA4	132851	broad.mit.edu	37	4	177116464	177116465	+	Intron	INS	-	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:177116464_177116465insG	uc003iuo.1	-							NM_144644	NP_653245			spermatogenesis associated 4						apoptosis|spermatogenesis						0		Breast(14;0.0011)|Prostate(90;0.0129)|Melanoma(52;0.0133)|Renal(120;0.0376)|all_hematologic(60;0.124)		all cancers(43;2.9e-20)|Epithelial(43;1.99e-17)|OV - Ovarian serous cystadenocarcinoma(60;2.58e-09)|GBM - Glioblastoma multiforme(59;0.000162)|STAD - Stomach adenocarcinoma(60;0.000543)|LUSC - Lung squamous cell carcinoma(193;0.096)														---	---	---	---
Unknown	0	broad.mit.edu	37	4	177414392	177414392	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:177414392delT								SPCS3 (160998 upstream) : VEGFC (190299 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	177463004	177463004	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:177463004delA								SPCS3 (209610 upstream) : VEGFC (141687 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	177554802	177554803	+	IGR	DEL	AA	-	-	rs76923022		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:177554802_177554803delAA								SPCS3 (301408 upstream) : VEGFC (49888 downstream)																																			---	---	---	---
VEGFC	7424	broad.mit.edu	37	4	177642583	177642583	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:177642583delA	uc003ius.1	-							NM_005429	NP_005420			vascular endothelial growth factor C						angiogenesis|induction of positive chemotaxis|platelet activation|platelet degranulation|positive regulation of cell division|positive regulation of mast cell chemotaxis|substrate-dependent cell migration|vascular endothelial growth factor receptor signaling pathway	membrane|platelet alpha granule lumen	chemoattractant activity|growth factor activity			lung(5)	5		Breast(14;0.000223)|Renal(120;0.00988)|Prostate(90;0.00996)|Melanoma(52;0.0101)|all_hematologic(60;0.107)|all_neural(102;0.164)		all cancers(43;1.59e-18)|Epithelial(43;3.68e-16)|OV - Ovarian serous cystadenocarcinoma(60;8.52e-09)|GBM - Glioblastoma multiforme(59;0.000546)|STAD - Stomach adenocarcinoma(60;0.00308)|Colorectal(24;0.025)|COAD - Colon adenocarcinoma(29;0.0359)|LUSC - Lung squamous cell carcinoma(193;0.0397)														---	---	---	---
Unknown	0	broad.mit.edu	37	4	177907134	177907134	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:177907134delA								VEGFC (193239 upstream) : NEIL3 (323857 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	178192765	178192765	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:178192765delA								VEGFC (478870 upstream) : NEIL3 (38226 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	178332495	178332495	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:178332495delT								NEIL3 (48403 upstream) : AGA (19429 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	178495211	178495211	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:178495211delT	uc003iux.1	+											Homo sapiens cDNA FLJ37626 fis, clone BRCOC2014748.																														---	---	---	---
Unknown	0	broad.mit.edu	37	4	178645753	178645753	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:178645753delT								AGA (282162 upstream) : LOC285501 (4154 downstream)																																			---	---	---	---
LOC285501	285501	broad.mit.edu	37	4	178827451	178827452	+	Intron	DEL	TG	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:178827451_178827452delTG	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	179192930	179192930	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:179192930delT								LOC285501 (281027 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	180071174	180071175	+	IGR	DEL	TG	-	-	rs72046640		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:180071174_180071175delTG								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	180081281	180081282	+	IGR	INS	-	AC	AC	rs138302185	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:180081281_180081282insAC								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	180109574	180109574	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:180109574delA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	180246995	180246996	+	IGR	DEL	AG	-	-	rs138139634		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:180246995_180246996delAG								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	180359696	180359696	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:180359696delA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	180831249	180831251	+	IGR	DEL	AAA	-	-	rs11300229		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:180831249_180831251delAAA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	180835137	180835138	+	IGR	DEL	TC	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:180835137_180835138delTC								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	181487086	181487101	+	IGR	DEL	GGGTGAATGCAGGTGA	-	-	rs76818314		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:181487086_181487101delGGGTGAATGCAGGTGA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	181695302	181695302	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:181695302delA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	181723798	181723799	+	IGR	DEL	TT	-	-	rs138679570		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:181723798_181723799delTT								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	181821411	181821412	+	IGR	DEL	TA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:181821411_181821412delTA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	181938828	181938830	+	IGR	DEL	AGA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:181938828_181938830delAGA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	182026439	182026439	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:182026439delA	uc003iuz.2	-											Homo sapiens full length insert cDNA clone YY72H05.																														---	---	---	---
Unknown	0	broad.mit.edu	37	4	182088727	182088727	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:182088727delT								None (None upstream) : MGC45800 (971432 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	182338196	182338196	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:182338196delT								None (None upstream) : MGC45800 (721963 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	182989039	182989039	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:182989039delT	uc003iva.1	-											Homo sapiens cDNA FLJ31634 fis, clone NT2RI2003419.																														---	---	---	---
WWC2	80014	broad.mit.edu	37	4	184207093	184207094	+	Intron	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:184207093_184207094delTT	uc010irx.2	+						WWC2_uc003ivk.3_Intron|WWC2_uc003ivl.3_Intron|WWC2_uc010iry.2_Intron|WWC2_uc003ivn.3_Intron|WWC2_uc010irz.2_Intron|WWC2_uc003ivo.3_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	184338384	184338384	+	IGR	DEL	T	-	-	rs5864830		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:184338384delT								WWC2 (96457 upstream) : CDKN2AIP (27405 downstream)																																			---	---	---	---
C4orf41	60684	broad.mit.edu	37	4	184614700	184614700	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:184614700delT	uc003ivx.2	+						C4orf41_uc003ivw.2_Intron|C4orf41_uc010isc.2_Intron|C4orf41_uc003ivy.2_Intron	NM_021942	NP_068761			hypothetical protein LOC60684 isoform a												0		all_lung(41;4.4e-14)|Lung NSC(41;1.03e-13)|Colorectal(36;0.00139)|all_hematologic(60;0.00756)|Hepatocellular(41;0.00826)|Renal(120;0.00988)|Prostate(90;0.0235)|all_neural(102;0.202)		all cancers(43;1.39e-26)|Epithelial(43;2.42e-22)|OV - Ovarian serous cystadenocarcinoma(60;6.85e-10)|GBM - Glioblastoma multiforme(59;6.71e-06)|Colorectal(24;9.67e-06)|STAD - Stomach adenocarcinoma(60;2.36e-05)|COAD - Colon adenocarcinoma(29;7.07e-05)|LUSC - Lung squamous cell carcinoma(40;0.00984)|READ - Rectum adenocarcinoma(43;0.171)														---	---	---	---
STOX2	56977	broad.mit.edu	37	4	184932899	184932899	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:184932899delT	uc003ivz.1	+						STOX2_uc003iwa.1_Intron	NM_020225	NP_064610			storkhead box 2						embryo development|maternal placenta development						0		all_lung(41;1.89e-12)|Lung NSC(41;3.48e-12)|Colorectal(36;0.00435)|Renal(120;0.0246)|Hepatocellular(41;0.0268)|all_hematologic(60;0.027)|Prostate(90;0.0283)		all cancers(43;2.85e-26)|Epithelial(43;2.27e-22)|OV - Ovarian serous cystadenocarcinoma(60;3.4e-10)|Colorectal(24;8.23e-06)|GBM - Glioblastoma multiforme(59;1.64e-05)|STAD - Stomach adenocarcinoma(60;3.6e-05)|COAD - Colon adenocarcinoma(29;4.37e-05)|LUSC - Lung squamous cell carcinoma(40;0.008)|READ - Rectum adenocarcinoma(43;0.227)														---	---	---	---
ENPP6	133121	broad.mit.edu	37	4	185140263	185140263	+	5'Flank	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:185140263delA	uc003iwc.2	-							NM_153343	NP_699174			ectonucleotide pyrophosphatase/phosphodiesterase						lipid catabolic process	extracellular region|integral to membrane|plasma membrane				central_nervous_system(1)	1		all_lung(41;7.99e-12)|Lung NSC(41;1.46e-11)|Colorectal(36;0.00435)|Renal(120;0.0246)|Hepatocellular(41;0.0268)|Prostate(90;0.0283)|all_hematologic(60;0.0749)		all cancers(43;4.98e-27)|Epithelial(43;3.15e-24)|OV - Ovarian serous cystadenocarcinoma(60;4.09e-12)|Colorectal(24;3.78e-05)|STAD - Stomach adenocarcinoma(60;4.5e-05)|COAD - Colon adenocarcinoma(29;0.000154)|GBM - Glioblastoma multiforme(59;0.000167)|BRCA - Breast invasive adenocarcinoma(30;0.000378)|LUSC - Lung squamous cell carcinoma(40;0.0151)														---	---	---	---
ACSL1	2180	broad.mit.edu	37	4	185683286	185683286	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:185683286delA	uc003iww.2	-						ACSL1_uc011ckm.1_Intron|ACSL1_uc003iwt.1_Intron|ACSL1_uc003iwu.1_Intron|ACSL1_uc011ckn.1_Intron|ACSL1_uc003iws.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)													---	---	---	---
Unknown	0	broad.mit.edu	37	4	185901002	185901005	+	IGR	DEL	AGAG	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:185901002_185901005delAGAG								ACSL1 (153787 upstream) : HELT (38990 downstream)																																			---	---	---	---
KIAA1430	57587	broad.mit.edu	37	4	186081250	186081250	+	3'UTR	DEL	A	-	-	rs59628395		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:186081250delA	uc003ixf.3	-	5						NM_020827	NP_065878			hypothetical protein LOC57587												0		all_lung(41;1.19e-13)|Lung NSC(41;3.16e-13)|Hepatocellular(41;0.00826)|Colorectal(36;0.00872)|Renal(120;0.00988)|Prostate(90;0.0235)|all_hematologic(60;0.0592)|all_neural(102;0.243)		all cancers(43;9.44e-26)|Epithelial(43;2.64e-23)|OV - Ovarian serous cystadenocarcinoma(60;1.66e-11)|Colorectal(24;6.03e-05)|BRCA - Breast invasive adenocarcinoma(30;8.01e-05)|GBM - Glioblastoma multiforme(59;0.000331)|COAD - Colon adenocarcinoma(29;0.000427)|STAD - Stomach adenocarcinoma(60;0.000777)|LUSC - Lung squamous cell carcinoma(40;0.00924)|READ - Rectum adenocarcinoma(43;0.165)														---	---	---	---
SNX25	83891	broad.mit.edu	37	4	186283364	186283364	+	Intron	DEL	A	-	-	rs78356496		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:186283364delA	uc003ixh.2	+						SNX25_uc010ish.2_Intron|SNX25_uc003ixi.2_Intron	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	186283992	186284000	+	Intron	DEL	TTTTTTTTT	-	-	rs67664115		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:186283992_186284000delTTTTTTTTT	uc003ixh.2	+						SNX25_uc010ish.2_Intron|SNX25_uc003ixi.2_Intron	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)														---	---	---	---
LRP2BP	55805	broad.mit.edu	37	4	186291741	186291741	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:186291741delA	uc003ixj.1	-						LRP2BP_uc003ixk.1_Intron|LRP2BP_uc011ckr.1_Intron	NM_018409	NP_060879			LRP2 binding protein							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)														---	---	---	---
CCDC110	256309	broad.mit.edu	37	4	186366423	186366423	+	3'UTR	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:186366423delC	uc003ixu.3	-	7					CCDC110_uc003ixv.3_3'UTR|C4orf47_uc003ixt.2_Intron|C4orf47_uc003ixs.2_Intron	NM_152775	NP_689988			coiled-coil domain containing 110 isoform a							nucleus				central_nervous_system(1)	1		all_lung(41;1.3e-11)|Lung NSC(41;2.25e-11)|Melanoma(20;7.86e-05)|Renal(120;0.0246)|Hepatocellular(41;0.0268)|Prostate(90;0.0283)|Colorectal(36;0.0381)|all_hematologic(60;0.0749)		OV - Ovarian serous cystadenocarcinoma(60;1.13e-10)|BRCA - Breast invasive adenocarcinoma(30;8.01e-05)|GBM - Glioblastoma multiforme(59;0.00014)|STAD - Stomach adenocarcinoma(60;0.000777)|LUSC - Lung squamous cell carcinoma(40;0.00921)|COAD - Colon adenocarcinoma(29;0.0105)|READ - Rectum adenocarcinoma(43;0.164)														---	---	---	---
Unknown	0	broad.mit.edu	37	4	187218905	187218905	+	Intron	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:187218905delC	uc003izb.1	-											Homo sapiens coagulation factor XI (plasma thromboplastin antecedent), mRNA (cDNA clone IMAGE:4831055).																														---	---	---	---
Unknown	0	broad.mit.edu	37	4	188064330	188064330	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:188064330delA								FAT1 (416480 upstream) : ZFP42 (852595 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	188492978	188492978	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:188492978delA								FAT1 (845128 upstream) : ZFP42 (423947 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	189045227	189045228	+	IGR	INS	-	T	T	rs150473973	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:189045227_189045228insT								TRIML2 (14805 upstream) : TRIML1 (15370 downstream)																																			---	---	---	---
TRIML1	339976	broad.mit.edu	37	4	189063815	189063815	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:189063815delA	uc003izm.1	+						TRIML1_uc003izn.1_5'Flank	NM_178556	NP_848651			tripartite motif family-like 1						multicellular organismal development		ligase activity|zinc ion binding			ovary(1)|pancreas(1)|breast(1)|skin(1)	4		all_cancers(14;1.33e-43)|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)|Hepatocellular(41;0.0218)|Renal(120;0.0376)|Prostate(90;0.0513)|all_hematologic(60;0.062)		OV - Ovarian serous cystadenocarcinoma(60;1.52e-11)|BRCA - Breast invasive adenocarcinoma(30;4.19e-06)|GBM - Glioblastoma multiforme(59;0.000232)|STAD - Stomach adenocarcinoma(60;0.000279)|LUSC - Lung squamous cell carcinoma(40;0.00902)|READ - Rectum adenocarcinoma(43;0.156)														---	---	---	---
Unknown	0	broad.mit.edu	37	4	189137576	189137579	+	IGR	DEL	TCCC	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:189137576_189137579delTCCC								TRIML1 (68927 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	189153730	189153731	+	IGR	INS	-	T	T	rs138041311	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:189153730_189153731insT								TRIML1 (85081 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	190201182	190201182	+	IGR	DEL	T	-	-	rs66862727		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:190201182delT								None (None upstream) : FRG1 (660792 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	190540544	190540544	+	IGR	DEL	A	-	-	rs68148160		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:190540544delA								None (None upstream) : FRG1 (321430 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	190551066	190551066	+	IGR	DEL	G	-	-	rs61341422	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:190551066delG								None (None upstream) : FRG1 (310908 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	190830807	190830807	+	Intron	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:190830807delC	uc003izq.2	-											Homo sapiens cDNA clone IMAGE:30384438.																														---	---	---	---
Unknown	0	broad.mit.edu	37	4	190853199	190853200	+	Intron	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:190853199_190853200delTT	uc003izq.2	-											Homo sapiens cDNA clone IMAGE:30384438.																														---	---	---	---
FRG1	2483	broad.mit.edu	37	4	190866602	190866603	+	Intron	INS	-	T	T	rs149585443	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:190866602_190866603insT	uc003izs.2	+							NM_004477	NP_004468			FSHD region gene 1						rRNA processing	Cajal body|catalytic step 2 spliceosome|nuclear speck|nucleolus					0		all_cancers(14;1.44e-58)|all_epithelial(14;6.32e-41)|all_lung(41;8.13e-17)|Lung NSC(41;2.13e-16)|Breast(6;2.54e-06)|Melanoma(20;0.000263)|Hepatocellular(41;0.00213)|Renal(120;0.0183)|all_hematologic(60;0.0358)|Prostate(90;0.0421)|all_neural(102;0.147)		all cancers(3;1.73e-30)|Epithelial(3;5.85e-30)|OV - Ovarian serous cystadenocarcinoma(60;5.56e-15)|BRCA - Breast invasive adenocarcinoma(30;9.14e-06)|Lung(3;3.54e-05)|STAD - Stomach adenocarcinoma(60;8.83e-05)|LUSC - Lung squamous cell carcinoma(40;0.000198)|GBM - Glioblastoma multiforme(59;0.00892)|READ - Rectum adenocarcinoma(43;0.161)														---	---	---	---
Unknown	0	broad.mit.edu	37	4	190963383	190963384	+	IGR	INS	-	A	A	rs77753899		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:190963383_190963384insA								TUBB4Q (57359 upstream) : LOC653545 (45182 downstream)																																			---	---	---	---
AHRR	57491	broad.mit.edu	37	5	326877	326877	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:326877delA	uc003jav.2	+						AHRR_uc003jaw.2_Intron|AHRR_uc010isy.2_Intron|AHRR_uc010isz.2_Intron	NM_020731	NP_065782			arylhydrocarbon receptor repressor						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)															---	---	---	---
AHRR	57491	broad.mit.edu	37	5	418773	418773	+	Intron	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:418773delC	uc003jav.2	+						AHRR_uc003jaw.2_Intron|AHRR_uc010isy.2_Intron|AHRR_uc010isz.2_Intron|AHRR_uc003jax.2_5'Flank|AHRR_uc003jay.2_5'Flank	NM_020731	NP_065782			arylhydrocarbon receptor repressor						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)															---	---	---	---
Unknown	0	broad.mit.edu	37	5	723043	723043	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:723043delA								TPPP (29533 upstream) : ZDHHC11 (72677 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	753932	753933	+	IGR	INS	-	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:753932_753933insC								TPPP (60422 upstream) : ZDHHC11 (41787 downstream)																																			---	---	---	---
ZDHHC11	79844	broad.mit.edu	37	5	822065	822065	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:822065delA	uc011cma.1	-						ZDHHC11_uc010itc.2_Intron|ZDHHC11_uc003jbj.2_Intron	NM_024786	NP_079062			zinc finger, DHHC-type containing 11							integral to membrane	acyltransferase activity|zinc ion binding			skin(1)|pancreas(1)	2			Epithelial(17;0.000445)|all cancers(22;0.00176)|OV - Ovarian serous cystadenocarcinoma(19;0.00227)|Lung(60;0.0863)															---	---	---	---
Unknown	0	broad.mit.edu	37	5	954158	954159	+	IGR	DEL	CA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:954158_954159delCA								TRIP13 (36000 upstream) : NKD2 (55009 downstream)																																			---	---	---	---
LPCAT1	79888	broad.mit.edu	37	5	1464801	1464802	+	Intron	DEL	AC	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:1464801_1464802delAC	uc003jcm.2	-						LPCAT1_uc003jcl.2_Intron	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)														---	---	---	---
Unknown	0	broad.mit.edu	37	5	2062516	2062516	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:2062516delT								IRX4 (179636 upstream) : IRX2 (683765 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	2145692	2145693	+	IGR	INS	-	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:2145692_2145693insC								IRX4 (262812 upstream) : IRX2 (600588 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	2535586	2535586	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:2535586delA								IRX4 (652706 upstream) : IRX2 (210695 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	2612775	2612776	+	IGR	DEL	AA	-	-	rs73735834	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-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	2799332	2799332	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:2799332delT								C5orf38 (43820 upstream) : IRX1 (796836 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	2819985	2819985	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:2819985delT								C5orf38 (64473 upstream) : IRX1 (776183 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	3184224	3184224	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:3184224delA								C5orf38 (428712 upstream) : IRX1 (411944 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	3187542	3187543	+	IGR	INS	-	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:3187542_3187543insT								C5orf38 (432030 upstream) : IRX1 (408625 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	3233251	3233251	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:3233251delA								C5orf38 (477739 upstream) : IRX1 (362917 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	3459970	3459971	+	Intron	DEL	AA	-	-	rs75518423		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:3459970_3459971delAA	uc003jdd.2	-											Homo sapiens cDNA clone IMAGE:4823480.																														---	---	---	---
Unknown	0	broad.mit.edu	37	5	3840402	3840403	+	IGR	INS	-	AA	AA	rs137970263	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:3840402_3840403insAA								IRX1 (238886 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	4409551	4409551	+	IGR	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:4409551delG								IRX1 (808035 upstream) : LOC340094 (624921 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	4439455	4439455	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:4439455delT								IRX1 (837939 upstream) : LOC340094 (595017 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	4657157	4657157	+	IGR	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:4657157delC								None (None upstream) : LOC340094 (377315 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	4675017	4675018	+	IGR	DEL	TT	-	-	rs71602173		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:4675017_4675018delTT								None (None upstream) : LOC340094 (359454 downstream)																																			---	---	---	---
LOC340094	340094	broad.mit.edu	37	5	5058117	5058117	+	Intron	DEL	A	-	-	rs71698222		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:5058117delA	uc003jdg.2	+						LOC340094_uc003jdh.2_Intron	NR_026994				Homo sapiens hypothetical protein LOC340094, mRNA (cDNA clone IMAGE:5295461).												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	5	5095065	5095066	+	IGR	INS	-	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:5095065_5095066insG								LOC340094 (24956 upstream) : ADAMTS16 (45377 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	5346143	5346145	+	IGR	DEL	AAA	-	-	rs74342465		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:5346143_5346145delAAA								ADAMTS16 (25732 upstream) : KIAA0947 (76662 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	5878145	5878145	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:5878145delA								KIAA0947 (387808 upstream) : FLJ33360 (432409 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	5891048	5891049	+	IGR	INS	-	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:5891048_5891049insT								KIAA0947 (400711 upstream) : FLJ33360 (419505 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	6031421	6031421	+	IGR	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:6031421delC								KIAA0947 (541084 upstream) : FLJ33360 (279133 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	6296394	6296394	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:6296394delA								KIAA0947 (806057 upstream) : FLJ33360 (14160 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	6361082	6361082	+	IGR	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:6361082delC								FLJ33360 (23677 upstream) : MED10 (10958 downstream)																																			---	---	---	---
PAPD7	11044	broad.mit.edu	37	5	6748371	6748372	+	Intron	INS	-	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:6748371_6748372insC	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																		---	---	---	---
Unknown	0	broad.mit.edu	37	5	7306657	7306657	+	RNA	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:7306657delT	uc003jdy.1	-	1		c.171delA								Homo sapiens cDNA FLJ42124 fis, clone TESTI2009477, weakly  similar to TRICHOHYALIN.																														---	---	---	---
ADCY2	108	broad.mit.edu	37	5	7701122	7701122	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:7701122delT	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																		---	---	---	---
Unknown	0	broad.mit.edu	37	5	8277192	8277192	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:8277192delA								MTRR (375959 upstream) : SEMA5A (757946 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	8512025	8512025	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:8512025delT								MTRR (610792 upstream) : SEMA5A (523113 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	8789845	8789846	+	IGR	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:8789845_8789846delAA								MTRR (888612 upstream) : SEMA5A (245292 downstream)																																			---	---	---	---
SEMA5A	9037	broad.mit.edu	37	5	9076459	9076459	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:9076459delA	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																		---	---	---	---
ROPN1L	83853	broad.mit.edu	37	5	10456613	10456613	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:10456613delA	uc003jex.3	+							NM_031916	NP_114122			ropporin 1-like						ciliary or flagellar motility|signal transduction	cytoplasm|motile cilium	cAMP-dependent protein kinase regulator activity|protein binding			ovary(1)	1																		---	---	---	---
DAP	1611	broad.mit.edu	37	5	10708498	10708499	+	Intron	DEL	AC	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:10708498_10708499delAC	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)																---	---	---	---
CTNND2	1501	broad.mit.edu	37	5	11225209	11225209	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:11225209delA	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	11886534	11886534	+	Intron	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:11886534delC	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	12044984	12044984	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:12044984delT								CTNND2 (140874 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	13283380	13283380	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:13283380delT								None (None upstream) : DNAH5 (407057 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	13456070	13456070	+	IGR	DEL	A	-	-	rs1529478	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:13456070delA								None (None upstream) : DNAH5 (234367 downstream)																																			---	---	---	---
DNAH5	1767	broad.mit.edu	37	5	13859314	13859315	+	Intron	INS	-	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:13859314_13859315insT	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	14123382	14123382	+	IGR	DEL	A	-	-	rs115220583	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-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	14622161	14622161	+	IGR	DEL	A	-	-	rs113417208		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:14622161delA								FAM105A (5876 upstream) : FAM105B (42622 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	14640377	14640378	+	IGR	INS	-	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:14640377_14640378insA								FAM105A (24092 upstream) : FAM105B (24405 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	14907567	14907568	+	IGR	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:14907567_14907568delAA								ANKH (35680 upstream) : FBXL7 (592737 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	14964407	14964408	+	IGR	DEL	TC	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:14964407_14964408delTC								ANKH (92520 upstream) : FBXL7 (535897 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	15029482	15029483	+	IGR	INS	-	TG	TG	rs138187214	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:15029482_15029483insTG								ANKH (157595 upstream) : FBXL7 (470822 downstream)																																			---	---	---	---
MARCH11	441061	broad.mit.edu	37	5	16101485	16101485	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:16101485delA	uc003jfo.2	-							NM_001102562	NP_001096032			membrane-associated ring finger (C3HC4) 11							cytoplasmic vesicle membrane|integral to membrane	ligase activity|zinc ion binding				0																		---	---	---	---
MYO10	4651	broad.mit.edu	37	5	16676266	16676266	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:16676266delA	uc003jft.3	-						MYO10_uc011cnb.1_Intron|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	16686649	16686650	+	Intron	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:16686649_16686650delTT	uc003jft.3	-						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	16766554	16766554	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:16766554delT	uc003jft.3	-						MYO10_uc010itx.2_5'Flank	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	16871717	16871717	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:16871717delA	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																		---	---	---	---
LOC285696	285696	broad.mit.edu	37	5	17158041	17158041	+	Intron	DEL	C	-	-	rs297182	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:17158041delC	uc003jfw.2	-							NR_027253				Homo sapiens cDNA FLJ34047 fis, clone FCBBF3000001.												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	5	17333068	17333068	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:17333068delT								BASP1 (56133 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	17498919	17498919	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:17498919delA								BASP1 (221984 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	17806879	17806880	+	IGR	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:17806879_17806880delTT								BASP1 (529944 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	17871649	17871649	+	Intron	DEL	G	-	-	rs70947637		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:17871649delG	uc003jgb.2	+											Homo sapiens cDNA clone IMAGE:5201079.																														---	---	---	---
Unknown	0	broad.mit.edu	37	5	17965184	17965184	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:17965184delT								BASP1 (688249 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	18010952	18010952	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:18010952delA								BASP1 (734017 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	18118598	18118599	+	IGR	DEL	TG	-	-	rs66993120	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:18118598_18118599delTG								BASP1 (841663 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	18632823	18632823	+	IGR	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:18632823delC								None (None upstream) : CDH18 (840334 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	18911494	18911494	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:18911494delT								None (None upstream) : CDH18 (561663 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	19391616	19391616	+	IGR	DEL	A	-	-	rs1398364	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:19391616delA								None (None upstream) : CDH18 (81541 downstream)																																			---	---	---	---
CDH18	1016	broad.mit.edu	37	5	19484608	19484608	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:19484608delA	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	19562464	19562464	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:19562464delT	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	21269852	21269853	+	IGR	DEL	TT	-	-	rs11355841		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:21269852_21269853delTT								None (None upstream) : GUSBP1 (72089 downstream)																																			---	---	---	---
GUSBP1	728411	broad.mit.edu	37	5	21480109	21480109	+	Intron	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:21480109delG	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	21489511	21489511	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:21489511delT	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	21491964	21491964	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:21491964delT	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	21534245	21534246	+	Intron	INS	-	TG	TG	rs143137704		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:21534245_21534246insTG	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																		---	---	---	---
GUSBP1	728411	broad.mit.edu	37	5	21543501	21543501	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:21543501delT	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	21609987	21609987	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:21609987delA								GUSBP1 (20508 upstream) : CDH12 (140986 downstream)																																			---	---	---	---
CDH12	1010	broad.mit.edu	37	5	21765315	21765315	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:21765315delA	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	22004157	22004157	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:22004157delA	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	22146151	22146151	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:22146151delA	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_Intron|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	22181375	22181375	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:22181375delT	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	22751027	22751028	+	Intron	DEL	AA	-	-	rs74533653		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:22751027_22751028delAA	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	23160349	23160350	+	IGR	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-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	23416754	23416755	+	IGR	INS	-	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:23416754_23416755insC								CDH12 (563023 upstream) : PRDM9 (90969 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	23428358	23428358	+	IGR	DEL	T	-	-	rs67390303		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:23428358delT								CDH12 (574627 upstream) : PRDM9 (79366 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	24321857	24321857	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:24321857delT								PRDM9 (793153 upstream) : CDH10 (165353 downstream)																																			---	---	---	---
CDH10	1008	broad.mit.edu	37	5	24584957	24584958	+	Intron	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:24584957_24584958delTT	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	24596480	24596481	+	Intron	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:24596480_24596481delTT	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	25029469	25029469	+	IGR	DEL	A	-	-	rs78457677	byFrequency;by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:25029469delA								CDH10 (384558 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	25032143	25032144	+	IGR	INS	-	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:25032143_25032144insT								CDH10 (387232 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	25267538	25267538	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:25267538delT								CDH10 (622627 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	25778186	25778186	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:25778186delA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	25804574	25804575	+	IGR	DEL	TG	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:25804574_25804575delTG								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	26701540	26701540	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:26701540delT								None (None upstream) : CDH9 (179169 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	27368038	27368038	+	IGR	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:27368038delG								CDH9 (329349 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	29171960	29171960	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:29171960delA	uc003jhb.1	+											Homo sapiens cDNA FLJ25704 fis, clone TST04756.																														---	---	---	---
Unknown	0	broad.mit.edu	37	5	29314900	29314900	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:29314900delT								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	29910305	29910306	+	IGR	INS	-	T	T	rs115035171	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:29910305_29910306insT								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	29996492	29996492	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:29996492delA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	30141806	30141806	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:30141806delT								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	31079594	31079594	+	IGR	DEL	T	-	-	rs11367264		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:31079594delT								None (None upstream) : CDH6 (114202 downstream)																																			---	---	---	---
CDH6	1004	broad.mit.edu	37	5	31293938	31293939	+	Intron	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:31293938_31293939delAA	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	31572742	31572744	+	IGR	DEL	AAA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:31572742_31572744delAAA								C5orf22 (17578 upstream) : PDZD2 (66773 downstream)																																			---	---	---	---
PDZD2	23037	broad.mit.edu	37	5	31643935	31643935	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:31643935delT	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	31723451	31723452	+	Intron	INS	-	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:31723451_31723452insT	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	31840576	31840576	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:31840576delT	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	31869675	31869675	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:31869675delA	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																		---	---	---	---
Unknown	0	broad.mit.edu	37	5	32119975	32119975	+	IGR	DEL	A	-	-	rs75826594		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:32119975delA								PDZD2 (8938 upstream) : GOLPH3 (4849 downstream)																																			---	---	---	---
MTMR12	54545	broad.mit.edu	37	5	32242341	32242342	+	Intron	DEL	TT	-	-	rs79086969	byFrequency;by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:32242341_32242342delTT	uc003jhq.2	-						MTMR12_uc010iuk.2_Intron|MTMR12_uc010iul.2_Intron	NM_001040446	NP_001035536			myotubularin related protein 12							cytoplasm	phosphatase activity			ovary(1)	1																		---	---	---	---
MTMR12	54545	broad.mit.edu	37	5	32296265	32296265	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:32296265delA	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	32353628	32353628	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:32353628delT								MTMR12 (40514 upstream) : ZFR (828 downstream)																																			---	---	---	---
ZFR	51663	broad.mit.edu	37	5	32397564	32397564	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:32397564delT	uc003jhr.1	-						MIR579_hsa-mir-579|MI0003586_5'Flank	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)														---	---	---	---
NPR3	4883	broad.mit.edu	37	5	32771157	32771158	+	Intron	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:32771157_32771158delTT	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	32917913	32917913	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:32917913delT								C5orf23 (126094 upstream) : TARS (522889 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	33372448	33372448	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:33372448delT								C5orf23 (580629 upstream) : TARS (68354 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	33381948	33381949	+	IGR	INS	-	TCTT	TCTT	rs139952588	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:33381948_33381949insTCTT								C5orf23 (590129 upstream) : TARS (58853 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	33405348	33405348	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:33405348delT								C5orf23 (613529 upstream) : TARS (35454 downstream)																																			---	---	---	---
ADAMTS12	81792	broad.mit.edu	37	5	33627479	33627481	+	Intron	DEL	TGG	-	-	rs149668162		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:33627479_33627481delTGG	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	33871692	33871692	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:33871692delA	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	33909762	33909765	+	IGR	DEL	TTAG	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:33909762_33909765delTTAG								ADAMTS12 (17638 upstream) : RXFP3 (26726 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	34177068	34177068	+	IGR	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:34177068delC								C1QTNF3 (133751 upstream) : RAI14 (479365 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	34468628	34468628	+	IGR	DEL	G	-	-	rs113231538		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:34468628delG								C1QTNF3 (425311 upstream) : RAI14 (187805 downstream)																																			---	---	---	---
DNAJC21	134218	broad.mit.edu	37	5	34941093	34941093	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:34941093delT	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)															---	---	---	---
DNAJC21	134218	broad.mit.edu	37	5	34944824	34944824	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:34944824delA	uc003jjc.2	+						DNAJC21_uc003jjb.2_Intron|DNAJC21_uc010iuu.1_Intron|DNAJC21_uc003jjd.2_5'Flank	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)															---	---	---	---
AGXT2	64902	broad.mit.edu	37	5	35013888	35013894	+	Intron	DEL	AAAAAAA	-	-	rs11301148		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:35013888_35013894delAAAAAAA	uc003jjf.2	-						AGXT2_uc003jje.1_Intron|AGXT2_uc011com.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	35066375	35066375	+	Intron	DEL	T	-	-	rs77557478		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:35066375delT	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	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	35068741	35068741	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:35068741delT	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)													---	---	---	---
Unknown	0	broad.mit.edu	37	5	35575091	35575091	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:35575091delT								PRLR (344297 upstream) : SPEF2 (42898 downstream)																																			---	---	---	---
SPEF2	79925	broad.mit.edu	37	5	35705894	35705894	+	Frame_Shift_Del	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:35705894delA	uc003jjo.2	+	18	2760	c.2649delA	c.(2647-2649)GCAfs	p.A883fs	SPEF2_uc003jjq.3_Frame_Shift_Del_p.A878fs|SPEF2_uc003jjp.1_Frame_Shift_Del_p.A369fs	NM_024867	NP_079143	Q9C093	SPEF2_HUMAN	KPL2 protein isoform 1	883	Potential.				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)															---	---	---	---
SPEF2	79925	broad.mit.edu	37	5	35719731	35719731	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:35719731delT	uc003jjo.2	+						SPEF2_uc003jjp.1_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)															---	---	---	---
SLC1A3	6507	broad.mit.edu	37	5	36637977	36637977	+	Intron	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:36637977delC	uc003jkj.3	+						SLC1A3_uc011cox.1_Intron|SLC1A3_uc010iuy.2_Intron	NM_004172	NP_004163			solute carrier family 1 (glial high affinity						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)													---	---	---	---
C5orf42	65250	broad.mit.edu	37	5	37169770	37169771	+	Intron	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:37169770_37169771delAA	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)															---	---	---	---
Unknown	0	broad.mit.edu	37	5	38233570	38233570	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:38233570delT								GDNF (393788 upstream) : EGFLAM (24963 downstream)																																			---	---	---	---
EGFLAM	133584	broad.mit.edu	37	5	38399029	38399029	+	Intron	DEL	G	-	-	rs113642316		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:38399029delG	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)																	---	---	---	---
EGFLAM	133584	broad.mit.edu	37	5	38402897	38402897	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:38402897delA	uc003jlc.1	+						EGFLAM_uc003jlb.1_Intron|EGFLAM_uc003jle.1_5'Flank|EGFLAM_uc003jlf.1_5'Flank|uc003jld.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)																	---	---	---	---
Unknown	0	broad.mit.edu	37	5	38661805	38661809	+	Intron	DEL	AAAAA	-	-	rs77509272		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:38661805_38661809delAAAAA	uc003jlj.2	+											Homo sapiens cDNA clone IMAGE:4829282.																														---	---	---	---
RICTOR	253260	broad.mit.edu	37	5	38978759	38978759	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:38978759delA	uc003jlp.2	-						RICTOR_uc003jlo.2_Intron|RICTOR_uc010ivf.2_Intron|RICTOR_uc003jlq.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	39047353	39047353	+	Intron	DEL	G	-	-	rs146119251	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:39047353delG	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	39077282	39077282	+	5'Flank	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:39077282delT	uc003jlp.2	-						RICTOR_uc003jlo.2_5'Flank|RICTOR_uc010ivf.2_5'Flank|RICTOR_uc003jlq.1_5'Flank|RICTOR_uc011cpk.1_5'Flank	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)																	---	---	---	---
DAB2	1601	broad.mit.edu	37	5	39404689	39404690	+	Intron	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:39404689_39404690delTT	uc003jlx.2	-							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	40487192	40487192	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:40487192delT								None (None upstream) : PTGER4 (192840 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	40595461	40595462	+	IGR	DEL	TT	-	-	rs66569864		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:40595461_40595462delTT								None (None upstream) : PTGER4 (84570 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	41110492	41110492	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:41110492delT								HEATR7B2 (39048 upstream) : C6 (31844 downstream)																																			---	---	---	---
PLCXD3	345557	broad.mit.edu	37	5	41458082	41458083	+	Intron	INS	-	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:41458082_41458083insA	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																		---	---	---	---
OXCT1	5019	broad.mit.edu	37	5	41810188	41810189	+	Intron	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:41810188_41810189delAA	uc003jmn.2	-							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)													---	---	---	---
OXCT1	5019	broad.mit.edu	37	5	41822920	41822921	+	Intron	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:41822920_41822921delTT	uc003jmn.2	-							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)													---	---	---	---
C5orf51	285636	broad.mit.edu	37	5	41909794	41909794	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:41909794delT	uc003jmo.2	+							NM_175921	NP_787117			hypothetical protein LOC285636												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	5	42183267	42183267	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:42183267delT								FBXO4 (241604 upstream) : GHR (240759 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	42326767	42326767	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:42326767delT								FBXO4 (385104 upstream) : GHR (97259 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	42734226	42734227	+	IGR	DEL	TC	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:42734226_42734227delTC								GHR (12301 upstream) : CCDC152 (22693 downstream)																																			---	---	---	---
ZNF131	7690	broad.mit.edu	37	5	43145764	43145764	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:43145764delA	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																		---	---	---	---
PAIP1	10605	broad.mit.edu	37	5	43535227	43535227	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-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)																	---	---	---	---
Unknown	0	broad.mit.edu	37	5	44070033	44070033	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:44070033delA								NNT (364366 upstream) : FGF10 (235064 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	45912701	45912701	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:45912701delT								HCN1 (216481 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	46347213	46347214	+	IGR	INS	-	CAT	CAT	rs138992399	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:46347213_46347214insCAT								HCN1 (650993 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	46364368	46364368	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:46364368delA								HCN1 (668148 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	49929660	49929660	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:49929660delA								EMB (192426 upstream) : PARP8 (32073 downstream)																																			---	---	---	---
PARP8	79668	broad.mit.edu	37	5	49978399	49978399	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:49978399delA	uc003jon.3	+						PARP8_uc011cpz.1_Intron|PARP8_uc003joo.2_Intron|PARP8_uc003jop.2_Intron	NM_024615	NP_078891			poly (ADP-ribose) polymerase family, member 8							intracellular	NAD+ ADP-ribosyltransferase activity			lung(3)|large_intestine(1)|ovary(1)	5		Lung NSC(810;0.0305)|Breast(144;0.222)																---	---	---	---
PARP8	79668	broad.mit.edu	37	5	50055619	50055619	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:50055619delT	uc003jon.3	+						PARP8_uc011cpz.1_Intron|PARP8_uc003joo.2_Intron|PARP8_uc003jop.2_Intron	NM_024615	NP_078891			poly (ADP-ribose) polymerase family, member 8							intracellular	NAD+ ADP-ribosyltransferase activity			lung(3)|large_intestine(1)|ovary(1)	5		Lung NSC(810;0.0305)|Breast(144;0.222)																---	---	---	---
PARP8	79668	broad.mit.edu	37	5	50092791	50092791	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:50092791delT	uc003jon.3	+						PARP8_uc011cpz.1_Intron|PARP8_uc003joo.2_Intron|PARP8_uc003jop.2_Intron	NM_024615	NP_078891			poly (ADP-ribose) polymerase family, member 8							intracellular	NAD+ ADP-ribosyltransferase activity			lung(3)|large_intestine(1)|ovary(1)	5		Lung NSC(810;0.0305)|Breast(144;0.222)																---	---	---	---
Unknown	0	broad.mit.edu	37	5	51273949	51273950	+	IGR	INS	-	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:51273949_51273950insA								ISL1 (583392 upstream) : ITGA1 (809824 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	51829804	51829804	+	IGR	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:51829804delC								None (None upstream) : ITGA1 (253970 downstream)																																			---	---	---	---
ITGA2	3673	broad.mit.edu	37	5	52370823	52370823	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:52370823delT	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)																---	---	---	---
ARL15	54622	broad.mit.edu	37	5	53496879	53496879	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:53496879delA	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	53654171	53654171	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:53654171delA								ARL15 (47768 upstream) : HSPB3 (97274 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	53774040	53774040	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:53774040delT								HSPB3 (21833 upstream) : SNX18 (39549 downstream)																																			---	---	---	---
GZMK	3003	broad.mit.edu	37	5	54324379	54324380	+	Intron	INS	-	T	T	rs72534330		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:54324379_54324380insT	uc003jpl.1	+							NM_002104	NP_002095			granzyme K precursor						proteolysis	extracellular region	serine-type endopeptidase activity				0		Lung NSC(810;4.08e-05)|Breast(144;0.0433)|Prostate(74;0.183)																---	---	---	---
GZMA	3001	broad.mit.edu	37	5	54398401	54398401	+	5'Flank	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:54398401delA	uc003jpm.2	+							NM_006144	NP_006135			granzyme A precursor						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	54558907	54558907	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:54558907delA	uc003jpx.2	-						DHX29_uc010ivw.2_Intron	NM_019030	NP_061903			DEAH (Asp-Glu-Ala-His) box polypeptide 29								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)																---	---	---	---
DHX29	54505	broad.mit.edu	37	5	54575567	54575567	+	Intron	DEL	T	-	-	rs5867979		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:54575567delT	uc003jpx.2	-						DHX29_uc010ivw.2_Intron	NM_019030	NP_061903			DEAH (Asp-Glu-Ala-His) box polypeptide 29								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)																---	---	---	---
DHX29	54505	broad.mit.edu	37	5	54594369	54594369	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:54594369delA	uc003jpx.2	-						DHX29_uc010ivw.2_Intron	NM_019030	NP_061903			DEAH (Asp-Glu-Ala-His) box polypeptide 29								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)																---	---	---	---
SKIV2L2	23517	broad.mit.edu	37	5	54641101	54641102	+	Intron	INS	-	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:54641101_54641102insT	uc003jpy.3	+						SKIV2L2_uc011cqi.1_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)																---	---	---	---
SKIV2L2	23517	broad.mit.edu	37	5	54642483	54642483	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:54642483delT	uc003jpy.3	+						SKIV2L2_uc011cqi.1_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)																---	---	---	---
IL31RA	133396	broad.mit.edu	37	5	55147283	55147283	+	5'Flank	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:55147283delA	uc003jql.2	+						IL31RA_uc003jqk.2_5'Flank|IL31RA_uc011cqj.1_5'Flank|IL31RA_uc003jqm.2_5'Flank|IL31RA_uc003jqn.2_5'Flank|IL31RA_uc010iwa.1_5'Flank|IL31RA_uc003jqo.2_5'Flank	NM_139017	NP_620586			gp130-like monocyte receptor						anti-apoptosis|defense response|homeostatic process|JAK-STAT cascade|macrophage differentiation|MAPKKK cascade|monocyte differentiation|negative regulation of macrophage activation|positive regulation of cell proliferation|positive regulation of transcription, DNA-dependent|positive regulation of tyrosine phosphorylation of Stat3 protein|positive regulation of tyrosine phosphorylation of Stat5 protein|transmembrane receptor protein tyrosine kinase signaling pathway	integral to membrane|plasma membrane	cytokine receptor activity|protein kinase binding|transcription coactivator activity			ovary(1)	1		Lung NSC(810;6.93e-05)|Prostate(74;0.00741)|Breast(144;0.0544)|Ovarian(174;0.223)																---	---	---	---
IL6ST	3572	broad.mit.edu	37	5	55240462	55240462	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:55240462delT	uc003jqq.2	-						IL6ST_uc010iwb.2_Intron|IL6ST_uc010iwc.2_Intron|IL6ST_uc010iwd.2_Intron|IL6ST_uc011cqk.1_Intron|IL6ST_uc003jqr.2_Intron	NM_002184	NP_002175			interleukin 6 signal transducer isoform 1						interleukin-6-mediated signaling pathway|leukemia inhibitory factor signaling pathway|negative regulation of interleukin-6-mediated signaling pathway|positive regulation of anti-apoptosis|positive regulation of cardiac muscle hypertrophy|positive regulation of osteoblast differentiation|positive regulation of T cell proliferation|positive regulation of tyrosine phosphorylation of Stat1 protein|positive regulation of tyrosine phosphorylation of Stat3 protein|positive regulation vascular endothelial growth factor production	ciliary neurotrophic factor receptor complex|extracellular region|extracellular space|interleukin-6 receptor complex|oncostatin-M receptor complex	ciliary neurotrophic factor receptor activity|ciliary neurotrophic factor receptor binding|growth factor binding|protein homodimerization activity			large_intestine(1)|ovary(1)	2		Lung NSC(810;8.69e-05)|Prostate(74;0.00308)|Breast(144;0.0544)|Ovarian(174;0.223)						O		hepatocellular ca								---	---	---	---
Unknown	0	broad.mit.edu	37	5	55342420	55342420	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:55342420delT								IL6ST (51657 upstream) : ANKRD55 (53088 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	55387847	55387847	+	IGR	DEL	A	-	-	rs67701385		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:55387847delA								IL6ST (97084 upstream) : ANKRD55 (7661 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	55578474	55578474	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:55578474delT								ANKRD55 (49288 upstream) : MAP3K1 (532426 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	55967752	55967753	+	IGR	INS	-	TG	TG	rs148889368	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:55967752_55967753insTG								ANKRD55 (438566 upstream) : MAP3K1 (143147 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	55976920	55976920	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:55976920delA								ANKRD55 (447734 upstream) : MAP3K1 (133980 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	56305968	56305968	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:56305968delA								MIER3 (38467 upstream) : GPBP1 (163807 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	56682852	56682852	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:56682852delA								GPBP1 (123442 upstream) : ACTBL2 (92992 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	56754020	56754020	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:56754020delA								GPBP1 (194610 upstream) : ACTBL2 (21824 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	56895090	56895090	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:56895090delT								ACTBL2 (116454 upstream) : PLK2 (854722 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	56940134	56940135	+	IGR	INS	-	TT	TT	rs146065299	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:56940134_56940135insTT								ACTBL2 (161498 upstream) : PLK2 (809677 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	57201721	57201721	+	IGR	DEL	A	-	-	rs35475958		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:57201721delA								ACTBL2 (423085 upstream) : PLK2 (548091 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	57365799	57365800	+	IGR	DEL	GT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:57365799_57365800delGT								ACTBL2 (587163 upstream) : PLK2 (384012 downstream)																																			---	---	---	---
PDE4D	5144	broad.mit.edu	37	5	59279867	59279867	+	Intron	DEL	C	-	-	rs76762048	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:59279867delC	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	59284181	59284182	+	3'UTR	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:59284181_59284182delTT	uc003jse.1	-	5					PDE4D_uc003jsb.2_Intron|PDE4D_uc010iwj.1_3'UTR					Homo sapiens cAMP-specific phosphodiesterase PDE4D7 (PDE4D) mRNA, complete cds; alternatively spliced.						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	59313457	59313457	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:59313457delT	uc003jsb.2	-						PDE4D_uc010iwj.1_Intron|PDE4D_uc003jse.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)													---	---	---	---
PDE4D	5144	broad.mit.edu	37	5	59742034	59742034	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:59742034delA	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)													---	---	---	---
ERCC8	1161	broad.mit.edu	37	5	60170513	60170514	+	Intron	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:60170513_60170514delAA	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					---	---	---	---
Unknown	0	broad.mit.edu	37	5	60913751	60913751	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:60913751delT								ZSWIM6 (71753 upstream) : FLJ37543 (19885 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	61441791	61441791	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:61441791delA								FLJ37543 (439429 upstream) : KIF2A (160198 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	61557189	61557191	+	IGR	DEL	AAA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:61557189_61557191delAAA								FLJ37543 (554827 upstream) : KIF2A (44798 downstream)																																			---	---	---	---
KIF2A	3796	broad.mit.edu	37	5	61648395	61648395	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:61648395delT	uc003jsy.3	+						KIF2A_uc003jsz.3_Intron|KIF2A_uc010iwp.2_Intron|KIF2A_uc003jsx.3_Intron|KIF2A_uc010iwq.2_Intron	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)														---	---	---	---
IPO11	51194	broad.mit.edu	37	5	61748470	61748470	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:61748470delT	uc003jtc.2	+						IPO11_uc011cqr.1_Intron|IPO11_uc003jtb.1_Intron	NM_016338	NP_057422			Ran binding protein 11 isoform 2							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	61802380	61802382	+	Intron	DEL	AAA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:61802380_61802382delAAA	uc003jtc.2	+						IPO11_uc011cqr.1_Intron|IPO11_uc003jtd.1_Intron	NM_016338	NP_057422			Ran binding protein 11 isoform 2							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	61849579	61849580	+	Intron	INS	-	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:61849579_61849580insT	uc003jtc.2	+						IPO11_uc011cqr.1_Intron|IPO11_uc003jtd.1_Intron|IPO11_uc010iwr.2_Intron	NM_016338	NP_057422			Ran binding protein 11 isoform 2							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)														---	---	---	---
Unknown	0	broad.mit.edu	37	5	62652895	62652895	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:62652895delT								ISCA1P1 (579725 upstream) : HTR1A (603384 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	64011625	64011626	+	IGR	INS	-	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:64011625_64011626insT								RGS7BP (103506 upstream) : SFRS12IP1 (2354 downstream)																																			---	---	---	---
SFRS12IP1	285672	broad.mit.edu	37	5	64037043	64037043	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:64037043delA	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)														---	---	---	---
CWC27	10283	broad.mit.edu	37	5	64240667	64240667	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:64240667delA	uc003jtn.1	+						CWC27_uc010iwt.1_Intron	NM_005869	NP_005860			serologically defined colon cancer antigen 10						protein folding	catalytic step 2 spliceosome	peptidyl-prolyl cis-trans isomerase activity				0																		---	---	---	---
CWC27	10283	broad.mit.edu	37	5	64294893	64294893	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:64294893delT	uc003jtn.1	+						CWC27_uc010iwt.1_Intron	NM_005869	NP_005860			serologically defined colon cancer antigen 10						protein folding	catalytic step 2 spliceosome	peptidyl-prolyl cis-trans isomerase activity				0																		---	---	---	---
ADAMTS6	11174	broad.mit.edu	37	5	64535091	64535093	+	Intron	DEL	AAA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:64535091_64535093delAAA	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)														---	---	---	---
ADAMTS6	11174	broad.mit.edu	37	5	64769520	64769520	+	5'UTR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:64769520delT	uc003jtp.2	-	2					ADAMTS6_uc003jto.2_RNA|ADAMTS6_uc003jtq.2_RNA|ADAMTS6_uc003jtr.1_5'UTR	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)														---	---	---	---
PPWD1	23398	broad.mit.edu	37	5	64863326	64863326	+	Intron	DEL	T	-	-	rs71674730		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:64863326delT	uc003jtv.3	+						PPWD1_uc011cqv.1_Intron|PPWD1_uc011cqw.1_Intron	NM_015342	NP_056157			peptidylprolyl isomerase domain and WD repeat						protein folding	catalytic step 2 spliceosome	peptidyl-prolyl cis-trans isomerase activity			ovary(1)	1		Lung NSC(167;7.21e-05)|Prostate(74;0.0174)|Ovarian(174;0.186)		Lung(70;0.00451)														---	---	---	---
SGTB	54557	broad.mit.edu	37	5	64972149	64972149	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:64972149delA	uc003jud.2	-							NM_019072	NP_061945			small glutamine-rich tetratricopeptide repeat								binding				0		Lung NSC(167;3.24e-06)|Prostate(74;0.0138)|Ovarian(174;0.0545)|Breast(144;0.174)|Colorectal(97;0.234)		UCEC - Uterine corpus endometrioid carcinoma (4;0.0657)|Lung(70;0.00487)														---	---	---	---
SGTB	54557	broad.mit.edu	37	5	64989226	64989229	+	Intron	DEL	GAAG	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:64989226_64989229delGAAG	uc003jud.2	-							NM_019072	NP_061945			small glutamine-rich tetratricopeptide repeat								binding				0		Lung NSC(167;3.24e-06)|Prostate(74;0.0138)|Ovarian(174;0.0545)|Breast(144;0.174)|Colorectal(97;0.234)		UCEC - Uterine corpus endometrioid carcinoma (4;0.0657)|Lung(70;0.00487)														---	---	---	---
Unknown	0	broad.mit.edu	37	5	65142557	65142557	+	IGR	DEL	G	-	-	rs11745984	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:65142557delG								NLN (23170 upstream) : ERBB2IP (79827 downstream)																																			---	---	---	---
ERBB2IP	55914	broad.mit.edu	37	5	65267960	65267960	+	Intron	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:65267960delG	uc003juk.1	+						ERBB2IP_uc003juh.1_Intron|ERBB2IP_uc003jui.1_Intron|ERBB2IP_uc003juj.1_Intron|ERBB2IP_uc011cqx.1_Intron|ERBB2IP_uc011cqy.1_Intron|ERBB2IP_uc011cqz.1_Intron	NM_018695	NP_061165			ERBB2 interacting protein isoform 2						basal protein localization|cell adhesion|cell cycle|cell growth|epidermal growth factor receptor signaling pathway|establishment or maintenance of epithelial cell apical/basal polarity|integrin-mediated signaling pathway|intermediate filament cytoskeleton organization	basement membrane|cytoplasm|hemidesmosome|nucleus	ErbB-2 class receptor binding|integrin binding|structural constituent of cytoskeleton			ovary(3)|lung(2)|central_nervous_system(2)	7		Lung NSC(167;9.45e-06)|Prostate(74;0.0139)|Ovarian(174;0.0547)|Breast(144;0.093)|Colorectal(97;0.234)		UCEC - Uterine corpus endometrioid carcinoma (4;0.0767)|Lung(70;0.00191)														---	---	---	---
Unknown	0	broad.mit.edu	37	5	65404088	65404088	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:65404088delA								ERBB2IP (27238 upstream) : SFRS12 (35997 downstream)																																			---	---	---	---
SFRS12	140890	broad.mit.edu	37	5	65458491	65458491	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:65458491delT	uc003juo.2	+						SFRS12_uc003jun.2_Intron|SFRS12_uc010iwy.2_Intron	NM_139168	NP_631907			splicing factor, arginine/serine-rich 12 isoform						mRNA processing|RNA splicing	spliceosomal complex	nucleic acid binding|nucleotide binding|protein binding				0		Lung NSC(167;9.34e-06)|Prostate(74;0.00187)|Ovarian(174;0.0545)|Breast(144;0.0928)|Colorectal(97;0.234)		Lung(70;0.00449)														---	---	---	---
MAST4	375449	broad.mit.edu	37	5	66300755	66300755	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:66300755delT	uc003jut.1	+						MAST4_uc003jus.2_Intron|MAST4_uc003juu.1_Intron|MAST4_uc011cra.1_Intron|MAST4_uc010ixa.2_RNA|MAST4_uc003juv.2_5'UTR|MAST4_uc003juw.2_5'Flank	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	66608376	66608379	+	IGR	DEL	AATG	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:66608376_66608379delAATG								CD180 (115759 upstream) : PIK3R1 (903225 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	66988647	66988647	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:66988647delT								CD180 (496030 upstream) : PIK3R1 (522957 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	67056885	67056885	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:67056885delA								CD180 (564268 upstream) : PIK3R1 (454719 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	67273922	67273922	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:67273922delT								CD180 (781305 upstream) : PIK3R1 (237682 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	67374116	67374116	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:67374116delT								CD180 (881499 upstream) : PIK3R1 (137488 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	67459834	67459834	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:67459834delT								CD180 (967217 upstream) : PIK3R1 (51770 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	67492157	67492162	+	IGR	DEL	TTTTTT	-	-	rs10534819		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:67492157_67492162delTTTTTT								CD180 (999540 upstream) : PIK3R1 (19442 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	67892400	67892400	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:67892400delA								PIK3R1 (294753 upstream) : SLC30A5 (497418 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	68284446	68284447	+	Intron	INS	-	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:68284446_68284447insA	uc003jvf.1	-											Homo sapiens cDNA FLJ46633 fis, clone TRACH2025705.																														---	---	---	---
CCNB1	891	broad.mit.edu	37	5	68470535	68470536	+	Intron	INS	-	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:68470535_68470536insA	uc003jvm.2	+						CCNB1_uc011crd.1_Intron|CCNB1_uc010ixb.2_Intron	NM_031966	NP_114172			cyclin B1						anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|cell division|G1/S transition of mitotic cell cycle|G2/M transition of mitotic cell cycle|mitotic cell cycle spindle checkpoint|mitotic metaphase plate congression|mitotic prometaphase|mitotic spindle stabilization|positive regulation of attachment of spindle microtubules to kinetochore|positive regulation of mitotic cell cycle|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|regulation of cyclin-dependent protein kinase activity	condensed nuclear chromosome outer kinetochore|cytosol|microtubule organizing center|nucleoplasm|spindle pole					0		Lung NSC(167;5.51e-05)|Prostate(74;0.00634)|Ovarian(174;0.0448)|Breast(144;0.198)		OV - Ovarian serous cystadenocarcinoma(47;1.24e-56)|Epithelial(20;1.12e-52)|all cancers(19;2.63e-48)|Lung(70;0.0177)														---	---	---	---
CDK7	1022	broad.mit.edu	37	5	68528188	68528188	+	5'Flank	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:68528188delT	uc003jvs.3	+						CDK7_uc010ixd.1_5'Flank|CDK7_uc003jvt.3_5'Flank|CDK7_uc003jvu.3_5'Flank	NM_001799	NP_001790			cyclin-dependent kinase 7						androgen receptor signaling pathway|cell division|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|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	holo TFIIH complex|mitochondrion	androgen receptor binding|ATP binding|cyclin-dependent protein kinase activity|DNA-dependent ATPase activity|protein C-terminus binding|RNA polymerase II carboxy-terminal domain kinase activity|transcription coactivator activity			lung(1)	1		Lung NSC(167;7.26e-05)|Prostate(74;0.00634)|Ovarian(174;0.0448)|Breast(144;0.198)		OV - Ovarian serous cystadenocarcinoma(47;2.98e-56)|Epithelial(20;3.54e-52)|all cancers(19;9.11e-48)|Lung(70;0.0185)									NER					---	---	---	---
SERF1A	8293	broad.mit.edu	37	5	69325574	69325574	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:69325574delT	uc003jyb.2	+						GUSBP3_uc003jxm.2_Intron|uc003jxp.3_Intron|uc011crh.1_Intron|uc011crl.1_Intron|SERF1A_uc003jya.2_Intron|SERF1A_uc003jxz.3_Intron	NM_022978	NP_075267			small EDRK-rich factor 1B, centromeric						nervous system development						0		Lung NSC(167;4.15e-05)|Prostate(74;0.00996)|Ovarian(174;0.0448)|Breast(144;0.198)		OV - Ovarian serous cystadenocarcinoma(47;3.04e-60)|Epithelial(20;7.09e-58)|all cancers(19;1.13e-53)|Lung(70;0.0174)														---	---	---	---
Unknown	0	broad.mit.edu	37	5	70251041	70251042	+	Intron	INS	-	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:70251041_70251042insA	uc010iyh.1	+						uc003jzx.2_Intron					Homo sapiens cDNA FLJ39772 fis, clone SPLEN2001157, highly similar to H.sapiens SMA4 mRNA.																														---	---	---	---
NAIP	4671	broad.mit.edu	37	5	70307058	70307059	+	Intron	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:70307058_70307059delAA	uc003kar.1	-						NAIP_uc003kat.1_Intron|NAIP_uc011crs.1_Intron|NAIP_uc003kas.1_Intron	NM_004536	NP_004527			NLR family, apoptosis inhibitory protein isoform						anti-apoptosis|apoptosis|nervous system development	basolateral plasma membrane|cytoplasm	caspase inhibitor activity|metal ion binding|nucleoside-triphosphatase activity|nucleotide binding			central_nervous_system(1)	1		Lung NSC(167;4.15e-05)|Prostate(74;0.00996)|Ovarian(174;0.0448)|Breast(144;0.198)		OV - Ovarian serous cystadenocarcinoma(47;3.04e-60)|Epithelial(20;7.09e-58)|all cancers(19;1.13e-53)|Lung(70;0.0174)														---	---	---	---
BDP1	55814	broad.mit.edu	37	5	70755338	70755338	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:70755338delA	uc003kbp.1	+						BDP1_uc003kbn.1_Intron|BDP1_uc003kbo.2_Intron	NM_018429	NP_060899			transcription factor-like nuclear regulator						regulation of transcription, DNA-dependent|transcription from RNA polymerase III promoter	nucleoplasm	DNA binding			skin(2)	2		Lung NSC(167;0.000422)|Prostate(74;0.00815)|Ovarian(174;0.0176)|Breast(144;0.198)		OV - Ovarian serous cystadenocarcinoma(47;5.28e-56)|Epithelial(20;2.31e-50)														---	---	---	---
Unknown	0	broad.mit.edu	37	5	70870218	70870218	+	IGR	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:70870218delG								BDP1 (6569 upstream) : MCCC2 (12897 downstream)																																			---	---	---	---
MAP1B	4131	broad.mit.edu	37	5	71500849	71500849	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:71500849delT	uc003kbw.3	+							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)														---	---	---	---
Unknown	0	broad.mit.edu	37	5	71998676	71998677	+	IGR	INS	-	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:71998676_71998677insA								ZNF366 (195427 upstream) : TNPO1 (113741 downstream)																																			---	---	---	---
TNPO1	3842	broad.mit.edu	37	5	72146953	72146953	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:72146953delA	uc003kck.3	+						TNPO1_uc011csi.1_Intron|TNPO1_uc011csj.1_Intron|TNPO1_uc003kch.2_Intron|TNPO1_uc003kci.3_Intron|TNPO1_uc003kcg.3_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	72406790	72406790	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:72406790delT								FCHO2 (20442 upstream) : TMEM171 (9598 downstream)																																			---	---	---	---
RGNEF	64283	broad.mit.edu	37	5	72946471	72946471	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:72946471delT	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	73426806	73426806	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:73426806delA								RGNEF (189393 upstream) : ENC1 (496429 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	73439547	73439549	+	IGR	DEL	AAG	-	-	rs149471924		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:73439547_73439549delAAG								RGNEF (202134 upstream) : ENC1 (483686 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	73716850	73716851	+	IGR	DEL	AA	-	-	rs113651546		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:73716850_73716851delAA								RGNEF (479437 upstream) : ENC1 (206384 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	73817078	73817079	+	IGR	INS	-	T	T	rs112314148		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:73817078_73817079insT								RGNEF (579665 upstream) : ENC1 (106156 downstream)																																			---	---	---	---
FAM169A	26049	broad.mit.edu	37	5	74135799	74135799	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-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	74339306	74339306	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:74339306delT								GCNT4 (12582 upstream) : ANKRD31 (103756 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	74564262	74564263	+	IGR	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:74564262_74564263delAA								ANKRD31 (31559 upstream) : HMGCR (67891 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	74662480	74662480	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:74662480delA								HMGCR (4556 upstream) : COL4A3BP (4449 downstream)																																			---	---	---	---
COL4A3BP	10087	broad.mit.edu	37	5	74780133	74780133	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:74780133delA	uc011csu.1	-						COL4A3BP_uc003kds.2_Intron|COL4A3BP_uc003kdt.2_Intron|COL4A3BP_uc003kdu.2_Intron	NM_005713	NP_005704			alpha 3 type IV collagen binding protein isoform						ER to Golgi ceramide transport|immune response	cytosol|endoplasmic reticulum membrane|Golgi apparatus	ceramide binding|phosphatidylinositol-4-phosphate binding|protein binding|protein kinase activity			skin(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;1e-53)														---	---	---	---
POC5	134359	broad.mit.edu	37	5	74982863	74982863	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:74982863delT	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	75120406	75120406	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:75120406delA								POC5 (107093 upstream) : SV2C (258899 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	75285808	75285809	+	IGR	DEL	TT	-	-	rs34463157		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:75285808_75285809delTT								POC5 (272495 upstream) : SV2C (93496 downstream)																																			---	---	---	---
SV2C	22987	broad.mit.edu	37	5	75522274	75522274	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:75522274delA	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)														---	---	---	---
SV2C	22987	broad.mit.edu	37	5	75533911	75533911	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:75533911delT	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)														---	---	---	---
Unknown	0	broad.mit.edu	37	5	75657149	75657150	+	IGR	INS	-	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:75657149_75657150insT								SV2C (35733 upstream) : IQGAP2 (41999 downstream)																																			---	---	---	---
IQGAP2	10788	broad.mit.edu	37	5	75725686	75725687	+	Intron	DEL	AC	-	-	rs71974018		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:75725686_75725687delAC	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)														---	---	---	---
IQGAP2	10788	broad.mit.edu	37	5	75842754	75842754	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:75842754delT	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)														---	---	---	---
IQGAP2	10788	broad.mit.edu	37	5	75890266	75890266	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:75890266delT	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)														---	---	---	---
IQGAP2	10788	broad.mit.edu	37	5	75943648	75943649	+	Intron	INS	-	CACA	CACA	rs34315403		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:75943648_75943649insCACA	uc003kek.2	+						IQGAP2_uc010izv.2_Intron|IQGAP2_uc011csv.1_Intron|IQGAP2_uc003kel.2_Intron	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)														---	---	---	---
Unknown	0	broad.mit.edu	37	5	76071767	76071768	+	IGR	DEL	TT	-	-	rs113327912		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:76071767_76071768delTT								F2R (40173 upstream) : F2RL1 (43065 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	76081373	76081373	+	IGR	DEL	A	-	-	rs74732662		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:76081373delA								F2R (49779 upstream) : F2RL1 (33460 downstream)																																			---	---	---	---
S100Z	170591	broad.mit.edu	37	5	76147426	76147426	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:76147426delA	uc003kep.1	+						S100Z_uc003keq.3_Intron	NM_130772	NP_570128			S100 calcium binding protein Z								calcium ion binding			ovary(1)	1		all_lung(232;0.000414)|Lung NSC(167;0.0011)|Ovarian(174;0.0129)|Prostate(461;0.11)		OV - Ovarian serous cystadenocarcinoma(54;8.91e-51)|Epithelial(54;5.43e-45)|all cancers(79;1.82e-40)														---	---	---	---
PDE8B	8622	broad.mit.edu	37	5	76542018	76542018	+	Intron	DEL	A	-	-	rs78250921		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:76542018delA	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)														---	---	---	---
PDE8B	8622	broad.mit.edu	37	5	76570836	76570837	+	Intron	INS	-	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:76570836_76570837insA	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)														---	---	---	---
PDE8B	8622	broad.mit.edu	37	5	76571219	76571219	+	Intron	DEL	A	-	-	rs34990832		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:76571219delA	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	76842129	76842129	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:76842129delA								WDR41 (53797 upstream) : OTP (82409 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	76851746	76851746	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:76851746delA								WDR41 (63414 upstream) : OTP (72792 downstream)																																			---	---	---	---
TBCA	6902	broad.mit.edu	37	5	77052828	77052828	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:77052828delT	uc003kfh.1	-						TBCA_uc003kfi.1_Intron	NM_004607	NP_004598			tubulin-specific chaperone a						'de novo' posttranslational protein folding|post-chaperonin tubulin folding pathway|tubulin complex assembly	cytoplasm|microtubule	chaperone binding|unfolded protein binding			ovary(1)	1		all_lung(232;0.000511)|Lung NSC(167;0.000601)|Ovarian(174;0.0105)|Prostate(461;0.214)		OV - Ovarian serous cystadenocarcinoma(54;1.02e-49)|Epithelial(54;1.05e-44)|all cancers(79;4.08e-40)														---	---	---	---
Unknown	0	broad.mit.edu	37	5	77235816	77235819	+	IGR	DEL	TTTT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:77235816_77235819delTTTT								TBCA (163631 upstream) : AP3B1 (62332 downstream)																																			---	---	---	---
AP3B1	8546	broad.mit.edu	37	5	77571308	77571308	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:77571308delT	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				---	---	---	---
SCAMP1	9522	broad.mit.edu	37	5	77663436	77663436	+	Intron	DEL	C	-	-	rs10065260	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:77663436delC	uc003kfl.2	+						SCAMP1_uc010jaa.2_Intron|SCAMP1_uc011ctc.1_Intron|SCAMP1_uc011ctd.1_Intron	NM_004866	NP_004857			secretory carrier membrane protein 1						post-Golgi vesicle-mediated transport|protein transport	integral to membrane|recycling endosome membrane|trans-Golgi network	protein binding				0		all_lung(232;0.000397)|Lung NSC(167;0.00105)|Ovarian(174;0.0105)|Prostate(461;0.214)		OV - Ovarian serous cystadenocarcinoma(54;1.9e-46)|Epithelial(54;9.4e-43)|all cancers(79;1.12e-37)														---	---	---	---
LHFPL2	10184	broad.mit.edu	37	5	77852786	77852788	+	Intron	DEL	TTT	-	-	rs149354359		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:77852786_77852788delTTT	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	77939394	77939394	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:77939394delT	uc003kfo.2	-						LHFPL2_uc003kfp.1_5'Flank	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)														---	---	---	---
JMY	133746	broad.mit.edu	37	5	78544886	78544886	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:78544886delT	uc003kfx.3	+							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	78858831	78858831	+	IGR	DEL	A	-	-	rs111435603	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:78858831delA								HOMER1 (49131 upstream) : PAPD4 (49412 downstream)																																			---	---	---	---
PAPD4	167153	broad.mit.edu	37	5	78936848	78936849	+	Intron	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:78936848_78936849delTT	uc010jae.1	+						PAPD4_uc003kgb.2_Intron|PAPD4_uc010jaf.1_Intron|PAPD4_uc003kga.2_Intron|PAPD4_uc003kfz.2_Intron	NM_001114393	NP_001107865			PAP associated domain containing 4						histone mRNA catabolic process|mRNA processing|RNA polyadenylation	cytoplasm	ATP binding|metal ion binding|polynucleotide adenylyltransferase activity			ovary(1)	1		Lung NSC(167;0.00293)|all_lung(232;0.00323)|Ovarian(174;0.0261)		OV - Ovarian serous cystadenocarcinoma(54;8.61e-47)|Epithelial(54;1.32e-41)|all cancers(79;2.45e-36)														---	---	---	---
THBS4	7060	broad.mit.edu	37	5	79334395	79334396	+	Intron	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:79334395_79334396delTT	uc003kgh.2	+							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)														---	---	---	---
THBS4	7060	broad.mit.edu	37	5	79338801	79338801	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:79338801delA	uc003kgh.2	+							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)														---	---	---	---
Unknown	0	broad.mit.edu	37	5	79568481	79568481	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:79568481delA								SERINC5 (16611 upstream) : LOC644936 (26438 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	79620457	79620458	+	5'Flank	DEL	TT	-	-	rs72183634		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:79620457_79620458delTT	uc011ctk.1	-											Homo sapiens cDNA FLJ25709 fis, clone TST04944.																														---	---	---	---
Unknown	0	broad.mit.edu	37	5	79900226	79900226	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:79900226delA								ANKRD34B (34128 upstream) : DHFR (21819 downstream)																																			---	---	---	---
MSH3	4437	broad.mit.edu	37	5	80045867	80045867	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:80045867delT	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					---	---	---	---
MSH3	4437	broad.mit.edu	37	5	80088494	80088494	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:80088494delT	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					---	---	---	---
RASGRF2	5924	broad.mit.edu	37	5	80434596	80434598	+	Intron	DEL	TTC	-	-	rs70994422		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:80434596_80434598delTTC	uc003kha.1	+						RASGRF2_uc011ctn.1_Intron	NM_006909	NP_008840			Ras protein-specific guanine						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	80538123	80538123	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:80538123delT	uc003khc.3	+						RNU5E_uc011cto.1_Intron|CKMT2_uc010jaq.2_Intron|CKMT2_uc003khd.3_Intron|uc003khe.1_Intron|uc003khf.1_Intron|uc003khg.1_Intron	NM_001825	NP_001816			sarcomeric mitochondrial creatine kinase						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)													---	---	---	---
ACOT12	134526	broad.mit.edu	37	5	80658986	80658986	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:80658986delA	uc003khl.3	-						RNU5E_uc011cto.1_Intron|ACOT12_uc003khm.2_Intron	NM_130767	NP_570123			acyl-CoA thioesterase 12						acyl-CoA metabolic process|fatty acid metabolic process	cytosol	acetyl-CoA hydrolase activity|carboxylesterase activity			ovary(1)|kidney(1)	2		Lung NSC(167;0.0176)|all_lung(232;0.0205)|Ovarian(174;0.135)		OV - Ovarian serous cystadenocarcinoma(54;1.37e-45)|Epithelial(54;1.25e-39)|all cancers(79;5.01e-34)														---	---	---	---
RNU5E	26829	broad.mit.edu	37	5	80714216	80714216	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:80714216delT	uc011cto.1	+							NR_002754				Homo sapiens RNA, U5E small nuclear (RNU5E), non-coding RNA.												0																		---	---	---	---
SSBP2	23635	broad.mit.edu	37	5	80738453	80738453	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:80738453delA	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	81387277	81387277	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:81387277delA	uc003khs.2	+						ATG10_uc003khq.2_Intron|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)														---	---	---	---
Unknown	0	broad.mit.edu	37	5	81569134	81569135	+	IGR	DEL	CA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:81569134_81569135delCA								ATG10 (17923 upstream) : RPS23 (6 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	81661457	81661457	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:81661457delT								ATP6AP1L (47311 upstream) : TMEM167A (687210 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	81904227	81904228	+	IGR	INS	-	A	A	rs148369260	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:81904227_81904228insA								ATP6AP1L (290081 upstream) : TMEM167A (444439 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	82275278	82275278	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:82275278delA								ATP6AP1L (661132 upstream) : TMEM167A (73389 downstream)																																			---	---	---	---
VCAN	1462	broad.mit.edu	37	5	82848471	82848472	+	Intron	DEL	AC	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:82848471_82848472delAC	uc003kii.3	+						VCAN_uc003kij.3_Intron|VCAN_uc010jau.2_Intron|VCAN_uc003kik.3_Intron|VCAN_uc003kil.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)														---	---	---	---
EDIL3	10085	broad.mit.edu	37	5	83586350	83586350	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:83586350delA	uc003kio.1	-						EDIL3_uc003kip.1_Intron	NM_005711	NP_005702			EGF-like repeats and discoidin I-like						cell adhesion|multicellular organismal development	extracellular region	calcium ion binding|integrin binding			skin(2)	2		Lung NSC(167;0.000121)|all_lung(232;0.000154)|Ovarian(174;0.0425)		OV - Ovarian serous cystadenocarcinoma(54;4.3e-40)|Epithelial(54;4.79e-32)|all cancers(79;1.54e-26)														---	---	---	---
Unknown	0	broad.mit.edu	37	5	84092400	84092403	+	IGR	DEL	TTTT	-	-	rs74598531		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:84092400_84092403delTTTT								EDIL3 (411789 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	84993904	84993904	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:84993904delA								None (None upstream) : NBPF22P (584358 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	85121961	85121961	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:85121961delT								None (None upstream) : NBPF22P (456301 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	85791009	85791009	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:85791009delT								NBPF22P (197647 upstream) : COX7C (122775 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	86069955	86069955	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:86069955delT								COX7C (153374 upstream) : RASA1 (494196 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	86557136	86557139	+	IGR	DEL	TTTT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:86557136_86557139delTTTT								COX7C (640555 upstream) : RASA1 (7012 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	86736691	86736691	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:86736691delT								CCNH (27855 upstream) : TMEM161B (754333 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	86831947	86831948	+	IGR	DEL	GT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:86831947_86831948delGT								CCNH (123111 upstream) : TMEM161B (659076 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	87485035	87485035	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:87485035delT								CCNH (776199 upstream) : TMEM161B (5989 downstream)																																			---	---	---	---
TMEM161B	153396	broad.mit.edu	37	5	87491918	87491918	+	3'UTR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-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)														---	---	---	---
Unknown	0	broad.mit.edu	37	5	87715371	87715373	+	Intron	DEL	AAA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:87715371_87715373delAAA	uc003kjd.2	+						uc003kje.2_Intron					Homo sapiens cDNA clone IMAGE:4814828.																														---	---	---	---
Unknown	0	broad.mit.edu	37	5	87758192	87758193	+	IGR	INS	-	A	A	rs150897245	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:87758192_87758193insA								TMEM161B (193527 upstream) : LOC645323 (78404 downstream)																																			---	---	---	---
LOC645323	645323	broad.mit.edu	37	5	87857040	87857040	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:87857040delA	uc011cua.1	-							NR_015436				Homo sapiens cDNA FLJ34037 fis, clone FCBBF2005439.												0																		---	---	---	---
LOC645323	645323	broad.mit.edu	37	5	87898998	87898998	+	Intron	DEL	A	-	-	rs11959094		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:87898998delA	uc011cua.1	-							NR_015436				Homo sapiens cDNA FLJ34037 fis, clone FCBBF2005439.												0																		---	---	---	---
LOC645323	645323	broad.mit.edu	37	5	87972384	87972385	+	Intron	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:87972384_87972385delTT	uc011cua.1	-						LOC645323_uc003kjg.2_5'Flank|LOC645323_uc011cub.1_Intron|LOC645323_uc003kjh.3_Intron	NR_015436				Homo sapiens cDNA FLJ34037 fis, clone FCBBF2005439.												0																		---	---	---	---
LOC645323	645323	broad.mit.edu	37	5	87977648	87977649	+	Intron	INS	-	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:87977648_87977649insT	uc011cua.1	-						LOC645323_uc003kjh.3_Intron	NR_015436				Homo sapiens cDNA FLJ34037 fis, clone FCBBF2005439.												0																		---	---	---	---
MEF2C	4208	broad.mit.edu	37	5	88053235	88053235	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:88053235delA	uc003kjj.2	-						MEF2C_uc003kji.2_Intron|MEF2C_uc003kjk.2_Intron|MEF2C_uc003kjm.2_Intron|MEF2C_uc003kjl.2_Intron	NM_002397	NP_002388			myocyte enhancer factor 2C isoform 1						apoptosis|B cell proliferation|innate immune response|learning or memory|muscle cell differentiation|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|neuron development|positive regulation of muscle cell differentiation|positive regulation of survival gene product expression|positive regulation of transcription from RNA polymerase II promoter|regulation of germinal center formation|regulation of megakaryocyte differentiation|regulation of synaptic 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	nuclear speck	activating transcription factor binding|protein heterodimerization activity|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding			lung(3)|breast(2)|ovary(1)|large_intestine(1)	7		all_cancers(142;6.67e-05)|all_epithelial(76;7.77e-07)|Lung NSC(167;0.00566)|all_lung(232;0.00732)|Colorectal(57;0.0959)|Ovarian(174;0.1)		OV - Ovarian serous cystadenocarcinoma(54;1.04e-33)|Epithelial(54;1.6e-28)|all cancers(79;2.9e-25)											HNSCC(66;0.2)			---	---	---	---
MEF2C	4208	broad.mit.edu	37	5	88105326	88105326	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:88105326delA	uc003kjj.2	-						MEF2C_uc003kji.2_Intron|MEF2C_uc003kjk.2_Intron|MEF2C_uc003kjm.2_Intron|MEF2C_uc003kjl.2_Intron	NM_002397	NP_002388			myocyte enhancer factor 2C isoform 1						apoptosis|B cell proliferation|innate immune response|learning or memory|muscle cell differentiation|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|neuron development|positive regulation of muscle cell differentiation|positive regulation of survival gene product expression|positive regulation of transcription from RNA polymerase II promoter|regulation of germinal center formation|regulation of megakaryocyte differentiation|regulation of synaptic 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	nuclear speck	activating transcription factor binding|protein heterodimerization activity|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding			lung(3)|breast(2)|ovary(1)|large_intestine(1)	7		all_cancers(142;6.67e-05)|all_epithelial(76;7.77e-07)|Lung NSC(167;0.00566)|all_lung(232;0.00732)|Colorectal(57;0.0959)|Ovarian(174;0.1)		OV - Ovarian serous cystadenocarcinoma(54;1.04e-33)|Epithelial(54;1.6e-28)|all cancers(79;2.9e-25)											HNSCC(66;0.2)			---	---	---	---
Unknown	0	broad.mit.edu	37	5	88296465	88296465	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:88296465delT								MEF2C (96596 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	88507723	88507724	+	IGR	INS	-	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:88507723_88507724insA								MEF2C (307854 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	88556172	88556172	+	IGR	DEL	A	-	-	rs34234582		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:88556172delA								MEF2C (356303 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	89070072	89070073	+	IGR	DEL	TA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:89070072_89070073delTA								MEF2C (870203 upstream) : CETN3 (619458 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	89121493	89121493	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:89121493delT								MEF2C (921624 upstream) : CETN3 (568038 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	89709133	89709133	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:89709133delT								CETN3 (3530 upstream) : MBLAC2 (44889 downstream)																																			---	---	---	---
GPR98	84059	broad.mit.edu	37	5	90086591	90086591	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-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	90160960	90160960	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:90160960delT	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)														---	---	---	---
Unknown	0	broad.mit.edu	37	5	91378474	91378474	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:91378474delA								LOC100129716 (661943 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	91722495	91722495	+	Intron	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:91722495delC	uc003kkb.1	+											Homo sapiens cDNA FLJ31923 fis, clone NT2RP7005323.																														---	---	---	---
Unknown	0	broad.mit.edu	37	5	92940465	92940468	+	IGR	DEL	TCCC	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:92940465_92940468delTCCC								NR2F1 (10687 upstream) : FAM172A (12964 downstream)																																			---	---	---	---
FAM172A	83989	broad.mit.edu	37	5	93089994	93089994	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:93089994delT	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	93382425	93382426	+	Intron	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:93382425_93382426delTT	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																		---	---	---	---
FAM172A	83989	broad.mit.edu	37	5	93388892	93388892	+	Frame_Shift_Del	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:93388892delT	uc010jbd.2	-	3	354	c.147delA	c.(145-147)AAAfs	p.K49fs	FAM172A_uc011cuf.1_Frame_Shift_Del_p.K3fs|FAM172A_uc011cug.1_Frame_Shift_Del_p.K3fs|FAM172A_uc011cuh.1_5'UTR|FAM172A_uc011cui.1_RNA|FAM172A_uc011cuj.1_5'UTR|FAM172A_uc003kkm.3_Frame_Shift_Del_p.K49fs	NM_032042	NP_114431	Q8WUF8	F172A_HUMAN	hypothetical protein LOC83989 isoform 1	49						endoplasmic reticulum|extracellular region					0																		---	---	---	---
MCTP1	79772	broad.mit.edu	37	5	94259574	94259575	+	Intron	INS	-	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:94259574_94259575insA	uc003kkx.2	-						MCTP1_uc003kkv.2_Intron|MCTP1_uc003kkw.2_Intron|MCTP1_uc003kkz.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)														---	---	---	---
TTC37	9652	broad.mit.edu	37	5	94805686	94805688	+	Intron	DEL	TTT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:94805686_94805688delTTT	uc003klb.2	-							NM_014639	NP_055454			tetratricopeptide repeat domain 37								binding			ovary(3)|pancreas(1)	4																		---	---	---	---
Unknown	0	broad.mit.edu	37	5	95325389	95325389	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:95325389delT								ELL2 (27614 upstream) : MIR583 (89453 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	95528865	95528865	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:95528865delT								MIR583 (113949 upstream) : PCSK1 (197254 downstream)																																			---	---	---	---
ERAP1	51752	broad.mit.edu	37	5	96143987	96143988	+	5'Flank	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:96143987_96143988delTT	uc003kmm.2	-						ERAP1_uc003kml.2_5'Flank|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	96392026	96392026	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:96392026delA								LNPEP (26911 upstream) : LIX1 (35549 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	96419119	96419119	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:96419119delT								LNPEP (54004 upstream) : LIX1 (8456 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	96481605	96481605	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:96481605delA								LIX1 (3085 upstream) : RIOK2 (14967 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	96576671	96576671	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:96576671delT								RIOK2 (57666 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	97076646	97076647	+	IGR	DEL	TC	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:97076646_97076647delTC								RIOK2 (557641 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	97675625	97675625	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:97675625delT								None (None upstream) : RGMB (429374 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	97938229	97938229	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:97938229delA								None (None upstream) : RGMB (166770 downstream)																																			---	---	---	---
CHD1	1105	broad.mit.edu	37	5	98228483	98228483	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:98228483delT	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	98524700	98524701	+	IGR	DEL	AG	-	-	rs35357687		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:98524700_98524701delAG								CHD1 (262462 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	98941569	98941572	+	IGR	DEL	TTGT	-	-	rs3850907	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:98941569_98941572delTTGT								CHD1 (679331 upstream) : LOC100133050 (773637 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	99059503	99059503	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:99059503delT								CHD1 (797265 upstream) : LOC100133050 (655706 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	99953103	99953103	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:99953103delT								FAM174A (30663 upstream) : ST8SIA4 (189537 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	101222411	101222411	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:101222411delT								ST8SIA4 (983424 upstream) : SLCO4C1 (347283 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	101320931	101320931	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:101320931delA								None (None upstream) : SLCO4C1 (248763 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	101678317	101678317	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:101678317delA								SLCO4C1 (46064 upstream) : SLCO6A1 (29333 downstream)																																			---	---	---	---
SLCO6A1	133482	broad.mit.edu	37	5	101755728	101755728	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:101755728delA	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)														---	---	---	---
Unknown	0	broad.mit.edu	37	5	101912714	101912715	+	IGR	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:101912714_101912715delTT								SLCO6A1 (77994 upstream) : PAM (288812 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	102368767	102368767	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:102368767delA								PAM (3351 upstream) : GIN1 (52937 downstream)																																			---	---	---	---
GIN1	54826	broad.mit.edu	37	5	102429990	102429990	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:102429990delA	uc003koa.1	-						GIN1_uc003kob.1_Intron|GIN1_uc003koc.1_Intron	NM_017676	NP_060146			zinc finger, H2C2 domain containing						DNA integration		DNA binding			ovary(1)|skin(1)	2		all_cancers(142;3.23e-07)|all_epithelial(76;3.64e-10)|Prostate(80;0.00914)|Ovarian(225;0.0139)|Lung NSC(167;0.0212)|Colorectal(57;0.0249)|all_lung(232;0.0283)		Epithelial(69;3.57e-14)|COAD - Colon adenocarcinoma(37;0.00794)														---	---	---	---
Unknown	0	broad.mit.edu	37	5	102669271	102669271	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:102669271delA								C5orf30 (54910 upstream) : NUDT12 (215286 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	102693595	102693595	+	IGR	DEL	T	-	-	rs140417919	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:102693595delT								C5orf30 (79234 upstream) : NUDT12 (190962 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	102908289	102908289	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:102908289delA								NUDT12 (9799 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	103056077	103056078	+	IGR	INS	-	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:103056077_103056078insG								NUDT12 (157587 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	103175853	103175853	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:103175853delA								NUDT12 (277363 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	105373838	105373839	+	IGR	INS	-	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:105373838_105373839insT								RAB9BP1 (938040 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	105584157	105584158	+	IGR	DEL	AC	-	-	rs57368963	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:105584157_105584158delAC								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	106070930	106070930	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:106070930delA								None (None upstream) : EFNA5 (641661 downstream)																																			---	---	---	---
EFNA5	1946	broad.mit.edu	37	5	106766238	106766239	+	Intron	INS	-	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:106766238_106766239insA	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)														---	---	---	---
EFNA5	1946	broad.mit.edu	37	5	106825689	106825689	+	Intron	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:106825689delC	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	107268574	107268575	+	Intron	INS	-	T	T	rs77877531	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:107268574_107268575insT	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	107270770	107270770	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:107270770delT	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	107703971	107703971	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:107703971delA	uc011cvc.1	-						FBXL17_uc003kon.3_5'Flank	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	107877136	107877136	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:107877136delA								FBXL17 (159337 upstream) : FER (206387 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	107928024	107928025	+	IGR	INS	-	T	T	rs150158519	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:107928024_107928025insT								FBXL17 (210225 upstream) : FER (155498 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	107957303	107957303	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:107957303delA								FBXL17 (239504 upstream) : FER (126220 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	108015061	108015062	+	IGR	DEL	TC	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:108015061_108015062delTC								FBXL17 (297262 upstream) : FER (68461 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	108041715	108041715	+	IGR	DEL	T	-	-	rs10707846		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:108041715delT								FBXL17 (323916 upstream) : FER (41808 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	108633569	108633569	+	IGR	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:108633569delC								FER (110196 upstream) : PJA2 (36842 downstream)																																			---	---	---	---
MAN2A1	4124	broad.mit.edu	37	5	109042453	109042453	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:109042453delA	uc003kou.1	+							NM_002372	NP_002363			mannosidase, alpha, class 2A, member 1						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)														---	---	---	---
Unknown	0	broad.mit.edu	37	5	109606366	109606366	+	IGR	DEL	T	-	-	rs71899267		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:109606366delT								MAN2A1 (402937 upstream) : TMEM232 (18568 downstream)																																			---	---	---	---
TMEM232	642987	broad.mit.edu	37	5	109916436	109916437	+	Intron	INS	-	T	T	rs145520042	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:109916436_109916437insT	uc011cvh.1	-						TMEM232_uc003kow.1_Intron|TMEM232_uc003kox.2_Intron|TMEM232_uc010jbs.2_Intron|TMEM232_uc003koy.3_Intron					SubName: Full=cDNA FLJ54480;							integral to membrane					0																		---	---	---	---
TMEM232	642987	broad.mit.edu	37	5	109940905	109940905	+	Frame_Shift_Del	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:109940905delT	uc011cvh.1	-	10	1247	c.1175delA	c.(1174-1176)AATfs	p.N392fs	TMEM232_uc003kow.1_Frame_Shift_Del_p.N200fs|TMEM232_uc003kox.2_RNA|TMEM232_uc010jbs.2_Frame_Shift_Del_p.N394fs|TMEM232_uc003koy.3_Frame_Shift_Del_p.N128fs			C9JQI7	TM232_HUMAN	SubName: Full=cDNA FLJ54480;	394						integral to membrane					0																		---	---	---	---
Unknown	0	broad.mit.edu	37	5	110159925	110159926	+	IGR	DEL	CC	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:110159925_110159926delCC								SLC25A46 (61443 upstream) : TSLP (245852 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	110329159	110329160	+	IGR	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:110329159_110329160delAA								SLC25A46 (230677 upstream) : TSLP (76618 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	110349051	110349051	+	IGR	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:110349051delG								SLC25A46 (250569 upstream) : TSLP (56727 downstream)																																			---	---	---	---
EPB41L4A	64097	broad.mit.edu	37	5	111560343	111560344	+	Intron	INS	-	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:111560343_111560344insT	uc003kpv.1	-						EPB41L4A_uc003kpp.1_Intron	NM_022140	NP_071423			erythrocyte protein band 4.1-like 4							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)														---	---	---	---
EPB41L4A	64097	broad.mit.edu	37	5	111628912	111628912	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:111628912delT	uc003kpv.1	-						EPB41L4A_uc003kpw.1_Intron	NM_022140	NP_071423			erythrocyte protein band 4.1-like 4							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)														---	---	---	---
Unknown	0	broad.mit.edu	37	5	111879324	111879324	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:111879324delA								FLJ11235 (122651 upstream) : APC (163894 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	111994544	111994544	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:111994544delT								FLJ11235 (237871 upstream) : APC (48674 downstream)																																			---	---	---	---
APC	324	broad.mit.edu	37	5	112101928	112101928	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:112101928delT	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)			---	---	---	---
APC	324	broad.mit.edu	37	5	112113962	112113962	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:112113962delA	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)			---	---	---	---
APC	324	broad.mit.edu	37	5	112162038	112162038	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:112162038delT	uc010jby.2	+						APC_uc011cvt.1_Intron|APC_uc003kpz.3_Intron|APC_uc003kpy.3_Intron|APC_uc010jbz.2_Intron|APC_uc010jca.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)			---	---	---	---
APC	324	broad.mit.edu	37	5	112163028	112163028	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:112163028delT	uc010jby.2	+						APC_uc011cvt.1_Intron|APC_uc003kpz.3_Intron|APC_uc003kpy.3_Intron|APC_uc010jbz.2_Intron|APC_uc010jca.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	p.?(1)		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)			---	---	---	---
Unknown	0	broad.mit.edu	37	5	113060003	113060003	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:113060003delT								YTHDC2 (129024 upstream) : KCNN2 (638013 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	113142658	113142658	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:113142658delT								YTHDC2 (211679 upstream) : KCNN2 (555358 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	113372703	113372703	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:113372703delT								YTHDC2 (441724 upstream) : KCNN2 (325313 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	113604641	113604641	+	IGR	DEL	G	-	-	rs10043191	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:113604641delG								YTHDC2 (673662 upstream) : KCNN2 (93375 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	113849725	113849726	+	Intron	DEL	CT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:113849725_113849726delCT	uc003kqr.1	-											Homo sapiens cDNA FLJ40367 fis, clone TESTI2034785.																														---	---	---	---
Unknown	0	broad.mit.edu	37	5	114328240	114328241	+	IGR	INS	-	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:114328240_114328241insA								KCNN2 (496044 upstream) : TRIM36 (132226 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	114520185	114520186	+	IGR	DEL	GG	-	-	rs5870642		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:114520185_114520186delGG								TRIM36 (3942 upstream) : PGGT1B (26342 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	114805820	114805821	+	IGR	INS	-	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:114805820_114805821insA								CCDC112 (173362 upstream) : FEM1C (50787 downstream)																																			---	---	---	---
CDO1	1036	broad.mit.edu	37	5	115148745	115148759	+	Intron	DEL	AAAAAAAAAAAAAAA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:115148745_115148759delAAAAAAAAAAAAAAA	uc003krg.2	-							NM_001801	NP_001792			cysteine dioxygenase						inflammatory response|sulfur amino acid biosynthetic process|taurine biosynthetic process	cytosol	cysteine dioxygenase activity			large_intestine(1)|skin(1)	2		all_cancers(142;0.0046)|all_epithelial(76;0.000161)|Prostate(80;0.0132)|Ovarian(225;0.0776)		OV - Ovarian serous cystadenocarcinoma(64;7.8e-08)|Epithelial(69;7.32e-07)|all cancers(49;3.24e-05)	L-Cysteine(DB00151)|NADH(DB00157)													---	---	---	---
SEMA6A	57556	broad.mit.edu	37	5	115822792	115822793	+	Intron	DEL	AA	-	-	rs111384042		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-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)														---	---	---	---
SEMA6A	57556	broad.mit.edu	37	5	115876839	115876839	+	Intron	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:115876839delG	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	116133315	116133315	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:116133315delA								SEMA6A (222764 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	116305313	116305313	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:116305313delA								SEMA6A (394762 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	116371626	116371626	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:116371626delA								SEMA6A (461075 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	116537983	116537983	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:116537983delT								SEMA6A (627432 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	117296081	117296081	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:117296081delA								None (None upstream) : DTWD2 (876490 downstream)																																			---	---	---	---
DTWD2	285605	broad.mit.edu	37	5	118310422	118310422	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:118310422delT	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)														---	---	---	---
DTWD2	285605	broad.mit.edu	37	5	118310505	118310505	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-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	118433665	118433665	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:118433665delT	uc003ksd.2	+						DMXL1_uc010jcl.1_Intron|DMXL1_uc003ksc.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)														---	---	---	---
DMXL1	1657	broad.mit.edu	37	5	118503285	118503285	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:118503285delT	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	118647840	118647841	+	Intron	DEL	GA	-	-	rs9327097	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:118647840_118647841delGA	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	118728496	118728498	+	Intron	DEL	TTT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:118728496_118728498delTTT	uc003ksh.2	+						TNFAIP8_uc003ksf.1_Intron|TNFAIP8_uc003ksg.2_Intron|TNFAIP8_uc011cwf.1_Intron|TNFAIP8_uc003ksi.2_Intron	NM_014350	NP_055165			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)														---	---	---	---
HSD17B4	3295	broad.mit.edu	37	5	118862722	118862722	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:118862722delT	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|HSD17B4_uc010jco.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	120829385	120829385	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:120829385delT								PRR16 (806423 upstream) : FTMT (358265 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	120966632	120966633	+	IGR	INS	-	A	A	rs141506910	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:120966632_120966633insA								PRR16 (943670 upstream) : FTMT (221017 downstream)																																			---	---	---	---
SNCAIP	9627	broad.mit.edu	37	5	121725581	121725581	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:121725581delT	uc003ksw.1	+						SNCAIP_uc011cwl.1_Intron|SNCAIP_uc010jct.2_Intron|SNCAIP_uc003ksx.1_Intron|SNCAIP_uc003ksy.1_Intron|SNCAIP_uc003ksz.1_Intron|SNCAIP_uc010jcu.2_Intron|SNCAIP_uc011cwm.1_Intron|SNCAIP_uc003kta.1_5'Flank|SNCAIP_uc010jcv.1_5'Flank|SNCAIP_uc010jcw.1_5'Flank|SNCAIP_uc010jcx.1_5'Flank	NM_005460	NP_005451			synuclein alpha interacting protein						cell death|dopamine metabolic process|regulation of inclusion body assembly|regulation of neurotransmitter secretion	cytoplasm|neuronal cell body|nucleolus|presynaptic membrane	ubiquitin protein ligase binding			ovary(1)|pancreas(1)	2		all_cancers(142;0.00787)|Prostate(80;0.0327)	KIRC - Kidney renal clear cell carcinoma(527;0.206)	OV - Ovarian serous cystadenocarcinoma(64;0.000625)|Epithelial(69;0.00216)|all cancers(49;0.0232)														---	---	---	---
SNX24	28966	broad.mit.edu	37	5	122199224	122199225	+	Intron	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:122199224_122199225delTT	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	122482293	122482295	+	Intron	DEL	TGT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:122482293_122482295delTGT	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																		---	---	---	---
Unknown	0	broad.mit.edu	37	5	122604437	122604437	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:122604437delT								PRDM6 (80693 upstream) : CEP120 (76143 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	122994054	122994054	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:122994054delT								CSNK1G3 (41592 upstream) : ZNF608 (978556 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	123170713	123170713	+	IGR	DEL	A	-	-	rs34883185		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:123170713delA								CSNK1G3 (218251 upstream) : ZNF608 (801897 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	123208760	123208760	+	IGR	DEL	A	-	-	rs75343390		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:123208760delA								CSNK1G3 (256298 upstream) : ZNF608 (763850 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	123326887	123326887	+	IGR	DEL	A	-	-	rs5871065		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:123326887delA								CSNK1G3 (374425 upstream) : ZNF608 (645723 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	123910688	123910689	+	IGR	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:123910688_123910689delTT								CSNK1G3 (958226 upstream) : ZNF608 (61921 downstream)																																			---	---	---	---
ZNF608	57507	broad.mit.edu	37	5	124026387	124026389	+	Intron	DEL	AAC	-	-	rs147697705	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:124026387_124026389delAAC	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	124189368	124189368	+	IGR	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:124189368delC								ZNF608 (104868 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	124207892	124207893	+	IGR	DEL	TG	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:124207892_124207893delTG								ZNF608 (123392 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	124367711	124367711	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:124367711delA								ZNF608 (283211 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	124686569	124686569	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:124686569delA								ZNF608 (602069 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	124877951	124877952	+	IGR	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:124877951_124877952delAA								ZNF608 (793451 upstream) : GRAMD3 (817836 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	124981183	124981183	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:124981183delA								ZNF608 (896683 upstream) : GRAMD3 (714605 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	125420365	125420365	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:125420365delT								None (None upstream) : GRAMD3 (275423 downstream)																																			---	---	---	---
GRAMD3	65983	broad.mit.edu	37	5	125795828	125795828	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:125795828delA	uc003ktu.2	+						GRAMD3_uc011cwt.1_Intron|GRAMD3_uc011cwv.1_Intron|GRAMD3_uc011cww.1_Intron|GRAMD3_uc011cwx.1_Intron|GRAMD3_uc011cwy.1_5'Flank|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)														---	---	---	---
ALDH7A1	501	broad.mit.edu	37	5	125890218	125890218	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:125890218delT	uc003ktx.2	-						ALDH7A1_uc003ktv.2_Intron|ALDH7A1_uc003kty.2_Intron|ALDH7A1_uc011cxa.1_Intron	NM_001182	NP_001173			aldehyde dehydrogenase 7 family, member A1						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)													---	---	---	---
C5orf48	389320	broad.mit.edu	37	5	125965807	125965807	+	5'Flank	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:125965807delA	uc003kub.1	+							NM_207408	NP_997291			hypothetical protein LOC389320											ovary(1)	1																		---	---	---	---
LMNB1	4001	broad.mit.edu	37	5	126172245	126172245	+	3'UTR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:126172245delT	uc003kud.1	+	11					LMNB1_uc010jdb.1_RNA|LMNB1_uc011cxb.1_3'UTR	NM_005573	NP_005564			lamin B1						cellular component disassembly involved in apoptosis	lamin filament|nuclear inner membrane	protein binding|structural molecule activity			kidney(1)|central_nervous_system(1)	2		all_cancers(142;0.103)|Prostate(80;0.081)	KIRC - Kidney renal clear cell carcinoma(527;0.0268)|Kidney(363;0.0488)	Epithelial(69;0.033)|OV - Ovarian serous cystadenocarcinoma(64;0.0398)|all cancers(49;0.0903)														---	---	---	---
MEGF10	84466	broad.mit.edu	37	5	126676295	126676295	+	Frame_Shift_Del	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:126676295delT	uc003kuh.3	+	5	654	c.292delT	c.(292-294)TTTfs	p.F98fs	MEGF10_uc010jdc.1_Frame_Shift_Del_p.F98fs|MEGF10_uc010jdd.1_Frame_Shift_Del_p.F98fs|MEGF10_uc003kui.3_Frame_Shift_Del_p.F98fs	NM_032446	NP_115822	Q96KG7	MEG10_HUMAN	multiple EGF-like-domains 10 precursor	98	Extracellular (Potential).|Necessary for interaction with AP2M1, self-assembly and formation of the irregular, mosaic-like adhesion pattern.|EMI.				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)														---	---	---	---
MEGF10	84466	broad.mit.edu	37	5	126734757	126734757	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:126734757delA	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)														---	---	---	---
MEGF10	84466	broad.mit.edu	37	5	126770267	126770267	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:126770267delT	uc003kuh.3	+						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)														---	---	---	---
SLC12A2	6558	broad.mit.edu	37	5	127520366	127520367	+	Intron	INS	-	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:127520366_127520367insT	uc003kus.2	+						SLC12A2_uc010jdf.2_Intron|SLC12A2_uc010jdg.2_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)													---	---	---	---
FBN2	2201	broad.mit.edu	37	5	127707231	127707231	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:127707231delT	uc003kuu.2	-						FBN2_uc003kuv.2_Intron	NM_001999	NP_001990			fibrillin 2 precursor						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)														---	---	---	---
Unknown	0	broad.mit.edu	37	5	128167758	128167758	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:128167758delA								FBN2 (293842 upstream) : SLC27A6 (133452 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	128546377	128546377	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:128546377delA								ISOC1 (96660 upstream) : ADAMTS19 (249726 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	128647635	128647636	+	IGR	INS	-	CCT	CCT	rs143163488	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:128647635_128647636insCCT								ISOC1 (197918 upstream) : ADAMTS19 (148467 downstream)																																			---	---	---	---
CHSY3	337876	broad.mit.edu	37	5	129507821	129507821	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:129507821delT	uc003kvd.2	+							NM_175856	NP_787052			chondroitin sulfate synthase 3							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)														---	---	---	---
Unknown	0	broad.mit.edu	37	5	129873588	129873588	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:129873588delA								CHSY3 (351262 upstream) : HINT1 (621287 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	129911609	129911609	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:129911609delT								CHSY3 (389283 upstream) : HINT1 (583266 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	129917968	129917968	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:129917968delT								CHSY3 (395642 upstream) : HINT1 (576907 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	130348438	130348438	+	IGR	DEL	A	-	-	rs79931009		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:130348438delA								CHSY3 (826112 upstream) : HINT1 (146437 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	130439686	130439686	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:130439686delA								CHSY3 (917360 upstream) : HINT1 (55189 downstream)																																			---	---	---	---
CDC42SE2	56990	broad.mit.edu	37	5	130611453	130611453	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:130611453delT	uc003kvh.2	+						CDC42SE2_uc003kvi.2_Intron|CDC42SE2_uc003kvj.2_Intron|CDC42SE2_uc003kvk.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)															---	---	---	---
RAPGEF6	51735	broad.mit.edu	37	5	131006382	131006383	+	Intron	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:131006382_131006383delAA	uc003kvp.1	-						FNIP1_uc003kvs.1_Intron|FNIP1_uc003kvt.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	131054951	131054951	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:131054951delA	uc003kvp.1	-						FNIP1_uc003kvs.1_Intron|FNIP1_uc003kvt.1_Intron|FNIP1_uc010jdm.1_Intron|FNIP1_uc003kvu.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)														---	---	---	---
RAPGEF6	51735	broad.mit.edu	37	5	131091114	131091114	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:131091114delA	uc003kvp.1	-						FNIP1_uc003kvs.1_Intron|FNIP1_uc003kvt.1_Intron|FNIP1_uc010jdm.1_Intron|FNIP1_uc003kvu.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)														---	---	---	---
Unknown	0	broad.mit.edu	37	5	131444336	131444336	+	IGR	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:131444336delG								CSF2 (32478 upstream) : P4HA2 (83970 downstream)																																			---	---	---	---
SLC22A4	6583	broad.mit.edu	37	5	131660561	131660561	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:131660561delA	uc003kwq.2	+						SLC22A4_uc010jdq.1_Intron|uc003kwr.3_Intron	NM_003059	NP_003050			solute carrier family 22 member 4						body fluid secretion|sodium ion transport	apical plasma membrane|integral to plasma membrane|mitochondrion	ATP binding|carnitine transporter activity|cation:cation antiporter activity|PDZ domain binding|secondary active organic cation transmembrane transporter activity|symporter activity				0		all_cancers(142;0.0752)|Breast(839;0.198)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)		L-Carnitine(DB00583)													---	---	---	---
Unknown	0	broad.mit.edu	37	5	131740488	131740488	+	IGR	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:131740488delC								SLC22A5 (9186 upstream) : C5orf56 (6185 downstream)																																			---	---	---	---
C5orf56	441108	broad.mit.edu	37	5	131791396	131791396	+	Intron	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:131791396delC	uc003kwy.1	+						C5orf56_uc003kwz.1_Intron|C5orf56_uc010jds.1_Intron|IRF1_uc003kxd.2_Intron	NM_001013717	NP_001013739			hypothetical protein LOC441108												0																		---	---	---	---
RAD50	10111	broad.mit.edu	37	5	131924364	131924364	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-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	132020069	132020072	+	IGR	DEL	AAAA	-	-	rs77277329		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:132020069_132020072delAAAA								IL4 (1701 upstream) : KIF3A (8253 downstream)																																			---	---	---	---
HSPA4	3308	broad.mit.edu	37	5	132414027	132414028	+	Intron	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:132414027_132414028delAA	uc003kyj.2	+							NM_002154	NP_002145			heat shock 70kDa protein 4						cellular chaperone-mediated protein complex assembly|protein import into mitochondrial outer membrane|response to unfolded protein	cytoplasm|nucleus	ATP binding			lung(1)|breast(1)	2			KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)															---	---	---	---
FSTL4	23105	broad.mit.edu	37	5	132535448	132535448	+	Frame_Shift_Del	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:132535448delT	uc003kyn.1	-	16	2086	c.1868delA	c.(1867-1869)AAGfs	p.K623fs	FSTL4_uc003kym.1_Frame_Shift_Del_p.K272fs	NM_015082	NP_055897	Q6MZW2	FSTL4_HUMAN	follistatin-like 4 precursor	623						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	132618951	132618956	+	Intron	DEL	TGTGTC	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:132618951_132618956delTGTGTC	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	132815969	132815969	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:132815969delA	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	132856736	132856736	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:132856736delT	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)															---	---	---	---
SKP1	6500	broad.mit.edu	37	5	133501940	133501941	+	Intron	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:133501940_133501941delAA	uc003kzc.3	-						SKP1_uc003kzd.3_Intron|SKP1_uc010jdv.2_Intron	NM_170679	NP_733779			S-phase kinase-associated protein 1 isoform b						anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|G1/S transition of mitotic cell cycle|histone H2A monoubiquitination|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|S phase of mitotic cell cycle|SCF-dependent proteasomal ubiquitin-dependent protein catabolic process|viral reproduction	cytosol|nucleoplasm|SCF ubiquitin ligase complex	protein binding|ubiquitin-protein ligase activity				0			KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)															---	---	---	---
CDKL3	51265	broad.mit.edu	37	5	133666524	133666524	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:133666524delA	uc003kzf.3	-						CDKL3_uc011cxm.1_Intron|CDKL3_uc011cxn.1_Intron|CDKL3_uc010jdw.2_Intron|CDKL3_uc011cxo.1_Intron|CDKL3_uc011cxp.1_Intron|CDKL3_uc011cxq.1_Intron|CDKL3_uc003kzg.3_Intron|CDKL3_uc011cxr.1_Intron	NM_001113575	NP_001107047			cyclin-dependent kinase-like 3 isoform 1							cytoplasm	ATP binding|cyclin-dependent protein kinase activity			breast(1)	1			KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)															---	---	---	---
PHF15	23338	broad.mit.edu	37	5	133867878	133867878	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:133867878delT	uc003kzo.1	+						PHF15_uc011cxt.1_Intron|PHF15_uc003kzk.2_Intron|PHF15_uc003kzl.2_Intron|PHF15_uc003kzm.2_Intron|PHF15_uc003kzn.2_Intron	NM_015288	NP_056103			PHD finger protein 15						histone H3 acetylation|histone H4-K12 acetylation|histone H4-K5 acetylation|histone H4-K8 acetylation	histone acetyltransferase complex	zinc ion binding				0			KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)															---	---	---	---
Unknown	0	broad.mit.edu	37	5	133925830	133925831	+	IGR	INS	-	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:133925830_133925831insT								PHF15 (6912 upstream) : SAR1B (16289 downstream)																																			---	---	---	---
SEC24A	10802	broad.mit.edu	37	5	133986228	133986229	+	Intron	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:133986228_133986229delTT	uc003kzs.2	+						SEC24A_uc011cxu.1_Intron	NM_021982	NP_068817			SEC24 related gene family, member 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	zinc ion binding				0			KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)															---	---	---	---
DDX46	9879	broad.mit.edu	37	5	134118927	134118927	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-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	134140602	134140602	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:134140602delT	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	134153425	134153425	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:134153425delT	uc003kzw.2	+							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	134778893	134778894	+	IGR	INS	-	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:134778893_134778894insT								H2AFY (43316 upstream) : C5orf20 (1011 downstream)																																			---	---	---	---
SPOCK1	6695	broad.mit.edu	37	5	136467377	136467377	+	Intron	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:136467377delC	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-4200-01A-01D-1126-08	TCGA-BR-4200-11A-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	136659834	136659834	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:136659834delA	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)															---	---	---	---
Unknown	0	broad.mit.edu	37	5	136950124	136950125	+	IGR	DEL	TC	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:136950124_136950125delTC								SPOCK1 (115106 upstream) : KLHL3 (3065 downstream)																																			---	---	---	---
MYOT	9499	broad.mit.edu	37	5	137217571	137217571	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:137217571delA	uc011cye.1	+						MYOT_uc003lbv.2_Intron|MYOT_uc011cyg.1_Intron|MYOT_uc011cyh.1_Intron	NM_001135940	NP_001129412			myotilin isoform b						muscle contraction	actin cytoskeleton|sarcolemma|sarcomere	actin binding|structural constituent of muscle			large_intestine(1)	1			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0109)															---	---	---	---
BRD8	10902	broad.mit.edu	37	5	137496058	137496058	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:137496058delT	uc003lcf.1	-						BRD8_uc003lcc.1_Intron|BRD8_uc011cyl.1_Intron|BRD8_uc003lcg.2_Intron|BRD8_uc003lci.2_Intron|BRD8_uc003lch.2_Intron|BRD8_uc011cym.1_Intron|BRD8_uc010jer.1_Intron|BRD8_uc011cyn.1_Intron	NM_139199	NP_631938			bromodomain containing 8 isoform 2						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)															---	---	---	---
BRD8	10902	broad.mit.edu	37	5	137501416	137501418	+	Intron	DEL	AAA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:137501416_137501418delAAA	uc003lcf.1	-						BRD8_uc003lcc.1_Intron|BRD8_uc011cyl.1_Intron|BRD8_uc003lcg.2_Intron|BRD8_uc003lci.2_Intron|BRD8_uc003lch.2_Intron|BRD8_uc011cym.1_Intron|BRD8_uc010jer.1_Intron|BRD8_uc011cyn.1_Intron	NM_139199	NP_631938			bromodomain containing 8 isoform 2						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	137664464	137664464	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:137664464delT	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	137691643	137691644	+	Intron	INS	-	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:137691643_137691644insT	uc003lcy.1	+							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																		---	---	---	---
KDM3B	51780	broad.mit.edu	37	5	137746178	137746178	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:137746178delA	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																		---	---	---	---
ETF1	2107	broad.mit.edu	37	5	137859225	137859225	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:137859225delA	uc003ldc.3	-						ETF1_uc011cyv.1_Intron|ETF1_uc010jex.2_Intron|ETF1_uc003ldd.3_Intron	NM_004730	NP_004721			eukaryotic translation termination factor 1						nuclear-transcribed mRNA catabolic process, nonsense-mediated decay|protein methylation|regulation of translational termination	cytoplasm	protein binding|ribosome binding|translation release factor activity, codon specific			ovary(2)	2			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00325)															---	---	---	---
Unknown	0	broad.mit.edu	37	5	137967662	137967663	+	IGR	INS	-	A	A	rs139790320	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:137967662_137967663insA								HSPA9 (56547 upstream) : CTNNA1 (121444 downstream)																																			---	---	---	---
SIL1	64374	broad.mit.edu	37	5	138495253	138495253	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:138495253delA	uc003ldo.2	-						SIL1_uc003ldn.2_Intron|SIL1_uc003ldp.2_Intron	NM_001037633	NP_001032722			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				---	---	---	---
DNAJC18	202052	broad.mit.edu	37	5	138771773	138771773	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:138771773delT	uc003len.2	-						DNAJC18_uc010jff.2_Intron	NM_152686	NP_689899			DnaJ (Hsp40) homolog, subfamily C, member 18						protein folding	integral to membrane	heat shock protein binding|unfolded protein binding			ovary(1)|kidney(1)	2			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00325)															---	---	---	---
ECSCR	641700	broad.mit.edu	37	5	138837559	138837559	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:138837559delA	uc011cze.1	-							NM_001077693	NP_001071161			endothelial cell-specific chemotaxis regulator						angiogenesis|cell differentiation|chemotaxis	integral to membrane|plasma membrane					0																		---	---	---	---
TMEM173	340061	broad.mit.edu	37	5	138858996	138858996	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:138858996delA	uc003lep.2	-							NM_198282	NP_938023			transmembrane protein 173						activation of innate immune response|apoptosis|cellular response to exogenous dsRNA|defense response to virus|innate immune response|interferon-beta production|positive regulation of defense response to virus by host|positive regulation of protein binding|positive regulation of protein import into nucleus, translocation|positive regulation of transcription factor import into nucleus|positive regulation of transcription from RNA polymerase II promoter	endoplasmic reticulum membrane|integral to membrane|mitochondrial outer membrane|perinuclear region of cytoplasm|plasma membrane	protein homodimerization activity|protein kinase binding|transcription factor binding			upper_aerodigestive_tract(1)	1			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00325)															---	---	---	---
UBE2D2	7322	broad.mit.edu	37	5	138970712	138970712	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:138970712delT	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)															---	---	---	---
Unknown	0	broad.mit.edu	37	5	139164349	139164350	+	IGR	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:139164349_139164350delTT								CXXC5 (101669 upstream) : PSD2 (11056 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	139428330	139428331	+	IGR	DEL	TT	-	-	rs78686998		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:139428330_139428331delTT								NRG2 (5451 upstream) : PURA (65377 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	139706240	139706243	+	IGR	DEL	TTTT	-	-	rs76777439		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:139706240_139706243delTTTT								PFDN1 (23551 upstream) : HBEGF (6186 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	139760534	139760534	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:139760534delA								SLC4A9 (5812 upstream) : ANKHD1 (20895 downstream)																																			---	---	---	---
ANKHD1-EIF4EBP3	404734	broad.mit.edu	37	5	139890404	139890405	+	Intron	DEL	GT	-	-	rs113479288		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:139890404_139890405delGT	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)															---	---	---	---
ANKHD1	54882	broad.mit.edu	37	5	139919068	139919068	+	3'UTR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:139919068delT	uc003lfr.2	+	34					ANKHD1-EIF4EBP3_uc003lfs.1_Intron|ANKHD1-EIF4EBP3_uc011czh.1_Intron|ANKHD1_uc003lfw.2_3'UTR|ANKHD1_uc010jfl.2_3'UTR|ANKHD1-EIF4EBP3_uc003lfx.1_Intron	NM_017747	NP_060217			ankyrin repeat and KH domain containing 1							cytoplasm|nucleus	protein binding|RNA binding			ovary(5)|skin(2)|lung(1)|breast(1)	9			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)															---	---	---	---
Unknown	0	broad.mit.edu	37	5	139982379	139982379	+	IGR	DEL	A	-	-	rs79422802		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:139982379delA								SLC35A4 (33696 upstream) : CD14 (28938 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	139993479	139993479	+	IGR	DEL	G	-	-	rs6579836		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:139993479delG								SLC35A4 (44796 upstream) : CD14 (17838 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	140448206	140448206	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140448206delT								PCDHB1 (14694 upstream) : PCDHB2 (26031 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	140505721	140505721	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140505721delA								PCDHB4 (520 upstream) : PCDHB5 (9079 downstream)																																			---	---	---	---
DIAPH1	1729	broad.mit.edu	37	5	140932849	140932849	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140932849delT	uc003llb.3	-						DIAPH1_uc003llc.3_Intron|DIAPH1_uc010jgc.1_Intron	NM_005219	NP_005210			diaphanous 1 isoform 1						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)															---	---	---	---
Unknown	0	broad.mit.edu	37	5	141101376	141101376	+	IGR	DEL	T	-	-	rs112642005		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:141101376delT								ARAP3 (39576 upstream) : PCDH1 (131307 downstream)																																			---	---	---	---
SPRY4	81848	broad.mit.edu	37	5	141699961	141699961	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-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				---	---	---	---
SPRY4	81848	broad.mit.edu	37	5	141703621	141703621	+	Intron	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:141703621delG	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	141818183	141818185	+	IGR	DEL	AAA	-	-	rs112702039		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:141818183_141818185delAAA								SPRY4 (113563 upstream) : FGF1 (153559 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	142133427	142133427	+	IGR	DEL	A	-	-	rs35138021		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:142133427delA								FGF1 (55792 upstream) : ARHGAP26 (16865 downstream)																																			---	---	---	---
NR3C1	2908	broad.mit.edu	37	5	142726903	142726906	+	Intron	DEL	ACAC	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:142726903_142726906delACAC	uc003lmz.2	-						NR3C1_uc003lmy.2_Intron|NR3C1_uc003lna.2_Intron|NR3C1_uc003lnb.2_Intron|NR3C1_uc011dbk.1_Intron|NR3C1_uc003lnc.2_Intron|NR3C1_uc003lnd.2_Intron|NR3C1_uc003lne.2_Intron|NR3C1_uc003lnf.2_Intron	NM_000176	NP_000167			glucocorticoid receptor isoform alpha						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)													---	---	---	---
Unknown	0	broad.mit.edu	37	5	142858453	142858453	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:142858453delT								NR3C1 (43376 upstream) : HMHB1 (333273 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	143336689	143336689	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:143336689delT								HMHB1 (136407 upstream) : YIPF5 (201042 downstream)																																			---	---	---	---
KCTD16	57528	broad.mit.edu	37	5	143812201	143812202	+	Intron	DEL	TG	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:143812201_143812202delTG	uc003lnm.1	+						KCTD16_uc003lnn.1_Intron	NM_020768	NP_065819			potassium channel tetramerisation domain							cell junction|postsynaptic membrane|presynaptic membrane|voltage-gated potassium channel complex	voltage-gated potassium channel activity			large_intestine(2)|ovary(1)|skin(1)	4		all_hematologic(541;0.118)	KIRC - Kidney renal clear cell carcinoma(527;0.00111)|Kidney(363;0.00176)															---	---	---	---
Unknown	0	broad.mit.edu	37	5	143933581	143933581	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:143933581delT								KCTD16 (76637 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	144405874	144405874	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:144405874delA								KCTD16 (548930 upstream) : PRELID2 (732708 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	144668705	144668705	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:144668705delT								KCTD16 (811761 upstream) : PRELID2 (469877 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	145017074	145017074	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:145017074delA								None (None upstream) : PRELID2 (121508 downstream)																																			---	---	---	---
LARS	51520	broad.mit.edu	37	5	145493481	145493481	+	3'UTR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:145493481delA	uc003lnx.1	-	32					LARS_uc003lnw.1_3'UTR|LARS_uc011dbq.1_3'UTR|LARS_uc011dbr.1_3'UTR|LARS_uc011dbs.1_3'UTR	NM_020117	NP_064502			leucyl-tRNA synthetase						leucyl-tRNA aminoacylation	cytosol	ATP binding|leucine-tRNA ligase activity|protein binding				0			KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)		L-Leucine(DB00149)													---	---	---	---
RBM27	54439	broad.mit.edu	37	5	145604252	145604252	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:145604252delA	uc003lnz.3	+						RBM27_uc003lny.2_Intron	NM_018989	NP_061862			RNA binding motif protein 27						mRNA processing	cytoplasm|nuclear speck	nucleotide binding|RNA binding|zinc ion binding			central_nervous_system(2)|pancreas(1)	3			KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)															---	---	---	---
Unknown	0	broad.mit.edu	37	5	145727702	145727702	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:145727702delT								POU4F3 (7619 upstream) : TCERG1 (99171 downstream)																																			---	---	---	---
PPP2R2B	5521	broad.mit.edu	37	5	146154066	146154066	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:146154066delA	uc003loe.2	-						PPP2R2B_uc010jgm.2_Intron|PPP2R2B_uc003log.3_Intron|PPP2R2B_uc003lof.3_Intron|PPP2R2B_uc003loi.3_Intron|PPP2R2B_uc003loh.3_Intron|PPP2R2B_uc003loj.3_Intron|PPP2R2B_uc003lok.3_Intron|PPP2R2B_uc011dbu.1_Intron|PPP2R2B_uc011dbv.1_Intron	NM_004576	NP_004567			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	146202534	146202534	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:146202534delT	uc003loe.2	-						PPP2R2B_uc010jgm.2_Intron|PPP2R2B_uc003log.3_Intron|PPP2R2B_uc003lof.3_Intron|PPP2R2B_uc003loi.3_Intron|PPP2R2B_uc003loh.3_Intron|PPP2R2B_uc003loj.3_Intron|PPP2R2B_uc003lok.3_Intron|PPP2R2B_uc011dbu.1_Intron|PPP2R2B_uc011dbv.1_Intron	NM_004576	NP_004567			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	146557133	146557135	+	IGR	DEL	TTT	-	-	rs112046589		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:146557133_146557135delTTT								PPP2R2B (96079 upstream) : STK32A (57444 downstream)																																			---	---	---	---
STK32A	202374	broad.mit.edu	37	5	146646593	146646596	+	Intron	DEL	AAAA	-	-	rs113418402		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:146646593_146646596delAAAA	uc010jgn.1	+						STK32A_uc003lol.3_Intron|STK32A_uc003lom.2_Intron|STK32A_uc011dbw.1_Intron	NM_001112724	NP_001106195			serine/threonine kinase 32A isoform 1								ATP binding|metal ion binding|protein serine/threonine kinase activity			lung(2)|skin(1)	3			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)															---	---	---	---
STK32A	202374	broad.mit.edu	37	5	146736896	146736896	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:146736896delA	uc010jgn.1	+						STK32A_uc003lom.2_Intron|STK32A_uc011dbw.1_Intron	NM_001112724	NP_001106195			serine/threonine kinase 32A isoform 1								ATP binding|metal ion binding|protein serine/threonine kinase activity			lung(2)|skin(1)	3			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)															---	---	---	---
JAKMIP2	9832	broad.mit.edu	37	5	147075214	147075215	+	Intron	DEL	TG	-	-	rs72394697		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:147075214_147075215delTG	uc003loq.1	-						JAKMIP2_uc011dbx.1_Intron|JAKMIP2_uc003lor.1_Intron	NM_014790	NP_055605			janus kinase and microtubule interacting protein							Golgi apparatus				large_intestine(1)|ovary(1)	2			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)															---	---	---	---
Unknown	0	broad.mit.edu	37	5	147182482	147182482	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:147182482delT								JAKMIP2 (20230 upstream) : SPINK1 (21661 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	147216697	147216697	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:147216697delT								SPINK1 (5437 upstream) : SCGB3A2 (41577 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	147745845	147745845	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:147745845delA	uc003lpb.1	-											Homo sapiens cDNA FLJ30191 fis, clone BRACE2001313.																														---	---	---	---
HTR4	3360	broad.mit.edu	37	5	147902626	147902626	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:147902626delA	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	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)													---	---	---	---
HTR4	3360	broad.mit.edu	37	5	147946527	147946528	+	Intron	INS	-	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:147946527_147946528insT	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)													---	---	---	---
HTR4	3360	broad.mit.edu	37	5	147986847	147986847	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:147986847delA	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	149038583	149038584	+	IGR	INS	-	ACTCTC	ACTCTC	rs142438198	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:149038583_149038584insACTCTC								ARHGEF37 (24056 upstream) : PPARGC1B (71280 downstream)																																			---	---	---	---
CSF1R	1436	broad.mit.edu	37	5	149446764	149446764	+	Intron	DEL	T	-	-	rs66517680		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:149446764delT	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)													---	---	---	---
CAMK2A	815	broad.mit.edu	37	5	149652503	149652503	+	Intron	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:149652503delC	uc003lru.2	-						CAMK2A_uc003lrt.2_Intron|CAMK2A_uc010jhe.2_Intron	NM_171825	NP_741960			calcium/calmodulin-dependent protein kinase II						interferon-gamma-mediated signaling pathway|positive regulation of NF-kappaB transcription factor activity|synaptic transmission	cell junction|cytosol|endocytic vesicle membrane|nucleoplasm|presynaptic membrane	ATP binding|calmodulin binding|calmodulin-dependent protein kinase activity			large_intestine(1)	1		all_hematologic(541;0.224)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)															---	---	---	---
CAMK2A	815	broad.mit.edu	37	5	149665309	149665310	+	Intron	DEL	CT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:149665309_149665310delCT	uc003lru.2	-						CAMK2A_uc003lrt.2_Intron|CAMK2A_uc010jhe.2_Intron	NM_171825	NP_741960			calcium/calmodulin-dependent protein kinase II						interferon-gamma-mediated signaling pathway|positive regulation of NF-kappaB transcription factor activity|synaptic transmission	cell junction|cytosol|endocytic vesicle membrane|nucleoplasm|presynaptic membrane	ATP binding|calmodulin binding|calmodulin-dependent protein kinase activity			large_intestine(1)	1		all_hematologic(541;0.224)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)															---	---	---	---
TCOF1	6949	broad.mit.edu	37	5	149774831	149774831	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:149774831delT	uc003lry.2	+						TCOF1_uc011dch.1_Intron|TCOF1_uc003lrz.2_Intron|TCOF1_uc003lrx.2_Intron|TCOF1_uc003lsa.2_Intron	NM_001135243	NP_001128715			Treacher Collins-Franceschetti syndrome 1						skeletal system development	nucleolus	protein binding|transporter activity			ovary(2)|large_intestine(1)	3		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	149873742	149873743	+	IGR	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:149873742_149873743delAA								RPS14 (44423 upstream) : NDST1 (3597 downstream)																																			---	---	---	---
NDST1	3340	broad.mit.edu	37	5	149912088	149912088	+	Intron	DEL	T	-	-	rs68113948		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:149912088delT	uc003lsk.3	+						NDST1_uc011dcj.1_Intron|NDST1_uc003lsl.2_Intron	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)															---	---	---	---
DCTN4	51164	broad.mit.edu	37	5	150111159	150111159	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:150111159delA	uc003lsv.2	-						DCTN4_uc003lsu.2_Intron|DCTN4_uc010jhi.2_Intron|DCTN4_uc010jhj.2_Intron|DCTN4_uc011dck.1_Intron	NM_016221	NP_057305			dynactin 4 (p62) isoform b							centrosome|nucleus	protein N-terminus binding			central_nervous_system(1)	1		Medulloblastoma(196;0.167)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)															---	---	---	---
ANXA6	309	broad.mit.edu	37	5	150500280	150500280	+	Intron	DEL	A	-	-	rs78586132		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:150500280delA	uc003ltl.1	-						ANXA6_uc011dcp.1_Intron|ANXA6_uc003ltm.1_Intron|ANXA6_uc003ltn.1_Intron|ANXA6_uc003lto.1_Intron	NM_001155	NP_001146			annexin VI isoform 1							melanosome	calcium ion binding|calcium-dependent phospholipid binding|protein binding				0		Medulloblastoma(196;0.0912)|all_hematologic(541;0.208)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)															---	---	---	---
SLC36A2	153201	broad.mit.edu	37	5	150718879	150718881	+	Intron	DEL	TTT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:150718879_150718881delTTT	uc003lty.2	-						GM2A_uc011dcs.1_Intron|SLC36A2_uc003ltz.2_Intron|SLC36A2_uc003lua.2_Intron|SLC36A2_uc010jhv.2_Intron|SLC36A2_uc011dct.1_Intron	NM_181776	NP_861441			solute carrier family 36, member 2						cellular nitrogen compound metabolic process	cytoplasm|integral to membrane|plasma membrane	glycine transmembrane transporter activity			ovary(1)|central_nervous_system(1)	2		Medulloblastoma(196;0.109)|all_hematologic(541;0.243)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)															---	---	---	---
GM2A	2760	broad.mit.edu	37	5	150759547	150759552	+	Intron	DEL	ATTAAC	-	-	rs144384954	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:150759547_150759552delATTAAC	uc011dcs.1	+							NM_000405				GM2 ganglioside activator precursor							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)															---	---	---	---
G3BP1	10146	broad.mit.edu	37	5	151174853	151174853	+	Intron	DEL	A	-	-	rs35887288		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:151174853delA	uc003lun.2	+						G3BP1_uc003lum.2_Intron|G3BP1_uc011dcu.1_Intron|G3BP1_uc010jhz.2_Intron|G3BP1_uc003luq.2_5'Flank	NM_005754	NP_005745			Ras-GTPase-activating protein SH3-domain-binding						Ras protein signal transduction|transport	cytosol|nucleus|plasma membrane	ATP binding|ATP-dependent DNA helicase activity|ATP-dependent RNA helicase activity|DNA binding|endonuclease activity|protein binding|RNA binding			skin(3)|ovary(1)	4		all_hematologic(541;0.0338)|Medulloblastoma(196;0.091)	Kidney(363;0.000171)|KIRC - Kidney renal clear cell carcinoma(527;0.000785)															---	---	---	---
GLRA1	2741	broad.mit.edu	37	5	151262752	151262752	+	Intron	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:151262752delC	uc003lut.2	-						GLRA1_uc003lur.2_Intron|GLRA1_uc003lus.2_Intron	NM_001146040	NP_001139512			glycine receptor, alpha 1 isoform 1 precursor						muscle contraction|negative regulation of transmission of nerve impulse|neuropeptide signaling pathway|positive regulation of acrosome reaction|regulation of membrane potential|startle response	cell junction|chloride channel complex|integral to plasma membrane|intracellular membrane-bounded organelle|postsynaptic membrane	extracellular-glycine-gated chloride channel activity|glycine binding|protein binding|receptor activity|taurine binding|transmitter-gated ion channel activity			ovary(1)|central_nervous_system(1)	2		all_hematologic(541;0.0341)|Medulloblastoma(196;0.0912)	Kidney(363;0.000171)|KIRC - Kidney renal clear cell carcinoma(527;0.000785)		Desflurane(DB01189)|Enflurane(DB00228)|Ethanol(DB00898)|Glycine(DB00145)|Halothane(DB01159)|Isoflurane(DB00753)|Methoxyflurane(DB01028)|Sevoflurane(DB01236)													---	---	---	---
Unknown	0	broad.mit.edu	37	5	151550851	151550852	+	Intron	INS	-	TG	TG			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:151550851_151550852insTG	uc003luu.1	+											Homo sapiens cDNA FLJ10720 fis, clone NT2RP3001116.																														---	---	---	---
Unknown	0	broad.mit.edu	37	5	151634399	151634400	+	Intron	INS	-	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:151634399_151634400insT	uc003luu.1	+											Homo sapiens cDNA FLJ10720 fis, clone NT2RP3001116.																														---	---	---	---
Unknown	0	broad.mit.edu	37	5	152793065	152793065	+	IGR	DEL	T	-	-	rs34156154		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:152793065delT								None (None upstream) : GRIA1 (76110 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	153562055	153562057	+	IGR	DEL	TTT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-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-4200-01A-01D-1126-08	TCGA-BR-4200-11A-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	153810615	153810615	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:153810615delA	uc003lvi.2	-											Homo sapiens cDNA FLJ38109 fis, clone D3OST2001788.																														---	---	---	---
C5orf4	10826	broad.mit.edu	37	5	154225233	154225234	+	Intron	INS	-	A	A	rs138531154	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:154225233_154225234insA	uc003lvs.3	-						C5orf4_uc011dde.1_Intron	NM_032385	NP_115761			hypothetical protein LOC10826						fatty acid biosynthetic process	integral to membrane	iron ion binding|oxidoreductase activity			ovary(1)	1	Renal(175;0.00488)	Medulloblastoma(196;0.0354)|all_neural(177;0.0999)	KIRC - Kidney renal clear cell carcinoma(527;0.00112)															---	---	---	---
GEMIN5	25929	broad.mit.edu	37	5	154292267	154292269	+	Intron	DEL	AAA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:154292267_154292269delAAA	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)															---	---	---	---
Unknown	0	broad.mit.edu	37	5	154707848	154707848	+	IGR	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:154707848delC								KIF4B (310163 upstream) : SGCD (427215 downstream)																																			---	---	---	---
SGCD	6444	broad.mit.edu	37	5	155414339	155414339	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:155414339delT	uc003lwa.1	+							NM_172244	NP_758447			delta-sarcoglycan isoform 2						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)															---	---	---	---
SGCD	6444	broad.mit.edu	37	5	155522003	155522003	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:155522003delA	uc003lwa.1	+							NM_172244	NP_758447			delta-sarcoglycan isoform 2						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)															---	---	---	---
SGCD	6444	broad.mit.edu	37	5	155692053	155692054	+	Intron	DEL	AT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:155692053_155692054delAT	uc003lwa.1	+							NM_172244	NP_758447			delta-sarcoglycan isoform 2						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)															---	---	---	---
SGCD	6444	broad.mit.edu	37	5	155713834	155713836	+	Intron	DEL	AAA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:155713834_155713836delAAA	uc003lwa.1	+							NM_172244	NP_758447			delta-sarcoglycan isoform 2						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)															---	---	---	---
SGCD	6444	broad.mit.edu	37	5	156126488	156126489	+	Intron	DEL	TT	-	-	rs113240058		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:156126488_156126489delTT	uc003lwd.3	+						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)															---	---	---	---
SGCD	6444	broad.mit.edu	37	5	156190092	156190092	+	3'UTR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:156190092delA	uc003lwd.3	+	8					SGCD_uc003lwc.3_3'UTR	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)															---	---	---	---
Unknown	0	broad.mit.edu	37	5	156543785	156543786	+	IGR	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:156543785_156543786delTT								HAVCR2 (7647 upstream) : MED7 (21667 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	156565151	156565151	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:156565151delA								HAVCR2 (29013 upstream) : MED7 (302 downstream)																																			---	---	---	---
C5orf52	100190949	broad.mit.edu	37	5	157099544	157099544	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:157099544delT	uc011ddt.1	+						SOX30_uc011dds.1_5'Flank	NM_001145132	NP_001138604			hypothetical protein LOC100190949												0																		---	---	---	---
LSM11	134353	broad.mit.edu	37	5	157183747	157183747	+	RNA	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:157183747delA	uc003lxf.1	+	1		c.868delA								Homo sapiens cDNA FLJ13097 fis, clone NT2RP3002173.						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)															---	---	---	---
Unknown	0	broad.mit.edu	37	5	157572763	157572763	+	IGR	DEL	A	-	-	rs71886663		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:157572763delA								CLINT1 (286595 upstream) : EBF1 (550161 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	157593005	157593005	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:157593005delT								CLINT1 (306837 upstream) : EBF1 (529919 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	157861070	157861072	+	IGR	DEL	TGA	-	-	rs68098066		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:157861070_157861072delTGA								CLINT1 (574902 upstream) : EBF1 (261852 downstream)																																			---	---	---	---
EBF1	1879	broad.mit.edu	37	5	158502281	158502281	+	Intron	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:158502281delC	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	158526597	158526597	+	5'UTR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:158526597delT	uc010jip.2	-	1					EBF1_uc011ddw.1_5'Flank|EBF1_uc011ddx.1_5'UTR|EBF1_uc003lxl.3_5'UTR|uc003lxm.1_5'Flank	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	158608883	158608883	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:158608883delA	uc003lxp.2	-						RNF145_uc011ddy.1_Intron|RNF145_uc003lxo.1_Intron|RNF145_uc011ddz.1_Intron|RNF145_uc010jiq.1_Intron|RNF145_uc011dea.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)															---	---	---	---
RNF145	153830	broad.mit.edu	37	5	158634513	158634513	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:158634513delA	uc003lxp.2	-						RNF145_uc011ddy.1_5'UTR|RNF145_uc003lxo.1_Intron|RNF145_uc011ddz.1_Intron|RNF145_uc010jiq.1_Intron|RNF145_uc011dea.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	159426589	159426589	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:159426589delA								ADRA1B (26572 upstream) : TTC1 (9591 downstream)																																			---	---	---	---
TTC1	7265	broad.mit.edu	37	5	159481665	159481665	+	Intron	DEL	A	-	-	rs74522071		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:159481665delA	uc003lxu.2	+							NM_003314	NP_003305			tetratricopeptide repeat domain 1						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)														---	---	---	---
TTC1	7265	broad.mit.edu	37	5	159490246	159490246	+	Intron	DEL	T	-	-	rs113638818		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:159490246delT	uc003lxu.2	+							NM_003314	NP_003305			tetratricopeptide repeat domain 1						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)														---	---	---	---
Unknown	0	broad.mit.edu	37	5	159608585	159608589	+	IGR	DEL	AAAAG	-	-	rs113532715		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:159608585_159608589delAAAAG								PWWP2A (62133 upstream) : FABP6 (5785 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	159611281	159611281	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:159611281delT								PWWP2A (64829 upstream) : FABP6 (3093 downstream)																																			---	---	---	---
CCNJL	79616	broad.mit.edu	37	5	159697452	159697453	+	Intron	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:159697452_159697453delAA	uc003lyb.1	-						CCNJL_uc011dee.1_Intron|CCNJL_uc003lyc.1_Intron|CCNJL_uc011def.1_Intron	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	159806342	159806343	+	IGR	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:159806342_159806343delAA								C1QTNF2 (8694 upstream) : C5orf54 (13812 downstream)																																			---	---	---	---
SLU7	10569	broad.mit.edu	37	5	159831737	159831737	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:159831737delA	uc003lyg.2	-							NM_006425	NP_006416			step II splicing factor SLU7						alternative nuclear mRNA splicing, via spliceosome|nuclear mRNA 3'-splice site recognition	catalytic step 2 spliceosome|cytoplasm|nuclear speck|small nuclear ribonucleoprotein complex	pre-mRNA 3'-splice site binding|second spliceosomal transesterification activity|zinc ion binding			ovary(1)	1	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)															---	---	---	---
ATP10B	23120	broad.mit.edu	37	5	160088194	160088194	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:160088194delA	uc003lym.1	-						ATP10B_uc003lyp.2_Intron|ATP10B_uc011deg.1_Intron|ATP10B_uc003lyo.2_Intron	NM_025153	NP_079429			ATPase, class V, type 10B						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(3)|central_nervous_system(1)|pancreas(1)	5	Renal(175;0.00196)	Medulloblastoma(196;0.0377)|all_neural(177;0.121)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)															---	---	---	---
ATP10B	23120	broad.mit.edu	37	5	160170560	160170560	+	Intron	DEL	T	-	-	rs72052865		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:160170560delT	uc003lym.1	-						ATP10B_uc003lyp.2_Intron|ATP10B_uc011deg.1_Intron	NM_025153	NP_079429			ATPase, class V, type 10B						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(3)|central_nervous_system(1)|pancreas(1)	5	Renal(175;0.00196)	Medulloblastoma(196;0.0377)|all_neural(177;0.121)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)															---	---	---	---
Unknown	0	broad.mit.edu	37	5	160570345	160570345	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:160570345delA								LOC285629 (204712 upstream) : GABRB2 (145091 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	160673641	160673641	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:160673641delT								LOC285629 (308008 upstream) : GABRB2 (41795 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	161162397	161162397	+	IGR	DEL	C	-	-	rs71611101	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:161162397delC								GABRA6 (32799 upstream) : GABRA1 (111800 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	162694152	162694153	+	IGR	INS	-	TGT	TGT	rs147329196	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:162694152_162694153insTGT								None (None upstream) : CCNG1 (170424 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	163111075	163111076	+	IGR	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-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	163851716	163851718	+	Intron	DEL	AAC	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:163851716_163851718delAAC	uc003lzn.2	+											Homo sapiens, clone IMAGE:4479080, mRNA, partial cds.																														---	---	---	---
Unknown	0	broad.mit.edu	37	5	164535644	164535645	+	IGR	INS	-	TC	TC	rs140017076	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:164535644_164535645insTC								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	164702818	164702820	+	IGR	DEL	TTT	-	-	rs79027016		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:164702818_164702820delTTT								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	164862046	164862046	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:164862046delA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	165858839	165858839	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:165858839delA								None (None upstream) : ODZ2 (853004 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	166133716	166133717	+	IGR	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:166133716_166133717delAA								None (None upstream) : ODZ2 (578126 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	166323185	166323186	+	IGR	DEL	AA	-	-	rs78756742		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:166323185_166323186delAA								None (None upstream) : ODZ2 (388657 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	166403054	166403055	+	IGR	INS	-	TGTG	TGTG	rs2861942		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:166403054_166403055insTGTG								None (None upstream) : ODZ2 (308788 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	166524535	166524535	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:166524535delA								None (None upstream) : ODZ2 (187308 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	166530851	166530851	+	IGR	DEL	A	-	-	rs112026301		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:166530851delA								None (None upstream) : ODZ2 (180992 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	166618792	166618792	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:166618792delT								None (None upstream) : ODZ2 (93051 downstream)																																			---	---	---	---
ODZ2	57451	broad.mit.edu	37	5	167208907	167208907	+	Intron	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:167208907delG	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	167343668	167343668	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:167343668delA	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	167350330	167350332	+	Intron	DEL	AAA	-	-	rs5873074		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:167350330_167350332delAAA	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	167371441	167371444	+	Intron	DEL	AAAA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:167371441_167371444delAAAA	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	167671782	167671782	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:167671782delT	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)														---	---	---	---
SLIT3	6586	broad.mit.edu	37	5	168324422	168324423	+	Intron	DEL	GA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:168324422_168324423delGA	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	168656101	168656102	+	Intron	DEL	AG	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:168656101_168656102delAG	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)															---	---	---	---
Unknown	0	broad.mit.edu	37	5	168788342	168788342	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:168788342delA								SLIT3 (60209 upstream) : CCDC99 (222296 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	168994879	168994879	+	IGR	DEL	T	-	-	rs79682451		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:168994879delT								SLIT3 (266746 upstream) : CCDC99 (15759 downstream)																																			---	---	---	---
DOCK2	1794	broad.mit.edu	37	5	169262764	169262764	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:169262764delT	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)															---	---	---	---
Unknown	0	broad.mit.edu	37	5	170277357	170277358	+	IGR	DEL	TA	-	-	rs35224291		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:170277357_170277358delTA								GABRP (36309 upstream) : RANBP17 (11664 downstream)																																			---	---	---	---
RANBP17	64901	broad.mit.edu	37	5	170341158	170341158	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:170341158delT	uc003mba.2	+						RANBP17_uc003max.1_Intron|RANBP17_uc003may.1_Intron|RANBP17_uc003maz.1_Intron|RANBP17_uc010jjr.1_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	170595849	170595850	+	Intron	DEL	TC	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:170595849_170595850delTC	uc003mba.2	+						RANBP17_uc003max.1_Intron|RANBP17_uc003may.1_Intron|RANBP17_uc003maz.1_Intron|RANBP17_uc010jjr.1_Intron|RANBP17_uc003mbb.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	170610064	170610064	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:170610064delT	uc003mba.2	+						RANBP17_uc003mbb.2_Intron|RANBP17_uc003mbd.2_5'Flank|RANBP17_uc010jjs.2_5'Flank|RANBP17_uc003mbc.2_5'Flank	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	170626448	170626449	+	Intron	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:170626448_170626449delAA	uc003mba.2	+						RANBP17_uc003mbb.2_Intron|RANBP17_uc003mbd.2_Intron|RANBP17_uc010jjs.2_Intron|RANBP17_uc003mbc.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	170649639	170649639	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:170649639delT	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	170655937	170655937	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:170655937delA	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	171077307	171077309	+	IGR	DEL	AAA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:171077307_171077309delAAA								FGF18 (193145 upstream) : FBXW11 (211247 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	171220959	171220959	+	IGR	DEL	C	-	-	rs11339138		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:171220959delC								FGF18 (336797 upstream) : FBXW11 (67597 downstream)																																			---	---	---	---
STK10	6793	broad.mit.edu	37	5	171614500	171614500	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:171614500delA	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)															---	---	---	---
UBTD2	92181	broad.mit.edu	37	5	171696495	171696497	+	Intron	DEL	AAA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:171696495_171696497delAAA	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	171750413	171750414	+	IGR	INS	-	TGTG	TGTG	rs71927486		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:171750413_171750414insTGTG								UBTD2 (39618 upstream) : SH3PXD2B (10091 downstream)																																			---	---	---	---
SH3PXD2B	285590	broad.mit.edu	37	5	171820954	171820955	+	Intron	DEL	TT	-	-	rs111904453		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:171820954_171820955delTT	uc003mbr.2	-						SH3PXD2B_uc003mbs.1_Intron	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	171898530	171898530	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:171898530delT								SH3PXD2B (17003 upstream) : NEURL1B (169746 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	172021116	172021116	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:172021116delA								SH3PXD2B (139589 upstream) : NEURL1B (47160 downstream)																																			---	---	---	---
NEURL1B	54492	broad.mit.edu	37	5	172109580	172109580	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:172109580delA	uc003mbt.2	+							NM_001142651	NP_001136123			neuralized homolog 1B								ligase activity|zinc ion binding				0																		---	---	---	---
ERGIC1	57222	broad.mit.edu	37	5	172303946	172303946	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:172303946delA	uc003mbw.3	+							NM_001031711	NP_001026881			endoplasmic reticulum-golgi intermediate						ER to Golgi vesicle-mediated transport	endoplasmic reticulum membrane|ER-Golgi intermediate compartment membrane|Golgi membrane|integral to membrane	protein binding			skin(2)|ovary(1)	3	Renal(175;0.000159)|Lung NSC(126;0.00344)|all_lung(126;0.00594)	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	172657122	172657122	+	IGR	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:172657122delC								BNIP1 (65733 upstream) : NKX2-5 (2016 downstream)																																			---	---	---	---
C5orf47	133491	broad.mit.edu	37	5	173418511	173418512	+	Intron	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:173418511_173418512delTT	uc003mcw.3	+						C5orf47_uc003mcv.2_Intron	NM_001144954	NP_001138426			hypothetical protein LOC133491												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	5	173638214	173638214	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:173638214delA								HMP19 (102033 upstream) : MSX2 (513361 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	173740020	173740021	+	IGR	DEL	AG	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:173740020_173740021delAG								HMP19 (203839 upstream) : MSX2 (411554 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	173789016	173789017	+	IGR	DEL	GA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:173789016_173789017delGA								HMP19 (252835 upstream) : MSX2 (362558 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	173945680	173945681	+	IGR	INS	-	C	C	rs12188599	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:173945680_173945681insC								HMP19 (409499 upstream) : MSX2 (205894 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	174012901	174012901	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:174012901delT								HMP19 (476720 upstream) : MSX2 (138674 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	174085664	174085664	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:174085664delT								HMP19 (549483 upstream) : MSX2 (65911 downstream)																																			---	---	---	---
SFXN1	94081	broad.mit.edu	37	5	174949356	174949356	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-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)															---	---	---	---
CLTB	1212	broad.mit.edu	37	5	175823955	175823956	+	Intron	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:175823955_175823956delTT	uc003meh.2	-						CLTB_uc003mei.2_Intron|CLTB_uc011dfn.1_Intron	NM_007097	NP_009028			clathrin, light polypeptide isoform b						intracellular protein transport|vesicle-mediated transport	clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle	protein binding|structural molecule activity				0	all_cancers(89;0.00522)|Renal(175;0.000269)|Lung NSC(126;0.0105)|all_lung(126;0.0168)	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;0.000178)	Kidney(146;0.098)														---	---	---	---
ZNF346	23567	broad.mit.edu	37	5	176495843	176495843	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:176495843delT	uc003mfk.1	+						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	176634924	176634925	+	Intron	INS	-	GT	GT	rs142847055	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:176634924_176634925insGT	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	176699883	176699884	+	Intron	INS	-	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:176699883_176699884insA	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)			---	---	---	---
Unknown	0	broad.mit.edu	37	5	177023943	177023943	+	IGR	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:177023943delG								TMED9 (846 upstream) : B4GALT7 (3229 downstream)																																			---	---	---	---
FAM153A	285596	broad.mit.edu	37	5	177146057	177146057	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:177146057delT	uc003mib.1	-							NM_173663				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	177859756	177859756	+	Intron	DEL	G	-	-	rs111857288		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:177859756delG	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	178107028	178107029	+	IGR	DEL	AA	-	-	rs76931826		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:178107028_178107029delAA								CLK4 (49412 upstream) : ZNF354A (31502 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	178186559	178186561	+	IGR	DEL	TTT	-	-	rs111822095		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:178186559_178186561delTTT								ZNF354A (28856 upstream) : AACSL (5305 downstream)																																			---	---	---	---
AACSL	729522	broad.mit.edu	37	5	178206421	178206421	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:178206421delT	uc011dgl.1	-						AACSL_uc003mjk.2_Intron					Homo sapiens acetoacetyl-CoA synthetase-like, mRNA (cDNA clone IMAGE:3945810), partial cds.												0																		---	---	---	---
AACSL	729522	broad.mit.edu	37	5	178223656	178223656	+	Intron	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-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																		---	---	---	---
AACSL	729522	broad.mit.edu	37	5	178237708	178237708	+	Intron	DEL	A	-	-	rs72101809		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:178237708delA	uc011dgl.1	-						AACSL_uc003mjk.2_Intron					Homo sapiens acetoacetyl-CoA synthetase-like, mRNA (cDNA clone IMAGE:3945810), partial cds.												0																		---	---	---	---
ZNF454	285676	broad.mit.edu	37	5	178372696	178372696	+	Intron	DEL	G	-	-	rs78217989		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:178372696delG	uc003mjo.1	+						ZNF454_uc010jkz.1_Intron|ZNF454_uc003mjp.2_Intron	NM_182594	NP_872400			zinc finger protein 454						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	178591151	178591152	+	Intron	DEL	CT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:178591151_178591152delCT	uc003mjw.2	-						ADAMTS2_uc011dgm.1_Intron	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)														---	---	---	---
CANX	821	broad.mit.edu	37	5	179135170	179135170	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-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)													---	---	---	---
MAML1	9794	broad.mit.edu	37	5	179218578	179218582	+	Intron	DEL	AAAAA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:179218578_179218582delAAAAA	uc003mkn.1	+						LTC4S_uc003mko.2_5'Flank	NM_014757	NP_055572			mastermind-like 1						Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	nuclear speck	peptide antigen binding|protein kinase binding|transcription coactivator activity			lung(4)|ovary(2)	6	all_cancers(89;0.000197)|all_epithelial(37;6.7e-05)|Renal(175;0.000159)|Lung NSC(126;0.00121)|all_lung(126;0.00218)	all_cancers(40;0.0308)|Medulloblastoma(196;0.00498)|all_neural(177;0.0138)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)															---	---	---	---
SQSTM1	8878	broad.mit.edu	37	5	179246978	179246980	+	5'Flank	DEL	CCT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:179246978_179246980delCCT	uc003mkw.3	+						SQSTM1_uc011dgr.1_Intron|SQSTM1_uc011dgs.1_Intron|SQSTM1_uc003mkv.3_5'Flank|SQSTM1_uc003mkx.2_5'Flank	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				---	---	---	---
TBC1D9B	23061	broad.mit.edu	37	5	179292509	179292509	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:179292509delA	uc003mlh.2	-						TBC1D9B_uc003mli.2_Intron|TBC1D9B_uc003mlj.2_Intron|TBC1D9B_uc003mlf.2_Intron|TBC1D9B_uc003mlg.2_Intron|TBC1D9B_uc011dgv.1_Intron	NM_198868	NP_942568			TBC1 domain family, member 9B (with GRAM domain)							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)															---	---	---	---
RNF130	55819	broad.mit.edu	37	5	179455563	179455566	+	Intron	DEL	GAAC	-	-	rs143317528		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:179455563_179455566delGAAC	uc003mll.1	-						RNF130_uc003mlm.1_Intron	NM_018434	NP_060904			ring finger protein 130 precursor						apoptosis	cytoplasm|integral to membrane|nucleus	ubiquitin-protein ligase activity|zinc ion binding			lung(2)|ovary(1)	3	all_cancers(89;5.49e-05)|all_epithelial(37;1.94e-05)|Renal(175;0.000159)|Lung NSC(126;0.00118)|all_lung(126;0.00212)	all_cancers(40;0.0294)|Medulloblastoma(196;0.00498)|all_neural(177;0.0138)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)															---	---	---	---
RNF130	55819	broad.mit.edu	37	5	179483083	179483084	+	Intron	INS	-	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:179483083_179483084insA	uc003mll.1	-						RNF130_uc003mlm.1_Intron	NM_018434	NP_060904			ring finger protein 130 precursor						apoptosis	cytoplasm|integral to membrane|nucleus	ubiquitin-protein ligase activity|zinc ion binding			lung(2)|ovary(1)	3	all_cancers(89;5.49e-05)|all_epithelial(37;1.94e-05)|Renal(175;0.000159)|Lung NSC(126;0.00118)|all_lung(126;0.00212)	all_cancers(40;0.0294)|Medulloblastoma(196;0.00498)|all_neural(177;0.0138)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)															---	---	---	---
Unknown	0	broad.mit.edu	37	5	179503032	179503032	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:179503032delT								RNF130 (3923 upstream) : RASGEF1C (24764 downstream)																																			---	---	---	---
MAPK9	5601	broad.mit.edu	37	5	179689017	179689017	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:179689017delA	uc003mls.3	-						MAPK9_uc003mlt.3_Intron|MAPK9_uc010jlc.2_Intron|MAPK9_uc003mlv.3_Intron|MAPK9_uc011dgx.1_Intron	NM_002752	NP_002743			mitogen-activated protein kinase 9 isoform JNK2						innate immune response|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|positive regulation of gene expression|positive regulation of macrophage derived foam cell differentiation|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|protein binding|protein binding			central_nervous_system(2)|upper_aerodigestive_tract(1)|large_intestine(1)	4	all_cancers(89;6.54e-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)	all_cancers(40;0.0236)|Medulloblastoma(196;0.0133)|all_neural(177;0.0199)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)															---	---	---	---
MAPK9	5601	broad.mit.edu	37	5	179696121	179696121	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:179696121delA	uc003mls.3	-						MAPK9_uc003mlt.3_Intron|MAPK9_uc010jlc.2_Intron|MAPK9_uc003mlv.3_Intron|MAPK9_uc011dgx.1_Intron	NM_002752	NP_002743			mitogen-activated protein kinase 9 isoform JNK2						innate immune response|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|positive regulation of gene expression|positive regulation of macrophage derived foam cell differentiation|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|protein binding|protein binding			central_nervous_system(2)|upper_aerodigestive_tract(1)|large_intestine(1)	4	all_cancers(89;6.54e-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)	all_cancers(40;0.0236)|Medulloblastoma(196;0.0133)|all_neural(177;0.0199)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)															---	---	---	---
CNOT6	57472	broad.mit.edu	37	5	179927107	179927107	+	Intron	DEL	C	-	-	rs11294788		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:179927107delC	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)														---	---	---	---
FLT4	2324	broad.mit.edu	37	5	180042675	180042676	+	Intron	INS	-	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:180042675_180042676insG	uc003mma.3	-						FLT4_uc003mlz.3_Intron	NM_002020	NP_002011			fms-related tyrosine kinase 4 isoform 2						positive regulation of cell proliferation	integral to plasma membrane	ATP binding|protein phosphatase binding|vascular endothelial growth factor receptor activity			lung(7)|skin(2)|ovary(2)|stomach(1)|central_nervous_system(1)|breast(1)|kidney(1)	15	all_cancers(89;2.21e-05)|all_epithelial(37;5.29e-06)|Renal(175;0.000159)|Lung NSC(126;0.00199)|all_lung(126;0.00351)|Breast(19;0.114)	all_cancers(40;0.00245)|Medulloblastoma(196;0.0133)|all_neural(177;0.0199)|all_hematologic(541;0.163)|Ovarian(839;0.238)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)	all cancers(165;0.134)	Sorafenib(DB00398)|Sunitinib(DB01268)									Congenital_Hereditary_Lymphedema				---	---	---	---
FLT4	2324	broad.mit.edu	37	5	180078901	180078901	+	5'Flank	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:180078901delT	uc003mma.3	-						FLT4_uc003mlz.3_5'Flank|FLT4_uc011dgy.1_5'Flank|FLT4_uc011dgz.1_5'Flank|FLT4_uc011dha.1_5'Flank	NM_002020	NP_002011			fms-related tyrosine kinase 4 isoform 2						positive regulation of cell proliferation	integral to plasma membrane	ATP binding|protein phosphatase binding|vascular endothelial growth factor receptor activity			lung(7)|skin(2)|ovary(2)|stomach(1)|central_nervous_system(1)|breast(1)|kidney(1)	15	all_cancers(89;2.21e-05)|all_epithelial(37;5.29e-06)|Renal(175;0.000159)|Lung NSC(126;0.00199)|all_lung(126;0.00351)|Breast(19;0.114)	all_cancers(40;0.00245)|Medulloblastoma(196;0.0133)|all_neural(177;0.0199)|all_hematologic(541;0.163)|Ovarian(839;0.238)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)	all cancers(165;0.134)	Sorafenib(DB00398)|Sunitinib(DB01268)									Congenital_Hereditary_Lymphedema				---	---	---	---
Unknown	0	broad.mit.edu	37	5	180553735	180553736	+	IGR	INS	-	AC	AC	rs149308949	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:180553735_180553736insAC								BTNL9 (65213 upstream) : OR2V2 (28207 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	180636234	180636234	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:180636234delA								TRIM7 (4057 upstream) : TRIM41 (14072 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	287793	287794	+	IGR	DEL	TC	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:287793_287794delTC								None (None upstream) : DUSP22 (4307 downstream)																																			---	---	---	---
DUSP22	56940	broad.mit.edu	37	6	293509	293510	+	Intron	INS	-	CCACC	CCACC	rs148652335	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:293509_293510insCCACC	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)														---	---	---	---
DUSP22	56940	broad.mit.edu	37	6	332645	332648	+	Intron	DEL	TTTT	-	-	rs67905135		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:332645_332648delTTTT	uc003msx.2	+						DUSP22_uc011dhn.1_Intron|DUSP22_uc003msy.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)														---	---	---	---
EXOC2	55770	broad.mit.edu	37	6	523075	523075	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:523075delA	uc003mtd.2	-						EXOC2_uc003mte.2_Intron|EXOC2_uc011dho.1_Intron	NM_018303	NP_060773			Sec5 protein						exocytosis|protein transport					breast(4)|ovary(2)|pancreas(1)	7	Ovarian(93;0.0733)	Breast(5;0.0014)|all_lung(73;0.0697)|all_hematologic(90;0.0897)		OV - Ovarian serous cystadenocarcinoma(45;0.0507)|BRCA - Breast invasive adenocarcinoma(62;0.14)														---	---	---	---
EXOC2	55770	broad.mit.edu	37	6	588804	588805	+	Intron	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:588804_588805delTT	uc003mtd.2	-						EXOC2_uc003mte.2_Intron|EXOC2_uc011dho.1_Intron	NM_018303	NP_060773			Sec5 protein						exocytosis|protein transport					breast(4)|ovary(2)|pancreas(1)	7	Ovarian(93;0.0733)	Breast(5;0.0014)|all_lung(73;0.0697)|all_hematologic(90;0.0897)		OV - Ovarian serous cystadenocarcinoma(45;0.0507)|BRCA - Breast invasive adenocarcinoma(62;0.14)														---	---	---	---
Unknown	0	broad.mit.edu	37	6	1426487	1426487	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:1426487delT								FOXF2 (30656 upstream) : FOXC1 (184194 downstream)																																			---	---	---	---
GMDS	2762	broad.mit.edu	37	6	1678814	1678814	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:1678814delT	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)														---	---	---	---
GMDS	2762	broad.mit.edu	37	6	1713004	1713004	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:1713004delA	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	2368007	2368007	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:2368007delT								GMDS (122161 upstream) : C6orf195 (254965 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	2556512	2556512	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:2556512delA								GMDS (310666 upstream) : C6orf195 (66460 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	2640089	2640089	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:2640089delT								C6orf195 (4791 upstream) : MYLK4 (23775 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	3569809	3569810	+	IGR	INS	-	AC	AC	rs138363962	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:3569809_3569810insAC								SLC22A23 (113016 upstream) : C6orf145 (153026 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	3982562	3982562	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:3982562delA								FAM50B (131012 upstream) : PRPF4B (39007 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	4424269	4424269	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:4424269delA								PECI (288438 upstream) : CDYL (282124 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	4463288	4463289	+	IGR	INS	-	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:4463288_4463289insA								PECI (327457 upstream) : CDYL (243104 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	4478577	4478577	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:4478577delA								PECI (342746 upstream) : CDYL (227816 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	4482052	4482055	+	IGR	DEL	AAAG	-	-	rs35835649		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:4482052_4482055delAAAG								PECI (346221 upstream) : CDYL (224338 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	4549420	4549423	+	IGR	DEL	AGGA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:4549420_4549423delAGGA								PECI (413589 upstream) : CDYL (156970 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	5072245	5072245	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:5072245delT	uc003mwn.1	+											Homo sapiens cDNA FLJ37615 fis, clone BRCOC2011996.																														---	---	---	---
FARS2	10667	broad.mit.edu	37	6	5406954	5406955	+	Intron	DEL	TA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:5406954_5406955delTA	uc010jnv.1	+						FARS2_uc003mwr.2_Intron|FARS2_uc003mws.1_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	6050855	6050855	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:6050855delT								NRN1 (43222 upstream) : F13A1 (93457 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	6340411	6340411	+	IGR	DEL	T	-	-	rs111530530		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:6340411delT								F13A1 (19487 upstream) : LOC285780 (6288 downstream)																																			---	---	---	---
LOC285780	285780	broad.mit.edu	37	6	6389653	6389654	+	Intron	DEL	TC	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:6389653_6389654delTC	uc003mww.3	-						LOC285780_uc003mwx.2_Intron	NR_026970				Homo sapiens cDNA FLJ33708 fis, clone BRAWH2007862.												0																		---	---	---	---
LOC285780	285780	broad.mit.edu	37	6	6434266	6434266	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:6434266delA	uc003mww.3	-						LOC285780_uc003mwx.2_Intron	NR_026970				Homo sapiens cDNA FLJ33708 fis, clone BRAWH2007862.												0																		---	---	---	---
LY86	9450	broad.mit.edu	37	6	6612749	6612750	+	Intron	INS	-	A	A	rs143724730	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:6612749_6612750insA	uc003mwy.1	+						LOC285780_uc003mww.3_Intron|LOC285780_uc003mwx.2_Intron	NM_004271	NP_004262			MD-1, RP105-associated precursor						apoptosis|cell proliferation|humoral immune response|inflammatory response|innate immune response	extracellular space|plasma membrane					0	Ovarian(93;0.0377)																	---	---	---	---
Unknown	0	broad.mit.edu	37	6	6771706	6771708	+	IGR	DEL	GAG	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:6771706_6771708delGAG								LY86 (116490 upstream) : RREB1 (336480 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	7016519	7016522	+	IGR	DEL	AAAA	-	-	rs76856171		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:7016519_7016522delAAAA								LY86 (361303 upstream) : RREB1 (91666 downstream)																																			---	---	---	---
RREB1	6239	broad.mit.edu	37	6	7160356	7160357	+	Intron	DEL	TT	-	-	rs66699485		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:7160356_7160357delTT	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	7216180	7216182	+	Intron	DEL	GAA	-	-	rs5874085		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:7216180_7216182delGAA	uc003mxc.2	+						RREB1_uc003mxb.2_Intron|RREB1_uc010jnx.2_Intron|RREB1_uc003mxd.2_3'UTR	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	7240518	7240519	+	Intron	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:7240518_7240519delTT	uc003mxc.2	+						RREB1_uc003mxb.2_Intron|RREB1_uc010jnx.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)																---	---	---	---
SSR1	6745	broad.mit.edu	37	6	7289894	7289894	+	3'UTR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:7289894delA	uc003mxf.3	-	8					SSR1_uc003mxg.3_3'UTR|SSR1_uc010jny.2_3'UTR	NM_003144	NP_003135			signal sequence receptor, alpha precursor						cotranslational protein targeting to membrane|positive regulation of cell proliferation	endoplasmic reticulum membrane|integral to membrane	signal sequence binding				0	Ovarian(93;0.0398)																	---	---	---	---
CAGE1	285782	broad.mit.edu	37	6	7338983	7338983	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:7338983delT	uc003mxi.2	-						CAGE1_uc003mxh.2_Intron|CAGE1_uc003mxj.2_Intron|CAGE1_uc003mxk.1_Intron	NM_205864	NP_995586			cancer antigen 1												0	Ovarian(93;0.0418)																	---	---	---	---
Unknown	0	broad.mit.edu	37	6	7443123	7443127	+	IGR	DEL	GTTTT	-	-	rs144397488		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:7443123_7443127delGTTTT								RIOK1 (24855 upstream) : DSP (98743 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	7503910	7503910	+	IGR	DEL	T	-	-	rs11340671		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:7503910delT								RIOK1 (85642 upstream) : DSP (37960 downstream)																																			---	---	---	---
SNRNP48	154007	broad.mit.edu	37	6	7595890	7595890	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:7595890delA	uc003mxr.2	+						SNRNP48_uc003mxs.2_Intron	NM_152551	NP_689764			U11/U12 snRNP 48K						mRNA processing	cytoplasm|U12-type spliceosomal complex	metal ion binding				0																		---	---	---	---
TXNDC5	81567	broad.mit.edu	37	6	7894500	7894502	+	Intron	DEL	TTT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:7894500_7894502delTTT	uc003mxv.2	-						TXNDC5_uc003mxw.2_Intron|TXNDC5_uc010jnz.2_Intron|TXNDC5_uc010joa.1_Intron	NM_030810	NP_110437			thioredoxin domain containing 5 isoform 1						anti-apoptosis|cell redox homeostasis|cellular membrane organization|glycerol ether metabolic process|post-Golgi vesicle-mediated transport	endoplasmic reticulum lumen|lysosomal lumen	electron carrier activity|isomerase activity|protein disulfide oxidoreductase activity				0	Ovarian(93;0.0398)																	---	---	---	---
TXNDC5	81567	broad.mit.edu	37	6	7961791	7961792	+	Intron	DEL	CT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:7961791_7961792delCT	uc003mxw.2	-							NM_001145549	NP_001139021			thioredoxin domain containing 5 isoform 3						anti-apoptosis|cell redox homeostasis|cellular membrane organization|glycerol ether metabolic process|post-Golgi vesicle-mediated transport	endoplasmic reticulum lumen|lysosomal lumen	electron carrier activity|isomerase activity|protein disulfide oxidoreductase activity				0	Ovarian(93;0.0398)																	---	---	---	---
Unknown	0	broad.mit.edu	37	6	8718266	8718266	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:8718266delT								HULC (64189 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	9197509	9197509	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:9197509delT								HULC (543432 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	9403970	9403970	+	IGR	DEL	A	-	-	rs145189978		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:9403970delA								HULC (749893 upstream) : TFAP2A (992947 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	9568735	9568735	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:9568735delA								HULC (914658 upstream) : TFAP2A (828182 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	9947189	9947189	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:9947189delA	uc003myn.2	-						uc010joi.1_Intron|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	10298356	10298356	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:10298356delA								None (None upstream) : TFAP2A (98561 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	10347189	10347189	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:10347189delT								None (None upstream) : TFAP2A (49728 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	10350392	10350392	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:10350392delT								None (None upstream) : TFAP2A (46525 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	10443693	10443693	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:10443693delA								C6orf218 (8638 upstream) : GCNT2 (48763 downstream)																																			---	---	---	---
C6orf52	347744	broad.mit.edu	37	6	10677769	10677769	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:10677769delT	uc011dij.1	-						C6orf52_uc011dik.1_Intron|C6orf52_uc003mzf.3_Intron|C6orf52_uc011dil.1_Intron	NM_001145020	NP_001138492			hypothetical protein LOC347744												0																		---	---	---	---
MAK	4117	broad.mit.edu	37	6	10800760	10800760	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:10800760delT	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)																---	---	---	---
MAK	4117	broad.mit.edu	37	6	10808864	10808864	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-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)																---	---	---	---
ELOVL2	54898	broad.mit.edu	37	6	11005392	11005392	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:11005392delA	uc003mzp.3	-							NM_017770	NP_060240			elongation of very long chain fatty acids-like						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	Breast(50;0.0418)|Ovarian(93;0.0919)	all_hematologic(90;0.117)	Epithelial(50;0.176)															---	---	---	---
HIVEP1	3096	broad.mit.edu	37	6	12162582	12162582	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:12162582delT	uc003nac.2	+						HIVEP1_uc011diq.1_Intron	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	12649345	12649345	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:12649345delT								EDN1 (351919 upstream) : PHACTR1 (67543 downstream)																																			---	---	---	---
PHACTR1	221692	broad.mit.edu	37	6	13050471	13050471	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:13050471delT	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	13251233	13251234	+	Intron	DEL	AC	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:13251233_13251234delAC	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)															---	---	---	---
RANBP9	10048	broad.mit.edu	37	6	13631076	13631077	+	Intron	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:13631076_13631077delTT	uc003nbb.2	-						RANBP9_uc003nba.2_Intron	NM_005493	NP_005484			RAN binding protein 9						axon guidance|microtubule nucleation|protein complex assembly	cytosol|microtubule associated complex|nucleus	Ran GTPase binding			lung(1)|skin(1)	2	Breast(50;0.00669)|Ovarian(93;0.0634)	all_hematologic(90;0.117)	Epithelial(50;0.223)															---	---	---	---
Unknown	0	broad.mit.edu	37	6	13757714	13757716	+	IGR	DEL	AAA	-	-	rs76912107		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:13757714_13757716delAAA								RANBP9 (45918 upstream) : CCDC90A (33305 downstream)																																			---	---	---	---
CD83	9308	broad.mit.edu	37	6	14134204	14134205	+	Intron	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:14134204_14134205delAA	uc003nbi.2	+						CD83_uc003nbh.2_Intron	NM_004233	NP_004224			CD83 antigen isoform a						defense response|humoral immune response|signal transduction	integral to plasma membrane					0	Breast(50;0.00245)|Ovarian(93;0.137)	all_hematologic(90;0.117)																---	---	---	---
Unknown	0	broad.mit.edu	37	6	14227961	14227961	+	IGR	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:14227961delG								CD83 (90815 upstream) : None (None downstream)																																	OREG0007352	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	6	14253455	14253455	+	IGR	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:14253455delC								CD83 (116309 upstream) : JARID2 (992279 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	14447943	14447943	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:14447943delA								CD83 (310797 upstream) : JARID2 (797791 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	14583014	14583014	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:14583014delT								CD83 (445868 upstream) : JARID2 (662720 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	15155866	15155866	+	IGR	DEL	T	-	-	rs35721781		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:15155866delT								None (None upstream) : JARID2 (89868 downstream)																																			---	---	---	---
JARID2	3720	broad.mit.edu	37	6	15280435	15280435	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:15280435delA	uc003nbj.2	+						JARID2_uc011diu.1_Intron|JARID2_uc011div.1_Intron	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)																---	---	---	---
JARID2	3720	broad.mit.edu	37	6	15405214	15405214	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:15405214delT	uc003nbj.2	+						JARID2_uc011diu.1_Intron|JARID2_uc011div.1_Intron|JARID2_uc011diw.1_Intron	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)																---	---	---	---
ATXN1	6310	broad.mit.edu	37	6	16304671	16304671	+	3'UTR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:16304671delA	uc003nbt.2	-	9					ATXN1_uc010jpi.2_3'UTR|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)																---	---	---	---
ATXN1	6310	broad.mit.edu	37	6	16578976	16578978	+	Intron	DEL	AAA	-	-	rs71748450		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:16578976_16578978delAAA	uc003nbt.2	-						ATXN1_uc010jpi.2_Intron|ATXN1_uc010jpj.1_Intron|ATXN1_uc003nbu.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)																---	---	---	---
ATXN1	6310	broad.mit.edu	37	6	16653263	16653263	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:16653263delA	uc003nbt.2	-						ATXN1_uc010jpi.2_Intron|ATXN1_uc010jpj.1_Intron|ATXN1_uc003nbu.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	17022286	17022286	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:17022286delT								ATXN1 (260565 upstream) : RBM24 (259523 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	17162943	17162947	+	IGR	DEL	AAAAA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:17162943_17162947delAAAAA								ATXN1 (401222 upstream) : RBM24 (118862 downstream)																																			---	---	---	---
CAP2	10486	broad.mit.edu	37	6	17409603	17409603	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:17409603delA	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)															---	---	---	---
Unknown	0	broad.mit.edu	37	6	17729836	17729836	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:17729836delT								NUP153 (23018 upstream) : KIF13A (30749 downstream)																																			---	---	---	---
KIF13A	63971	broad.mit.edu	37	6	17773037	17773037	+	Intron	DEL	T	-	-	rs35738577		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:17773037delT	uc003ncg.3	-						KIF13A_uc003ncf.2_Intron|KIF13A_uc003nch.3_Intron|KIF13A_uc003nci.3_Intron|KIF13A_uc003nce.1_Intron	NM_022113	NP_071396			kinesin family member 13A isoform a						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)															---	---	---	---
KIF13A	63971	broad.mit.edu	37	6	17773894	17773894	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:17773894delT	uc003ncg.3	-						KIF13A_uc003ncf.2_Intron|KIF13A_uc003nch.3_Intron|KIF13A_uc003nci.3_Intron|KIF13A_uc003nce.1_Intron	NM_022113	NP_071396			kinesin family member 13A isoform a						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)															---	---	---	---
KDM1B	221656	broad.mit.edu	37	6	18171050	18171050	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:18171050delT	uc003ncn.1	+							NM_153042	NP_694587			amine oxidase (flavin containing) domain 1						multicellular organismal development|regulation of DNA methylation|regulation of gene expression by genetic imprinting|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	histone demethylase activity (H3-dimethyl-K4 specific)|histone demethylase activity (H3-monomethyl-K4 specific)|oxidoreductase activity|zinc ion binding			skin(1)	1																		---	---	---	---
KDM1B	221656	broad.mit.edu	37	6	18221153	18221153	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:18221153delT	uc003nco.1	+						KDM1B_uc003ncn.1_Intron|KDM1B_uc003ncp.1_Intron|KDM1B_uc003ncq.1_Intron	NM_153042	NP_694587			amine oxidase (flavin containing) domain 1						multicellular organismal development|regulation of DNA methylation|regulation of gene expression by genetic imprinting|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	histone demethylase activity (H3-dimethyl-K4 specific)|histone demethylase activity (H3-monomethyl-K4 specific)|oxidoreductase activity|zinc ion binding			skin(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	6	18566545	18566545	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:18566545delT	uc003nct.1	+											Homo sapiens cDNA FLJ25799 fis, clone TST07088.																														---	---	---	---
Unknown	0	broad.mit.edu	37	6	18663991	18663991	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:18663991delT	uc003nct.1	+											Homo sapiens cDNA FLJ25799 fis, clone TST07088.																														---	---	---	---
Unknown	0	broad.mit.edu	37	6	19332430	19332430	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:19332430delT								MIR548A1 (760319 upstream) : ID4 (505187 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	19501893	19501893	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:19501893delA								MIR548A1 (929782 upstream) : ID4 (335724 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	19683569	19683569	+	IGR	DEL	T	-	-	rs11288466		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:19683569delT								None (None upstream) : ID4 (154048 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	19727909	19727913	+	IGR	DEL	AAAAA	-	-	rs76695570		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:19727909_19727913delAAAAA								None (None upstream) : ID4 (109704 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	19979080	19979080	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:19979080delT								ID4 (138166 upstream) : MBOAT1 (121855 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	20048301	20048301	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:20048301delT								ID4 (207387 upstream) : MBOAT1 (52634 downstream)																																			---	---	---	---
CDKAL1	54901	broad.mit.edu	37	6	20688893	20688894	+	Intron	INS	-	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:20688893_20688894insT	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	20938998	20938998	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:20938998delT	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	21207750	21207750	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:21207750delA	uc003ndc.1	+						CDKAL1_uc003ndd.1_Intron|CDKAL1_uc003nde.1_Intron|CDKAL1_uc003ndf.1_Intron|CDKAL1_uc003ndg.2_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	21393600	21393600	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:21393600delA								CDKAL1 (160968 upstream) : SOX4 (200372 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	21431140	21431140	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:21431140delA								CDKAL1 (198508 upstream) : SOX4 (162832 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	21534178	21534178	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:21534178delT								CDKAL1 (301546 upstream) : SOX4 (59794 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	21590827	21590827	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:21590827delA								CDKAL1 (358195 upstream) : SOX4 (3145 downstream)																																			---	---	---	---
FLJ22536	401237	broad.mit.edu	37	6	21792895	21792895	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:21792895delT	uc010jpp.1	+						FLJ22536_uc003ndj.2_Intron|FLJ22536_uc011djk.1_Intron|FLJ22536_uc011djj.1_Intron					Homo sapiens cDNA FLJ12803 fis, clone NT2RP2002172.												0																		---	---	---	---
FLJ22536	401237	broad.mit.edu	37	6	21922022	21922022	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:21922022delA	uc003ndj.2	+						FLJ22536_uc011djk.1_Intron|FLJ22536_uc003ndl.2_Intron|FLJ22536_uc011djj.1_Intron|FLJ22536_uc003ndk.1_Intron	NR_015410				Homo sapiens cDNA FLJ12803 fis, clone NT2RP2002172.												0																		---	---	---	---
FLJ22536	401237	broad.mit.edu	37	6	21994704	21994705	+	Intron	DEL	TG	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:21994704_21994705delTG	uc003ndj.2	+						FLJ22536_uc011djk.1_Intron|FLJ22536_uc003ndl.2_Intron	NR_015410				Homo sapiens cDNA FLJ12803 fis, clone NT2RP2002172.												0																		---	---	---	---
FLJ22536	401237	broad.mit.edu	37	6	22102424	22102424	+	Intron	DEL	T	-	-	rs5874850		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:22102424delT	uc003ndj.2	+						FLJ22536_uc011djk.1_Intron|FLJ22536_uc003ndl.2_Intron	NR_015410				Homo sapiens cDNA FLJ12803 fis, clone NT2RP2002172.												0																		---	---	---	---
FLJ22536	401237	broad.mit.edu	37	6	22125350	22125350	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:22125350delT	uc003ndj.2	+						FLJ22536_uc011djk.1_Intron|FLJ22536_uc003ndl.2_Intron	NR_015410				Homo sapiens cDNA FLJ12803 fis, clone NT2RP2002172.												0																		---	---	---	---
FLJ22536	401237	broad.mit.edu	37	6	22133415	22133416	+	Intron	INS	-	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:22133415_22133416insA	uc003ndj.2	+						FLJ22536_uc011djk.1_Intron|FLJ22536_uc003ndl.2_Intron	NR_015410				Homo sapiens cDNA FLJ12803 fis, clone NT2RP2002172.												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	6	22705173	22705173	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:22705173delA								HDGFL1 (134424 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	22807275	22807275	+	IGR	DEL	A	-	-	rs34923624		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:22807275delA								HDGFL1 (236526 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	22811353	22811354	+	IGR	DEL	CA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:22811353_22811354delCA								HDGFL1 (240604 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	23640939	23640939	+	IGR	DEL	T	-	-	rs75145806		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:23640939delT								None (None upstream) : NRSN1 (485475 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	23645809	23645809	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:23645809delT								None (None upstream) : NRSN1 (480605 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	23893331	23893331	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:23893331delT								None (None upstream) : NRSN1 (233083 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	23916846	23916846	+	IGR	DEL	T	-	-	rs10715713		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:23916846delT								None (None upstream) : NRSN1 (209568 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	23931919	23931919	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:23931919delA								None (None upstream) : NRSN1 (194495 downstream)																																			---	---	---	---
MRS2	57380	broad.mit.edu	37	6	24418169	24418169	+	Intron	DEL	A	-	-	rs71542670		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:24418169delA	uc003neb.2	+						MRS2_uc003nea.2_Intron|MRS2_uc011djl.1_Intron|MRS2_uc011djm.1_Intron|MRS2_uc011djn.1_Intron|MRS2_uc003nec.2_Intron	NM_020662	NP_065713			MRS2-like, magnesium homeostasis factor						ion transport	integral to membrane|mitochondrial inner membrane					0																		---	---	---	---
ALDH5A1	7915	broad.mit.edu	37	6	24522707	24522708	+	Intron	DEL	GT	-	-	rs72282015		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:24522707_24522708delGT	uc003neg.2	+						ALDH5A1_uc003nef.2_Intron	NM_001080	NP_001071			aldehyde dehydrogenase 5A1 isoform 2 precursor						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)													---	---	---	---
FAM65B	9750	broad.mit.edu	37	6	25025707	25025707	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:25025707delA	uc011dju.1	-							NM_015864	NP_056948			hypothetical protein LOC9750 isoform 2						cell differentiation|muscle organ development	cytoskeleton|filopodium|mitochondrion	binding			ovary(1)	1																		---	---	---	---
LRRC16A	55604	broad.mit.edu	37	6	25333805	25333806	+	Intron	DEL	AT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:25333805_25333806delAT	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	25489016	25489016	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:25489016delT	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																		---	---	---	---
Unknown	0	broad.mit.edu	37	6	25948458	25948459	+	IGR	DEL	TG	-	-	rs11757088	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:25948458_25948459delTG								SLC17A2 (17619 upstream) : TRIM38 (14612 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	25949442	25949442	+	IGR	DEL	T	-	-	rs76984275		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:25949442delT								SLC17A2 (18603 upstream) : TRIM38 (13629 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	25953274	25953275	+	IGR	DEL	TT	-	-	rs199727	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:25953274_25953275delTT								SLC17A2 (22435 upstream) : TRIM38 (9796 downstream)																																			---	---	---	---
HIST1H4B	8366	broad.mit.edu	37	6	26029501	26029502	+	5'Flank	INS	-	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:26029501_26029502insT	uc003nfr.2	-							NM_003544	NP_003535			histone cluster 1, H4b						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																		---	---	---	---
HIST1H4C	8364	broad.mit.edu	37	6	26101430	26101430	+	5'Flank	DEL	T	-	-	rs150747425	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:26101430delT	uc003ngi.2	+							NM_003542	NP_003533			histone cluster 1, H4c						CenH3-containing nucleosome assembly at centromere|negative regulation of megakaryocyte differentiation|phosphatidylinositol-mediated signaling|telomere maintenance	nucleoplasm|nucleosome	DNA binding|protein binding				0																		---	---	---	---
BTN2A3	54718	broad.mit.edu	37	6	26428451	26428453	+	Intron	DEL	AAA	-	-	rs139821417		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:26428451_26428453delAAA	uc011dkl.1	+						BTN2A3_uc011dkm.1_Intron					RecName: Full=Butyrophilin subfamily 2 member A3; Flags: Precursor;												0																		---	---	---	---
BTN2A3	54718	broad.mit.edu	37	6	26430817	26430821	+	Intron	DEL	AAAAA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:26430817_26430821delAAAAA	uc011dkl.1	+						BTN2A3_uc011dkm.1_Intron					RecName: Full=Butyrophilin subfamily 2 member A3; Flags: Precursor;												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	6	26493449	26493449	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:26493449delA								BTN2A1 (23584 upstream) : BTN1A1 (8046 downstream)																																			---	---	---	---
HMGN4	10473	broad.mit.edu	37	6	26537583	26537583	+	5'Flank	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:26537583delG	uc003nig.2	+							NM_006353	NP_006344			high mobility group nucleosomal binding domain							chromatin|nucleus	DNA binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	6	27310648	27310649	+	IGR	DEL	TT	-	-	rs75050573		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:27310648_27310649delTT								FKSG83 (16909 upstream) : ZNF204P (14953 downstream)																																			---	---	---	---
HIST1H2BM	8342	broad.mit.edu	37	6	27781389	27781389	+	5'Flank	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:27781389delT	uc003njo.2	+							NM_003521	NP_003512			histone cluster 1, H2bm						nucleosome assembly	nucleosome|nucleus	DNA binding			large_intestine(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	6	27833798	27833798	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:27833798delA								HIST1H2AL (223 upstream) : HIST1H1B (773 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	28419536	28419536	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:28419536delT								ZSCAN23 (8257 upstream) : GPX6 (51537 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	28930099	28930099	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:28930099delA								TRIM27 (38331 upstream) : ZNF311 (32495 downstream)																																			---	---	---	---
GABBR1	2550	broad.mit.edu	37	6	29545639	29545640	+	Intron	INS	-	TG	TG			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:29545639_29545640insTG	uc003nmp.3	-							NM_021903	NP_068703			gamma-aminobutyric acid (GABA) B receptor 1						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)													---	---	---	---
HLA-A	3105	broad.mit.edu	37	6	29912653	29912655	+	Intron	DEL	AGA	-	-	rs9278467		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:29912653_29912655delAGA	uc003nol.2	+						HLA-G_uc011dmb.1_Intron|HCG4P6_uc003nog.1_5'Flank|HLA-A_uc003nok.2_Intron|HLA-A_uc003non.2_Intron|HLA-A_uc003noo.2_Intron|HLA-A_uc010jrr.2_Intron|HLA-A_uc003nom.2_Intron|HLA-A_uc010klp.2_Intron|HLA-A_uc011dmc.1_Intron|HLA-A_uc011dmd.1_3'UTR	NM_002116	NP_002107			major histocompatibility complex, class I, A						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			upper_aerodigestive_tract(1)|ovary(1)	2														Melanoma_Familial_Clustering_of|Lichen_Sclerosis_et_Atrophicus_Familial_Clustering_of|Osteosarcoma_Familial_Clustering_of|Naso-/Oropharyngeal/Laryngeal_Cancer_Familial_Clustering_of	Multiple Myeloma(9;0.094)			---	---	---	---
Unknown	0	broad.mit.edu	37	6	30644133	30644133	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:30644133delT								DHX16 (3303 upstream) : KIAA1949 (35 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	31078498	31078499	+	IGR	INS	-	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:31078498_31078499insA								HCG22 (50845 upstream) : C6orf15 (501 downstream)																																			---	---	---	---
C6orf48	50854	broad.mit.edu	37	6	31803324	31803329	+	Intron	DEL	TTTTTT	-	-	rs71552087		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:31803324_31803329delTTTTTT	uc003rjx.1	+						C6orf48_uc003rjy.1_Intron|C6orf48_uc003rjz.1_Intron|SNORD52_uc003nxp.2_5'Flank	NM_001040437	NP_001035527			G8 protein												0																		---	---	---	---
ATF6B	1388	broad.mit.edu	37	6	32085618	32085619	+	Intron	DEL	CT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:32085618_32085619delCT	uc003nzn.2	-						TNXB_uc010jts.1_5'Flank|ATF6B_uc003nzm.1_Intron|ATF6B_uc003nzo.2_Intron|ATF6B_uc003nzp.1_Intron	NM_004381	NP_004372			activating transcription factor 6 beta isoform						response to unfolded protein|signal transduction	endoplasmic reticulum membrane|integral to membrane|nucleus	protein dimerization activity|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity				0																		---	---	---	---
C6orf10	10665	broad.mit.edu	37	6	32267548	32267549	+	Intron	INS	-	GG	GG	rs150721951	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:32267548_32267549insGG	uc011dpy.1	-							NM_006781	NP_006772			chromosome 6 open reading frame 10							integral to membrane				skin(1)	1																		---	---	---	---
C6orf10	10665	broad.mit.edu	37	6	32272515	32272515	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:32272515delT	uc011dpy.1	-							NM_006781	NP_006772			chromosome 6 open reading frame 10							integral to membrane				skin(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	6	32398614	32398614	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:32398614delT								BTNL2 (23714 upstream) : HLA-DRA (9033 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	32417245	32417246	+	IGR	INS	-	A	A	rs28788562		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:32417245_32417246insA								HLA-DRA (4424 upstream) : HLA-DRB1 (67917 downstream)																																			---	---	---	---
HLA-DRB5	3127	broad.mit.edu	37	6	32508818	32508822	+	Intron	DEL	ATGTC	-	-	rs148505568		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:32508818_32508822delATGTC	uc003obk.3	-						HLA-DRB1_uc011dqa.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-DPB1	3115	broad.mit.edu	37	6	33047685	33047686	+	Intron	INS	-	A	A	rs149161332	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:33047685_33047686insA	uc003ocu.1	+						HLA-DPA1_uc003oct.1_Intron|HLA-DPB1_uc011dqn.1_Intron|HLA-DPB1_uc011dqo.1_Intron|HLA-DPB1_uc011dqp.1_Intron|HLA-DPB1_uc011dqq.1_5'Flank	NM_002121	NP_002112			major histocompatibility complex, class II, DP						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				ovary(1)	1																		---	---	---	---
COL11A2	1302	broad.mit.edu	37	6	33140009	33140009	+	Intron	DEL	T	-	-	rs973233	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:33140009delT	uc003ocx.1	-						COL11A2_uc010jul.1_Intron|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																		---	---	---	---
Unknown	0	broad.mit.edu	37	6	33307389	33307391	+	IGR	DEL	TTT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:33307389_33307391delTTT								DAXX (16596 upstream) : LYPLA2P1 (25124 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	33537363	33537364	+	IGR	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:33537363_33537364delTT								ZBTB9 (112045 upstream) : BAK1 (2960 downstream)																																			---	---	---	---
GRM4	2914	broad.mit.edu	37	6	34012407	34012408	+	Intron	INS	-	CACA	CACA	rs141185968	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:34012407_34012408insCACA	uc003oir.3	-						GRM4_uc011dsn.1_Intron|GRM4_uc010jvh.2_Intron|GRM4_uc010jvi.2_Intron|GRM4_uc003oio.2_Intron|GRM4_uc003oip.2_Intron|GRM4_uc011dsl.1_Intron|GRM4_uc003oiq.2_Intron|GRM4_uc011dsm.1_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)													---	---	---	---
GRM4	2914	broad.mit.edu	37	6	34055909	34055909	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:34055909delT	uc003oir.3	-						GRM4_uc011dsn.1_Intron|GRM4_uc010jvh.2_Intron|GRM4_uc010jvi.2_Intron|GRM4_uc011dsl.1_Intron|GRM4_uc003oiq.2_Intron|GRM4_uc011dsm.1_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)													---	---	---	---
GRM4	2914	broad.mit.edu	37	6	34065228	34065229	+	Intron	DEL	GC	-	-	rs4990430		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:34065228_34065229delGC	uc003oir.3	-						GRM4_uc011dsn.1_Intron|GRM4_uc010jvh.2_Intron|GRM4_uc010jvi.2_Intron|GRM4_uc010jvk.1_Intron|GRM4_uc011dsl.1_Intron|GRM4_uc003oiq.2_Intron|GRM4_uc011dsm.1_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)													---	---	---	---
NUDT3	11165	broad.mit.edu	37	6	34258465	34258465	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:34258465delT	uc003ojl.2	-							NM_006703	NP_006694			nudix-type motif 3						cell-cell signaling|diadenosine polyphosphate catabolic process|diphosphoinositol polyphosphate catabolic process	cytoplasm	diphosphoinositol-polyphosphate diphosphatase activity|magnesium ion binding				0																		---	---	---	---
NUDT3	11165	broad.mit.edu	37	6	34291344	34291344	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:34291344delA	uc003ojl.2	-							NM_006703	NP_006694			nudix-type motif 3						cell-cell signaling|diadenosine polyphosphate catabolic process|diphosphoinositol polyphosphate catabolic process	cytoplasm	diphosphoinositol-polyphosphate diphosphatase activity|magnesium ion binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	6	34374517	34374517	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:34374517delA								NUDT3 (14076 upstream) : RPS10 (10716 downstream)																																			---	---	---	---
C6orf106	64771	broad.mit.edu	37	6	34632918	34632919	+	Intron	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:34632918_34632919delTT	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	35034229	35034229	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:35034229delA	uc003ojx.3	+						ANKS1A_uc011dss.1_Intron|ANKS1A_uc011dst.1_Intron|ANKS1A_uc010jvp.1_Intron	NM_015245	NP_056060			ankyrin repeat and sterile alpha motif domain							cytoplasm	protein binding			ovary(3)|upper_aerodigestive_tract(1)	4																		---	---	---	---
ANKS1A	23294	broad.mit.edu	37	6	35082651	35082651	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:35082651delA	uc010jvp.1	+											SubName: Full=ANKS1A protein;							cytoplasm	protein binding			ovary(3)|upper_aerodigestive_tract(1)	4																		---	---	---	---
TCP11	6954	broad.mit.edu	37	6	35087761	35087761	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:35087761delT	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																		---	---	---	---
TEAD3	7005	broad.mit.edu	37	6	35442470	35442470	+	3'UTR	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:35442470delC	uc003oku.3	-	13					TEAD3_uc003okt.2_3'UTR|TEAD3_uc010jvx.2_3'UTR	NM_003214	NP_003205			TEA domain family member 3						female pregnancy|hippo signaling cascade		DNA binding|protein binding|sequence-specific DNA binding transcription factor activity			ovary(1)	1																		---	---	---	---
FKBP5	2289	broad.mit.edu	37	6	35689954	35689954	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:35689954delT	uc003oky.2	-							NM_001145775	NP_001139247			FK506 binding protein 5 isoform 1						protein folding	cytoplasm|membrane|nucleus	FK506 binding|heat shock protein binding|peptidyl-prolyl cis-trans isomerase activity			ovary(1)	1																		---	---	---	---
C6orf126	389383	broad.mit.edu	37	6	35745414	35745414	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:35745414delA	uc010jvz.1	+						C6orf126_uc003olc.1_Intron	NM_207409	NP_997292			hypothetical protein LOC389383 precursor						digestion|lipid catabolic process	extracellular region	enzyme activator activity				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	6	35757671	35757671	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:35757671delA								C6orf127 (1831 upstream) : CLPS (5089 downstream)																																			---	---	---	---
KCTD20	222658	broad.mit.edu	37	6	36442433	36442433	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:36442433delT	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																		---	---	---	---
STK38	11329	broad.mit.edu	37	6	36482982	36482982	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:36482982delA	uc003omg.2	-						STK38_uc003omh.2_Intron|STK38_uc003omi.2_Intron	NM_007271	NP_009202			serine/threonine kinase 38						intracellular protein kinase cascade|negative regulation of MAP kinase activity	cytoplasm|MLL5-L complex	ATP binding|magnesium ion binding|mitogen-activated protein kinase kinase kinase binding|protein serine/threonine kinase activity			ovary(3)|upper_aerodigestive_tract(1)|lung(1)|skin(1)	6																		---	---	---	---
Unknown	0	broad.mit.edu	37	6	36588765	36588765	+	IGR	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:36588765delG								SFRS3 (16522 upstream) : CDKN1A (56823 downstream)																																			---	---	---	---
CPNE5	57699	broad.mit.edu	37	6	36733013	36733014	+	Intron	INS	-	G	G	rs41272184	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:36733013_36733014insG	uc003omr.1	-						CPNE5_uc003oms.1_Intron	NM_020939	NP_065990			copine V											skin(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	6	37041377	37041377	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:37041377delT								FGD2 (44532 upstream) : PIM1 (96545 downstream)																																			---	---	---	---
TBC1D22B	55633	broad.mit.edu	37	6	37254734	37254735	+	Intron	INS	-	A	A	rs140231399	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:37254734_37254735insA	uc003onn.2	+						TBC1D22B_uc010jwt.2_Intron	NM_017772	NP_060242			TBC1 domain family, member 22B							intracellular	Rab GTPase activator activity				0			OV - Ovarian serous cystadenocarcinoma(102;0.241)															---	---	---	---
Unknown	0	broad.mit.edu	37	6	37314655	37314655	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:37314655delA								TBC1D22B (13910 upstream) : RNF8 (7093 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	37394315	37394315	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:37394315delT								RNF8 (31802 upstream) : FTSJD2 (6592 downstream)																																			---	---	---	---
ZFAND3	60685	broad.mit.edu	37	6	38028556	38028556	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:38028556delT	uc003onx.2	+							NM_021943	NP_068762			zinc finger, AN1-type domain 3								DNA binding|zinc ion binding			ovary(1)	1																		---	---	---	---
DNAH8	1769	broad.mit.edu	37	6	38701675	38701675	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:38701675delA	uc003ooe.1	+						DNAH8_uc003ood.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	38775211	38775211	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:38775211delA	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	38817974	38817974	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:38817974delT	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																		---	---	---	---
Unknown	0	broad.mit.edu	37	6	39211085	39211085	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:39211085delT								KCNK5 (13834 upstream) : KCNK17 (55693 downstream)																																			---	---	---	---
KIF6	221458	broad.mit.edu	37	6	39517004	39517005	+	Intron	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:39517004_39517005delAA	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																		---	---	---	---
KIF6	221458	broad.mit.edu	37	6	39633492	39633492	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:39633492delT	uc003oot.2	-						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	39770220	39770221	+	Intron	INS	-	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:39770220_39770221insA	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	39933904	39933904	+	IGR	DEL	G	-	-	rs11362289		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:39933904delG								MOCS1 (31650 upstream) : TDRG1 (412259 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	39936849	39936849	+	IGR	DEL	A	-	-	rs74364823		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:39936849delA								MOCS1 (34595 upstream) : TDRG1 (409314 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	40687579	40687579	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:40687579delA								LRFN2 (132453 upstream) : UNC5CL (307193 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	40745595	40745596	+	IGR	DEL	TA	-	-	rs150913041	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:40745595_40745596delTA								LRFN2 (190469 upstream) : UNC5CL (249176 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	40910540	40910540	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:40910540delA								LRFN2 (355414 upstream) : UNC5CL (84232 downstream)																																			---	---	---	---
UNC5CL	222643	broad.mit.edu	37	6	41025625	41025625	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:41025625delT	uc010jxe.1	-						APOBEC2_uc003opl.2_Intron|APOBEC2_uc010jxf.2_Intron	NM_173561	NP_775832			unc-5 homolog C-like						signal transduction	cytoplasm|integral to membrane				ovary(2)	2	Ovarian(28;0.0418)|Colorectal(47;0.196)																	---	---	---	---
Unknown	0	broad.mit.edu	37	6	41583313	41583314	+	IGR	INS	-	AG	AG	rs143052628	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:41583313_41583314insAG								FOXP4 (13192 upstream) : MDFI (21616 downstream)																																			---	---	---	---
PRICKLE4	29964	broad.mit.edu	37	6	41752028	41752029	+	Intron	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:41752028_41752029delTT	uc011duf.1	+						PRICKLE4_uc003ord.2_Intron|TOMM6_uc003org.2_5'Flank	NM_013397	NP_037529			over-expressed breast tumor protein							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)															---	---	---	---
TRERF1	55809	broad.mit.edu	37	6	42297732	42297732	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:42297732delA	uc003osd.2	-						TRERF1_uc003osb.2_Intron|TRERF1_uc003osc.2_Intron|TRERF1_uc003ose.2_Intron|TRERF1_uc010jxu.1_Intron	NM_033502	NP_277037			transcriptional regulating factor 1						cholesterol catabolic process|homeostatic process|multicellular organismal development|positive regulation of transcription, DNA-dependent|regulation of hormone biosynthetic process|steroid biosynthetic process	nucleus	DNA bending activity|ligand-dependent nuclear receptor transcription coactivator activity|RNA polymerase II transcription cofactor activity|sequence-specific DNA binding transcription factor activity|transcription factor binding|zinc ion binding			ovary(3)|pancreas(1)|skin(1)	5	Colorectal(47;0.196)		Colorectal(64;0.00062)|COAD - Colon adenocarcinoma(64;0.00152)															---	---	---	---
Unknown	0	broad.mit.edu	37	6	42445632	42445632	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:42445632delT								TRERF1 (25767 upstream) : UBR2 (86426 downstream)																																			---	---	---	---
UBR2	23304	broad.mit.edu	37	6	42600675	42600676	+	Intron	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:42600675_42600676delTT	uc011dur.1	+						UBR2_uc011dus.1_Intron|UBR2_uc010jxv.1_Intron|UBR2_uc003osh.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	42610142	42610142	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:42610142delT	uc011dur.1	+						UBR2_uc011dus.1_Intron|UBR2_uc010jxv.1_Intron|UBR2_uc003osh.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	42643695	42643695	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:42643695delA	uc011dur.1	+						UBR2_uc011dus.1_Intron|UBR2_uc003osh.2_Intron|UBR2_uc011dut.1_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)															---	---	---	---
KIAA0240	23506	broad.mit.edu	37	6	42765176	42765176	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:42765176delA	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)															---	---	---	---
KIAA0240	23506	broad.mit.edu	37	6	42820976	42820976	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:42820976delA	uc003osn.1	+						KIAA0240_uc011duw.1_Intron|KIAA0240_uc003osp.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)															---	---	---	---
Unknown	0	broad.mit.edu	37	6	42839979	42839981	+	IGR	DEL	AAA	-	-	rs113520282		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:42839979_42839981delAAA								KIAA0240 (3683 upstream) : RPL7L1 (7690 downstream)																																			---	---	---	---
KLHDC3	116138	broad.mit.edu	37	6	42987302	42987302	+	Intron	DEL	A	-	-	rs112870593		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:42987302delA	uc003otl.2	+						C6orf153_uc003otp.1_5'Flank|KLHDC3_uc003otm.2_Intron|KLHDC3_uc010jyf.2_Intron|KLHDC3_uc003otn.2_Intron|KLHDC3_uc003oto.2_Intron	NM_057161	NP_476502			kelch domain containing 3						reciprocal meiotic recombination	cytoplasm|nuclear chromatin	chromatin binding|protein binding			upper_aerodigestive_tract(1)	1			Colorectal(64;0.00237)|all cancers(41;0.0034)|COAD - Colon adenocarcinoma(64;0.00473)|OV - Ovarian serous cystadenocarcinoma(102;0.0539)|KIRC - Kidney renal clear cell carcinoma(15;0.133)|Kidney(15;0.188)															---	---	---	---
PTK7	5754	broad.mit.edu	37	6	43118950	43118951	+	Intron	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:43118950_43118951delTT	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	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)															---	---	---	---
Unknown	0	broad.mit.edu	37	6	43429886	43429886	+	IGR	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:43429886delC								DLK2 (6100 upstream) : TJAP1 (15375 downstream)																																			---	---	---	---
RSPH9	221421	broad.mit.edu	37	6	43620055	43620056	+	Intron	INS	-	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:43620055_43620056insA	uc003ovw.1	+						RSPH9_uc003ovx.1_Intron	NM_152732	NP_689945			radial spoke head 9 homolog						cilium axoneme assembly|cilium movement	cytoplasm|cytoskeleton				upper_aerodigestive_tract(1)|skin(1)	2														Kartagener_syndrome				---	---	---	---
LOC100132354	100132354	broad.mit.edu	37	6	43875519	43875519	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:43875519delT	uc011dvm.1	+							NR_024478				Homo sapiens cDNA FLJ38229 fis, clone FCBBF2004256.												0																		---	---	---	---
SPATS1	221409	broad.mit.edu	37	6	44339040	44339041	+	Intron	DEL	AA	-	-	rs77255646		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:44339040_44339041delAA	uc003oxk.2	+						SPATS1_uc003oxg.2_Intron|SPATS1_uc010jzb.2_Intron	NM_145026	NP_659463			spermatogenesis associated, serine-rich 1											skin(1)	1	all_lung(25;0.00469)|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	44357995	44357995	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:44357995delT	uc003oxl.2	+							NM_001253	NP_001244			CDC5-like						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	45070685	45070685	+	Intron	DEL	A	-	-	rs75311913		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:45070685delA	uc003oxo.2	-						SUPT3H_uc003oxn.1_Intron|SUPT3H_uc011dvv.1_Intron|SUPT3H_uc003oxp.2_Intron|SUPT3H_uc011dvw.1_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																		---	---	---	---
RUNX2	860	broad.mit.edu	37	6	45354374	45354374	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:45354374delT	uc011dvx.1	+						RUNX2_uc011dvy.1_Intron	NM_001024630	NP_001019801			runt-related transcription factor 2 isoform a						negative regulation of transcription, DNA-dependent|osteoblast differentiation|positive regulation of transcription, DNA-dependent	nucleus	ATP binding|DNA binding|protein binding|sequence-specific DNA binding transcription factor activity			ovary(2)|skin(1)	3																		---	---	---	---
CLIC5	53405	broad.mit.edu	37	6	45890545	45890546	+	Intron	DEL	AG	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:45890545_45890546delAG	uc003oxv.3	-						CLIC5_uc003oxu.3_Intron|CLIC5_uc003oxw.2_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																OREG0017483	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
CLIC5	53405	broad.mit.edu	37	6	45931390	45931390	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-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																		---	---	---	---
RCAN2	10231	broad.mit.edu	37	6	46312490	46312490	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:46312490delA	uc003oyc.1	-						RCAN2_uc003oyd.1_Intron					SubName: Full=cDNA, FLJ92723, highly similar to Homo sapiens Down syndrome critical region gene 1-like 1 (DSCR1L1), mRNA;						calcium-mediated signaling|central nervous system development		nucleotide binding|protein phosphatase 2B binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	6	47072725	47072725	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:47072725delA								GPR110 (62643 upstream) : TNFRSF21 (126544 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	47168011	47168011	+	IGR	DEL	T	-	-	rs113379734		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:47168011delT								GPR110 (157929 upstream) : TNFRSF21 (31258 downstream)																																			---	---	---	---
OPN5	221391	broad.mit.edu	37	6	47781899	47781899	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:47781899delT	uc003ozc.2	+						OPN5_uc003ozd.2_Intron	NM_181744	NP_859528			opsin 5 isoform 1						phototransduction|protein-chromophore linkage|visual perception	integral to membrane	G-protein coupled receptor activity|photoreceptor activity			ovary(1)	1																		---	---	---	---
C6orf138	442213	broad.mit.edu	37	6	47884387	47884388	+	Intron	DEL	AC	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:47884387_47884388delAC	uc011dwm.1	-						C6orf138_uc011dwn.1_Intron|C6orf138_uc003ozf.2_Intron	NM_001013732	NP_001013754			hypothetical protein LOC442213							integral to membrane	hedgehog receptor activity			central_nervous_system(1)	1																		---	---	---	---
C6orf138	442213	broad.mit.edu	37	6	48053763	48053763	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:48053763delA	uc011dwn.1	-							NM_001013732	NP_001013754			hypothetical protein LOC442213							integral to membrane	hedgehog receptor activity			central_nervous_system(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	6	49076660	49076660	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:49076660delA								C6orf138 (997717 upstream) : MUT (322334 downstream)																																			---	---	---	---
CRISP3	10321	broad.mit.edu	37	6	49701364	49701364	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-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)															---	---	---	---
DEFB114	245928	broad.mit.edu	37	6	49928267	49928267	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:49928267delA	uc011dwp.1	-							NM_001037499	NP_001032588			beta-defensin 114 precursor						defense response to bacterium	extracellular region				ovary(1)	1	Lung NSC(77;0.042)																	---	---	---	---
Unknown	0	broad.mit.edu	37	6	50260386	50260386	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:50260386delT								DEFB112 (244022 upstream) : TFAP2D (420871 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	50942951	50942951	+	IGR	DEL	A	-	-	rs67748791		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:50942951delA								TFAP2B (127626 upstream) : PKHD1 (537194 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	51034397	51034397	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:51034397delT								TFAP2B (219072 upstream) : PKHD1 (445748 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	51171480	51171481	+	IGR	INS	-	C	C	rs141640946	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:51171480_51171481insC								TFAP2B (356155 upstream) : PKHD1 (308664 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	51332297	51332297	+	IGR	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:51332297delC								TFAP2B (516972 upstream) : PKHD1 (147848 downstream)																																			---	---	---	---
PKHD1	5314	broad.mit.edu	37	6	51921383	51921383	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:51921383delT	uc003pah.1	-						PKHD1_uc003pai.2_Intron	NM_138694	NP_619639			fibrocystin isoform 1						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)																	---	---	---	---
Unknown	0	broad.mit.edu	37	6	52098848	52098848	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:52098848delT								IL17A (43412 upstream) : IL17F (2636 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	52163976	52163976	+	IGR	DEL	T	-	-	rs35593834		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:52163976delT								MCM3 (14394 upstream) : PAQR8 (62950 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	52186272	52186273	+	IGR	INS	-	A	A	rs144688340	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:52186272_52186273insA								MCM3 (36690 upstream) : PAQR8 (40653 downstream)																																			---	---	---	---
TMEM14A	28978	broad.mit.edu	37	6	52546594	52546594	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:52546594delT	uc003pax.2	+							NM_014051	NP_054770			transmembrane protein 14A							integral to membrane					0	Lung NSC(77;0.118)																	---	---	---	---
Unknown	0	broad.mit.edu	37	6	52553653	52553653	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:52553653delA								TMEM14A (2270 upstream) : GSTA2 (61235 downstream)																																			---	---	---	---
GSTA4	2941	broad.mit.edu	37	6	52862573	52862573	+	5'Flank	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:52862573delA	uc003pbf.2	-							NM_001512	NP_001503			glutathione S-transferase alpha 4						glutathione metabolic process|xenobiotic metabolic process	cytosol	glutathione transferase activity|protein homodimerization activity				0	Lung NSC(77;0.103)				Glutathione(DB00143)													---	---	---	---
GCLC	2729	broad.mit.edu	37	6	53380582	53380582	+	Intron	DEL	A	-	-	rs5876317		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:53380582delA	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)													---	---	---	---
LRRC1	55227	broad.mit.edu	37	6	53742255	53742255	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:53742255delT	uc003pcd.1	+							NM_018214	NP_060684			leucine rich repeat containing 1							cytoplasm|membrane				ovary(1)	1	Lung NSC(77;0.0147)			BRCA - Breast invasive adenocarcinoma(397;0.0745)														---	---	---	---
LRRC1	55227	broad.mit.edu	37	6	53769018	53769018	+	Intron	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:53769018delC	uc003pcd.1	+							NM_018214	NP_060684			leucine rich repeat containing 1							cytoplasm|membrane				ovary(1)	1	Lung NSC(77;0.0147)			BRCA - Breast invasive adenocarcinoma(397;0.0745)														---	---	---	---
C6orf142	90523	broad.mit.edu	37	6	54066861	54066861	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:54066861delT	uc003pcg.3	+						C6orf142_uc003pcf.2_Intron|C6orf142_uc003pch.3_Intron|C6orf142_uc011dxa.1_Intron	NM_138569	NP_612636			hypothetical protein LOC90523							nuclear envelope|PML body	protein binding				0	Lung NSC(77;0.0317)																	---	---	---	---
C6orf142	90523	broad.mit.edu	37	6	54071937	54071938	+	Intron	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:54071937_54071938delTT	uc003pcg.3	+						C6orf142_uc003pcf.2_Intron|C6orf142_uc003pch.3_Intron|C6orf142_uc011dxa.1_Intron	NM_138569	NP_612636			hypothetical protein LOC90523							nuclear envelope|PML body	protein binding				0	Lung NSC(77;0.0317)																	---	---	---	---
C6orf142	90523	broad.mit.edu	37	6	54125968	54125968	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:54125968delT	uc003pcg.3	+						C6orf142_uc003pch.3_Intron|C6orf142_uc011dxa.1_Intron	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	54330798	54330799	+	IGR	DEL	TC	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:54330798_54330799delTC								TINAG (75848 upstream) : FAM83B (380770 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	54563456	54563457	+	IGR	DEL	TC	-	-	rs77079892		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:54563456_54563457delTC								TINAG (308506 upstream) : FAM83B (148112 downstream)																																			---	---	---	---
HCRTR2	3062	broad.mit.edu	37	6	55068672	55068672	+	Intron	DEL	T	-	-	rs71708373		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:55068672delT	uc003pcl.2	+						HCRTR2_uc010jzv.2_Intron	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)															---	---	---	---
HCRTR2	3062	broad.mit.edu	37	6	55128706	55128706	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:55128706delT	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)															---	---	---	---
GFRAL	389400	broad.mit.edu	37	6	55191594	55191594	+	5'Flank	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:55191594delA	uc003pcm.1	+							NM_207410	NP_997293			GDNF family receptor alpha like precursor							integral to membrane	receptor activity			ovary(1)|breast(1)	2	Lung NSC(77;0.0875)|Renal(3;0.122)		LUSC - Lung squamous cell carcinoma(124;0.23)															---	---	---	---
Unknown	0	broad.mit.edu	37	6	55860909	55860910	+	IGR	DEL	AG	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:55860909_55860910delAG								BMP5 (120534 upstream) : COL21A1 (60479 downstream)																																			---	---	---	---
COL21A1	81578	broad.mit.edu	37	6	55946046	55946046	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:55946046delT	uc003pcs.2	-						COL21A1_uc010jzz.2_Intron|COL21A1_uc011dxg.1_Intron|COL21A1_uc011dxh.1_Intron|COL21A1_uc003pcr.2_Intron	NM_030820	NP_110447			collagen, type XXI, alpha 1 precursor						cell adhesion	collagen|cytoplasm	structural molecule activity			ovary(2)	2	Lung NSC(77;0.0483)		LUSC - Lung squamous cell carcinoma(124;0.181)															---	---	---	---
COL21A1	81578	broad.mit.edu	37	6	56047463	56047463	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:56047463delA	uc003pcs.2	-						COL21A1_uc003pct.1_Intron|COL21A1_uc011dxi.1_Intron|COL21A1_uc003pcu.1_Intron	NM_030820	NP_110447			collagen, type XXI, alpha 1 precursor						cell adhesion	collagen|cytoplasm	structural molecule activity			ovary(2)	2	Lung NSC(77;0.0483)		LUSC - Lung squamous cell carcinoma(124;0.181)															---	---	---	---
DST	667	broad.mit.edu	37	6	56818104	56818104	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:56818104delA	uc003pdf.2	-						BEND6_uc010kab.2_5'Flank|BEND6_uc003pdg.2_5'Flank	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)															---	---	---	---
ZNF451	26036	broad.mit.edu	37	6	57014629	57014629	+	Intron	DEL	T	-	-	rs66838312		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57014629delT	uc003pdm.1	+						ZNF451_uc003pdl.2_Intron|ZNF451_uc003pdn.1_Intron|uc003pdq.1_Intron|ZNF451_uc003pdk.1_Intron	NM_001031623	NP_001026794			zinc finger protein 451 isoform 1						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)															---	---	---	---
RAB23	51715	broad.mit.edu	37	6	57087981	57087981	+	5'Flank	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57087981delA	uc003pds.2	-						RAB23_uc003pdt.2_5'Flank|RAB23_uc010kac.2_5'Flank|RAB23_uc010kad.2_5'Flank	NM_183227	NP_899050			Ras-related protein Rab-23						protein transport|small GTPase mediated signal transduction	plasma membrane	GTP binding			skin(1)	1	Lung NSC(77;0.121)		LUSC - Lung squamous cell carcinoma(124;0.0785)|Lung(124;0.13)															---	---	---	---
PRIM2	5558	broad.mit.edu	37	6	57243174	57243174	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57243174delA	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	57262516	57262516	+	Intron	DEL	A	-	-	rs75873741		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57262516delA	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	57295806	57295806	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57295806delT	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	57323077	57323077	+	Intron	DEL	G	-	-	rs67240761		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57323077delG	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	57346959	57346959	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57346959delT	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	57360568	57360569	+	Intron	DEL	AT	-	-	rs140251188		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57360568_57360569delAT	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	57436915	57436916	+	Intron	INS	-	TTCTT	TTCTT	rs142426424		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57436915_57436916insTTCTT	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	57438024	57438026	+	Intron	DEL	AAT	-	-	rs67074144		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57438024_57438026delAAT	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	57460919	57460919	+	Intron	DEL	A	-	-	rs67751161		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57460919delA	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	57487931	57487931	+	Intron	DEL	T	-	-	rs74294531		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57487931delT	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	57502416	57502416	+	Intron	DEL	T	-	-	rs67317872		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57502416delT	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	57504529	57504529	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57504529delA	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	57513815	57513816	+	IGR	INS	-	TAAAT	TAAAT	rs145501425		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57513815_57513816insTAAAT								PRIM2 (440 upstream) : GUSBL2 (732343 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	57515828	57515828	+	IGR	DEL	C	-	-	rs11292500		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57515828delC								PRIM2 (2453 upstream) : GUSBL2 (730331 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	57522595	57522595	+	IGR	DEL	C	-	-	rs111414309		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57522595delC								PRIM2 (9220 upstream) : GUSBL2 (723564 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	57542931	57542931	+	IGR	DEL	G	-	-	rs112793267		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57542931delG								PRIM2 (29556 upstream) : GUSBL2 (703228 downstream)																																			---	---	---	---
GUSBL2	375513	broad.mit.edu	37	6	58251803	58251803	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:58251803delA	uc011dxq.1	-						GUSBL2_uc011dxp.1_Intron					SubName: Full=Putative uncharacterized protein ENSP00000348869; Flags: Fragment;												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	6	62051921	62051923	+	IGR	DEL	TTT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:62051921_62051923delTTT								None (None upstream) : KHDRBS2 (337942 downstream)																																			---	---	---	---
KHDRBS2	202559	broad.mit.edu	37	6	62545662	62545663	+	Intron	DEL	GA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:62545662_62545663delGA	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	62696609	62696609	+	Intron	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:62696609delC	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	62763262	62763262	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:62763262delA	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	62883102	62883103	+	Intron	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:62883102_62883103delAA	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	63351102	63351103	+	IGR	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:63351102_63351103delTT								KHDRBS2 (355002 upstream) : LGSN (634754 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	63829966	63829966	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:63829966delA								KHDRBS2 (833866 upstream) : LGSN (155891 downstream)																																			---	---	---	---
LGSN	51557	broad.mit.edu	37	6	63989792	63989792	+	3'UTR	DEL	A	-	-	rs79900249		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:63989792delA	uc003peh.2	-	4					LGSN_uc003pei.2_3'UTR	NM_016571	NP_057655			lengsin, lens protein with glutamine synthetase						glutamine biosynthetic process		glutamate-ammonia ligase activity			skin(2)	2					L-Glutamic Acid(DB00142)													---	---	---	---
Unknown	0	broad.mit.edu	37	6	64043530	64043530	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:64043530delA								LGSN (13648 upstream) : PTP4A1 (188121 downstream)																																			---	---	---	---
PTP4A1	7803	broad.mit.edu	37	6	64259472	64259472	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:64259472delT	uc003pek.2	+							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)															---	---	---	---
Unknown	0	broad.mit.edu	37	6	64325784	64325784	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:64325784delA								PTP4A1 (32296 upstream) : PHF3 (19941 downstream)																																			---	---	---	---
PHF3	23469	broad.mit.edu	37	6	64415953	64415953	+	Frame_Shift_Del	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:64415953delA	uc003pep.1	+	11	3428	c.3402delA	c.(3400-3402)CCAfs	p.P1134fs	PHF3_uc010kah.1_Frame_Shift_Del_p.P948fs|PHF3_uc003pen.2_Frame_Shift_Del_p.P1046fs|PHF3_uc011dxs.1_Frame_Shift_Del_p.P403fs	NM_015153	NP_055968	Q92576	PHF3_HUMAN	PHD finger protein 3	1134					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)															---	---	---	---
EYS	346007	broad.mit.edu	37	6	65471192	65471192	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:65471192delT	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	65548510	65548511	+	Intron	INS	-	ACAC	ACAC	rs139024905	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:65548510_65548511insACAC	uc011dxu.1	-							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	65561665	65561665	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:65561665delA	uc011dxu.1	-							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	65687098	65687098	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:65687098delT	uc011dxu.1	-							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	66054075	66054075	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:66054075delA	uc011dxu.1	-						EYS_uc003peq.2_Intron|EYS_uc003per.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																		---	---	---	---
Unknown	0	broad.mit.edu	37	6	66436914	66436914	+	IGR	DEL	T	-	-	rs151216402		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:66436914delT								EYS (19796 upstream) : MCART3P (60858 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	67066008	67066008	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:67066008delT								MCART3P (566633 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	67076342	67076342	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:67076342delA								MCART3P (576967 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	67189605	67189605	+	IGR	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:67189605delG								MCART3P (690230 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	67958311	67958311	+	IGR	DEL	T	-	-	rs9363731	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:67958311delT								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	68785308	68785308	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:68785308delA								None (None upstream) : BAI3 (560324 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	69026466	69026468	+	IGR	DEL	AAC	-	-	rs79624424		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:69026466_69026468delAAC								None (None upstream) : BAI3 (319164 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	69263850	69263850	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:69263850delA								None (None upstream) : BAI3 (81782 downstream)																																			---	---	---	---
BAI3	577	broad.mit.edu	37	6	69550580	69550581	+	Intron	INS	-	AAAC	AAAC	rs139446106	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:69550580_69550581insAAAC	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)																---	---	---	---
BAI3	577	broad.mit.edu	37	6	69625661	69625661	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:69625661delA	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)																---	---	---	---
BAI3	577	broad.mit.edu	37	6	69763076	69763077	+	Intron	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:69763076_69763077delAA	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	70459210	70459210	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:70459210delA	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																		---	---	---	---
Unknown	0	broad.mit.edu	37	6	70557450	70557451	+	IGR	DEL	CA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:70557450_70557451delCA								LMBRD1 (50562 upstream) : COL19A1 (18997 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	71079653	71079653	+	IGR	DEL	T	-	-	rs11306367		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:71079653delT								COL9A1 (66867 upstream) : FAM135A (43454 downstream)																																			---	---	---	---
SMAP1	60682	broad.mit.edu	37	6	71424084	71424084	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:71424084delT	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	71821988	71821989	+	IGR	DEL	CA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:71821988_71821989delCA								B3GAT2 (155200 upstream) : OGFRL1 (176488 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	72232506	72232506	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:72232506delT								C6orf155 (102058 upstream) : RIMS1 (364144 downstream)																																			---	---	---	---
RIMS1	22999	broad.mit.edu	37	6	72660089	72660090	+	Intron	INS	-	G	G	rs11373059		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:72660089_72660090insG	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)																---	---	---	---
RIMS1	22999	broad.mit.edu	37	6	72960181	72960181	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:72960181delA	uc003pga.2	+						RIMS1_uc011dyb.1_Intron|RIMS1_uc003pgc.2_Intron|RIMS1_uc010kaq.2_Intron|RIMS1_uc011dyc.1_Intron|RIMS1_uc010kar.2_Intron|RIMS1_uc011dyd.1_Intron|RIMS1_uc003pgf.2_Intron|RIMS1_uc003pgg.2_Intron|RIMS1_uc003pgi.2_Intron|RIMS1_uc003pgh.2_Intron|RIMS1_uc003pgd.2_Intron|RIMS1_uc003pge.2_Intron|RIMS1_uc011dye.1_5'Flank|RIMS1_uc003pgb.3_Intron|RIMS1_uc010kas.1_Intron	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)																---	---	---	---
RIMS1	22999	broad.mit.edu	37	6	73073980	73073980	+	Intron	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:73073980delG	uc003pga.2	+						RIMS1_uc011dyb.1_Intron|RIMS1_uc003pgc.2_Intron|RIMS1_uc010kaq.2_Intron|RIMS1_uc011dyc.1_Intron|RIMS1_uc010kar.2_Intron|RIMS1_uc011dyd.1_Intron|RIMS1_uc003pgf.2_Intron|RIMS1_uc003pgg.2_Intron|RIMS1_uc003pgi.2_Intron|RIMS1_uc003pgh.2_Intron|RIMS1_uc003pgd.2_Intron|RIMS1_uc003pge.2_Intron|RIMS1_uc011dye.1_Intron|RIMS1_uc011dyf.1_Intron|RIMS1_uc011dyg.1_5'Flank	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)																---	---	---	---
C6orf150	115004	broad.mit.edu	37	6	74162892	74162893	+	5'Flank	INS	-	ACAAA	ACAAA	rs140774106	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:74162892_74162893insACAAA	uc003pgx.1	-							NM_138441	NP_612450			hypothetical protein LOC115004												0																		---	---	---	---
CD109	135228	broad.mit.edu	37	6	74521908	74521908	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:74521908delT	uc003php.2	+						CD109_uc010kaz.2_Intron|CD109_uc003phq.2_Intron|CD109_uc010kba.2_Intron	NM_133493	NP_598000			CD109 antigen isoform 1 precursor							anchored to membrane|extracellular space|plasma membrane	serine-type endopeptidase inhibitor activity			large_intestine(2)|ovary(2)	4																		---	---	---	---
Unknown	0	broad.mit.edu	37	6	74691002	74691002	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:74691002delT								CD109 (152962 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	75040856	75040856	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:75040856delT	uc003phr.2	+											Homo sapiens full length insert cDNA clone ZD50H02.																														---	---	---	---
Unknown	0	broad.mit.edu	37	6	75071899	75071900	+	Intron	INS	-	AAC	AAC			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:75071899_75071900insAAC	uc003phr.2	+											Homo sapiens full length insert cDNA clone ZD50H02.																														---	---	---	---
FILIP1	27145	broad.mit.edu	37	6	76072773	76072773	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:76072773delT	uc003pia.2	-						FILIP1_uc003phy.1_Intron|FILIP1_uc003phz.2_5'Flank|FILIP1_uc010kbe.2_Intron	NM_015687	NP_056502			filamin A interacting protein 1											skin(3)|ovary(1)	4																		---	---	---	---
SENP6	26054	broad.mit.edu	37	6	76419522	76419522	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:76419522delA	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	76421202	76421202	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-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)																---	---	---	---
MYO6	4646	broad.mit.edu	37	6	76576840	76576840	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:76576840delT	uc003pih.1	+						MYO6_uc003pig.1_Intron|MYO6_uc003pii.1_Intron	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)														---	---	---	---
Unknown	0	broad.mit.edu	37	6	76955706	76955706	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:76955706delT								IMPG1 (173371 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	78436760	78436760	+	IGR	DEL	T	-	-	rs76954147	byFrequency;by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:78436760delT								HTR1B (263640 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	78448916	78448916	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:78448916delT								HTR1B (275796 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	78587212	78587213	+	IGR	INS	-	AGA	AGA	rs141335411	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:78587212_78587213insAGA								HTR1B (414092 upstream) : IRAK1BP1 (989976 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	78679973	78679974	+	IGR	INS	-	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:78679973_78679974insA								HTR1B (506853 upstream) : IRAK1BP1 (897215 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	79291656	79291656	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:79291656delA								None (None upstream) : IRAK1BP1 (285533 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	79388050	79388050	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:79388050delA								None (None upstream) : IRAK1BP1 (189139 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	79563335	79563335	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:79563335delA								None (None upstream) : IRAK1BP1 (13854 downstream)																																			---	---	---	---
SH3BGRL2	83699	broad.mit.edu	37	6	80409424	80409424	+	3'UTR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:80409424delT	uc003piz.1	+	4						NM_031469	NP_113657			SH3 domain binding glutamic acid-rich protein							nucleus	SH3 domain binding				0		all_cancers(76;0.00188)|Acute lymphoblastic leukemia(125;1.24e-05)|all_hematologic(105;0.00223)|all_epithelial(107;0.174)		BRCA - Breast invasive adenocarcinoma(397;0.0278)														---	---	---	---
Unknown	0	broad.mit.edu	37	6	80502316	80502317	+	IGR	DEL	AC	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:80502316_80502317delAC								RNY4 (50647 upstream) : ELOVL4 (122219 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	80555799	80555800	+	IGR	INS	-	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:80555799_80555800insA								RNY4 (104130 upstream) : ELOVL4 (68736 downstream)																																			---	---	---	---
BCKDHB	594	broad.mit.edu	37	6	80878332	80878333	+	Intron	INS	-	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:80878332_80878333insG	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	81084530	81084530	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:81084530delT								BCKDHB (28543 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	81208666	81208669	+	IGR	DEL	TTTT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:81208666_81208669delTTTT								BCKDHB (152679 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	81218010	81218011	+	IGR	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:81218010_81218011delTT								BCKDHB (162023 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	82023347	82023347	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:82023347delA								BCKDHB (967360 upstream) : FAM46A (432101 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	82717260	82717260	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:82717260delT								FAM46A (254832 upstream) : IBTK (162696 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	82851572	82851572	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:82851572delA								FAM46A (389144 upstream) : IBTK (28384 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	83287557	83287557	+	IGR	DEL	A	-	-	rs111705010		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:83287557delA								TPBG (210943 upstream) : UBE2CBP (314629 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	83313294	83313294	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:83313294delA								TPBG (236680 upstream) : UBE2CBP (288892 downstream)																																			---	---	---	---
DOPEY1	23033	broad.mit.edu	37	6	83839311	83839311	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:83839311delT	uc003pjs.1	+						DOPEY1_uc011dyy.1_Intron|DOPEY1_uc010kbl.1_Intron	NM_015018	NP_055833			dopey family member 1						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)														---	---	---	---
ME1	4199	broad.mit.edu	37	6	83931805	83931806	+	Intron	INS	-	AG	AG			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:83931805_83931806insAG	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)													---	---	---	---
ME1	4199	broad.mit.edu	37	6	84024803	84024803	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:84024803delA	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)													---	---	---	---
ME1	4199	broad.mit.edu	37	6	84026329	84026329	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:84026329delA	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)													---	---	---	---
ME1	4199	broad.mit.edu	37	6	84121956	84121957	+	Intron	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:84121956_84121957delAA	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)													---	---	---	---
SNAP91	9892	broad.mit.edu	37	6	84368820	84368823	+	Intron	DEL	AAAA	-	-	rs7770662		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:84368820_84368823delAAAA	uc011dze.1	-						SNAP91_uc003pkb.2_Intron|SNAP91_uc003pkc.2_Intron|SNAP91_uc003pkd.2_Intron|SNAP91_uc003pka.2_Intron|SNAP91_uc011dzf.1_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)														---	---	---	---
Unknown	0	broad.mit.edu	37	6	84487355	84487355	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:84487355delA								SNAP91 (68228 upstream) : RIPPLY2 (75630 downstream)																																			---	---	---	---
CYB5R4	51167	broad.mit.edu	37	6	84588621	84588621	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-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	85760953	85760955	+	IGR	DEL	AGC	-	-	rs10600230		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:85760953_85760955delAGC								TBX18 (287054 upstream) : NT5E (398347 downstream)																																			---	---	---	---
SNX14	57231	broad.mit.edu	37	6	86246422	86246422	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:86246422delA	uc003pkr.2	-						SNX14_uc003pkp.2_Intron|SNX14_uc003pkq.2_Intron|SNX14_uc011dzg.1_Intron|SNX14_uc003pks.2_Intron|SNX14_uc003pkt.2_Intron	NM_153816	NP_722523			sorting nexin 14 isoform a						cell communication|protein transport	integral to membrane	phosphatidylinositol binding|signal transducer activity				0		all_cancers(76;4.83e-07)|Acute lymphoblastic leukemia(125;3.3e-08)|Prostate(29;2.55e-07)|all_hematologic(105;3.66e-05)|all_epithelial(107;0.000695)|Lung NSC(302;0.197)|all_lung(197;0.24)		BRCA - Breast invasive adenocarcinoma(108;0.0423)														---	---	---	---
SYNCRIP	10492	broad.mit.edu	37	6	86350406	86350408	+	Intron	DEL	AAA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:86350406_86350408delAAA	uc003pla.2	-						SYNCRIP_uc003pku.2_Intron|SYNCRIP_uc003pkw.2_Intron|SYNCRIP_uc003pky.2_Intron|SYNCRIP_uc003pkv.2_Intron|SYNCRIP_uc003pkx.2_Intron|SYNCRIP_uc003pkz.2_Intron	NM_006372	NP_006363			synaptotagmin binding, cytoplasmic RNA						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)														---	---	---	---
Unknown	0	broad.mit.edu	37	6	86501477	86501479	+	IGR	DEL	TTT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:86501477_86501479delTTT								SNHG5 (113026 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	86946336	86946336	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:86946336delT								SNHG5 (557885 upstream) : HTR1E (700688 downstream)																																			---	---	---	---
ZNF292	23036	broad.mit.edu	37	6	87954956	87954956	+	Intron	DEL	A	-	-	rs75723743		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:87954956delA	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)														---	---	---	---
ZNF292	23036	broad.mit.edu	37	6	87955207	87955208	+	Intron	DEL	TT	-	-	rs72438234		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-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)														---	---	---	---
Unknown	0	broad.mit.edu	37	6	88516969	88516969	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:88516969delT	uc003pmm.2	+											Homo sapiens mRNA sequence.																														---	---	---	---
Unknown	0	broad.mit.edu	37	6	88538487	88538488	+	Intron	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:88538487_88538488delTT	uc003pmm.2	+											Homo sapiens mRNA sequence.																														---	---	---	---
Unknown	0	broad.mit.edu	37	6	88566330	88566331	+	Intron	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:88566330_88566331delAA	uc003pmm.2	+											Homo sapiens mRNA sequence.																														---	---	---	---
Unknown	0	broad.mit.edu	37	6	88740443	88740443	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-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	89284174	89284174	+	IGR	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:89284174delG								CNR1 (408407 upstream) : RNGTT (35815 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	89766582	89766582	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:89766582delA								RNGTT (93234 upstream) : PNRC1 (23847 downstream)																																			---	---	---	---
ANKRD6	22881	broad.mit.edu	37	6	90245961	90245961	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:90245961delA	uc003pni.3	+						ANKRD6_uc003pne.3_Intron|ANKRD6_uc003pnf.3_Intron	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	90371716	90371716	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:90371716delA	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)														---	---	---	---
CASP8AP2	9994	broad.mit.edu	37	6	90567787	90567787	+	Intron	DEL	A	-	-	rs79317675		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:90567787delA	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)														---	---	---	---
BACH2	60468	broad.mit.edu	37	6	90825211	90825211	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:90825211delT	uc011eab.1	-						BACH2_uc003pnw.2_Intron|BACH2_uc010kch.2_Intron	NM_021813	NP_068585			BTB and CNC homology 1, basic leucine zipper							nucleus	protein dimerization activity|sequence-specific DNA binding			ovary(3)|pancreas(1)|lung(1)|skin(1)	6		all_cancers(76;7.37e-06)|Acute lymphoblastic leukemia(125;2.23e-10)|Prostate(29;5.55e-10)|all_hematologic(105;2.42e-06)|all_epithelial(107;0.0063)		BRCA - Breast invasive adenocarcinoma(108;0.0799)														---	---	---	---
BACH2	60468	broad.mit.edu	37	6	90918982	90918983	+	Intron	INS	-	AGAG	AGAG	rs146123942	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:90918982_90918983insAGAG	uc011eab.1	-						BACH2_uc003pnw.2_Intron|BACH2_uc010kch.2_Intron	NM_021813	NP_068585			BTB and CNC homology 1, basic leucine zipper							nucleus	protein dimerization activity|sequence-specific DNA binding			ovary(3)|pancreas(1)|lung(1)|skin(1)	6		all_cancers(76;7.37e-06)|Acute lymphoblastic leukemia(125;2.23e-10)|Prostate(29;5.55e-10)|all_hematologic(105;2.42e-06)|all_epithelial(107;0.0063)		BRCA - Breast invasive adenocarcinoma(108;0.0799)														---	---	---	---
Unknown	0	broad.mit.edu	37	6	91069585	91069590	+	Intron	DEL	GCGCGC	-	-	rs58786579	byFrequency;by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:91069585_91069590delGCGCGC	uc003pnx.1	+											full-length cDNA clone CS0DL001YH04 of B cells (Ramos cell line) Cot 25-normalized of Homo sapiens (human).																														---	---	---	---
Unknown	0	broad.mit.edu	37	6	91905851	91905851	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:91905851delT								MAP3K7 (608944 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	92125693	92125694	+	IGR	INS	-	TGTGTGTG	TGTGTGTG	rs146155376	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:92125693_92125694insTGTGTGTG								MAP3K7 (828786 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	92764915	92764915	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:92764915delA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	92993171	92993171	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:92993171delT								None (None upstream) : EPHA7 (956571 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	93561216	93561216	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:93561216delT								None (None upstream) : EPHA7 (388526 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	93886594	93886594	+	IGR	DEL	T	-	-	rs67793519		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:93886594delT								None (None upstream) : EPHA7 (63148 downstream)																																			---	---	---	---
EPHA7	2045	broad.mit.edu	37	6	93988426	93988426	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:93988426delT	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	96019915	96019916	+	IGR	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:96019915_96019916delTT								None (None upstream) : MANEA (5497 downstream)																																			---	---	---	---
MANEA	79694	broad.mit.edu	37	6	96051893	96051894	+	Intron	DEL	AT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:96051893_96051894delAT	uc003poo.1	+							NM_024641	NP_078917			mannosidase, endo-alpha						post-translational protein modification|protein N-linked glycosylation via asparagine	Golgi membrane|integral to membrane	glycoprotein endo-alpha-1,2-mannosidase activity			ovary(2)|breast(1)	3		all_cancers(76;1.01e-06)|Acute lymphoblastic leukemia(125;3.58e-09)|all_hematologic(75;1.22e-06)|all_epithelial(107;0.00433)|Colorectal(196;0.0341)		BRCA - Breast invasive adenocarcinoma(108;0.148)														---	---	---	---
Unknown	0	broad.mit.edu	37	6	96078395	96078395	+	IGR	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:96078395delG								MANEA (21069 upstream) : FUT9 (385450 downstream)																																			---	---	---	---
FUT9	10690	broad.mit.edu	37	6	96659402	96659402	+	3'UTR	DEL	A	-	-	rs73757755		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:96659402delA	uc003pop.3	+	3						NM_006581	NP_006572			fucosyltransferase 9 (alpha (1,3)						L-fucose catabolic process|protein glycosylation	Golgi cisterna membrane|integral to membrane	alpha(1,3)-fucosyltransferase activity			skin(4)|ovary(1)	5		all_cancers(76;4.77e-07)|Acute lymphoblastic leukemia(125;4.01e-09)|all_hematologic(75;1.25e-06)|all_epithelial(107;0.00279)|Colorectal(196;0.0356)		BRCA - Breast invasive adenocarcinoma(108;0.08)														---	---	---	---
GPR63	81491	broad.mit.edu	37	6	97274923	97274923	+	Intron	DEL	A	-	-	rs66603309		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:97274923delA	uc010kcl.2	-						GPR63_uc003pou.2_Intron	NM_001143957	NP_001137429			G protein-coupled receptor 63							integral to membrane|plasma membrane	G-protein coupled receptor activity|protein binding			upper_aerodigestive_tract(1)|ovary(1)	2		all_cancers(76;6.89e-05)|Acute lymphoblastic leukemia(125;7.02e-10)|all_hematologic(75;1.23e-06)|all_epithelial(107;0.0618)|Colorectal(196;0.0721)		BRCA - Breast invasive adenocarcinoma(108;0.0912)														---	---	---	---
KLHL32	114792	broad.mit.edu	37	6	97500960	97500961	+	Intron	DEL	AC	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:97500960_97500961delAC	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	98092623	98092623	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:98092623delT	uc003ppd.1	+											Homo sapiens cDNA FLJ34046 fis, clone FCBBF2007610.																														---	---	---	---
Unknown	0	broad.mit.edu	37	6	98183159	98183159	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:98183159delT								C6orf167 (452098 upstream) : MIR2113 (289248 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	98206671	98206672	+	IGR	DEL	AC	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:98206671_98206672delAC								C6orf167 (475610 upstream) : MIR2113 (265735 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	98983607	98983607	+	IGR	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:98983607delG								MIR2113 (511110 upstream) : POU3F2 (298973 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	99028235	99028235	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:99028235delA								MIR2113 (555738 upstream) : POU3F2 (254345 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	99505661	99505662	+	IGR	DEL	TC	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:99505661_99505662delTC								FBXL4 (109812 upstream) : C6orf168 (215132 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	100078375	100078375	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:100078375delT								PRDM13 (14921 upstream) : MCHR2 (289411 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	100090103	100090103	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:100090103delT								PRDM13 (26649 upstream) : MCHR2 (277683 downstream)																																			---	---	---	---
ASCC3	10973	broad.mit.edu	37	6	101053476	101053476	+	Frame_Shift_Del	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:101053476delT	uc003pqk.2	-	33	5474	c.5145delA	c.(5143-5145)AAAfs	p.K1715fs		NM_006828	NP_006819	Q8N3C0	HELC1_HUMAN	activating signal cointegrator 1 complex subunit	1715	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)														---	---	---	---
ASCC3	10973	broad.mit.edu	37	6	101054815	101054815	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:101054815delA	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	101354113	101354113	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:101354113delT								ASCC3 (24889 upstream) : GRIK2 (492792 downstream)																																			---	---	---	---
GRIK2	2898	broad.mit.edu	37	6	101930381	101930381	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:101930381delT	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	101936446	101936446	+	Intron	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:101936446delG	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	102493563	102493563	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:102493563delA	uc003pqp.3	+						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)													---	---	---	---
Unknown	0	broad.mit.edu	37	6	102739097	102739097	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:102739097delT								GRIK2 (221140 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	103189191	103189191	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:103189191delT								GRIK2 (671234 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	103678911	103678913	+	IGR	DEL	AAA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:103678911_103678913delAAA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	104024454	104024454	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:104024454delT								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	105085963	105085963	+	IGR	DEL	A	-	-	rs67254499		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:105085963delA								None (None upstream) : HACE1 (90005 downstream)																																			---	---	---	---
HACE1	57531	broad.mit.edu	37	6	105300084	105300085	+	Intron	INS	-	TT	TT	rs45443697		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:105300084_105300085insTT	uc003pqu.1	-						HACE1_uc010kcy.1_Intron|HACE1_uc010kcz.1_Intron	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	105340744	105340747	+	IGR	DEL	AAAA	-	-	rs68041433		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:105340744_105340747delAAAA								HACE1 (32950 upstream) : LIN28B (64176 downstream)																																			---	---	---	---
POPDC3	64208	broad.mit.edu	37	6	105606725	105606725	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:105606725delT	uc003prb.2	-						uc003pqz.2_Intron|POPDC3_uc003pra.2_Intron	NM_022361	NP_071756			popeye protein 3							integral to membrane				skin(3)|ovary(2)	5		all_cancers(87;4.87e-05)|Acute lymphoblastic leukemia(125;1.9e-08)|all_hematologic(75;9.25e-07)|all_epithelial(87;0.0157)|Colorectal(196;0.202)|Lung NSC(302;0.238)																---	---	---	---
Unknown	0	broad.mit.edu	37	6	107134006	107134007	+	IGR	DEL	AC	-	-	rs72282228		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:107134006_107134007delAC								QRSL1 (17716 upstream) : MIR587 (97993 downstream)																																			---	---	---	---
C6orf203	51250	broad.mit.edu	37	6	107362906	107362907	+	Intron	INS	-	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:107362906_107362907insT	uc003prq.2	+						C6orf203_uc011eaj.1_Intron|C6orf203_uc010kde.2_Intron	NM_016487	NP_057571			hypothetical protein LOC51250 isoform a												0	Breast(9;0.00124)|all_epithelial(6;0.0729)	all_cancers(87;0.00461)|Acute lymphoblastic leukemia(125;3.07e-08)|all_hematologic(75;3.33e-06)|Colorectal(196;0.171)|all_epithelial(87;0.23)	BRCA - Breast invasive adenocarcinoma(8;0.000395)|all cancers(7;0.00065)|Epithelial(6;0.000834)|OV - Ovarian serous cystadenocarcinoma(5;0.244)	BRCA - Breast invasive adenocarcinoma(108;0.117)														---	---	---	---
PDSS2	57107	broad.mit.edu	37	6	107655273	107655273	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:107655273delT	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)														---	---	---	---
SEC63	11231	broad.mit.edu	37	6	108200060	108200060	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:108200060delA	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	108391166	108391168	+	Intron	DEL	AAG	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:108391166_108391168delAAG	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)														---	---	---	---
Unknown	0	broad.mit.edu	37	6	108424665	108424666	+	IGR	INS	-	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:108424665_108424666insA								OSTM1 (28724 upstream) : NR2E1 (62549 downstream)																																			---	---	---	---
SNX3	8724	broad.mit.edu	37	6	108549020	108549021	+	Intron	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:108549020_108549021delTT	uc003psh.2	-						SNX3_uc003psi.2_Intron|SNX3_uc010kdi.2_Intron	NM_003795	NP_003786			sorting nexin 3 isoform a						cell communication|endocytosis|protein transport	early endosome|endosome membrane	phosphatidylinositol-3-phosphate binding|protein phosphatase binding				0		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;0.0136)|Epithelial(106;0.0564)|OV - Ovarian serous cystadenocarcinoma(136;0.0717)|all cancers(137;0.0743)														---	---	---	---
LACE1	246269	broad.mit.edu	37	6	108687358	108687358	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:108687358delA	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	108938999	108938999	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:108938999delA	uc003psk.2	+						FOXO3_uc003psn.2_Intron|FOXO3_uc003psm.2_Intron|FOXO3_uc011ean.1_Intron	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-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:109636544delT								C6orf182 (151431 upstream) : CD164 (51174 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	110275066	110275066	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:110275066delA								FIG4 (128432 upstream) : GPR6 (24443 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	110291652	110291653	+	IGR	INS	-	TTC	TTC	rs146963606	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:110291652_110291653insTTC								FIG4 (145018 upstream) : GPR6 (7856 downstream)																																			---	---	---	---
CDC40	51362	broad.mit.edu	37	6	110551052	110551052	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-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)														---	---	---	---
C6orf186	728464	broad.mit.edu	37	6	110652554	110652554	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:110652554delA	uc010kdu.1	-						C6orf186_uc003pub.2_Intron	NM_001123364	NP_001116836			chromosome 6 open reading frame 186 precursor							extracellular region					0																		---	---	---	---
SLC22A16	85413	broad.mit.edu	37	6	110763381	110763382	+	Intron	DEL	AC	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:110763381_110763382delAC	uc003puf.2	-						SLC22A16_uc003pue.2_Intron	NM_033125	NP_149116			solute carrier family 22, member 16						acid secretion|cell differentiation|multicellular organismal development|single fertilization|sperm motility|spermatogenesis	integral to membrane	carnitine transporter activity			ovary(1)	1		all_cancers(87;0.00221)|Acute lymphoblastic leukemia(125;2.27e-07)|all_hematologic(75;1.38e-05)|all_epithelial(87;0.0485)|Colorectal(196;0.101)		OV - Ovarian serous cystadenocarcinoma(136;0.0513)|Epithelial(106;0.0921)|all cancers(137;0.115)														---	---	---	---
CDK19	23097	broad.mit.edu	37	6	110932989	110932990	+	3'UTR	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:110932989_110932990delAA	uc003puh.1	-	13					CDK19_uc003pui.1_3'UTR|CDK19_uc011eax.1_3'UTR	NM_015076	NP_055891			cell division cycle 2-like 6 (CDK8-like)								ATP binding|cyclin-dependent protein kinase activity|protein binding			ovary(2)|central_nervous_system(1)|skin(1)	4																		---	---	---	---
CDK19	23097	broad.mit.edu	37	6	111062866	111062867	+	Intron	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:111062866_111062867delAA	uc003puh.1	-						CDK19_uc003pui.1_Intron	NM_015076	NP_055891			cell division cycle 2-like 6 (CDK8-like)								ATP binding|cyclin-dependent protein kinase activity|protein binding			ovary(2)|central_nervous_system(1)|skin(1)	4																		---	---	---	---
CDK19	23097	broad.mit.edu	37	6	111125726	111125728	+	Intron	DEL	TAT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:111125726_111125728delTAT	uc003puh.1	-						CDK19_uc003pui.1_Intron	NM_015076	NP_055891			cell division cycle 2-like 6 (CDK8-like)								ATP binding|cyclin-dependent protein kinase activity|protein binding			ovary(2)|central_nervous_system(1)|skin(1)	4																		---	---	---	---
AMD1	262	broad.mit.edu	37	6	111144541	111144543	+	Intron	DEL	CTT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:111144541_111144543delCTT	uc011eay.1	+							NM_001033059	NP_001028231			adenosylmethionine decarboxylase 1 isoform 2						spermidine biosynthetic process|spermine biosynthetic process	cytosol	adenosylmethionine decarboxylase activity			upper_aerodigestive_tract(1)	1		all_cancers(87;3.83e-05)|Acute lymphoblastic leukemia(125;2.13e-07)|all_hematologic(75;5.28e-06)|all_epithelial(87;0.00225)|Colorectal(196;0.0209)		OV - Ovarian serous cystadenocarcinoma(136;0.0522)|Epithelial(106;0.111)|all cancers(137;0.143)	S-Adenosylmethionine(DB00118)													---	---	---	---
Unknown	0	broad.mit.edu	37	6	111223216	111223216	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:111223216delA								AMD1 (6303 upstream) : GTF3C6 (56547 downstream)																																			---	---	---	---
KIAA1919	91749	broad.mit.edu	37	6	111584143	111584143	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:111584143delT	uc003puv.3	+							NM_153369	NP_699200			sodium-dependent glucose transporter 1						carbohydrate transport|sodium ion transport	apical plasma membrane|integral to membrane	symporter activity			ovary(3)	3		all_cancers(87;2.35e-05)|Acute lymphoblastic leukemia(125;2.13e-07)|all_hematologic(75;5.28e-06)|all_epithelial(87;0.00138)|Colorectal(196;0.0209)		OV - Ovarian serous cystadenocarcinoma(136;0.055)|all cancers(137;0.0871)|Epithelial(106;0.0884)														---	---	---	---
REV3L	5980	broad.mit.edu	37	6	111718294	111718294	+	Intron	DEL	T	-	-	rs78978536		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:111718294delT	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					---	---	---	---
REV3L	5980	broad.mit.edu	37	6	111770604	111770605	+	Intron	INS	-	AA	AA	rs145393485	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:111770604_111770605insAA	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					---	---	---	---
REV3L	5980	broad.mit.edu	37	6	111794430	111794431	+	Intron	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:111794430_111794431delTT	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					---	---	---	---
TRAF3IP2	10758	broad.mit.edu	37	6	111901780	111901780	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:111901780delT	uc011ebc.1	-						TRAF3IP2_uc003pvg.2_Intron|TRAF3IP2_uc003pvf.2_Intron|TRAF3IP2_uc010kdw.2_Intron|TRAF3IP2_uc010kdx.2_Intron	NM_147686	NP_679211			TRAF3 interacting protein 2 isoform 2						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)														---	---	---	---
FYN	2534	broad.mit.edu	37	6	112025372	112025372	+	Intron	DEL	T	-	-	rs67511839		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:112025372delT	uc003pvj.2	-						FYN_uc003pvi.2_Intron|FYN_uc003pvk.2_Intron|FYN_uc003pvh.2_Intron|FYN_uc010kdy.1_5'Flank	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)													---	---	---	---
FYN	2534	broad.mit.edu	37	6	112184545	112184545	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:112184545delA	uc003pvk.2	-							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)													---	---	---	---
WISP3	8838	broad.mit.edu	37	6	112377575	112377575	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:112377575delT	uc003pvm.2	+						WISP3_uc003pvn.2_Intron|WISP3_uc003pvo.2_Intron	NM_003880	NP_003871			WNT1 inducible signaling pathway protein 3						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)														---	---	---	---
WISP3	8838	broad.mit.edu	37	6	112382541	112382541	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:112382541delT	uc003pvm.2	+						WISP3_uc003pvn.2_Intron|WISP3_uc003pvo.2_Intron	NM_003880	NP_003871			WNT1 inducible signaling pathway protein 3						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)														---	---	---	---
WISP3	8838	broad.mit.edu	37	6	112389434	112389434	+	Frame_Shift_Del	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:112389434delA	uc003pvm.2	+	5	726	c.616delA	c.(616-618)AAAfs	p.K206fs	WISP3_uc003pvn.2_RNA|WISP3_uc003pvo.2_Frame_Shift_Del_p.K224fs	NM_003880	NP_003871	O95389	WISP3_HUMAN	WNT1 inducible signaling pathway protein 3	206					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	112462354	112462354	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:112462354delT	uc003pvu.2	-						LAMA4_uc003pvv.2_Intron|LAMA4_uc003pvt.2_Intron	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	112709772	112709773	+	IGR	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:112709772_112709773delTT								RFPL4B (37274 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	113285580	113285580	+	IGR	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:113285580delC								RFPL4B (613082 upstream) : MARCKS (892947 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	113615524	113615524	+	IGR	DEL	A	-	-	rs149115595		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:113615524delA								RFPL4B (943026 upstream) : MARCKS (563003 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	114156465	114156466	+	IGR	INS	-	AT	AT			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:114156465_114156466insAT								None (None upstream) : MARCKS (22061 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	114160856	114160856	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:114160856delA								None (None upstream) : MARCKS (17671 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	114167176	114167177	+	IGR	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:114167176_114167177delAA								None (None upstream) : MARCKS (11350 downstream)																																			---	---	---	---
HDAC2	3066	broad.mit.edu	37	6	114292040	114292040	+	Frame_Shift_Del	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:114292040delT	uc003pwd.1	-	1	315	c.315delA	c.(313-315)AAAfs	p.K105fs	uc003pwf.2_Intron|HDAC2_uc003pwc.1_5'Flank|HDAC2_uc003pwe.1_5'UTR	NM_001527	NP_001518	Q92769	HDAC2_HUMAN	histone deacetylase 2	11	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)													---	---	---	---
HS3ST5	222537	broad.mit.edu	37	6	114455136	114455137	+	Intron	DEL	GA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:114455136_114455137delGA	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	114598379	114598379	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:114598379delT	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)														---	---	---	---
Unknown	0	broad.mit.edu	37	6	114743073	114743074	+	IGR	INS	-	GA	GA			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:114743073_114743074insGA								HS3ST5 (79533 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	114765899	114765899	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:114765899delT								HS3ST5 (102359 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	114785205	114785207	+	IGR	DEL	TTT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:114785205_114785207delTTT								HS3ST5 (121665 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	114881749	114881749	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:114881749delT								HS3ST5 (218209 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	115091579	115091579	+	IGR	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:115091579delG								HS3ST5 (428039 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	115202837	115202837	+	IGR	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:115202837delG								HS3ST5 (539297 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	116163871	116163871	+	IGR	DEL	A	-	-	rs75083929		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:116163871delA								None (None upstream) : FRK (98822 downstream)																																			---	---	---	---
NT5DC1	221294	broad.mit.edu	37	6	116429154	116429155	+	Intron	DEL	TG	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:116429154_116429155delTG	uc003pwj.2	+						NT5DC1_uc003pwk.2_Intron|NT5DC1_uc003pwl.2_5'Flank	NM_152729	NP_689942			5'-nucleotidase, cytosolic II-like 1 protein								hydrolase activity|metal ion binding				0		all_cancers(87;0.00367)|all_epithelial(87;0.00449)|Colorectal(196;0.0469)		all cancers(137;0.0327)|OV - Ovarian serous cystadenocarcinoma(136;0.0445)|GBM - Glioblastoma multiforme(226;0.0719)|Epithelial(106;0.112)														---	---	---	---
Unknown	0	broad.mit.edu	37	6	116918000	116918000	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:116918000delT								RWDD1 (3568 upstream) : RSPH4A (19642 downstream)																																			---	---	---	---
KPNA5	3841	broad.mit.edu	37	6	117026218	117026218	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:117026218delT	uc003pxh.2	+							NM_002269	NP_002260			karyopherin alpha 5						NLS-bearing substrate import into nucleus	cytoplasm|nuclear pore	protein binding|protein transporter activity			breast(3)|skin(1)	4		all_cancers(87;0.0314)|all_epithelial(87;0.0216)|Colorectal(196;0.234)		GBM - Glioblastoma multiforme(226;0.0298)|all cancers(137;0.0461)|OV - Ovarian serous cystadenocarcinoma(136;0.0513)|Epithelial(106;0.212)														---	---	---	---
KPNA5	3841	broad.mit.edu	37	6	117045743	117045746	+	Intron	DEL	TTTA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:117045743_117045746delTTTA	uc003pxh.2	+							NM_002269	NP_002260			karyopherin alpha 5						NLS-bearing substrate import into nucleus	cytoplasm|nuclear pore	protein binding|protein transporter activity			breast(3)|skin(1)	4		all_cancers(87;0.0314)|all_epithelial(87;0.0216)|Colorectal(196;0.234)		GBM - Glioblastoma multiforme(226;0.0298)|all cancers(137;0.0461)|OV - Ovarian serous cystadenocarcinoma(136;0.0513)|Epithelial(106;0.212)														---	---	---	---
ROS1	6098	broad.mit.edu	37	6	117726831	117726831	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:117726831delA	uc003pxp.1	-						ROS1_uc011ebi.1_Intron|GOPC_uc003pxq.1_Intron	NM_002944	NP_002935			proto-oncogene c-ros-1 protein precursor						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	117732383	117732386	+	Intron	DEL	TCTC	-	-	rs111822815		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:117732383_117732386delTCTC	uc003pxp.1	-						ROS1_uc011ebi.1_Intron|GOPC_uc003pxq.1_Intron	NM_002944	NP_002935			proto-oncogene c-ros-1 protein precursor						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								---	---	---	---
GOPC	57120	broad.mit.edu	37	6	117752525	117752526	+	Intron	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:117752525_117752526delTT	uc003pxq.1	-							NM_001017408	NP_001017408			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								---	---	---	---
DCBLD1	285761	broad.mit.edu	37	6	117884562	117884562	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:117884562delA	uc003pxs.2	+						GOPC_uc003pxq.1_Intron|GOPC_uc003pxu.2_Intron|GOPC_uc003pxv.2_Intron	NM_173674	NP_775945			discoidin, CUB and LCCL domain containing 1						cell adhesion	integral to membrane				ovary(1)	1		all_cancers(87;0.171)		GBM - Glioblastoma multiforme(226;0.0447)|OV - Ovarian serous cystadenocarcinoma(136;0.0921)|all cancers(137;0.125)														---	---	---	---
Unknown	0	broad.mit.edu	37	6	117989584	117989584	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:117989584delA								GOPC (65903 upstream) : NUS1 (7033 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	118080795	118080796	+	IGR	DEL	TT	-	-	rs671737	byFrequency;by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:118080795_118080796delTT								NUS1 (48911 upstream) : SLC35F1 (147893 downstream)																																			---	---	---	---
SLC35F1	222553	broad.mit.edu	37	6	118598986	118598986	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-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)														---	---	---	---
Unknown	0	broad.mit.edu	37	6	118670148	118670149	+	IGR	DEL	CT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:118670148_118670149delCT								SLC35F1 (31311 upstream) : C6orf204 (116090 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	118744521	118744521	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:118744521delA								SLC35F1 (105684 upstream) : C6orf204 (41718 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	118758941	118758941	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:118758941delT								SLC35F1 (120104 upstream) : C6orf204 (27298 downstream)																																			---	---	---	---
C6orf204	387119	broad.mit.edu	37	6	118902589	118902589	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:118902589delT	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)														---	---	---	---
Unknown	0	broad.mit.edu	37	6	119131020	119131021	+	IGR	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:119131020_119131021delTT								C6orf204 (99782 upstream) : ASF1A (84220 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	119146435	119146435	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:119146435delT	uc011ebm.1	-											RecName: Full=DNA replication licensing factor MCM9; AltName: Full=Mini-chromosome maintenance deficient 9;          Short=hMCM9; AltName: Full=Mini-chromosome maintenance deficient domain-containing protein 1;																														---	---	---	---
FAM184A	79632	broad.mit.edu	37	6	119472426	119472429	+	5'Flank	DEL	TGCT	-	-	rs35513453	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:119472426_119472429delTGCT	uc003pyk.3	-						FAM184A_uc003pyl.3_5'Flank	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	119511121	119511121	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:119511121delA	uc003pym.1	-							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	120087396	120087397	+	IGR	INS	-	GC	GC	rs140194627	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:120087396_120087397insGC								MAN1A1 (416470 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	120397705	120397705	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:120397705delT								MAN1A1 (726779 upstream) : None (None downstream)																																			---	---	---	---
C6orf170	221322	broad.mit.edu	37	6	121447899	121447899	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:121447899delA	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	121989499	121989501	+	IGR	DEL	TTT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:121989499_121989501delTTT								GJA1 (218627 upstream) : HSF2 (731195 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	122213177	122213177	+	IGR	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:122213177delG								GJA1 (442305 upstream) : HSF2 (507519 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	122696637	122696638	+	IGR	INS	-	G	G	rs141553463	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:122696637_122696638insG								GJA1 (925765 upstream) : HSF2 (24058 downstream)																																			---	---	---	---
PKIB	5570	broad.mit.edu	37	6	122847328	122847328	+	Intron	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:122847328delC	uc003pyz.2	+							NM_181794	NP_861459			cAMP-dependent protein kinase inhibitor beta								cAMP-dependent protein kinase inhibitor activity				0				GBM - Glioblastoma multiforme(226;0.164)														---	---	---	---
TRDN	10345	broad.mit.edu	37	6	123702474	123702474	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:123702474delA	uc003pzj.1	-						TRDN_uc003pzk.1_Intron|TRDN_uc003pzl.1_Intron|TRDN_uc010kem.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)														---	---	---	---
TRDN	10345	broad.mit.edu	37	6	123737413	123737415	+	Intron	DEL	ATA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:123737413_123737415delATA	uc003pzj.1	-						TRDN_uc003pzk.1_Intron|TRDN_uc003pzl.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)														---	---	---	---
TRDN	10345	broad.mit.edu	37	6	123783630	123783630	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:123783630delT	uc003pzj.1	-						TRDN_uc003pzk.1_Intron|TRDN_uc003pzl.1_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)														---	---	---	---
TRDN	10345	broad.mit.edu	37	6	123812250	123812250	+	Intron	DEL	A	-	-	rs5879684		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:123812250delA	uc003pzj.1	-						TRDN_uc003pzk.1_Intron|TRDN_uc003pzl.1_Intron|TRDN_uc010ken.2_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)														---	---	---	---
Unknown	0	broad.mit.edu	37	6	124096419	124096419	+	IGR	DEL	T	-	-	rs11321371		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:124096419delT								TRDN (138477 upstream) : NKAIN2 (28650 downstream)																																			---	---	---	---
NKAIN2	154215	broad.mit.edu	37	6	124476744	124476746	+	Intron	DEL	TTT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:124476744_124476746delTTT	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	124814034	124814034	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:124814034delT	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	125090706	125090706	+	Intron	DEL	A	-	-	rs140429910	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:125090706delA	uc003pzo.2	+						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)														---	---	---	---
RNF217	154214	broad.mit.edu	37	6	125330620	125330620	+	Intron	DEL	A	-	-	rs112538609		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:125330620delA	uc003pzs.2	+						RNF217_uc003pzr.2_Intron|RNF217_uc003pzt.2_Intron	NM_152553	NP_689766			ring finger protein 217						protein ubiquitination involved in ubiquitin-dependent protein catabolic process	integral to membrane	ubiquitin-protein ligase activity|zinc ion binding				0			LUSC - Lung squamous cell carcinoma(4;0.0263)|Lung(4;0.0828)	GBM - Glioblastoma multiforme(226;0.0162)														---	---	---	---
Unknown	0	broad.mit.edu	37	6	125763454	125763455	+	IGR	DEL	AC	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:125763454_125763455delAC								HDDC2 (140172 upstream) : HEY2 (305325 downstream)																																			---	---	---	---
RNF146	81847	broad.mit.edu	37	6	127588743	127588743	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:127588743delT	uc003qav.2	+						RNF146_uc003qat.2_Intron|RNF146_uc003qau.2_Intron	NM_030963	NP_112225			ring finger protein 146						positive regulation of canonical Wnt receptor signaling pathway|protein autoubiquitination|protein K48-linked ubiquitination|protein ubiquitination involved in ubiquitin-dependent protein catabolic process|Wnt receptor signaling pathway	cytosol	poly-ADP-D-ribose binding|protein binding|ubiquitin-protein ligase activity|zinc ion binding			kidney(1)	1				GBM - Glioblastoma multiforme(226;0.0407)|all cancers(137;0.2)														---	---	---	---
THEMIS	387357	broad.mit.edu	37	6	128031170	128031170	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:128031170delA	uc003qbi.2	-						THEMIS_uc010kfa.2_Intron|THEMIS_uc011ebt.1_Intron|THEMIS_uc010kfb.2_Intron	NM_001010923	NP_001010923			thymocyte selection pathway associated isoform						negative T cell selection|positive T cell selection|T cell receptor signaling pathway	cytoplasm|nucleus				ovary(2)|skin(2)	4																		---	---	---	---
PTPRK	5796	broad.mit.edu	37	6	128291226	128291226	+	3'UTR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:128291226delA	uc003qbk.2	-	30					PTPRK_uc003qbj.2_3'UTR|PTPRK_uc010kfc.2_3'UTR|PTPRK_uc011ebu.1_3'UTR	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	128318089	128318089	+	Frame_Shift_Del	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:128318089delT	uc003qbk.2	-	17	3088	c.2721delA	c.(2719-2721)AAAfs	p.K907fs	PTPRK_uc003qbj.2_Frame_Shift_Del_p.K908fs|PTPRK_uc010kfc.2_Frame_Shift_Del_p.K908fs|PTPRK_uc011ebu.1_Frame_Shift_Del_p.K924fs	NM_002844	NP_002835	Q15262	PTPRK_HUMAN	protein tyrosine phosphatase, receptor type, K	907	Tyrosine-protein phosphatase 1.|Cytoplasmic (Potential).				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)														---	---	---	---
LAMA2	3908	broad.mit.edu	37	6	129277957	129277957	+	Intron	DEL	T	-	-	rs113330072		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:129277957delT	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)														---	---	---	---
LAMA2	3908	broad.mit.edu	37	6	129763128	129763131	+	Intron	DEL	AAAA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:129763128_129763131delAAAA	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)														---	---	---	---
Unknown	0	broad.mit.edu	37	6	130314387	130314387	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-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	130407269	130407269	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:130407269delT	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)														---	---	---	---
L3MBTL3	84456	broad.mit.edu	37	6	130425541	130425541	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:130425541delT	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)														---	---	---	---
L3MBTL3	84456	broad.mit.edu	37	6	130460736	130460736	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:130460736delT	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)														---	---	---	---
TMEM200A	114801	broad.mit.edu	37	6	130761753	130761753	+	Frame_Shift_Del	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:130761753delT	uc003qca.2	+	3	1057	c.186delT	c.(184-186)GGTfs	p.G62fs	TMEM200A_uc010kfh.2_Frame_Shift_Del_p.G62fs|TMEM200A_uc010kfi.2_Frame_Shift_Del_p.G62fs|TMEM200A_uc003qcb.2_Frame_Shift_Del_p.G62fs	NM_052913	NP_443145	Q86VY9	T200A_HUMAN	transmembrane protein 200A	62	Helical; (Potential).					integral to membrane				ovary(1)	1				GBM - Glioblastoma multiforme(226;0.0139)|OV - Ovarian serous cystadenocarcinoma(155;0.12)														---	---	---	---
Unknown	0	broad.mit.edu	37	6	130936688	130936688	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:130936688delA								TMEM200A (172480 upstream) : LOC285733 (211636 downstream)																																			---	---	---	---
EPB41L2	2037	broad.mit.edu	37	6	131218365	131218366	+	Intron	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:131218365_131218366delAA	uc003qch.2	-						EPB41L2_uc003qcg.1_Intron|EPB41L2_uc011eby.1_Intron|EPB41L2_uc003qci.2_Intron|EPB41L2_uc010kfk.2_Intron|EPB41L2_uc010kfl.1_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	131430140	131430141	+	IGR	DEL	GT	-	-	rs34397018		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:131430140_131430141delGT								EPB41L2 (45678 upstream) : AKAP7 (26730 downstream)																																			---	---	---	---
AKAP7	9465	broad.mit.edu	37	6	131530391	131530391	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:131530391delT	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)														---	---	---	---
Unknown	0	broad.mit.edu	37	6	131887398	131887401	+	IGR	DEL	AAAA	-	-	rs112277244		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:131887398_131887401delAAAA								AKAP7 (282725 upstream) : ARG1 (6964 downstream)																																			---	---	---	---
MED23	9439	broad.mit.edu	37	6	131900087	131900087	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:131900087delA	uc003qcq.2	-						ARG1_uc003qco.1_Intron|ARG1_uc003qcp.1_Intron|ARG1_uc010kfm.1_Intron	NM_015979	NP_057063			mediator complex subunit 23 isoform b						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	132157258	132157259	+	Intron	DEL	TT	-	-	rs71728181		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:132157258_132157259delTT	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)													---	---	---	---
ENPP1	5167	broad.mit.edu	37	6	132176897	132176898	+	Intron	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:132176897_132176898delTT	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	132356790	132356791	+	IGR	DEL	AA	-	-	rs113454047		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:132356790_132356791delAA								CTGF (84272 upstream) : MOXD1 (260404 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	132424529	132424529	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:132424529delT								CTGF (152011 upstream) : MOXD1 (192666 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	132448604	132448604	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:132448604delT								CTGF (176086 upstream) : MOXD1 (168591 downstream)																																			---	---	---	---
MOXD1	26002	broad.mit.edu	37	6	132705418	132705418	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:132705418delT	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)														---	---	---	---
STX7	8417	broad.mit.edu	37	6	132812413	132812413	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:132812413delA	uc003qdg.2	-						STX7_uc011ecg.1_Intron|STX7_uc011ech.1_Intron	NM_003569	NP_003560			syntaxin 7						intracellular protein transport|post-Golgi vesicle-mediated transport	early endosome membrane|integral to membrane	SNAP receptor activity				0	Breast(56;0.0615)			OV - Ovarian serous cystadenocarcinoma(155;0.00532)|GBM - Glioblastoma multiforme(226;0.0114)														---	---	---	---
Unknown	0	broad.mit.edu	37	6	132994969	132994969	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:132994969delT								TAAR1 (27827 upstream) : VNN1 (7029 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	133152647	133152647	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:133152647delT								RPS12 (13945 upstream) : LOC285735 (256572 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	133495903	133495903	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:133495903delT								LOC285735 (68193 upstream) : EYA4 (65833 downstream)																																			---	---	---	---
EYA4	2070	broad.mit.edu	37	6	133698703	133698711	+	Intron	DEL	TTTTTTTTT	-	-	rs66883615		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:133698703_133698711delTTTTTTTTT	uc003qec.3	+						EYA4_uc011ecq.1_Intron|EYA4_uc011ecr.1_Intron|EYA4_uc003qed.3_Intron|EYA4_uc003qee.3_Intron|EYA4_uc011ecs.1_Intron	NM_004100	NP_004091			eyes absent 4 isoform a						anatomical structure morphogenesis|chromatin modification|DNA repair|multicellular organismal development|regulation of transcription, DNA-dependent|transcription, DNA-dependent|visual perception	cytoplasm|nucleus	metal ion binding|protein tyrosine phosphatase activity			large_intestine(2)	2	Colorectal(23;0.221)			GBM - Glioblastoma multiforme(68;0.00457)|OV - Ovarian serous cystadenocarcinoma(155;0.0152)														---	---	---	---
EYA4	2070	broad.mit.edu	37	6	133744173	133744173	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:133744173delT	uc003qec.3	+						EYA4_uc011ecq.1_Intron|EYA4_uc011ecr.1_Intron|EYA4_uc003qed.3_Intron|EYA4_uc003qee.3_Intron|EYA4_uc011ecs.1_Intron	NM_004100	NP_004091			eyes absent 4 isoform a						anatomical structure morphogenesis|chromatin modification|DNA repair|multicellular organismal development|regulation of transcription, DNA-dependent|transcription, DNA-dependent|visual perception	cytoplasm|nucleus	metal ion binding|protein tyrosine phosphatase activity			large_intestine(2)	2	Colorectal(23;0.221)			GBM - Glioblastoma multiforme(68;0.00457)|OV - Ovarian serous cystadenocarcinoma(155;0.0152)														---	---	---	---
Unknown	0	broad.mit.edu	37	6	133992611	133992611	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:133992611delT	uc003qeg.1	-											Homo sapiens cDNA FLJ36194 fis, clone TESTI2027615.																														---	---	---	---
Unknown	0	broad.mit.edu	37	6	134128218	134128218	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:134128218delA	uc003qeg.1	-											Homo sapiens cDNA FLJ36194 fis, clone TESTI2027615.																														---	---	---	---
Unknown	0	broad.mit.edu	37	6	134429488	134429488	+	IGR	DEL	C	-	-	rs9321425	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:134429488delC								SLC2A12 (55699 upstream) : SGK1 (60897 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	135212267	135212268	+	IGR	DEL	AG	-	-	rs76655717		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:135212267_135212268delAG								SGK1 (573071 upstream) : ALDH8A1 (26261 downstream)																																			---	---	---	---
AHI1	54806	broad.mit.edu	37	6	135734617	135734617	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:135734617delA	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)														---	---	---	---
C6orf217	100131814	broad.mit.edu	37	6	135854399	135854399	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:135854399delT	uc003qgn.2	+						C6orf217_uc003qgo.2_Intron|C6orf217_uc010kgo.2_Intron|C6orf217_uc003qgm.2_Intron					Homo sapiens cDNA clone IMAGE:4795512.												0																		---	---	---	---
C6orf217	100131814	broad.mit.edu	37	6	136026174	136026175	+	Intron	DEL	AG	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:136026174_136026175delAG	uc003qgn.2	+						C6orf217_uc003qgo.2_Intron					Homo sapiens cDNA clone IMAGE:4795512.												0																		---	---	---	---
BCLAF1	9774	broad.mit.edu	37	6	136605971	136605971	+	Intron	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:136605971delG	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)														---	---	---	---
MAP7	9053	broad.mit.edu	37	6	136790131	136790131	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:136790131delT	uc003qgz.2	-						MAP7_uc011edf.1_5'Flank|MAP7_uc011edg.1_Intron|MAP7_uc010kgu.2_Intron|MAP7_uc011edh.1_Intron|MAP7_uc010kgv.2_Intron|MAP7_uc010kgs.2_Intron|MAP7_uc011edi.1_Intron|MAP7_uc010kgq.1_Intron|MAP7_uc003qha.1_Intron|MAP7_uc010kgr.2_Intron|MAP7_uc010kgt.2_Intron	NM_003980	NP_003971			microtubule-associated protein 7						establishment or maintenance of cell polarity|microtubule cytoskeleton organization|protein localization in plasma membrane|response to osmotic stress	basolateral plasma membrane|microtubule|microtubule associated complex|nucleus|perinuclear region of cytoplasm	receptor binding|structural molecule activity				0	Colorectal(23;0.24)			GBM - Glioblastoma multiforme(68;0.00199)|OV - Ovarian serous cystadenocarcinoma(155;0.00643)														---	---	---	---
MAP3K5	4217	broad.mit.edu	37	6	136883805	136883805	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:136883805delT	uc003qhc.2	-						MAP3K5_uc011edj.1_Intron|MAP3K5_uc011edk.1_Intron	NM_005923	NP_005914			mitogen-activated protein kinase kinase kinase						activation of JUN kinase activity|activation of MAPKK activity|cellular response to hydrogen peroxide|induction of apoptosis by extracellular signals|interspecies interaction between organisms		ATP binding|caspase activator activity|magnesium ion binding|MAP kinase kinase kinase activity|protein homodimerization activity|protein phosphatase binding			ovary(2)|skin(2)|lung(1)	5	Colorectal(23;0.24)			GBM - Glioblastoma multiforme(68;0.00137)|OV - Ovarian serous cystadenocarcinoma(155;0.00569)														---	---	---	---
Unknown	0	broad.mit.edu	37	6	137401972	137401972	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:137401972delA								IL20RA (35674 upstream) : IL22RA2 (62986 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	137662523	137662523	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:137662523delT								IFNGR1 (121956 upstream) : OLIG3 (150813 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	137772840	137772840	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:137772840delT								IFNGR1 (232273 upstream) : OLIG3 (40496 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	137951073	137951073	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:137951073delA								OLIG3 (135542 upstream) : TNFAIP3 (237508 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	138020158	138020160	+	IGR	DEL	CTC	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:138020158_138020160delCTC								OLIG3 (204627 upstream) : TNFAIP3 (168421 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	138288316	138288316	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:138288316delA								TNFAIP3 (83871 upstream) : PERP (121326 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	138319619	138319620	+	IGR	DEL	AG	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:138319619_138319620delAG								TNFAIP3 (115174 upstream) : PERP (90022 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	138376195	138376195	+	IGR	DEL	A	-	-	rs138937311		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:138376195delA								TNFAIP3 (171750 upstream) : PERP (33447 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	138399054	138399054	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:138399054delT								TNFAIP3 (194609 upstream) : PERP (10588 downstream)																																			---	---	---	---
KIAA1244	57221	broad.mit.edu	37	6	138524042	138524043	+	Intron	DEL	CA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:138524042_138524043delCA	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)														---	---	---	---
NHSL1	57224	broad.mit.edu	37	6	138892291	138892291	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:138892291delA	uc003qhx.2	-							NM_020464	NP_065197			NHS-like 1 isoform 1												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	6	138929691	138929691	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:138929691delA								NHSL1 (36023 upstream) : CCDC28A (164966 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	139056726	139056727	+	Intron	INS	-	A	A	rs11431423		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:139056726_139056727insA	uc003qid.1	-											Homo sapiens cDNA FLJ35273 fis, clone PROST2006020.																														---	---	---	---
CCDC28A	25901	broad.mit.edu	37	6	139096998	139096999	+	Intron	INS	-	AAAAC	AAAAC			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:139096998_139096999insAAAAC	uc003qie.2	+						uc003qid.1_5'Flank	NM_015439	NP_056254			coiled-coil domain containing 28A												0				OV - Ovarian serous cystadenocarcinoma(155;0.000201)|GBM - Glioblastoma multiforme(68;0.000306)														---	---	---	---
CCDC28A	25901	broad.mit.edu	37	6	139106548	139106548	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:139106548delA	uc003qie.2	+							NM_015439	NP_056254			coiled-coil domain containing 28A												0				OV - Ovarian serous cystadenocarcinoma(155;0.000201)|GBM - Glioblastoma multiforme(68;0.000306)														---	---	---	---
Unknown	0	broad.mit.edu	37	6	139788010	139788011	+	IGR	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:139788010_139788011delTT								CITED2 (92225 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	139849322	139849322	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:139849322delA								CITED2 (153537 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	140952119	140952120	+	IGR	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:140952119_140952120delTT								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	141359010	141359010	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:141359010delT								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	141377541	141377542	+	IGR	INS	-	CACA	CACA	rs146850096	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:141377541_141377542insCACA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	141746566	141746566	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:141746566delA								None (None upstream) : NMBR (650180 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	141999364	141999364	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:141999364delT	uc003qit.1	-											SubName: Full=ORF2-like protein; Flags: Fragment;																														---	---	---	---
Unknown	0	broad.mit.edu	37	6	142013848	142013849	+	Intron	INS	-	TG	TG			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:142013848_142013849insTG	uc003qit.1	-											SubName: Full=ORF2-like protein; Flags: Fragment;																														---	---	---	---
Unknown	0	broad.mit.edu	37	6	142232571	142232572	+	Intron	DEL	AC	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:142232571_142232572delAC	uc003qit.1	-											SubName: Full=ORF2-like protein; Flags: Fragment;																														---	---	---	---
Unknown	0	broad.mit.edu	37	6	142276210	142276210	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:142276210delT	uc003qit.1	-											SubName: Full=ORF2-like protein; Flags: Fragment;																														---	---	---	---
VTA1	51534	broad.mit.edu	37	6	142494115	142494117	+	Intron	DEL	AAG	-	-	rs71723726		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:142494115_142494117delAAG	uc003qiw.2	+						VTA1_uc011edt.1_Intron|VTA1_uc011edu.1_Intron	NM_016485	NP_057569			Vps20-associated 1 homolog						cellular membrane organization|endosome transport|protein transport	cytosol|endosome membrane	protein binding				0	Breast(32;0.155)			OV - Ovarian serous cystadenocarcinoma(155;1.34e-05)|GBM - Glioblastoma multiforme(68;0.00182)														---	---	---	---
VTA1	51534	broad.mit.edu	37	6	142507705	142507705	+	Intron	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:142507705delG	uc003qiw.2	+						VTA1_uc011edt.1_Intron|VTA1_uc011edu.1_Intron	NM_016485	NP_057569			Vps20-associated 1 homolog						cellular membrane organization|endosome transport|protein transport	cytosol|endosome membrane	protein binding				0	Breast(32;0.155)			OV - Ovarian serous cystadenocarcinoma(155;1.34e-05)|GBM - Glioblastoma multiforme(68;0.00182)														---	---	---	---
Unknown	0	broad.mit.edu	37	6	142555609	142555609	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:142555609delA								VTA1 (13526 upstream) : GPR126 (67447 downstream)																																			---	---	---	---
AIG1	51390	broad.mit.edu	37	6	143382375	143382375	+	Intron	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:143382375delC	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)														---	---	---	---
Unknown	0	broad.mit.edu	37	6	144154167	144154167	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:144154167delA								PHACTR2 (1846 upstream) : LTV1 (10341 downstream)																																			---	---	---	---
LTV1	84946	broad.mit.edu	37	6	144179191	144179191	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:144179191delT	uc003qjs.2	+						LTV1_uc003qju.1_Intron|C6orf94_uc010khj.2_Intron	NM_032860	NP_116249			LTV1 homolog											ovary(1)	1				OV - Ovarian serous cystadenocarcinoma(155;2.72e-06)|GBM - Glioblastoma multiforme(68;0.0372)														---	---	---	---
UTRN	7402	broad.mit.edu	37	6	144697061	144697061	+	Intron	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:144697061delC	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	145097094	145097094	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:145097094delA	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	145167012	145167012	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:145167012delT	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	145199970	145199970	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:145199970delT								UTRN (25802 upstream) : EPM2A (746476 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	145551277	145551277	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:145551277delA								UTRN (377109 upstream) : EPM2A (395169 downstream)																																			---	---	---	---
SHPRH	257218	broad.mit.edu	37	6	146264759	146264759	+	Frame_Shift_Del	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:146264759delT	uc003qlf.2	-	9	2157	c.1758delA	c.(1756-1758)AAAfs	p.K586fs	SHPRH_uc003qld.2_Frame_Shift_Del_p.K586fs|SHPRH_uc003qle.2_Frame_Shift_Del_p.K586fs|SHPRH_uc003qlg.1_Frame_Shift_Del_p.K142fs|SHPRH_uc003qlj.1_Frame_Shift_Del_p.K475fs	NM_001042683	NP_001036148	Q149N8	SHPRH_HUMAN	SNF2 histone linker PHD RING helicase isoform a	586					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)														---	---	---	---
RAB32	10981	broad.mit.edu	37	6	146872270	146872270	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:146872270delA	uc003qln.1	+							NM_006834	NP_006825			RAB32, member RAS oncogene family						protein transport|small GTPase mediated signal transduction	mitochondrion	GTP binding				0		Ovarian(120;0.142)		OV - Ovarian serous cystadenocarcinoma(155;2.68e-09)|GBM - Glioblastoma multiforme(68;0.00608)														---	---	---	---
Unknown	0	broad.mit.edu	37	6	146916672	146916673	+	IGR	INS	-	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:146916672_146916673insA								RAB32 (40586 upstream) : C6orf103 (3463 downstream)																																			---	---	---	---
C6orf103	79747	broad.mit.edu	37	6	146935344	146935359	+	Intron	DEL	CCTTCCTTCCTCCCTT	-	-	rs67622688	by1000genomes;by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:146935344_146935359delCCTTCCTTCCTCCCTT	uc010khx.2	+						C6orf103_uc003qlp.2_Intron	NM_024694	NP_078970			hypothetical protein LOC79747						oxygen transport|proteolysis	intracellular	calcium-dependent cysteine-type endopeptidase activity|heme binding|oxygen binding			central_nervous_system(2)|lung(1)	3		Ovarian(120;0.142)		OV - Ovarian serous cystadenocarcinoma(155;2.04e-08)|GBM - Glioblastoma multiforme(68;0.0113)														---	---	---	---
Unknown	0	broad.mit.edu	37	6	147469302	147469303	+	Intron	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:147469302_147469303delTT	uc003qlt.1	-						uc003qlu.1_Intron					Homo sapiens cDNA FLJ34275 fis, clone FEBRA2003454.																														---	---	---	---
STXBP5	134957	broad.mit.edu	37	6	147543087	147543087	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:147543087delT	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	147785821	147785821	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:147785821delT								STXBP5 (77114 upstream) : SAMD5 (44242 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	147812179	147812179	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:147812179delA								STXBP5 (103472 upstream) : SAMD5 (17884 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	147826490	147826490	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:147826490delA								STXBP5 (117783 upstream) : SAMD5 (3573 downstream)																																			---	---	---	---
TAB2	23118	broad.mit.edu	37	6	149656234	149656234	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:149656234delT	uc003qmj.2	+						TAB2_uc011eec.1_Intron|TAB2_uc010kia.1_Intron|TAB2_uc010kib.1_Intron	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																		---	---	---	---
KATNA1	11104	broad.mit.edu	37	6	149937890	149937890	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:149937890delA	uc003qmr.1	-						KATNA1_uc003qms.2_Intron|KATNA1_uc003qmt.2_Intron|KATNA1_uc011eed.1_Intron	NM_007044	NP_008975			katanin p60 subunit A 1						cell division|interphase of mitotic cell cycle|mitosis	microtubule|microtubule organizing center|spindle pole	ATP binding|microtubule binding|microtubule-severing ATPase activity|protein heterodimerization activity			skin(1)	1		Ovarian(120;0.0164)		OV - Ovarian serous cystadenocarcinoma(155;2.95e-12)|GBM - Glioblastoma multiforme(68;0.173)														---	---	---	---
LATS1	9113	broad.mit.edu	37	6	150019859	150019859	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:150019859delT	uc003qmu.1	-						LATS1_uc010kif.1_Intron|LATS1_uc003qmv.1_Intron|LATS1_uc003qmw.2_Intron|LATS1_uc010kig.1_Intron	NM_004690	NP_004681			LATS homolog 1						cell division|cytoplasmic sequestering of protein|G2/M transition of mitotic cell cycle|hippo signaling cascade|hormone-mediated signaling pathway|mitosis|negative regulation of canonical Wnt receptor signaling pathway|negative regulation of cyclin-dependent protein kinase activity|positive regulation of peptidyl-serine phosphorylation|regulation of actin filament polymerization|sister chromatid segregation	microtubule organizing center|spindle pole	ATP binding|magnesium ion binding|protein kinase binding|protein serine/threonine kinase activity			lung(5)|central_nervous_system(1)	6		Ovarian(120;0.0164)		OV - Ovarian serous cystadenocarcinoma(155;6.93e-13)|GBM - Glioblastoma multiforme(68;0.116)														---	---	---	---
PCMT1	5110	broad.mit.edu	37	6	150096678	150096679	+	Intron	INS	-	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:150096678_150096679insA	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)														---	---	---	---
Unknown	0	broad.mit.edu	37	6	150192850	150192850	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:150192850delT	uc003qni.1	+											Homo sapiens low density lipoprotein receptor-related protein 11, mRNA (cDNA clone IMAGE:4072521), partial cds.																														---	---	---	---
RAET1G	353091	broad.mit.edu	37	6	150245280	150245280	+	5'Flank	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:150245280delT	uc010kii.1	-						RAET1G_uc003qnm.2_5'Flank	NM_001001788	NP_001001788			retinoic acid early transcript 1G precursor						antigen processing and presentation|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;2.73e-12)														---	---	---	---
MTHFD1L	25902	broad.mit.edu	37	6	151395017	151395017	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:151395017delA	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)														---	---	---	---
Unknown	0	broad.mit.edu	37	6	151541994	151541995	+	Intron	DEL	AA	-	-	rs71715393		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:151541994_151541995delAA	uc003qod.2	-											Homo sapiens cDNA clone IMAGE:4838370.																														---	---	---	---
ZBTB2	57621	broad.mit.edu	37	6	151701276	151701276	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:151701276delA	uc003qoh.2	-							NM_020861	NP_065912			zinc finger and BTB domain containing 2						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)														---	---	---	---
ESR1	2099	broad.mit.edu	37	6	152203897	152203899	+	Intron	DEL	TTT	-	-	rs111742105		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:152203897_152203899delTTT	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)													---	---	---	---
ESR1	2099	broad.mit.edu	37	6	152229904	152229904	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:152229904delA	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	152671640	152671640	+	Intron	DEL	A	-	-	rs76305112		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:152671640delA	uc010kiw.2	-						SYNE1_uc003qot.3_Intron|SYNE1_uc003qou.3_Intron|SYNE1_uc010kja.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	152832668	152832668	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:152832668delA	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	153490203	153490203	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:153490203delT								RGS17 (37814 upstream) : OPRM1 (841433 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	153603371	153603372	+	IGR	DEL	TT	-	-	rs113533278	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:153603371_153603372delTT								RGS17 (150982 upstream) : OPRM1 (728264 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	153750006	153750006	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:153750006delA								RGS17 (297617 upstream) : OPRM1 (581630 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	154111035	154111036	+	IGR	INS	-	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:154111035_154111036insA								RGS17 (658646 upstream) : OPRM1 (220600 downstream)																																			---	---	---	---
IPCEF1	26034	broad.mit.edu	37	6	154505625	154505625	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:154505625delT	uc003qpx.2	-						OPRM1_uc003qpt.1_Intron|IPCEF1_uc003qpv.2_Intron|IPCEF1_uc003qpw.2_Intron|IPCEF1_uc010kjh.2_Intron	NM_015553	NP_056368			phosphoinositide-binding protein PIP3-E isoform						response to oxidative stress	cytoplasm|plasma membrane	oxygen transporter activity|peroxidase activity				0																		---	---	---	---
IPCEF1	26034	broad.mit.edu	37	6	154582864	154582864	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:154582864delT	uc003qpx.2	-						IPCEF1_uc003qpw.2_Intron|IPCEF1_uc010kjh.2_Intron	NM_015553	NP_056368			phosphoinositide-binding protein PIP3-E isoform						response to oxidative stress	cytoplasm|plasma membrane	oxygen transporter activity|peroxidase activity				0																		---	---	---	---
TIAM2	26230	broad.mit.edu	37	6	155510103	155510103	+	Intron	DEL	T	-	-	rs71927167		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:155510103delT	uc003qqb.2	+						TIAM2_uc003qqe.2_Intron|TIAM2_uc010kjj.2_Intron|TIAM2_uc003qqf.2_Intron|TIAM2_uc011efl.1_Intron|TIAM2_uc003qqg.2_Intron	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)														---	---	---	---
TIAM2	26230	broad.mit.edu	37	6	155510484	155510484	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:155510484delT	uc003qqb.2	+						TIAM2_uc003qqe.2_Intron|TIAM2_uc010kjj.2_Intron|TIAM2_uc003qqf.2_Intron|TIAM2_uc011efl.1_Intron|TIAM2_uc003qqg.2_Intron	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	155761274	155761274	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:155761274delA	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	155773091	155773091	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:155773091delT	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	155976308	155976308	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:155976308delT								NOX3 (199271 upstream) : MIR1202 (291623 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	156220767	156220767	+	IGR	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:156220767delG								NOX3 (443730 upstream) : MIR1202 (47164 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	156450243	156450244	+	IGR	DEL	TC	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:156450243_156450244delTC								MIR1202 (182230 upstream) : ARID1B (648842 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	157031811	157031812	+	IGR	DEL	GT	-	-	rs72067053		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:157031811_157031812delGT								MIR1202 (763798 upstream) : ARID1B (67274 downstream)																																			---	---	---	---
ARID1B	57492	broad.mit.edu	37	6	157296203	157296203	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:157296203delT	uc003qqn.2	+						ARID1B_uc003qqo.2_Intron|ARID1B_uc003qqp.2_Intron|ARID1B_uc003qqq.1_Intron	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)														---	---	---	---
ARID1B	57492	broad.mit.edu	37	6	157495668	157495669	+	Intron	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:157495668_157495669delTT	uc003qqn.2	+						ARID1B_uc003qqo.2_Intron|ARID1B_uc003qqp.2_Intron|ARID1B_uc010kjl.2_Intron	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	157558474	157558475	+	IGR	DEL	GC	-	-	rs143179613	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:157558474_157558475delGC								ARID1B (28073 upstream) : C6orf35 (151580 downstream)																																			---	---	---	---
SERAC1	84947	broad.mit.edu	37	6	158535189	158535189	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:158535189delA	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	158633759	158633759	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:158633759delA								GTF2H5 (13393 upstream) : TULP4 (99933 downstream)																																			---	---	---	---
SYTL3	94120	broad.mit.edu	37	6	159166783	159166783	+	Intron	DEL	A	-	-	rs67759405		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:159166783delA	uc003qrp.2	+						SYTL3_uc011efp.1_Intron|SYTL3_uc003qro.2_Intron|SYTL3_uc003qrq.2_Intron|SYTL3_uc003qrr.2_Intron|SYTL3_uc003qrs.2_Intron|SYTL3_uc011efq.1_Intron	NM_001009991	NP_001009991			synaptotagmin-like 3						intracellular protein transport	endomembrane system|membrane	Rab GTPase binding				0		Breast(66;0.000776)|Ovarian(120;0.0303)		OV - Ovarian serous cystadenocarcinoma(65;1.54e-17)|BRCA - Breast invasive adenocarcinoma(81;8.24e-06)														---	---	---	---
SYTL3	94120	broad.mit.edu	37	6	159184493	159184494	+	Frame_Shift_Del	DEL	CT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:159184493_159184494delCT	uc003qrp.2	+	16	1919_1920	c.1675_1676delCT	c.(1675-1677)CTCfs	p.L559fs	SYTL3_uc011efp.1_Frame_Shift_Del_p.L559fs|SYTL3_uc003qro.2_Frame_Shift_Del_p.L491fs|SYTL3_uc003qrq.2_Frame_Shift_Del_p.L491fs|SYTL3_uc003qrr.2_Frame_Shift_Del_p.L559fs|SYTL3_uc003qrs.2_Frame_Shift_Del_p.L491fs|SYTL3_uc011efq.1_Frame_Shift_Del_p.L285fs	NM_001009991	NP_001009991	Q4VX76	SYTL3_HUMAN	synaptotagmin-like 3	559	C2 2.				intracellular protein transport	endomembrane system|membrane	Rab GTPase binding				0		Breast(66;0.000776)|Ovarian(120;0.0303)		OV - Ovarian serous cystadenocarcinoma(65;1.54e-17)|BRCA - Breast invasive adenocarcinoma(81;8.24e-06)														---	---	---	---
OSTCL	202459	broad.mit.edu	37	6	159262512	159262512	+	3'UTR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:159262512delA	uc003qrw.2	-	3						NM_145303	NP_660346			oligosaccharyltransferase complex subunit-like												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	6	159308435	159308435	+	IGR	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:159308435delG								OSTCL (29771 upstream) : RSPH3 (89833 downstream)																																			---	---	---	---
RSPH3	83861	broad.mit.edu	37	6	159414159	159414160	+	Intron	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:159414159_159414160delTT	uc003qrx.2	-						RSPH3_uc010kju.2_Intron|RSPH3_uc003qry.1_Intron	NM_031924	NP_114130			radial spoke 3 homolog											ovary(1)|skin(1)	2		Breast(66;0.00519)|Ovarian(120;0.123)		OV - Ovarian serous cystadenocarcinoma(65;2.36e-16)|BRCA - Breast invasive adenocarcinoma(81;5.92e-06)														---	---	---	---
Unknown	0	broad.mit.edu	37	6	160053803	160053803	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:160053803delA								FNDC1 (360664 upstream) : SOD2 (46348 downstream)																																			---	---	---	---
SLC22A1	6580	broad.mit.edu	37	6	160567092	160567093	+	Intron	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:160567092_160567093delTT	uc003qtc.2	+						SLC22A1_uc003qtd.2_Intron	NM_003057	NP_003048			solute carrier family 22 member 1 isoform a							basolateral plasma membrane|integral to plasma membrane|membrane fraction	organic cation transmembrane transporter activity|protein binding				0		Breast(66;0.000776)|Ovarian(120;0.00556)		OV - Ovarian serous cystadenocarcinoma(65;2.73e-17)|BRCA - Breast invasive adenocarcinoma(81;1.1e-06)														---	---	---	---
SLC22A2	6582	broad.mit.edu	37	6	160616340	160616340	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:160616340delT	uc003qte.1	-							NM_003058	NP_003049			solute carrier family 22 member 2						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)														---	---	---	---
SLC22A3	6581	broad.mit.edu	37	6	160773547	160773547	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:160773547delA	uc003qti.2	+						SLC22A3_uc011efx.1_Intron	NM_021977	NP_068812			solute carrier family 22 member 3							integral to plasma membrane|membrane fraction	protein binding|quaternary ammonium group transmembrane transporter activity			skin(2)|ovary(1)|central_nervous_system(1)	4		Breast(66;0.00028)|Ovarian(120;0.0308)|Prostate(117;0.218)		OV - Ovarian serous cystadenocarcinoma(65;9.47e-17)|BRCA - Breast invasive adenocarcinoma(81;9.75e-06)														---	---	---	---
SLC22A3	6581	broad.mit.edu	37	6	160787006	160787007	+	Intron	INS	-	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:160787006_160787007insG	uc003qti.2	+						SLC22A3_uc011efx.1_Intron	NM_021977	NP_068812			solute carrier family 22 member 3							integral to plasma membrane|membrane fraction	protein binding|quaternary ammonium group transmembrane transporter activity			skin(2)|ovary(1)|central_nervous_system(1)	4		Breast(66;0.00028)|Ovarian(120;0.0308)|Prostate(117;0.218)		OV - Ovarian serous cystadenocarcinoma(65;9.47e-17)|BRCA - Breast invasive adenocarcinoma(81;9.75e-06)														---	---	---	---
SLC22A3	6581	broad.mit.edu	37	6	160868943	160868943	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:160868943delA	uc003qti.2	+						SLC22A3_uc011efx.1_Intron	NM_021977	NP_068812			solute carrier family 22 member 3							integral to plasma membrane|membrane fraction	protein binding|quaternary ammonium group transmembrane transporter activity			skin(2)|ovary(1)|central_nervous_system(1)	4		Breast(66;0.00028)|Ovarian(120;0.0308)|Prostate(117;0.218)		OV - Ovarian serous cystadenocarcinoma(65;9.47e-17)|BRCA - Breast invasive adenocarcinoma(81;9.75e-06)														---	---	---	---
LPA	4018	broad.mit.edu	37	6	161017426	161017428	+	Intron	DEL	TTT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-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	161111166	161111167	+	IGR	INS	-	GT	GT	rs148094949	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:161111166_161111167insGT								LPA (23759 upstream) : PLG (12107 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	161211638	161211638	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:161211638delA								PLG (37293 upstream) : MAP3K4 (201184 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	161542054	161542055	+	IGR	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:161542054_161542055delTT								MAP3K4 (3638 upstream) : AGPAT4 (9002 downstream)																																			---	---	---	---
PARK2	5071	broad.mit.edu	37	6	161822657	161822658	+	Intron	DEL	AA	-	-	rs143757495		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:161822657_161822658delAA	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	161843734	161843734	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:161843734delA	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	161881959	161881960	+	Intron	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:161881959_161881960delTT	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	161947159	161947159	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:161947159delA	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	162002111	162002112	+	Intron	INS	-	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:162002111_162002112insT	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	162010979	162010980	+	Intron	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:162010979_162010980delTT	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	162511096	162511096	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:162511096delT	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	162511173	162511174	+	Intron	DEL	TG	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:162511173_162511174delTG	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	163012655	163012655	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:163012655delT	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)														---	---	---	---
QKI	9444	broad.mit.edu	37	6	163987695	163987695	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:163987695delT	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	164004567	164004567	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:164004567delA								QKI (9675 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	164086789	164086790	+	IGR	INS	-	AC	AC			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:164086789_164086790insAC								QKI (91897 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	164930806	164930806	+	IGR	DEL	A	-	-	rs67422531		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:164930806delA								QKI (935914 upstream) : C6orf118 (762349 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	164999479	164999479	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:164999479delA								None (None upstream) : C6orf118 (693676 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	165607728	165607731	+	IGR	DEL	AAAA	-	-	rs67773716		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:165607728_165607731delAAAA								None (None upstream) : C6orf118 (85424 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	166096909	166096910	+	IGR	DEL	CA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:166096909_166096910delCA								PDE10A (21325 upstream) : C6orf176 (240626 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	166115265	166115266	+	IGR	DEL	GT	-	-	rs114265542	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:166115265_166115266delGT								PDE10A (39681 upstream) : C6orf176 (222270 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	166432247	166432247	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:166432247delA								LOC441177 (29144 upstream) : T (138839 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	166501349	166501350	+	IGR	INS	-	G	G	rs147619371	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:166501349_166501350insG								LOC441177 (98246 upstream) : T (69736 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	167294424	167294424	+	IGR	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:167294424delG								RPS6KA2 (18653 upstream) : RNASET2 (48584 downstream)																																			---	---	---	---
RNASET2	8635	broad.mit.edu	37	6	167377923	167377923	+	Intron	DEL	T	-	-	rs145188497		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-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)														---	---	---	---
FGFR1OP	11116	broad.mit.edu	37	6	167446007	167446008	+	Intron	INS	-	T	T	rs3752519	byFrequency;by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:167446007_167446008insT	uc003qvj.2	+						CCR6_uc003qvl.2_Intron|FGFR1OP_uc011egp.1_Intron|FGFR1OP_uc003qvk.2_Intron	NM_007045	NP_008976			FGFR1 oncogene partner isoform a						G2/M transition of mitotic cell cycle|microtubule anchoring|positive regulation of cell growth|positive regulation of cell migration|positive regulation of cell proliferation	centrosome|cytosol|nucleus|perinuclear region of cytoplasm	protein homodimerization activity|protein kinase binding|protein tyrosine kinase inhibitor activity			ovary(1)	1		Breast(66;1.48e-05)|Ovarian(120;0.0607)		OV - Ovarian serous cystadenocarcinoma(33;1.73e-19)|BRCA - Breast invasive adenocarcinoma(81;5.1e-06)|GBM - Glioblastoma multiforme(31;0.00231)				T	FGFR1	MPD|NHL								---	---	---	---
FRMD1	79981	broad.mit.edu	37	6	168478917	168478917	+	Intron	DEL	G	-	-	rs4708633	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:168478917delG	uc003qwo.3	-						FRMD1_uc003qwn.3_5'Flank	NM_024919	NP_079195			FERM domain containing 1 isoform 1							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)														---	---	---	---
Unknown	0	broad.mit.edu	37	6	168732156	168732157	+	IGR	DEL	TG	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:168732156_168732157delTG								DACT2 (11754 upstream) : SMOC2 (109874 downstream)																																			---	---	---	---
SMOC2	64094	broad.mit.edu	37	6	168937404	168937404	+	Intron	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:168937404delC	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	168940880	168940880	+	Intron	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:168940880delG	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	168957498	168957499	+	Intron	INS	-	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:168957498_168957499insT	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	168959486	168959487	+	Intron	DEL	TG	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:168959486_168959487delTG	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	168999703	168999703	+	Intron	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:168999703delC	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	169410264	169410267	+	IGR	DEL	TTTT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:169410264_169410267delTTTT								SMOC2 (341593 upstream) : THBS2 (205609 downstream)																																			---	---	---	---
THBS2	7058	broad.mit.edu	37	6	169616608	169616609	+	3'UTR	INS	-	G	G	rs78222213	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:169616608_169616609insG	uc003qwt.2	-	23						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)														---	---	---	---
THBS2	7058	broad.mit.edu	37	6	169636387	169636388	+	Intron	INS	-	C	C	rs145507173	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:169636387_169636388insC	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)														---	---	---	---
PHF10	55274	broad.mit.edu	37	6	170116197	170116197	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:170116197delA	uc011egy.1	-						PHF10_uc011egz.1_Intron|PHF10_uc011eha.1_5'Flank	NM_018288	NP_060758			PHD finger protein 10 isoform a						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)														---	---	---	---
PHF10	55274	broad.mit.edu	37	6	170118007	170118007	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:170118007delA	uc011egy.1	-						PHF10_uc011egz.1_Intron|PHF10_uc011eha.1_5'Flank	NM_018288	NP_060758			PHD finger protein 10 isoform a						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)														---	---	---	---
Unknown	0	broad.mit.edu	37	6	170530538	170530538	+	IGR	DEL	C	-	-	rs67985666		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:170530538delC								C6orf208 (327569 upstream) : LOC154449 (32884 downstream)																																			---	---	---	---
PSMB1	5689	broad.mit.edu	37	6	170821774	170821775	+	Intron	DEL	AC	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:170821774_170821775delAC	uc003qxq.2	-							NM_002793				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)													---	---	---	---
Unknown	0	broad.mit.edu	37	7	414108	414111	+	IGR	DEL	GGAG	-	-	rs139925018	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:414108_414111delGGAG								FAM20C (113397 upstream) : PDGFA (122788 downstream)																																			---	---	---	---
SUN1	23353	broad.mit.edu	37	7	881566	881566	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:881566delT	uc011jvp.1	+						SUN1_uc010ksa.1_Intron|SUN1_uc003sje.1_Intron|SUN1_uc003sjf.2_Intron|SUN1_uc011jvq.1_Intron|SUN1_uc003sjg.2_5'Flank	NM_001130965	NP_001124437			unc-84 homolog A isoform a						cytoskeletal anchoring at nuclear membrane|nuclear matrix anchoring at nuclear membrane	integral to membrane|nuclear inner membrane|SUN-KASH complex	protein binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	7	1253471	1253471	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:1253471delA								ZFAND2A (53616 upstream) : UNCX (19183 downstream)																																			---	---	---	---
INTS1	26173	broad.mit.edu	37	7	1532995	1532996	+	Intron	INS	-	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:1532995_1532996insG	uc003skn.2	-						INTS1_uc003skp.1_Intron	NM_001080453	NP_001073922			integrator complex subunit 1						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	1605945	1605945	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:1605945delA								TMEM184A (9879 upstream) : PSMG3 (1025 downstream)																																			---	---	---	---
KIAA1908	114796	broad.mit.edu	37	7	1627871	1627872	+	RNA	INS	-	C	C	rs148656502	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:1627871_1627872insC	uc003sla.2	+	6		c.2469_2470insC			KIAA1908_uc003sky.1_RNA|KIAA1908_uc003skz.1_RNA	NR_021487				Homo sapiens mRNA for KIAA1908 protein, partial cds.												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	7	1634961	1634962	+	IGR	INS	-	ATCC	ATCC	rs141966771	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:1634961_1634962insATCC								KIAA1908 (5702 upstream) : TFAMP1 (19144 downstream)																																			---	---	---	---
EIF3B	8662	broad.mit.edu	37	7	2403106	2403106	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:2403106delA	uc003slx.2	+						EIF3B_uc003sly.2_Intron|EIF3B_uc003slz.1_Intron|EIF3B_uc003sma.2_Intron	NM_003751	NP_003742			eukaryotic translation initiation factor 3,						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)														---	---	---	---
EIF3B	8662	broad.mit.edu	37	7	2413963	2413963	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:2413963delT	uc003slx.2	+						EIF3B_uc003sly.2_Intron|EIF3B_uc003sma.2_Intron|EIF3B_uc003smb.2_5'Flank	NM_003751	NP_003742			eukaryotic translation initiation factor 3,						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)														---	---	---	---
Unknown	0	broad.mit.edu	37	7	2477835	2477836	+	Intron	INS	-	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:2477835_2477836insG	uc003sme.2	+											Homo sapiens, clone IMAGE:4778475, mRNA.																														---	---	---	---
Unknown	0	broad.mit.edu	37	7	2529484	2529484	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:2529484delA								CHST12 (55270 upstream) : LFNG (29995 downstream)																																			---	---	---	---
GNA12	2768	broad.mit.edu	37	7	2877776	2877776	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-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)														---	---	---	---
Unknown	0	broad.mit.edu	37	7	3201981	3201982	+	Intron	INS	-	A	A	rs72088635		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:3201981_3201982insA	uc003smw.1	-											Homo sapiens hypothetical protein LOC389457, mRNA (cDNA clone IMAGE:5267367).																														---	---	---	---
Unknown	0	broad.mit.edu	37	7	3271764	3271765	+	IGR	DEL	TG	-	-	rs112345450		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:3271764_3271765delTG								CARD11 (188185 upstream) : SDK1 (69315 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	3283740	3283740	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:3283740delA								CARD11 (200161 upstream) : SDK1 (57340 downstream)																																			---	---	---	---
SDK1	221935	broad.mit.edu	37	7	3591477	3591477	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:3591477delT	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	4251251	4251252	+	Intron	INS	-	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:4251251_4251252insT	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	4322060	4322060	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:4322060delA								SDK1 (13431 upstream) : FOXK1 (361328 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	4566900	4566901	+	IGR	DEL	TT	-	-	rs75582801		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:4566900_4566901delTT								SDK1 (258271 upstream) : FOXK1 (116487 downstream)																																			---	---	---	---
MMD2	221938	broad.mit.edu	37	7	4956703	4956703	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:4956703delA	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	5169949	5169950	+	Intron	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:5169949_5169950delAA	uc003snu.1	-						uc010ksu.1_Intron|uc011jwf.1_Intron					SubName: Full=cDNA FLJ60262, weakly similar to Zinc finger protein 81;																														---	---	---	---
TNRC18	84629	broad.mit.edu	37	7	5396370	5396370	+	Intron	DEL	C	-	-	rs67430912		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:5396370delC	uc003soi.3	-						TNRC18_uc003soj.2_Intron	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	5903978	5903979	+	IGR	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:5903978_5903979delAA								ZNF815 (9912 upstream) : OCM (16450 downstream)																																			---	---	---	---
C7orf28A	51622	broad.mit.edu	37	7	5942261	5942261	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:5942261delT	uc003spf.2	+							NM_015622	NP_056437			hypothetical protein LOC51622							lysosomal membrane					0		Ovarian(82;0.0694)		UCEC - Uterine corpus endometrioid carcinoma (126;0.0974)|OV - Ovarian serous cystadenocarcinoma(56;7.91e-15)														---	---	---	---
CYTH3	9265	broad.mit.edu	37	7	6261335	6261336	+	Intron	INS	-	A	A	rs145837937	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:6261335_6261336insA	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																		---	---	---	---
C7orf70	84792	broad.mit.edu	37	7	6380775	6380775	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:6380775delA	uc003spu.2	-							NM_001037163	NP_001032240			hypothetical protein LOC84792							nucleus					0																		---	---	---	---
DAGLB	221955	broad.mit.edu	37	7	6474587	6474587	+	Frame_Shift_Del	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:6474587delT	uc003sqa.2	-	4	654	c.484delA	c.(484-486)ATGfs	p.M162fs	DAGLB_uc011jwt.1_Translation_Start_Site|DAGLB_uc011jwu.1_Intron|DAGLB_uc003sqb.2_Intron|DAGLB_uc003sqc.2_Intron|DAGLB_uc011jwv.1_RNA|DAGLB_uc003sqd.3_Frame_Shift_Del_p.M121fs|DAGLB_uc011jww.1_Intron	NM_139179	NP_631918	Q8NCG7	DGLB_HUMAN	diacylglycerol lipase, beta isoform 1	162	Cytoplasmic (Potential).				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)														---	---	---	---
PMS2CL	441194	broad.mit.edu	37	7	6775133	6775133	+	Intron	DEL	T	-	-	rs138405905		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:6775133delT	uc011jxb.1	+						PMS2CL_uc003squ.2_Intron|PMS2CL_uc003sqv.1_Intron					SubName: Full=cDNA FLJ60281, highly similar to PMS1 protein homolog 2;												0																		---	---	---	---
COL28A1	340267	broad.mit.edu	37	7	7498049	7498049	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:7498049delA	uc003src.1	-						COL28A1_uc011jxe.1_Intron|COL28A1_uc003srd.2_Intron	NM_001037763	NP_001032852			collagen, type XXVIII precursor						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)														---	---	---	---
COL28A1	340267	broad.mit.edu	37	7	7557619	7557621	+	Intron	DEL	AAA	-	-	rs67184564		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:7557619_7557621delAAA	uc003src.1	-						COL28A1_uc011jxe.1_Intron|COL28A1_uc003srd.2_5'Flank	NM_001037763	NP_001032852			collagen, type XXVIII precursor						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)														---	---	---	---
ICA1	3382	broad.mit.edu	37	7	8166181	8166181	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:8166181delT	uc003srm.2	-						ICA1_uc010ktr.2_Intron|ICA1_uc003srl.2_Intron|ICA1_uc003srn.3_Intron|ICA1_uc003srp.3_Intron|ICA1_uc010kts.2_Intron|ICA1_uc003srq.2_Intron|ICA1_uc003srr.2_Intron|ICA1_uc003sro.3_Intron	NM_022307	NP_071682			islet cell autoantigen 1						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)														---	---	---	---
ICA1	3382	broad.mit.edu	37	7	8260714	8260714	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:8260714delA	uc003srm.2	-						ICA1_uc010ktr.2_Intron|ICA1_uc003srl.2_Intron|ICA1_uc003srn.3_Intron|ICA1_uc003srp.3_Intron|ICA1_uc010kts.2_Intron|ICA1_uc003srq.2_Intron|ICA1_uc003srr.2_Intron|ICA1_uc003sro.3_Intron|ICA1_uc011jxg.1_Intron|ICA1_uc003srs.1_Intron	NM_022307	NP_071682			islet cell autoantigen 1						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)														---	---	---	---
NXPH1	30010	broad.mit.edu	37	7	8475126	8475126	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:8475126delT	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	8884785	8884786	+	IGR	INS	-	AC	AC			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:8884785_8884786insAC								NXPH1 (92193 upstream) : PER4 (789114 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	9051387	9051387	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:9051387delT								NXPH1 (258795 upstream) : PER4 (622513 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	9170788	9170788	+	IGR	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:9170788delC								NXPH1 (378196 upstream) : PER4 (503112 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	10656792	10656792	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:10656792delA								PER4 (981345 upstream) : NDUFA4 (316023 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	10697349	10697350	+	IGR	INS	-	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:10697349_10697350insG								None (None upstream) : NDUFA4 (275465 downstream)																																			---	---	---	---
PHF14	9678	broad.mit.edu	37	7	11126825	11126825	+	Intron	DEL	T	-	-	rs71998835		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:11126825delT	uc003sry.1	+						PHF14_uc011jxi.1_Intron|PHF14_uc003srz.2_Intron|PHF14_uc011jxj.1_Intron	NM_014660	NP_055475			PHD finger protein 14 isoform 2								zinc ion binding			kidney(2)|skin(1)	3				UCEC - Uterine corpus endometrioid carcinoma (126;0.205)														---	---	---	---
Unknown	0	broad.mit.edu	37	7	11323878	11323878	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:11323878delT	uc003ssb.2	+											Homo sapiens cDNA clone IMAGE:4830466.																														---	---	---	---
Unknown	0	broad.mit.edu	37	7	11334100	11334101	+	Intron	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:11334100_11334101delTT	uc003ssb.2	+											Homo sapiens cDNA clone IMAGE:4830466.																														---	---	---	---
THSD7A	221981	broad.mit.edu	37	7	11433315	11433315	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:11433315delA	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	11441364	11441364	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:11441364delT	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	11688265	11688266	+	Intron	DEL	GT	-	-	rs67629582		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:11688265_11688266delGT	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)			---	---	---	---
VWDE	221806	broad.mit.edu	37	7	12397273	12397273	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:12397273delT	uc003ssj.2	-						VWDE_uc011jxl.1_Intron|VWDE_uc011jxm.1_Intron	NM_001135924	NP_001129396			von Willebrand factor D and EGF domains							extracellular region					0																		---	---	---	---
VWDE	221806	broad.mit.edu	37	7	12399366	12399366	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:12399366delA	uc003ssj.2	-						VWDE_uc011jxl.1_Intron|VWDE_uc011jxm.1_Intron	NM_001135924	NP_001129396			von Willebrand factor D and EGF domains							extracellular region					0																		---	---	---	---
Unknown	0	broad.mit.edu	37	7	13700145	13700146	+	IGR	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:13700145_13700146delTT								ARL4A (969589 upstream) : ETV1 (230712 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	13845362	13845362	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:13845362delA								None (None upstream) : ETV1 (85496 downstream)																																			---	---	---	---
ETV1	2115	broad.mit.edu	37	7	14027675	14027675	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:14027675delA	uc011jxq.1	-						ETV1_uc011jxn.1_5'Flank|ETV1_uc011jxo.1_5'Flank|ETV1_uc011jxp.1_5'Flank|ETV1_uc003ssw.3_Intron|ETV1_uc003ssx.2_Intron|ETV1_uc011jxr.1_Intron|ETV1_uc011jxs.1_Intron|ETV1_uc010ktv.2_5'Flank	NM_004956	NP_004947			ets variant gene 1 isoform a						transcription from RNA polymerase II promoter	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity		TMPRSS2/ETV1(24)|EWSR1/ETV1(7)	prostate(24)|soft_tissue(4)|bone(3)|lung(2)|central_nervous_system(1)|ovary(1)	35								T	EWSR1|TMPRSS2|SLC45A3|C15orf21|HNRNPA2B1. ACSL3	Ewing sarcoma|prostate								---	---	---	---
Unknown	0	broad.mit.edu	37	7	15144575	15144575	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:15144575delT								DGKB (202025 upstream) : TMEM195 (95368 downstream)																																			---	---	---	---
TMEM195	392636	broad.mit.edu	37	7	15424538	15424538	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:15424538delA	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	15556385	15556386	+	Intron	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:15556385_15556386delTT	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	15885922	15885922	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:15885922delA								MEOX2 (159614 upstream) : ISPD (241230 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	16086473	16086473	+	IGR	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:16086473delG								MEOX2 (360165 upstream) : ISPD (40679 downstream)																																			---	---	---	---
ISPD	729920	broad.mit.edu	37	7	16384455	16384456	+	Intron	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:16384455_16384456delAA	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	16539020	16539020	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:16539020delA	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)														---	---	---	---
SOSTDC1	25928	broad.mit.edu	37	7	16569074	16569074	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:16569074delT	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)														---	---	---	---
TSPAN13	27075	broad.mit.edu	37	7	16820034	16820034	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:16820034delT	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)														---	---	---	---
Unknown	0	broad.mit.edu	37	7	17045976	17045977	+	IGR	DEL	TC	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:17045976_17045977delTC								AGR3 (124363 upstream) : AHR (292299 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	17051296	17051296	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:17051296delT								AGR3 (129683 upstream) : AHR (286980 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	17569721	17569721	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:17569721delT								AHR (183946 upstream) : SNX13 (260665 downstream)																																			---	---	---	---
HDAC9	9734	broad.mit.edu	37	7	18617556	18617556	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:18617556delA	uc003suh.2	+						HDAC9_uc003sue.2_Intron|HDAC9_uc011jyd.1_Intron|HDAC9_uc003sui.2_Intron|HDAC9_uc003suj.2_Intron|HDAC9_uc011jya.1_Intron|HDAC9_uc003sua.1_Intron|HDAC9_uc011jyb.1_Intron|HDAC9_uc003sud.1_Intron|HDAC9_uc011jyc.1_Intron|HDAC9_uc003suf.1_Intron|HDAC9_uc010kud.1_Intron|HDAC9_uc011jye.1_Intron|HDAC9_uc011jyf.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)													---	---	---	---
HDAC9	9734	broad.mit.edu	37	7	18747478	18747479	+	Intron	DEL	GT	-	-	rs72528001		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:18747478_18747479delGT	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)													---	---	---	---
HDAC9	9734	broad.mit.edu	37	7	18873218	18873219	+	Intron	INS	-	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:18873218_18873219insT	uc003suh.2	+						HDAC9_uc003sue.2_Intron|HDAC9_uc011jyd.1_Intron|HDAC9_uc003sui.2_Intron|HDAC9_uc003suj.2_Intron|HDAC9_uc003suk.2_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)													---	---	---	---
Unknown	0	broad.mit.edu	37	7	19375251	19375252	+	IGR	DEL	GT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:19375251_19375252delGT								FERD3L (190207 upstream) : TWISTNB (359833 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	19448491	19448491	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:19448491delT								FERD3L (263447 upstream) : TWISTNB (286594 downstream)																																			---	---	---	---
MACC1	346389	broad.mit.edu	37	7	20239647	20239648	+	Intron	DEL	TG	-	-	rs149308215	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:20239647_20239648delTG	uc003sus.3	-						MACC1_uc010kug.2_Intron	NM_182762	NP_877439			putative binding protein 7a5						positive regulation of cell division|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus|plasma membrane	growth factor activity			ovary(2)|skin(1)	3																		---	---	---	---
Unknown	0	broad.mit.edu	37	7	20316281	20316282	+	IGR	INS	-	AC	AC			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:20316281_20316282insAC								MACC1 (59268 upstream) : ITGB8 (54043 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	20363566	20363567	+	IGR	INS	-	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:20363566_20363567insC								MACC1 (106553 upstream) : ITGB8 (6758 downstream)																																			---	---	---	---
ITGB8	3696	broad.mit.edu	37	7	20445606	20445606	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:20445606delT	uc003suu.2	+						ITGB8_uc011jyh.1_Intron	NM_002214	NP_002205			integrin, beta 8 precursor						cell-matrix adhesion|integrin-mediated signaling pathway|placenta blood vessel development	integrin complex	protein binding|receptor activity			skin(3)	3																		---	---	---	---
Unknown	0	broad.mit.edu	37	7	20850978	20850979	+	IGR	INS	-	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:20850978_20850979insT								SP8 (24470 upstream) : RPL23P8 (15938 downstream)																																			---	---	---	---
DNAH11	8701	broad.mit.edu	37	7	21633525	21633526	+	Intron	DEL	TC	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:21633525_21633526delTC	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	21786061	21786061	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:21786061delT	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	21943615	21943615	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:21943615delA	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	22368448	22368448	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:22368448delA	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																		---	---	---	---
Unknown	0	broad.mit.edu	37	7	23331223	23331223	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:23331223delT								GPNMB (16495 upstream) : C7orf30 (7717 downstream)																																			---	---	---	---
C7orf30	115416	broad.mit.edu	37	7	23346373	23346373	+	Intron	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:23346373delG	uc003swd.1	+						C7orf30_uc003swe.2_5'Flank	NM_138446	NP_612455			hypothetical protein LOC115416							mitochondrion					0			GBM - Glioblastoma multiforme(13;0.154)															---	---	---	---
IGF2BP3	10643	broad.mit.edu	37	7	23403992	23403993	+	Intron	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:23403992_23403993delAA	uc003swg.2	-							NM_006547	NP_006538			insulin-like growth factor 2 mRNA binding						anatomical structure morphogenesis|negative regulation of translation|translation	cytosol|nucleus	mRNA 3'-UTR binding|mRNA 5'-UTR binding|nucleotide binding|protein binding|translation regulator activity			ovary(2)	2																		---	---	---	---
IGF2BP3	10643	broad.mit.edu	37	7	23453770	23453771	+	Intron	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:23453770_23453771delAA	uc003swg.2	-						IGF2BP3_uc003swh.1_RNA	NM_006547	NP_006538			insulin-like growth factor 2 mRNA binding						anatomical structure morphogenesis|negative regulation of translation|translation	cytosol|nucleus	mRNA 3'-UTR binding|mRNA 5'-UTR binding|nucleotide binding|protein binding|translation regulator activity			ovary(2)	2																		---	---	---	---
STK31	56164	broad.mit.edu	37	7	23776840	23776840	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:23776840delT	uc003sws.3	+						STK31_uc003swt.3_Intron|STK31_uc011jze.1_Intron|STK31_uc010kuq.2_Intron	NM_031414	NP_113602			serine/threonine kinase 31 isoform a								ATP binding|nucleic acid binding|protein serine/threonine kinase activity			skin(3)|lung(2)|ovary(2)|stomach(2)	9																		---	---	---	---
STK31	56164	broad.mit.edu	37	7	23809127	23809127	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:23809127delT	uc003sws.3	+						STK31_uc003swt.3_Intron|STK31_uc011jze.1_Intron|STK31_uc010kuq.2_Intron	NM_031414	NP_113602			serine/threonine kinase 31 isoform a								ATP binding|nucleic acid binding|protein serine/threonine kinase activity			skin(3)|lung(2)|ovary(2)|stomach(2)	9																		---	---	---	---
OSBPL3	26031	broad.mit.edu	37	7	24871967	24871967	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:24871967delA	uc003sxf.2	-						OSBPL3_uc003sxd.2_Intron|OSBPL3_uc003sxe.2_Intron|OSBPL3_uc003sxg.2_Intron|OSBPL3_uc003sxh.2_Intron|OSBPL3_uc003sxi.2_Intron	NM_015550	NP_056365			oxysterol-binding protein-like protein 3 isoform						lipid transport		lipid binding|protein binding			skin(1)	1																		---	---	---	---
OSBPL3	26031	broad.mit.edu	37	7	24911905	24911906	+	Intron	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:24911905_24911906delTT	uc003sxf.2	-						OSBPL3_uc003sxd.2_Intron|OSBPL3_uc003sxe.2_Intron|OSBPL3_uc003sxg.2_Intron|OSBPL3_uc003sxh.2_Intron|OSBPL3_uc003sxi.2_Intron	NM_015550	NP_056365			oxysterol-binding protein-like protein 3 isoform						lipid transport		lipid binding|protein binding			skin(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	7	25230039	25230039	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:25230039delT								C7orf31 (10222 upstream) : NPVF (34154 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	25255954	25255954	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:25255954delA								C7orf31 (36137 upstream) : NPVF (8239 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	25276737	25276738	+	IGR	INS	-	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:25276737_25276738insT								NPVF (8632 upstream) : MIR148A (712801 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	25729106	25729106	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:25729106delT								NPVF (461001 upstream) : MIR148A (260433 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	25818287	25818287	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:25818287delA								NPVF (550182 upstream) : MIR148A (171252 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	25826830	25826830	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:25826830delA								NPVF (558725 upstream) : MIR148A (162709 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	26316251	26316251	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:26316251delA								CBX3 (63277 upstream) : SNX10 (15264 downstream)																																			---	---	---	---
SNX10	29887	broad.mit.edu	37	7	26411424	26411424	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:26411424delT	uc003sxx.2	+						SNX10_uc011jzg.1_Intron|SNX10_uc010kuu.2_Intron|SNX10_uc010kuv.2_Intron|SNX10_uc010kuw.2_Intron	NM_013322	NP_037454			sorting nexin 10						cell communication|endosome organization|protein transport	extrinsic to endosome membrane	1-phosphatidylinositol binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	7	26418080	26418080	+	IGR	DEL	A	-	-	rs80023032		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:26418080delA								SNX10 (4143 upstream) : LOC441204 (20259 downstream)																																			---	---	---	---
LOC441204	441204	broad.mit.edu	37	7	26491881	26491881	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:26491881delT	uc003sxy.1	+						LOC441204_uc003sxz.2_Intron					Homo sapiens cDNA FLJ31922 fis, clone NT2RP7005219.												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	7	26590175	26590175	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:26590175delA								KIAA0087 (11731 upstream) : C7orf71 (87315 downstream)																																			---	---	---	---
SKAP2	8935	broad.mit.edu	37	7	27009307	27009307	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:27009307delT	uc011jzj.1	-							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																		---	---	---	---
Unknown	0	broad.mit.edu	37	7	27190810	27190811	+	Intron	INS	-	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:27190810_27190811insA	uc003syp.1	+						HOXA6_uc003syq.1_Intron|uc003syr.1_5'Flank					Homo sapiens cDNA FLJ34614 fis, clone KIDNE2014268.																												OREG0017913	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	27314121	27314122	+	IGR	DEL	TG	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:27314121_27314122delTG								EVX1 (27929 upstream) : HIBADH (250941 downstream)																																			---	---	---	---
JAZF1	221895	broad.mit.edu	37	7	28016319	28016319	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:28016319delA	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	28753949	28753949	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:28753949delT	uc003szq.2	+						CREB5_uc003szo.2_Intron|CREB5_uc003szr.2_Intron|CREB5_uc003szs.2_Intron|CREB5_uc011jzr.1_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	29152222	29152222	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:29152222delT	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																		---	---	---	---
CPVL	54504	broad.mit.edu	37	7	29160776	29160776	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:29160776delA	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																		---	---	---	---
CHN2	1124	broad.mit.edu	37	7	29252170	29252170	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:29252170delA	uc003szz.2	+						CHN2_uc011jzs.1_Intron|CHN2_uc010kva.2_Intron|CHN2_uc010kvb.2_Intron|CHN2_uc010kvc.2_Intron|CHN2_uc011jzt.1_Intron|CHN2_uc010kvd.2_Intron|CHN2_uc011jzu.1_Intron	NM_004067	NP_004058			beta chimerin isoform 2						regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol|membrane	GTPase activator activity|metal ion binding|SH3/SH2 adaptor activity			ovary(2)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	7	29586514	29586515	+	Intron	INS	-	A	A	rs71557418		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:29586514_29586515insA	uc003tab.2	-											Homo sapiens, clone IMAGE:4347271, mRNA.																														---	---	---	---
Unknown	0	broad.mit.edu	37	7	29736490	29736491	+	Intron	INS	-	A	A	rs139218961	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:29736490_29736491insA	uc003tah.1	+											Homo sapiens DPY-19-like 2 pseudogene 3 (DPY19L2P3) pseudogene mRNA, complete sequence.																														---	---	---	---
Unknown	0	broad.mit.edu	37	7	29760233	29760233	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:29760233delT	uc003tai.2	+											Homo sapiens DPY-19-like 2 pseudogene 3 (DPY19L2P3) pseudogene mRNA, complete sequence.																														---	---	---	---
Unknown	0	broad.mit.edu	37	7	29771801	29771801	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:29771801delA	uc003tai.2	+											Homo sapiens DPY-19-like 2 pseudogene 3 (DPY19L2P3) pseudogene mRNA, complete sequence.																														---	---	---	---
WIPF3	644150	broad.mit.edu	37	7	29936240	29936240	+	Intron	DEL	T	-	-	rs75499288		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:29936240delT	uc003taj.1	+							NM_001080529	NP_001073998			WAS/WASL interacting protein family, member 3											ovary(1)	1																		---	---	---	---
PLEKHA8	84725	broad.mit.edu	37	7	30074662	30074662	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:30074662delT	uc003tam.1	+						PLEKHA8_uc003tao.2_Intron|PLEKHA8_uc003tap.1_Intron|PLEKHA8_uc003tan.2_Intron	NM_032639	NP_116028			pleckstrin homology domain containing, family A						protein transport	cytoplasm	glycolipid binding|glycolipid transporter activity			breast(3)|ovary(1)	4																		---	---	---	---
Unknown	0	broad.mit.edu	37	7	30412640	30412640	+	IGR	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:30412640delC								DKFZP586I1420 (232 upstream) : NOD1 (51504 downstream)																																			---	---	---	---
GARS	2617	broad.mit.edu	37	7	30643333	30643333	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:30643333delT	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)													---	---	---	---
GARS	2617	broad.mit.edu	37	7	30644136	30644136	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:30644136delT	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	30713840	30713840	+	Intron	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:30713840delG	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																		---	---	---	---
INMT	11185	broad.mit.edu	37	7	30754637	30754638	+	Intron	INS	-	A	A	rs138069915	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:30754637_30754638insA	uc010kwc.1	+											Homo sapiens indolethylamine N-methyltransferase (INMT) mRNA, INMT-1 allele, complete cds.							cytoplasm	amine N-methyltransferase activity				0																		---	---	---	---
FAM188B	84182	broad.mit.edu	37	7	30828483	30828483	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:30828483delA	uc003tbt.2	+						FAM188B_uc010kwe.2_Intron	NM_032222	NP_115598			hypothetical protein LOC84182												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	7	31165192	31165192	+	IGR	DEL	T	-	-	rs71987796		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:31165192delT								ADCYAP1R1 (18881 upstream) : NEUROD6 (211890 downstream)																																			---	---	---	---
PDE1C	5137	broad.mit.edu	37	7	32310362	32310362	+	Intron	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:32310362delG	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	32581329	32581331	+	Intron	DEL	TTT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:32581329_32581331delTTT	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	32594260	32594260	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:32594260delT	uc003tcv.1	+						AVL9_uc011kai.1_Intron|AVL9_uc010kwj.1_Intron	NM_015060	NP_055875			AVL9 homolog (S. cerevisiase)							integral to membrane					0																		---	---	---	---
AVL9	23080	broad.mit.edu	37	7	32952451	32952451	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:32952451delT	uc011kai.1	+							NM_015060	NP_055875			AVL9 homolog (S. cerevisiase)							integral to membrane					0																		---	---	---	---
Unknown	0	broad.mit.edu	37	7	33117040	33117040	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:33117040delT								NT5C3 (14631 upstream) : RP9 (17372 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	33120321	33120321	+	IGR	DEL	T	-	-	rs76888589		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:33120321delT								NT5C3 (17912 upstream) : RP9 (14091 downstream)																																			---	---	---	---
BBS9	27241	broad.mit.edu	37	7	33300679	33300680	+	Intron	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:33300679_33300680delTT	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	33331841	33331842	+	Intron	DEL	TT	-	-	rs34411260		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:33331841_33331842delTT	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	33521702	33521703	+	Intron	DEL	TT	-	-	rs111659756		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:33521702_33521703delTT	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				---	---	---	---
BBS9	27241	broad.mit.edu	37	7	33534180	33534180	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:33534180delA	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	33740292	33740293	+	IGR	INS	-	CA	CA			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:33740292_33740293insCA								BBS9 (94612 upstream) : BMPER (204819 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	34272969	34272970	+	IGR	INS	-	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:34272969_34272970insT								BMPER (78858 upstream) : AAA1 (117065 downstream)																																			---	---	---	---
AAA1	404744	broad.mit.edu	37	7	34430927	34430927	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:34430927delT	uc010kwo.1	-						AAA1_uc010kwp.1_Intron|AAA1_uc003tdz.2_Intron|AAA1_uc010kwq.1_Intron					Homo sapiens AAA1 variant IA mRNA, complete cds; alternatively spliced.												0																		---	---	---	---
NPSR1	387129	broad.mit.edu	37	7	34870926	34870929	+	Intron	DEL	CACA	-	-	rs113899398		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:34870926_34870929delCACA	uc003teg.1	+						AAA1_uc010kwq.1_Intron|AAA1_uc011kaq.1_Intron|NPSR1_uc003teh.1_Intron|NPSR1_uc010kwt.1_Intron|NPSR1_uc010kwu.1_Intron|NPSR1_uc010kwv.1_Intron|NPSR1_uc003tei.1_Intron|NPSR1_uc010kww.1_Intron|NPSR1_uc011kar.1_Intron|AAA1_uc010kwy.2_Intron|AAA1_uc003tek.3_Intron	NM_207172	NP_997055			G protein-coupled receptor for asthma							cytoplasm|integral to membrane|plasma membrane	vasopressin receptor activity			skin(3)|pancreas(1)	4					Halothane(DB01159)													---	---	---	---
Unknown	0	broad.mit.edu	37	7	34938484	34938484	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:34938484delA								NPSR1 (20540 upstream) : DPY19L1 (22597 downstream)																																			---	---	---	---
DPY19L1	23333	broad.mit.edu	37	7	34964111	34964111	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:34964111delA	uc003tel.1	-											Homo sapiens mRNA for KIAA0877 protein, partial cds.							integral to membrane					0																		---	---	---	---
DPY19L1	23333	broad.mit.edu	37	7	34979746	34979748	+	Intron	DEL	TTC	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:34979746_34979748delTTC	uc003tem.3	-						DPY19L1_uc003tel.1_5'Flank	NM_015283	NP_056098			dpy-19-like 1							integral to membrane					0																		---	---	---	---
DPY19L1	23333	broad.mit.edu	37	7	35043698	35043699	+	Intron	INS	-	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:35043698_35043699insG	uc003tem.3	-							NM_015283	NP_056098			dpy-19-like 1							integral to membrane					0																		---	---	---	---
Unknown	0	broad.mit.edu	37	7	35378897	35378897	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:35378897delA								TBX20 (85655 upstream) : HERPUD2 (293375 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	35461637	35461637	+	IGR	DEL	A	-	-	rs77112027	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:35461637delA								TBX20 (168395 upstream) : HERPUD2 (210635 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	35646045	35646045	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:35646045delT								TBX20 (352803 upstream) : HERPUD2 (26227 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	36093586	36093587	+	IGR	DEL	CT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:36093586_36093587delCT								SEPT7 (148671 upstream) : EEPD1 (99249 downstream)																																			---	---	---	---
ELMO1	9844	broad.mit.edu	37	7	37081929	37081929	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:37081929delT	uc003tfk.1	-						ELMO1_uc011kbc.1_Intron|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	37638429	37638429	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:37638429delT								ELMO1 (149899 upstream) : GPR141 (141567 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	37860780	37860781	+	Intron	DEL	AC	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:37860780_37860781delAC	uc003tfl.2	+											Homo sapiens, clone IMAGE:3881224, mRNA.																														---	---	---	---
SFRP4	6424	broad.mit.edu	37	7	37955475	37955475	+	Intron	DEL	T	-	-	rs36048041		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:37955475delT	uc003tfo.3	-							NM_003014	NP_003005			secreted frizzled-related  protein 4 precursor						brain development|cell differentiation|decidualization|embryo development|epithelium development|gonad development|mammary gland involution|menstrual cycle phase|negative regulation of canonical Wnt receptor signaling pathway|negative regulation of cell proliferation|negative regulation of JNK cascade|negative regulation of sequence-specific DNA binding transcription factor activity|negative regulation of sodium-dependent phosphate transport|phosphate ion homeostasis|positive regulation of apoptosis|positive regulation of canonical Wnt receptor signaling pathway|positive regulation of epidermal cell differentiation|positive regulation of gene expression|positive regulation of receptor internalization|vasculature development|Wnt receptor signaling pathway	cell surface|cytoplasm|extracellular space|nucleus	PDZ domain binding|Wnt receptor activity|Wnt-protein binding			lung(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	7	38113777	38113778	+	IGR	DEL	TG	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:38113777_38113778delTG								EPDR1 (122238 upstream) : STARD3NL (104155 downstream)																																			---	---	---	---
VPS41	27072	broad.mit.edu	37	7	38801051	38801054	+	Intron	DEL	TTTT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:38801051_38801054delTTTT	uc003tgy.2	-						VPS41_uc003tgz.2_Intron|VPS41_uc010kxn.2_Intron	NM_014396	NP_055211			vacuolar protein sorting 41 isoform 1						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																		---	---	---	---
VPS41	27072	broad.mit.edu	37	7	38919101	38919101	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:38919101delA	uc003tgy.2	-						VPS41_uc003tgz.2_Intron|VPS41_uc010kxn.2_Intron	NM_014396	NP_055211			vacuolar protein sorting 41 isoform 1						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																		---	---	---	---
Unknown	0	broad.mit.edu	37	7	38974369	38974370	+	IGR	INS	-	AC	AC			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:38974369_38974370insAC								VPS41 (25569 upstream) : POU6F2 (72038 downstream)																																			---	---	---	---
POU6F2	11281	broad.mit.edu	37	7	39247285	39247285	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:39247285delA	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																		---	---	---	---
POU6F2	11281	broad.mit.edu	37	7	39342765	39342765	+	Intron	DEL	T	-	-	rs139011776	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:39342765delT	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-4200-01A-01D-1126-08	TCGA-BR-4200-11A-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																		---	---	---	---
LOC349114	349114	broad.mit.edu	37	7	39795338	39795338	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:39795338delA	uc003thf.2	+							NR_026999				Homo sapiens cDNA FLJ40085 fis, clone TESTI2002993.												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	7	39905812	39905813	+	IGR	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:39905812_39905813delTT								LOC349114 (71591 upstream) : CDK13 (84146 downstream)																																			---	---	---	---
CDK13	8621	broad.mit.edu	37	7	40102943	40102943	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:40102943delT	uc003thh.3	+						CDK13_uc003thi.3_Intron|CDK13_uc011kbf.1_Intron|CDK13_uc003thj.2_Intron	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																		---	---	---	---
CDK13	8621	broad.mit.edu	37	7	40105082	40105082	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:40105082delA	uc003thh.3	+						CDK13_uc003thi.3_Intron|CDK13_uc011kbf.1_Intron|CDK13_uc003thj.2_Intron	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																		---	---	---	---
Unknown	0	broad.mit.edu	37	7	40136177	40136177	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:40136177delT								CDK13 (1032 upstream) : C7orf11 (36166 downstream)																																			---	---	---	---
C7orf10	79783	broad.mit.edu	37	7	40341873	40341873	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:40341873delT	uc003thn.1	+						C7orf10_uc003thm.1_Intron|C7orf10_uc003tho.1_Intron	NM_024728	NP_079004			dermal papilla derived protein 13								transferase activity			ovary(2)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	7	41041620	41041620	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:41041620delT								C7orf10 (141263 upstream) : INHBA (686983 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	41504879	41504880	+	IGR	DEL	TT	-	-	rs5883792		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:41504879_41504880delTT								C7orf10 (604522 upstream) : INHBA (223723 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	41527810	41527810	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:41527810delT								C7orf10 (627453 upstream) : INHBA (200793 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	41869619	41869619	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:41869619delA								LOC285954 (50645 upstream) : GLI3 (130931 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	41961008	41961010	+	IGR	DEL	AAA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:41961008_41961010delAAA								LOC285954 (142034 upstream) : GLI3 (39540 downstream)																																			---	---	---	---
GLI3	2737	broad.mit.edu	37	7	42123809	42123809	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:42123809delT	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	42336658	42336659	+	IGR	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:42336658_42336659delTT								GLI3 (60040 upstream) : C7orf25 (612215 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	42865971	42865971	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:42865971delT								GLI3 (589353 upstream) : C7orf25 (82903 downstream)																																			---	---	---	---
C7orf25	79020	broad.mit.edu	37	7	42949153	42949153	+	3'UTR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:42949153delT	uc003thw.2	-	2					C7orf25_uc010kxq.2_3'UTR|C7orf25_uc003thx.3_3'UTR|C7orf25_uc010kxr.2_3'UTR	NM_024054	NP_076959			hypothetical protein LOC79020 b											skin(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	7	43005509	43005510	+	IGR	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:43005509_43005510delTT								MRPL32 (28058 upstream) : HECW1 (146688 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	43068446	43068447	+	IGR	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:43068446_43068447delAA								MRPL32 (90995 upstream) : HECW1 (83751 downstream)																																			---	---	---	---
C7orf44	55744	broad.mit.edu	37	7	43694181	43694181	+	Intron	DEL	A	-	-	rs68106305		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:43694181delA	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																		---	---	---	---
PGAM2	5224	broad.mit.edu	37	7	44107833	44107836	+	5'Flank	DEL	GGTA	-	-	rs113218565		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:44107833_44107836delGGTA	uc003tjs.2	-							NM_000290	NP_000281			phosphoglycerate mutase 2						gluconeogenesis|glycolysis|striated muscle contraction	cytosol	2,3-bisphospho-D-glycerate 2-phosphohydrolase activity|bisphosphoglycerate mutase activity				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	7	44168792	44168793	+	IGR	INS	-	AT	AT	rs79629508		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:44168792_44168793insAT								POLD2 (5645 upstream) : MYL7 (9672 downstream)																																			---	---	---	---
GCK	2645	broad.mit.edu	37	7	44199353	44199353	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:44199353delA	uc003tkl.2	-						GCK_uc003tkj.1_5'Flank|GCK_uc003tkk.1_5'Flank	NM_000162	NP_000153			glucokinase isoform 1						cellular response to insulin stimulus|cellular response to leptin stimulus|detection of glucose|endocrine pancreas development|glucose homeostasis|glucose transport|glycolysis|negative regulation of gluconeogenesis|positive regulation of glycogen biosynthetic process|positive regulation of insulin secretion|regulation of glucose transport|regulation of glycolysis|transmembrane transport	cytosol|nucleoplasm	ATP binding|glucokinase activity|glucose binding|protein binding			skin(3)|lung(1)	4																		---	---	---	---
CAMK2B	816	broad.mit.edu	37	7	44347473	44347473	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:44347473delT	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																		---	---	---	---
TMED4	222068	broad.mit.edu	37	7	44622715	44622715	+	5'Flank	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:44622715delA	uc003tli.2	-						TMED4_uc003tlj.2_5'Flank|TMED4_uc003tlk.2_5'Flank|uc003tll.2_RNA	NM_182547	NP_872353			transmembrane emp24 protein transport domain						positive regulation of I-kappaB kinase/NF-kappaB cascade|transport	endoplasmic reticulum membrane|integral to membrane	signal transducer activity				0																		---	---	---	---
OGDH	4967	broad.mit.edu	37	7	44745159	44745159	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:44745159delT	uc003tln.2	+						OGDH_uc011kbx.1_Intron|OGDH_uc011kby.1_Intron|OGDH_uc003tlp.2_Intron|OGDH_uc011kbz.1_Intron	NM_002541	NP_002532			oxoglutarate dehydrogenase isoform 1 precursor						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	45010111	45010112	+	Intron	INS	-	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:45010111_45010112insC	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																		---	---	---	---
Unknown	0	broad.mit.edu	37	7	45166457	45166457	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:45166457delT								TBRG4 (15140 upstream) : RAMP3 (30910 downstream)																																			---	---	---	---
RAMP3	10268	broad.mit.edu	37	7	45196027	45196027	+	5'Flank	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:45196027delA	uc003tnb.2	+							NM_005856	NP_005847			receptor activity modifying protein 3 precursor						intracellular protein transport|receptor-mediated endocytosis|regulation of G-protein coupled receptor protein signaling pathway	integral to plasma membrane|lysosome	protein transporter activity				0					Pramlintide(DB01278)													---	---	---	---
Unknown	0	broad.mit.edu	37	7	45293409	45293410	+	IGR	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:45293409_45293410delTT								RAMP3 (69562 upstream) : ADCY1 (320329 downstream)																																			---	---	---	---
ADCY1	107	broad.mit.edu	37	7	45639232	45639234	+	Intron	DEL	TTT	-	-	rs113156682		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:45639232_45639234delTTT	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	46318590	46318592	+	IGR	DEL	TTT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:46318590_46318592delTTT								IGFBP3 (357719 upstream) : TNS3 (996161 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	46611243	46611244	+	IGR	INS	-	C	C	rs78653257	byFrequency;by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:46611243_46611244insC								IGFBP3 (650372 upstream) : TNS3 (703509 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	46672827	46672828	+	IGR	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:46672827_46672828delTT								IGFBP3 (711956 upstream) : TNS3 (641925 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	46969561	46969562	+	IGR	DEL	TT	-	-	rs75893737		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:46969561_46969562delTT								None (None upstream) : TNS3 (345191 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	47237476	47237476	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:47237476delA								None (None upstream) : TNS3 (77277 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	47302320	47302320	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:47302320delA								None (None upstream) : TNS3 (12433 downstream)																																			---	---	---	---
C7orf69	80099	broad.mit.edu	37	7	47859242	47859242	+	3'UTR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:47859242delA	uc003tnz.3	+	3					PKD1L1_uc003tny.1_Intron|C7orf69_uc003toa.1_Intron|PKD1L1_uc003tob.2_Intron	NM_025031	NP_079307			hypothetical protein LOC80099 precursor							extracellular region					0																		---	---	---	---
SUN3	256979	broad.mit.edu	37	7	48064090	48064090	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:48064090delA	uc003tof.2	-						SUN3_uc003tog.2_Intron|SUN3_uc011kcf.1_Intron	NM_152782	NP_689995			Sad1 and UNC84 domain containing 1							integral to membrane				central_nervous_system(1)	1																		---	---	---	---
UPP1	7378	broad.mit.edu	37	7	48146282	48146282	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:48146282delA	uc003toj.2	+						UPP1_uc003tok.2_Intron|UPP1_uc003tol.2_Intron|UPP1_uc011kch.1_Intron|UPP1_uc003ton.2_Intron|UPP1_uc003too.2_Intron	NM_181597	NP_853628			uridine phosphorylase 1						nucleotide catabolic process|pyrimidine base metabolic process|pyrimidine nucleoside catabolic process|pyrimidine nucleoside salvage	cytosol	uridine phosphorylase activity				0																		---	---	---	---
ABCA13	154664	broad.mit.edu	37	7	48270766	48270769	+	Intron	DEL	AAAA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:48270766_48270769delAAAA	uc003toq.2	+						ABCA13_uc010kyr.2_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	48278659	48278659	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:48278659delT	uc003toq.2	+						ABCA13_uc010kyr.2_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	48396768	48396768	+	Intron	DEL	A	-	-	rs11973210	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:48396768delA	uc003toq.2	+						ABCA13_uc010kys.1_Intron|ABCA13_uc003tos.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	48814559	48814560	+	IGR	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:48814559_48814560delTT								ABCA13 (127468 upstream) : CDC14C (149597 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	49088584	49088584	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:49088584delT								CDC14C (121535 upstream) : VWC2 (724673 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	49469204	49469205	+	IGR	DEL	AC	-	-	rs149238834		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:49469204_49469205delAC								CDC14C (502155 upstream) : VWC2 (344052 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	49509894	49509894	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:49509894delT								CDC14C (542845 upstream) : VWC2 (303363 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	50221585	50221586	+	IGR	INS	-	ACACACAC	ACACACAC	rs144888736	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:50221585_50221586insACACACAC								C7orf72 (22227 upstream) : IKZF1 (122792 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	50251697	50251699	+	IGR	DEL	AGG	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:50251697_50251699delAGG								C7orf72 (52339 upstream) : IKZF1 (92679 downstream)																																			---	---	---	---
DDC	1644	broad.mit.edu	37	7	50596888	50596888	+	Intron	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:50596888delC	uc003tpf.3	-						DDC_uc010kza.2_Intron|DDC_uc003tpg.3_Intron	NM_000790	NP_000781			dopa decarboxylase (aromatic L-amino acid						cellular amino acid metabolic process|hormone biosynthetic process|neurotransmitter secretion	cytosol	aromatic-L-amino-acid decarboxylase activity|protein binding|pyridoxal phosphate binding			ovary(2)	2	Glioma(55;0.08)|all_neural(89;0.245)				Amantadine(DB00915)|Carbidopa(DB00190)|Flupenthixol(DB00875)|L-Tryptophan(DB00150)|Levodopa(DB01235)|Pimozide(DB01100)|Pyridoxal Phosphate(DB00114)|Remoxipride(DB00409)													---	---	---	---
GRB10	2887	broad.mit.edu	37	7	50763686	50763687	+	Intron	INS	-	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:50763686_50763687insT	uc003tpi.2	-						GRB10_uc003tph.3_Intron|GRB10_uc003tpj.2_Intron|GRB10_uc003tpk.2_Intron|GRB10_uc010kzb.2_Intron|GRB10_uc003tpl.2_Intron|GRB10_uc003tpm.2_Intron|GRB10_uc003tpn.2_Intron	NM_005311	NP_005302			growth factor receptor-bound protein 10 isoform						insulin receptor signaling pathway|insulin receptor signaling pathway|negative regulation of glucose import|negative regulation of glycogen biosynthetic process|negative regulation of insulin receptor signaling pathway|negative regulation of Wnt receptor signaling pathway|positive regulation of phosphorylation|positive regulation of vascular endothelial growth factor receptor signaling pathway	cytosol|plasma membrane	insulin receptor binding|insulin receptor binding|SH3/SH2 adaptor activity			lung(3)|ovary(2)|upper_aerodigestive_tract(1)	6	Glioma(55;0.08)|all_neural(89;0.245)													Russell-Silver_syndrome				---	---	---	---
Unknown	0	broad.mit.edu	37	7	51023216	51023216	+	IGR	DEL	A	-	-	rs113517226		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:51023216delA								GRB10 (162057 upstream) : COBL (60694 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	51851034	51851035	+	IGR	DEL	TT	-	-	rs66786980		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:51851034_51851035delTT								COBL (466519 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	52481639	52481640	+	IGR	INS	-	AGGA	AGGA	rs139820965	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:52481639_52481640insAGGA								None (None upstream) : POM121L12 (621709 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	53000029	53000029	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:53000029delT								None (None upstream) : POM121L12 (103320 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	53254224	53254225	+	IGR	INS	-	A	A	rs138176553	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:53254224_53254225insA								POM121L12 (149607 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	53321184	53321184	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:53321184delT								POM121L12 (216567 upstream) : HPVC1 (947733 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	53322590	53322590	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:53322590delT								POM121L12 (217973 upstream) : HPVC1 (946327 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	53911992	53911992	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:53911992delT								POM121L12 (807375 upstream) : HPVC1 (356925 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	54098887	54098887	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:54098887delA								POM121L12 (994270 upstream) : HPVC1 (170030 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	54144233	54144233	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:54144233delT								None (None upstream) : HPVC1 (124684 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	54181562	54181562	+	IGR	DEL	C	-	-	rs10707655		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:54181562delC								None (None upstream) : HPVC1 (87355 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	54487051	54487052	+	IGR	INS	-	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:54487051_54487052insA								HPVC1 (216937 upstream) : VSTM2A (122967 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	54488037	54488037	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:54488037delT								HPVC1 (217923 upstream) : VSTM2A (121982 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	54494781	54494781	+	IGR	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:54494781delG								HPVC1 (224667 upstream) : VSTM2A (115238 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	54734131	54734131	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:54734131delT								VSTM2A (95944 upstream) : SEC61G (85810 downstream)																																			---	---	---	---
LANCL2	55915	broad.mit.edu	37	7	55492376	55492376	+	Intron	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:55492376delC	uc003tqp.2	+							NM_018697	NP_061167			LanC lantibiotic synthetase component C-like 2						negative regulation of transcription, DNA-dependent|positive regulation of abscisic acid mediated signaling pathway	cortical actin cytoskeleton|cytosol|nucleus|plasma membrane	ATP binding|catalytic activity|GTP binding|phosphatidylinositol-3-phosphate binding|phosphatidylinositol-4-phosphate binding|phosphatidylinositol-5-phosphate binding			ovary(1)|skin(1)	2	Breast(14;0.0379)		Lung(13;4.65e-05)|LUSC - Lung squamous cell carcinoma(13;0.000168)|STAD - Stomach adenocarcinoma(5;0.00128)|Epithelial(13;0.0706)															---	---	---	---
LOC442308	442308	broad.mit.edu	37	7	55713246	55713246	+	5'Flank	DEL	A	-	-	rs77079107		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:55713246delA	uc010kzj.2	+							NR_003598				Homo sapiens similar to tubulin, beta 5 (LOC442308), non-coding RNA.												0																		---	---	---	---
SEPT14	346288	broad.mit.edu	37	7	55898873	55898873	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:55898873delA	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)															---	---	---	---
MRPS17	51373	broad.mit.edu	37	7	56021075	56021075	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:56021075delA	uc003trd.2	+						MRPS17_uc003trb.2_Intron	NM_015969	NP_057053			mitochondrial ribosomal protein S17 precursor						translation	mitochondrial small ribosomal subunit	rRNA binding|structural constituent of ribosome				0	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-4200-01A-01D-1126-08	TCGA-BR-4200-11A-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	56699457	56699457	+	IGR	DEL	A	-	-	rs78077053		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:56699457delA								DKFZp434L192 (134480 upstream) : ZNF479 (487871 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	56905713	56905713	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:56905713delT								DKFZp434L192 (340736 upstream) : ZNF479 (281615 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	57216044	57216045	+	IGR	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:57216044_57216045delTT								ZNF479 (8473 upstream) : ZNF716 (293838 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	57607520	57607525	+	IGR	DEL	TCTTAT	-	-	rs141563333		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:57607520_57607525delTCTTAT								ZNF716 (74255 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	57734142	57734143	+	IGR	INS	-	T	T	rs144782587	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:57734142_57734143insT								ZNF716 (200877 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	57747484	57747485	+	IGR	INS	-	ATAAAC	ATAAAC	rs113514951		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:57747484_57747485insATAAAC								ZNF716 (214219 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	57918471	57918471	+	IGR	DEL	T	-	-	rs112384733		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:57918471delT								ZNF716 (385206 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	61535924	61535924	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:61535924delT								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	61555218	61555220	+	IGR	DEL	CTT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:61555218_61555220delCTT								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	61803150	61803150	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:61803150delT								None (None upstream) : LOC643955 (948522 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	62018607	62018607	+	IGR	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:62018607delC								None (None upstream) : LOC643955 (733065 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	62030467	62030468	+	IGR	INS	-	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:62030467_62030468insT								None (None upstream) : LOC643955 (721204 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	62054904	62054906	+	IGR	DEL	AGA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:62054904_62054906delAGA								None (None upstream) : LOC643955 (696766 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	62085990	62085990	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:62085990delA								None (None upstream) : LOC643955 (665682 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	62197178	62197178	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:62197178delT								None (None upstream) : LOC643955 (554494 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	62206720	62206721	+	IGR	DEL	CA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:62206720_62206721delCA								None (None upstream) : LOC643955 (544951 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	62520256	62520256	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:62520256delT								None (None upstream) : LOC643955 (231416 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	62557310	62557310	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:62557310delA								None (None upstream) : LOC643955 (194362 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	62559506	62559506	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:62559506delT								None (None upstream) : LOC643955 (192166 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	62578800	62578801	+	IGR	INS	-	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:62578800_62578801insA								None (None upstream) : LOC643955 (172871 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	62580897	62580897	+	IGR	DEL	A	-	-	rs77485035		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:62580897delA								None (None upstream) : LOC643955 (170775 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	62603897	62603897	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:62603897delT								None (None upstream) : LOC643955 (147775 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	62686065	62686065	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:62686065delT								None (None upstream) : LOC643955 (65607 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	63035543	63035543	+	IGR	DEL	T	-	-	rs74552050		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:63035543delT								LOC100287704 (223392 upstream) : ZNF727 (470278 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	63037983	63037983	+	IGR	DEL	T	-	-	rs77073931		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:63037983delT								LOC100287704 (225832 upstream) : ZNF727 (467838 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	63351578	63351578	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:63351578delT								LOC100287704 (539427 upstream) : ZNF727 (154243 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	63582426	63582426	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:63582426delA								ZNF727 (43501 upstream) : ZNF735 (85155 downstream)																																			---	---	---	---
ZNF679	168417	broad.mit.edu	37	7	63710230	63710230	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:63710230delT	uc003tsx.2	+							NM_153363	NP_699194			zinc finger protein 679						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			skin(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	7	64513332	64513332	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-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	64890540	64890540	+	IGR	DEL	A	-	-	rs113305093		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:64890540delA								ZNF92 (24543 upstream) : INTS4L2 (222237 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	64927813	64927814	+	IGR	INS	-	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:64927813_64927814insT								ZNF92 (61816 upstream) : INTS4L2 (184963 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	65187608	65187608	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:65187608delT	uc003tud.1	-											Homo sapiens hypothetical LOC441242, mRNA (cDNA clone MGC:87648 IMAGE:5267764), complete cds.																														---	---	---	---
VKORC1L1	154807	broad.mit.edu	37	7	65358946	65358949	+	Intron	DEL	TTTT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:65358946_65358949delTTTT	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	65439090	65439090	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:65439090delA	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	65523499	65523499	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:65523499delT								GUSB (76253 upstream) : ASL (17277 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	65572980	65572981	+	IGR	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:65572980_65572981delAA								ASL (14659 upstream) : CRCP (6824 downstream)																																			---	---	---	---
CRCP	27297	broad.mit.edu	37	7	65609974	65609974	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:65609974delA	uc003tus.2	+						CRCP_uc003tuv.2_Intron|CRCP_uc011kdw.1_Intron|CRCP_uc003tut.2_Intron|CRCP_uc003tuu.2_Intron	NM_014478	NP_055293			calcitonin gene-related peptide-receptor						acrosome reaction|innate immune response|response to virus|transcription from RNA polymerase III promoter	DNA polymerase III complex|nucleus|plasma membrane	calcitonin receptor activity|DNA-directed RNA polymerase activity|nucleotide binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	7	65662382	65662383	+	IGR	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:65662382_65662383delTT								CRCP (42831 upstream) : TPST1 (7876 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	65899617	65899617	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-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	66842913	66842913	+	IGR	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:66842913delC								STAG3L4 (56401 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	67106874	67106876	+	IGR	DEL	AAA	-	-	rs34038578		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:67106874_67106876delAAA								STAG3L4 (320362 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	67154559	67154559	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:67154559delT								STAG3L4 (368047 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	67422990	67422993	+	IGR	DEL	AAAA	-	-	rs74586212		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:67422990_67422993delAAAA								STAG3L4 (636478 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	67489052	67489053	+	IGR	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:67489052_67489053delAA								STAG3L4 (702540 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	67771486	67771487	+	IGR	DEL	AA	-	-	rs77994491		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:67771486_67771487delAA								STAG3L4 (984974 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	67790283	67790283	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:67790283delA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	67875359	67875362	+	IGR	DEL	GGAA	-	-	rs113313047		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:67875359_67875362delGGAA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	68276492	68276492	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:68276492delA								None (None upstream) : AUTS2 (787413 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	68602855	68602855	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:68602855delA								None (None upstream) : AUTS2 (461050 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	68626936	68626936	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:68626936delT								None (None upstream) : AUTS2 (436969 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	68689933	68689933	+	IGR	DEL	A	-	-	rs113250115		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:68689933delA								None (None upstream) : AUTS2 (373972 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	68804870	68804870	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:68804870delA								None (None upstream) : AUTS2 (259035 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	68872683	68872683	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:68872683delA								None (None upstream) : AUTS2 (191222 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	69017885	69017885	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:69017885delT								None (None upstream) : AUTS2 (46020 downstream)																																			---	---	---	---
AUTS2	26053	broad.mit.edu	37	7	69156844	69156844	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:69156844delT	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	69448501	69448502	+	Intron	DEL	TG	-	-	rs35678805		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:69448501_69448502delTG	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	69553596	69553596	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:69553596delT	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	69975232	69975232	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:69975232delT	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	70094744	70094744	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:70094744delT	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	70110929	70110929	+	Intron	DEL	T	-	-	rs11323206		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:70110929delT	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	70195204	70195204	+	Intron	DEL	T	-	-	rs72347688		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:70195204delT	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	70217046	70217047	+	Intron	INS	-	G	G	rs148193760	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:70217046_70217047insG	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)														---	---	---	---
Unknown	0	broad.mit.edu	37	7	70335287	70335287	+	IGR	DEL	T	-	-	rs80119664		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:70335287delT								AUTS2 (77403 upstream) : WBSCR17 (262502 downstream)																																			---	---	---	---
WBSCR17	64409	broad.mit.edu	37	7	70625452	70625452	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:70625452delT	uc003tvy.2	+							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	70879970	70879971	+	Intron	DEL	TT	-	-	rs72245504		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:70879970_70879971delTT	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	71065234	71065237	+	Intron	DEL	AAAA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:71065234_71065237delAAAA	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)																---	---	---	---
CALN1	83698	broad.mit.edu	37	7	71458032	71458032	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:71458032delT	uc003twa.3	-						CALN1_uc003twb.3_Intron|CALN1_uc003twc.3_Intron	NM_001017440	NP_001017440			calneuron 1 isoform 2							Golgi apparatus|integral to membrane|perinuclear region of cytoplasm|plasma membrane	calcium ion binding			skin(1)	1		all_cancers(73;0.069)|Lung NSC(55;0.0658)|all_lung(88;0.0912)|all_epithelial(88;0.161)																---	---	---	---
CALN1	83698	broad.mit.edu	37	7	71535744	71535745	+	Intron	DEL	CT	-	-	rs74802286		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:71535744_71535745delCT	uc003twa.3	-						CALN1_uc003twb.3_Intron|CALN1_uc003twc.3_Intron	NM_001017440	NP_001017440			calneuron 1 isoform 2							Golgi apparatus|integral to membrane|perinuclear region of cytoplasm|plasma membrane	calcium ion binding			skin(1)	1		all_cancers(73;0.069)|Lung NSC(55;0.0658)|all_lung(88;0.0912)|all_epithelial(88;0.161)																---	---	---	---
CALN1	83698	broad.mit.edu	37	7	71647258	71647258	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:71647258delA	uc003twa.3	-						CALN1_uc003twb.3_Intron|CALN1_uc003twc.3_Intron	NM_001017440	NP_001017440			calneuron 1 isoform 2							Golgi apparatus|integral to membrane|perinuclear region of cytoplasm|plasma membrane	calcium ion binding			skin(1)	1		all_cancers(73;0.069)|Lung NSC(55;0.0658)|all_lung(88;0.0912)|all_epithelial(88;0.161)																---	---	---	---
CALN1	83698	broad.mit.edu	37	7	71733316	71733316	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:71733316delA	uc003twa.3	-						CALN1_uc003twb.3_Intron|CALN1_uc003twc.3_Intron	NM_001017440	NP_001017440			calneuron 1 isoform 2							Golgi apparatus|integral to membrane|perinuclear region of cytoplasm|plasma membrane	calcium ion binding			skin(1)	1		all_cancers(73;0.069)|Lung NSC(55;0.0658)|all_lung(88;0.0912)|all_epithelial(88;0.161)																---	---	---	---
CALN1	83698	broad.mit.edu	37	7	71810287	71810287	+	Intron	DEL	A	-	-	rs113213573		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:71810287delA	uc003twb.3	-						CALN1_uc003twc.3_Intron	NM_031468	NP_113656			calneuron 1 isoform 1							Golgi apparatus|integral to membrane|perinuclear region of cytoplasm|plasma membrane	calcium ion binding			skin(1)	1		all_cancers(73;0.069)|Lung NSC(55;0.0658)|all_lung(88;0.0912)|all_epithelial(88;0.161)																---	---	---	---
TYW1B	441250	broad.mit.edu	37	7	72289732	72289732	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:72289732delA	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																		---	---	---	---
GTF2IRD2P1	401375	broad.mit.edu	37	7	72683456	72683457	+	Intron	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:72683456_72683457delTT	uc003txs.1	-						FKBP6_uc003twz.2_Intron|GTF2IRD2P1_uc011ket.1_5'Flank	NR_002164				RecName: Full=General transcription factor II-I repeat domain-containing protein 2B; AltName: Full=GTF2I repeat domain-containing protein 2B; AltName: Full=Transcription factor GTF2IRD2-beta;												0																		---	---	---	---
FKBP6	8468	broad.mit.edu	37	7	72764387	72764388	+	Intron	DEL	TG	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:72764387_72764388delTG	uc003tya.2	+						FKBP6_uc003twz.2_Intron|FKBP6_uc011kew.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	73072399	73072400	+	IGR	INS	-	C	C	rs141894458	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:73072399_73072400insC								MLXIPL (33529 upstream) : VPS37D (9774 downstream)																																			---	---	---	---
RFC2	5982	broad.mit.edu	37	7	73176319	73176319	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:73176319delA	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	73271843	73271843	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:73271843delT	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	73329417	73329417	+	Intron	DEL	T	-	-	rs72306274		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:73329417delT	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	73354033	73354034	+	Intron	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:73354033_73354034delTT	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	73385919	73385920	+	Intron	INS	-	TC	TC	rs148790281	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:73385919_73385920insTC	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																		---	---	---	---
ELN	2006	broad.mit.edu	37	7	73446150	73446151	+	Intron	DEL	GA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:73446150_73446151delGA	uc003tzw.2	+						RFC2_uc011kfa.1_Intron|ELN_uc003tzm.1_Intron|ELN_uc011kfe.1_Intron|ELN_uc003tzn.2_Intron|ELN_uc003tzz.2_Intron|ELN_uc003tzo.2_Intron|ELN_uc003tzp.2_Intron|ELN_uc003tzq.2_Intron|ELN_uc003tzr.2_Intron|ELN_uc003tzs.2_Intron|ELN_uc003tzt.2_Intron|ELN_uc003tzu.2_Intron|ELN_uc003tzv.2_Intron|ELN_uc003tzx.2_Intron|ELN_uc011kff.1_Intron|ELN_uc003tzy.2_Intron	NM_000501	NP_001075224			elastin isoform a precursor						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						---	---	---	---
EIF4H	7458	broad.mit.edu	37	7	73600243	73600243	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:73600243delA	uc003uad.1	+						RFC2_uc011kfa.1_Intron|EIF4H_uc011kfg.1_Intron|EIF4H_uc010lbm.2_Intron|EIF4H_uc003uae.1_Intron|EIF4H_uc003uaf.1_Intron	NM_022170	NP_071496			eukaryotic translation initiation factor 4H						interspecies interaction between organisms|regulation of translational initiation	cytosol|eukaryotic translation initiation factor 4F complex|perinuclear region of cytoplasm	nucleotide binding|protein binding|translation initiation factor activity				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	7	73681291	73681292	+	IGR	DEL	TG	-	-	rs111645563		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:73681291_73681292delTG								RFC2 (12553 upstream) : CLIP2 (22513 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	74027382	74027382	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:74027382delT								GTF2IRD1 (10464 upstream) : GTF2I (44648 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	74035398	74035399	+	IGR	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:74035398_74035399delTT								GTF2IRD1 (18480 upstream) : GTF2I (36631 downstream)																																			---	---	---	---
GTF2I	2969	broad.mit.edu	37	7	74105135	74105135	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:74105135delT	uc003uau.2	+						GTF2I_uc003uat.2_Intron|GTF2I_uc003uav.2_Intron|GTF2I_uc003uaw.2_Intron|GTF2I_uc003uay.2_Intron|GTF2I_uc003uax.2_Intron	NM_032999	NP_127492			general transcription factor IIi isoform 1						negative regulation of angiogenesis|signal transduction|transcription initiation from RNA polymerase II promoter	cytoplasm|nucleus	DNA binding|protein binding|sequence-specific DNA binding transcription factor activity				0																		---	---	---	---
GTF2I	2969	broad.mit.edu	37	7	74129127	74129127	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:74129127delT	uc003uau.2	+						GTF2I_uc003uat.2_Intron|GTF2I_uc003uav.2_Intron|GTF2I_uc003uaw.2_Intron|GTF2I_uc003uay.2_Intron|GTF2I_uc003uax.2_Intron|uc003uaz.2_Intron	NM_032999	NP_127492			general transcription factor IIi isoform 1						negative regulation of angiogenesis|signal transduction|transcription initiation from RNA polymerase II promoter	cytoplasm|nucleus	DNA binding|protein binding|sequence-specific DNA binding transcription factor activity				0																		---	---	---	---
GTF2I	2969	broad.mit.edu	37	7	74160131	74160131	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:74160131delA	uc003uau.2	+						GTF2I_uc003uav.2_Intron|GTF2I_uc003uaw.2_Intron|GTF2I_uc003uay.2_Intron|GTF2I_uc003uax.2_Intron	NM_032999	NP_127492			general transcription factor IIi isoform 1						negative regulation of angiogenesis|signal transduction|transcription initiation from RNA polymerase II promoter	cytoplasm|nucleus	DNA binding|protein binding|sequence-specific DNA binding transcription factor activity				0																		---	---	---	---
GTF2I	2969	broad.mit.edu	37	7	74163252	74163252	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:74163252delA	uc003uau.2	+						GTF2I_uc003uav.2_Intron|GTF2I_uc003uaw.2_Intron|GTF2I_uc003uay.2_Intron|GTF2I_uc003uax.2_Intron|GTF2I_uc003uba.2_5'Flank	NM_032999	NP_127492			general transcription factor IIi isoform 1						negative regulation of angiogenesis|signal transduction|transcription initiation from RNA polymerase II promoter	cytoplasm|nucleus	DNA binding|protein binding|sequence-specific DNA binding transcription factor activity				0																		---	---	---	---
PMS2L5	5383	broad.mit.edu	37	7	74319634	74319634	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:74319634delT	uc003ubl.2	+						PMS2L5_uc003ubk.2_Intron|PMS2L5_uc010lbw.2_Intron|PMS2L5_uc003ubm.3_Intron	NR_027775				SubName: Full=Postmeiotic segregation increased 2-like 5;												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	7	75456726	75456726	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:75456726delA								CCL24 (13693 upstream) : RHBDD2 (51591 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	75489930	75489930	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:75489930delT								CCL24 (46897 upstream) : RHBDD2 (18387 downstream)																																			---	---	---	---
POR	5447	broad.mit.edu	37	7	75593324	75593324	+	Intron	DEL	T	-	-	rs112808473		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:75593324delT	uc003udy.2	+							NM_000941	NP_000932			cytochrome P450 reductase						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)													---	---	---	---
POR	5447	broad.mit.edu	37	7	75602147	75602147	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:75602147delT	uc003udy.2	+						POR_uc011kgb.1_Intron	NM_000941	NP_000932			cytochrome P450 reductase						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)													---	---	---	---
Unknown	0	broad.mit.edu	37	7	76074067	76074067	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:76074067delA								ZP3 (2680 upstream) : DTX2 (16905 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	76381444	76381444	+	IGR	DEL	T	-	-	rs75868695		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:76381444delT								POMZP3 (124824 upstream) : PMS2L11 (228695 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	76477215	76477215	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:76477215delA								POMZP3 (220595 upstream) : PMS2L11 (132924 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	77100898	77100899	+	IGR	INS	-	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:77100898_77100899insA								PION (55181 upstream) : PTPN12 (65874 downstream)																																			---	---	---	---
PTPN12	5782	broad.mit.edu	37	7	77206014	77206014	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:77206014delA	uc003ugh.2	+						PTPN12_uc011kgp.1_Intron|PTPN12_uc011kgq.1_Intron|PTPN12_uc010ldq.1_Intron|PTPN12_uc010ldr.1_Intron	NM_002835	NP_002826			protein tyrosine phosphatase, non-receptor type							soluble fraction	non-membrane spanning protein tyrosine phosphatase activity|SH3 domain binding			ovary(1)|breast(1)|pancreas(1)	3																		---	---	---	---
Unknown	0	broad.mit.edu	37	7	77295273	77295273	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:77295273delT	uc003ugj.1	-											Homo sapiens clone 124-1V1, mRNA sequence.																														---	---	---	---
MAGI2	9863	broad.mit.edu	37	7	77848880	77848880	+	Intron	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:77848880delC	uc003ugx.2	-						MAGI2_uc003ugy.2_Intron|MAGI2_uc010ldx.1_Intron|MAGI2_uc010ldy.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	78623166	78623166	+	Intron	DEL	A	-	-	rs33986318		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:78623166delA	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	78685545	78685545	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:78685545delA	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	78940793	78940793	+	Intron	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:78940793delC	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	79219091	79219091	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:79219091delA								MAGI2 (136201 upstream) : GNAI1 (545049 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	79347768	79347768	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:79347768delA								MAGI2 (264878 upstream) : GNAI1 (416372 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	79481750	79481750	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:79481750delA								MAGI2 (398860 upstream) : GNAI1 (282390 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	79510634	79510634	+	IGR	DEL	T	-	-	rs112241390		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:79510634delT								MAGI2 (427744 upstream) : GNAI1 (253506 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	79734210	79734215	+	IGR	DEL	TGTGTG	-	-	rs10572441		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:79734210_79734215delTGTGTG								MAGI2 (651320 upstream) : GNAI1 (29925 downstream)																																			---	---	---	---
GNAI1	2770	broad.mit.edu	37	7	79785047	79785047	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:79785047delA	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																		---	---	---	---
GNAI1	2770	broad.mit.edu	37	7	79835898	79835898	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:79835898delT	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	80087548	80087548	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:80087548delA	uc003uhc.2	+							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	80269306	80269306	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:80269306delT	uc003uhc.2	+						CD36_uc003uhd.3_Intron|CD36_uc011kgv.1_Intron|CD36_uc003uhe.3_Intron|CD36_uc003uhf.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																		---	---	---	---
Unknown	0	broad.mit.edu	37	7	81097478	81097478	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:81097478delA								SEMA3C (545803 upstream) : HGF (233967 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	82133629	82133629	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:82133629delA								CACNA2D1 (60598 upstream) : PCLO (249692 downstream)																																			---	---	---	---
PCLO	27445	broad.mit.edu	37	7	82595469	82595469	+	Frame_Shift_Del	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:82595469delT	uc003uhx.2	-	4	3924	c.3635delA	c.(3634-3636)AAGfs	p.K1212fs	PCLO_uc003uhv.2_Frame_Shift_Del_p.K1212fs	NM_033026	NP_149015	Q9Y6V0	PCLO_HUMAN	piccolo isoform 1	1151					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	82595811	82595811	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:82595811delA	uc003uhx.2	-						PCLO_uc003uhv.2_Intron	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																		---	---	---	---
PCLO	27445	broad.mit.edu	37	7	82780049	82780049	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:82780049delT	uc003uhx.2	-						PCLO_uc003uhv.2_Intron	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																		---	---	---	---
SEMA3E	9723	broad.mit.edu	37	7	83035550	83035550	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:83035550delT	uc003uhy.1	-							NM_012431	NP_036563			semaphorin 3E precursor						axon guidance	extracellular space|membrane	receptor activity			ovary(3)	3		Medulloblastoma(109;0.109)																---	---	---	---
Unknown	0	broad.mit.edu	37	7	83978300	83978300	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:83978300delA								SEMA3A (154083 upstream) : SEMA3D (646574 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	84069395	84069395	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:84069395delA								SEMA3A (245178 upstream) : SEMA3D (555479 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	85667314	85667314	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:85667314delT								SEMA3D (851143 upstream) : GRM3 (605916 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	85863377	85863378	+	IGR	INS	-	A	A	rs111489508		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:85863377_85863378insA								None (None upstream) : GRM3 (409852 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	86085362	86085362	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:86085362delT								None (None upstream) : GRM3 (187868 downstream)																																			---	---	---	---
GRM3	2913	broad.mit.edu	37	7	86431915	86431916	+	Intron	DEL	AA	-	-	rs111893340		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:86431915_86431916delAA	uc003uid.2	+						GRM3_uc010lef.2_Intron|GRM3_uc010leg.2_Intron|GRM3_uc010leh.2_Intron	NM_000840	NP_000831			glutamate receptor, metabotropic 3 precursor						synaptic transmission	integral to plasma membrane				lung(4)|ovary(3)|central_nervous_system(2)|skin(2)|haematopoietic_and_lymphoid_tissue(1)|prostate(1)	13	Esophageal squamous(14;0.0058)|all_lung(186;0.132)|Lung NSC(181;0.142)				Acamprosate(DB00659)|Nicotine(DB00184)													---	---	---	---
ABCB1	5243	broad.mit.edu	37	7	87164655	87164658	+	Intron	DEL	TTTT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:87164655_87164658delTTTT	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)													---	---	---	---
DBF4	10926	broad.mit.edu	37	7	87516630	87516630	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:87516630delT	uc003ujf.1	+						DBF4_uc003ujh.1_Intron|DBF4_uc003ujg.1_Intron|DBF4_uc011khf.1_Intron	NM_006716	NP_006707			activator of S phase kinase						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)																---	---	---	---
ADAM22	53616	broad.mit.edu	37	7	87594423	87594423	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:87594423delA	uc003ujn.2	+						ADAM22_uc003uji.1_Intron|ADAM22_uc003ujj.1_Intron|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	88138125	88138126	+	IGR	INS	-	T	T	rs147008415	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:88138125_88138126insT								STEAP4 (201916 upstream) : ZNF804B (250627 downstream)																																			---	---	---	---
ZNF804B	219578	broad.mit.edu	37	7	88483925	88483925	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:88483925delT	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	88771349	88771349	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:88771349delT	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	89443210	89443210	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:89443210delA								ZNF804B (476866 upstream) : DPY19L2P4 (305504 downstream)																																			---	---	---	---
C7orf63	79846	broad.mit.edu	37	7	89912077	89912077	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:89912077delA	uc010lep.2	+						C7orf63_uc003ukf.2_Intron|C7orf63_uc003ukg.2_Intron|C7orf63_uc011khj.1_Intron|C7orf63_uc011khk.1_Intron	NM_001039706	NP_001034795			hypothetical protein LOC79846 isoform 1								binding			ovary(1)	1																		---	---	---	---
GTPBP10	85865	broad.mit.edu	37	7	89982117	89982117	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-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	90827575	90827575	+	Intron	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:90827575delG	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																		---	---	---	---
Unknown	0	broad.mit.edu	37	7	91140689	91140689	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:91140689delA								FZD1 (242558 upstream) : MTERF (290771 downstream)																																			---	---	---	---
AKAP9	10142	broad.mit.edu	37	7	91622509	91622509	+	Intron	DEL	T	-	-	rs75639681		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:91622509delT	uc003ulg.2	+						AKAP9_uc003uld.3_Intron|AKAP9_uc003ule.2_Intron|AKAP9_uc003ulf.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								---	---	---	---
CYP51A1	1595	broad.mit.edu	37	7	91767899	91767900	+	Intron	DEL	AA	-	-	rs113941377		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:91767899_91767900delAA	uc003uln.3	-						uc003ulo.1_Intron	NM_001146152	NP_001139624			cytochrome P450, family 51, subfamily A,						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	91937039	91937040	+	Intron	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:91937039_91937040delTT	uc003ulw.2	+							NM_019004	NP_061877			ankyrin repeat and IBR domain containing 1								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)															---	---	---	---
ANKIB1	54467	broad.mit.edu	37	7	91978104	91978104	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:91978104delA	uc003ulw.2	+							NM_019004	NP_061877			ankyrin repeat and IBR domain containing 1								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)															---	---	---	---
HEPACAM2	253012	broad.mit.edu	37	7	92844696	92844696	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:92844696delA	uc003umm.2	-						HEPACAM2_uc003uml.2_Intron|HEPACAM2_uc010lff.2_Intron|HEPACAM2_uc011khy.1_Intron	NM_001039372	NP_001034461			HEPACAM family member 2 isoform 1							integral to membrane				ovary(3)|breast(1)|kidney(1)	5																		---	---	---	---
CCDC132	55610	broad.mit.edu	37	7	92883251	92883251	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:92883251delA	uc003umo.2	+						CCDC132_uc003umq.2_Intron|CCDC132_uc003ump.2_Intron|CCDC132_uc003umr.2_Intron|CCDC132_uc011khz.1_Intron|CCDC132_uc003umn.2_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)															---	---	---	---
CCDC132	55610	broad.mit.edu	37	7	92926367	92926367	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-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	93667284	93667285	+	IGR	INS	-	G	G	rs150694132	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:93667284_93667285insG								BET1 (33594 upstream) : COL1A2 (356588 downstream)																																			---	---	---	---
COL1A2	1278	broad.mit.edu	37	7	94049911	94049911	+	Frame_Shift_Del	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:94049911delA	uc003ung.1	+	37	2717	c.2246delA	c.(2245-2247)GAAfs	p.E749fs	COL1A2_uc011kib.1_Intron|COL1A2_uc010lfi.1_Intron	NM_000089	NP_000080	P08123	CO1A2_HUMAN	alpha 2 type I collagen precursor	749			Missing (in OI2A).		axon guidance|blood vessel development|collagen fibril organization|leukocyte migration|odontogenesis|platelet activation|regulation of blood pressure|Rho protein signal transduction|skeletal system development|skin morphogenesis|transforming growth factor beta receptor signaling pathway	collagen type I|extracellular space|plasma membrane	extracellular matrix structural constituent|identical protein binding|platelet-derived growth factor binding|protein binding, bridging		COL1A2/PLAG1(3)	soft_tissue(3)|central_nervous_system(3)|ovary(2)|skin(1)	9	all_cancers(62;2.46e-09)|all_epithelial(64;2.7e-08)		STAD - Stomach adenocarcinoma(171;0.0031)		Collagenase(DB00048)										HNSCC(75;0.22)			---	---	---	---
ASB4	51666	broad.mit.edu	37	7	95146914	95146914	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-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)															---	---	---	---
PDK4	5166	broad.mit.edu	37	7	95221168	95221168	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:95221168delA	uc003uoa.2	-						PDK4_uc003unz.2_Intron	NM_002612	NP_002603			pyruvate dehydrogenase kinase 4 precursor						glucose metabolic process|peptidyl-histidine phosphorylation|pyruvate metabolic process|regulation of acetyl-CoA biosynthetic process from pyruvate	mitochondrial matrix	ATP binding|pyruvate dehydrogenase (acetyl-transferring) kinase activity|two-component sensor activity				0	all_cancers(62;1.06e-10)|all_epithelial(64;1.04e-09)|Lung NSC(181;0.128)|all_lung(186;0.151)		STAD - Stomach adenocarcinoma(171;0.0151)															---	---	---	---
SLC25A13	10165	broad.mit.edu	37	7	95775777	95775778	+	Intron	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:95775777_95775778delAA	uc003uof.3	-						SLC25A13_uc003uog.3_Intron|SLC25A13_uc011kik.1_Intron	NM_014251	NP_055066			solute carrier family 25, member 13 isoform 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)													---	---	---	---
Unknown	0	broad.mit.edu	37	7	96289226	96289230	+	Intron	DEL	AAAAA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:96289226_96289230delAAAAA	uc010lfm.1	-											Homo sapiens cDNA, FLJ17342.																														---	---	---	---
Unknown	0	broad.mit.edu	37	7	96377093	96377094	+	IGR	INS	-	CCTT	CCTT	rs6953216		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:96377093_96377094insCCTT								SHFM1 (37890 upstream) : DLX6AS (220734 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	96963257	96963258	+	IGR	INS	-	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:96963257_96963258insA								ACN9 (152184 upstream) : TAC1 (398013 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	97096757	97096759	+	IGR	DEL	TTT	-	-	rs34688567		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:97096757_97096759delTTT								ACN9 (285684 upstream) : TAC1 (264512 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	97116386	97116388	+	IGR	DEL	AAA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:97116386_97116388delAAA								ACN9 (305313 upstream) : TAC1 (244883 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	97337112	97337112	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:97337112delA								ACN9 (526039 upstream) : TAC1 (24159 downstream)																																			---	---	---	---
TECPR1	25851	broad.mit.edu	37	7	97858327	97858327	+	Intron	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:97858327delG	uc003upg.2	-						TECPR1_uc003uph.1_Intron	NM_015395	NP_056210			tectonin beta-propeller repeat containing 1							integral to membrane	protein binding			pancreas(1)	1																		---	---	---	---
TECPR1	25851	broad.mit.edu	37	7	97862098	97862099	+	Intron	DEL	AA	-	-	rs139511001		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:97862098_97862099delAA	uc003upg.2	-						TECPR1_uc003uph.1_Intron	NM_015395	NP_056210			tectonin beta-propeller repeat containing 1							integral to membrane	protein binding			pancreas(1)	1																		---	---	---	---
BAIAP2L1	55971	broad.mit.edu	37	7	97939976	97939977	+	Intron	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:97939976_97939977delTT	uc003upj.2	-							NM_018842	NP_061330			BAI1-associated protein 2-like 1						filopodium assembly|positive regulation of actin cytoskeleton reorganization|positive regulation of actin filament polymerization|response to bacterium|signal transduction	cell junction|cytoskeleton|cytosol|nucleus	actin binding|cytoskeletal adaptor activity|proline-rich region binding|SH3 domain binding			ovary(1)	1	all_cancers(62;4.34e-10)|all_epithelial(64;5e-10)|Esophageal squamous(72;0.00918)|Lung NSC(181;0.0113)|all_lung(186;0.0126)		STAD - Stomach adenocarcinoma(171;0.215)															---	---	---	---
BAIAP2L1	55971	broad.mit.edu	37	7	97999419	97999419	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:97999419delA	uc003upj.2	-							NM_018842	NP_061330			BAI1-associated protein 2-like 1						filopodium assembly|positive regulation of actin cytoskeleton reorganization|positive regulation of actin filament polymerization|response to bacterium|signal transduction	cell junction|cytoskeleton|cytosol|nucleus	actin binding|cytoskeletal adaptor activity|proline-rich region binding|SH3 domain binding			ovary(1)	1	all_cancers(62;4.34e-10)|all_epithelial(64;5e-10)|Esophageal squamous(72;0.00918)|Lung NSC(181;0.0113)|all_lung(186;0.0126)		STAD - Stomach adenocarcinoma(171;0.215)															---	---	---	---
BAIAP2L1	55971	broad.mit.edu	37	7	98015049	98015049	+	Intron	DEL	G	-	-	rs1635612	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:98015049delG	uc003upj.2	-							NM_018842	NP_061330			BAI1-associated protein 2-like 1						filopodium assembly|positive regulation of actin cytoskeleton reorganization|positive regulation of actin filament polymerization|response to bacterium|signal transduction	cell junction|cytoskeleton|cytosol|nucleus	actin binding|cytoskeletal adaptor activity|proline-rich region binding|SH3 domain binding			ovary(1)	1	all_cancers(62;4.34e-10)|all_epithelial(64;5e-10)|Esophageal squamous(72;0.00918)|Lung NSC(181;0.0113)|all_lung(186;0.0126)		STAD - Stomach adenocarcinoma(171;0.215)															---	---	---	---
TMEM130	222865	broad.mit.edu	37	7	98444482	98444483	+	3'UTR	INS	-	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:98444482_98444483insT	uc003upo.2	-	8					TMEM130_uc011kiq.1_3'UTR|TMEM130_uc011kir.1_3'UTR|TMEM130_uc003upn.2_3'UTR	NM_001134450	NP_001127922			transmembrane protein 130 isoform a							Golgi membrane|integral to membrane				ovary(1)|central_nervous_system(1)	2	all_cancers(62;4.05e-09)|all_epithelial(64;2.62e-09)|Lung NSC(181;0.01)|all_lung(186;0.0115)|Esophageal squamous(72;0.0274)		STAD - Stomach adenocarcinoma(171;0.215)															---	---	---	---
TMEM130	222865	broad.mit.edu	37	7	98446426	98446426	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:98446426delT	uc003upo.2	-						TMEM130_uc011kiq.1_Intron|TMEM130_uc011kir.1_Intron|TMEM130_uc003upn.2_Intron	NM_001134450	NP_001127922			transmembrane protein 130 isoform a							Golgi membrane|integral to membrane				ovary(1)|central_nervous_system(1)	2	all_cancers(62;4.05e-09)|all_epithelial(64;2.62e-09)|Lung NSC(181;0.01)|all_lung(186;0.0115)|Esophageal squamous(72;0.0274)		STAD - Stomach adenocarcinoma(171;0.215)															---	---	---	---
TRRAP	8295	broad.mit.edu	37	7	98518469	98518469	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:98518469delT	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	98546867	98546868	+	Intron	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:98546867_98546868delAA	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	98550574	98550574	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:98550574delT	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	98581179	98581179	+	Intron	DEL	T	-	-	rs57779646		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:98581179delT	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	98618827	98618827	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:98618827delA	uc003ups.2	+											Homo sapiens TRRAP protein (TRRAP) mRNA, complete cds.						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)															---	---	---	---
SMURF1	57154	broad.mit.edu	37	7	98722276	98722276	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:98722276delA	uc003upu.1	-						SMURF1_uc003upv.1_Intron|SMURF1_uc003upt.2_Intron	NM_020429	NP_065162			Smad ubiquitination regulatory factor 1 isoform						BMP signaling pathway|cell differentiation|ectoderm development|negative regulation of BMP signaling pathway|negative regulation of transforming growth factor beta receptor signaling pathway|positive regulation of protein ubiquitination|proteasomal ubiquitin-dependent protein catabolic process|protein export from nucleus|protein localization at cell surface|protein polyubiquitination|protein ubiquitination involved in ubiquitin-dependent protein catabolic process|receptor catabolic process|transforming growth factor beta receptor signaling pathway|ubiquitin-dependent SMAD protein catabolic process	cytosol|plasma membrane	activin binding|I-SMAD binding|R-SMAD binding|ubiquitin-protein ligase activity			skin(2)|ovary(1)|lung(1)	4	all_cancers(62;1.05e-08)|all_epithelial(64;4.34e-09)|Lung NSC(181;0.00902)|all_lung(186;0.0145)|Esophageal squamous(72;0.0274)		STAD - Stomach adenocarcinoma(171;0.215)|Lung(104;0.224)															---	---	---	---
SMURF1	57154	broad.mit.edu	37	7	98743258	98743259	+	5'Flank	DEL	TG	-	-	rs113552071		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:98743258_98743259delTG	uc003upu.1	-						SMURF1_uc003upv.1_5'Flank|SMURF1_uc003upt.2_5'Flank	NM_020429	NP_065162			Smad ubiquitination regulatory factor 1 isoform						BMP signaling pathway|cell differentiation|ectoderm development|negative regulation of BMP signaling pathway|negative regulation of transforming growth factor beta receptor signaling pathway|positive regulation of protein ubiquitination|proteasomal ubiquitin-dependent protein catabolic process|protein export from nucleus|protein localization at cell surface|protein polyubiquitination|protein ubiquitination involved in ubiquitin-dependent protein catabolic process|receptor catabolic process|transforming growth factor beta receptor signaling pathway|ubiquitin-dependent SMAD protein catabolic process	cytosol|plasma membrane	activin binding|I-SMAD binding|R-SMAD binding|ubiquitin-protein ligase activity			skin(2)|ovary(1)|lung(1)	4	all_cancers(62;1.05e-08)|all_epithelial(64;4.34e-09)|Lung NSC(181;0.00902)|all_lung(186;0.0145)|Esophageal squamous(72;0.0274)		STAD - Stomach adenocarcinoma(171;0.215)|Lung(104;0.224)															---	---	---	---
Unknown	0	broad.mit.edu	37	7	98819080	98819082	+	IGR	DEL	TTT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:98819080_98819082delTTT								KPNA7 (13991 upstream) : MYH16 (51842 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	98827170	98827170	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:98827170delT								KPNA7 (22081 upstream) : MYH16 (43754 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	98912360	98912361	+	IGR	DEL	CA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:98912360_98912361delCA								MYH16 (16768 upstream) : ARPC1A (11149 downstream)																																			---	---	---	---
ARPC1B	10095	broad.mit.edu	37	7	98985523	98985525	+	Intron	DEL	AAA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:98985523_98985525delAAA	uc003upz.2	+						ARPC1A_uc011kit.1_Intron|ARPC1B_uc003uqa.2_Intron|ARPC1B_uc003uqb.2_Intron|ARPC1B_uc003uqc.2_Intron|ARPC1B_uc003uqd.2_5'Flank	NM_005720	NP_005711			actin related protein 2/3 complex subunit 1B						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)															---	---	---	---
CYP3A4	1576	broad.mit.edu	37	7	99355990	99355990	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:99355990delA	uc003urv.1	-						CYP3A4_uc003urw.1_Intron|CYP3A4_uc011kiz.1_Intron|CYP3A4_uc011kja.1_Intron|CYP3A4_uc011kjb.1_Intron	NM_017460	NP_059488			cytochrome P450, family 3, subfamily A,						alkaloid catabolic process|androgen metabolic process|exogenous drug catabolic process|heterocycle metabolic process|monoterpenoid metabolic process|oxidative demethylation|steroid catabolic process|xenobiotic metabolic process	cell surface|endoplasmic reticulum membrane|integral to membrane|microsome	albendazole monooxygenase activity|caffeine oxidase activity|electron carrier activity|enzyme binding|heme binding|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|quinine 3-monooxygenase activity|steroid binding|taurochenodeoxycholate 6alpha-hydroxylase activity|testosterone 6-beta-hydroxylase activity|vitamin D 24-hydroxylase activity|vitamin D3 25-hydroxylase activity			central_nervous_system(3)|ovary(1)	4	Lung NSC(181;0.0144)|Esophageal squamous(72;0.0166)|all_lung(186;0.0228)				Albendazole(DB00518)|Alclometasone(DB00240)|Alfentanil(DB00802)|Alfuzosin(DB00346)|Aliskiren(DB01258)|Almotriptan(DB00918)|Alosetron(DB00969)|Alprazolam(DB00404)|Amlodipine(DB00381)|Amprenavir(DB00701)|Aprepitant(DB00673)|Aripiprazole(DB01238)|Astemizole(DB00637)|Atazanavir(DB01072)|Atorvastatin(DB01076)|Benazepril(DB00542)|Bepridil(DB01244)|Betamethasone(DB00443)|Bexarotene(DB00307)|Bortezomib(DB00188)|Bosentan(DB00559)|Bromocriptine(DB01200)|Budesonide(DB01222)|Bupivacaine(DB00297)|Buprenorphine(DB00921)|Buspirone(DB00490)|Busulfan(DB01008)|Carbamazepine(DB00564)|Cevimeline(DB00185)|Chlorpheniramine(DB01114)|Ciclesonide(DB01410)|Cilostazol(DB01166)|Cinacalcet(DB01012)|Cisapride(DB00604)|Clarithromycin(DB01211)|Clindamycin(DB01190)|Clofibrate(DB00636)|Clonazepam(DB01068)|Clopidogrel(DB00758)|Cocaine(DB00907)|Conivaptan(DB00872)|Conjugated Estrogens(DB00286)|Cyproterone(DB04839)|Darifenacin(DB00496)|Darunavir(DB01264)|Dasatinib(DB01254)|Delavirdine(DB00705)|Desogestrel(DB00304)|Dexamethasone(DB01234)|Diazepam(DB00829)|Dihydroergotamine(DB00320)|Diltiazem(DB00343)|Diphenhydramine(DB01075)|Disopyramide(DB00280)|Dofetilide(DB00204)|Dolasetron(DB00757)|Domperidone(DB01184)|Donepezil(DB00843)|Doxorubicin(DB00997)|Drospirenone(DB01395)|Dutasteride(DB01126)|Efavirenz(DB00625)|Eletriptan(DB00216)|Enalapril(DB00584)|Epirubicin(DB00445)|Eplerenone(DB00700)|Ergotamine(DB00696)|Erlotinib(DB00530)|Erythromycin(DB00199)|Escitalopram(DB01175)|Esomeprazole(DB00736)|Estazolam(DB01215)|Eszopiclone(DB00402)|Ethinyl Estradiol(DB00977)|Ethosuximide(DB00593)|Etonogestrel(DB00294)|Etoposide(DB00773)|Etoricoxib(DB01628)|Exemestane(DB00990)|Felodipine(DB01023)|Fentanyl(DB00813)|Fexofenadine(DB00950)|Finasteride(DB01216)|Fluconazole(DB00196)|Flumethasone Pivalate(DB00663)|Flunisolide(DB00180)|Fluocinolone Acetonide(DB00591)|Fluocinonide(DB01047)|Fluorometholone(DB00324)|Flurandrenolide(DB00846)|Fluticasone Propionate(DB00588)|Fosamprenavir(DB01319)|Fulvestrant(DB00947)|Galantamine(DB00674)|Gefitinib(DB00317)|Gemfibrozil(DB01241)|Granisetron(DB00889)|Grepafloxacin(DB00365)|Halofantrine(DB01218)|Hydrocodone(DB00956)|Hydrocortamate(DB00769)|Hydrocortisone(DB00741)|Hydromorphone(DB00327)|Imatinib(DB00619)|Indinavir(DB00224)|Ipratropium(DB00332)|Irinotecan(DB00762)|Isosorbide Dinitrate(DB00883)|Isosorbide Mononitrate(DB01020)|Isradipine(DB00270)|Itraconazole(DB01167)|Ketoconazole(DB01026)|Lapatinib(DB01259)|Lercanidipine(DB00528)|Letrozole(DB01006)|Levobupivacaine(DB01002)|Levomethadyl Acetate(DB01227)|Levothyroxine(DB00451)|Lomustine(DB01206)|Loperamide(DB00836)|Lopinavir(DB01601)|Loratadine(DB00455)|Losartan(DB00678)|Lovastatin(DB00227)|Maraviroc(DB04835)|Marinol(DB00470)|Mebendazole(DB00643)|Medroxyprogesterone(DB00603)|Methadone(DB00333)|Methylprednisolone(DB00959)|Metyrapone(DB01011)|Mibefradil(DB01388)|Midazolam(DB00683)|Mifepristone(DB00834)|Mirtazapine(DB00370)|Modafinil(DB00745)|Mometasone(DB00764)|Montelukast(DB00471)|Nateglinide(DB00731)|Nefazodone(DB01149)|Nelfinavir(DB00220)|Nevirapine(DB00238)|Nicardipine(DB00622)|Nifedipine(DB01115)|Nimodipine(DB00393)|Nisoldipine(DB00401)|Nitrendipine(DB01054)|Norethindrone(DB00717)|Norgestrel(DB00506)|Nystatin(DB00646)|Ondansetron(DB00904)|Oxybutynin(DB01062)|Paclitaxel(DB01229)|Paliperidone(DB01267)|Palonosetron(DB00377)|Pantoprazole(DB00213)|Paricalcitol(DB00910)|Phenmetrazine(DB00830)|Pimecrolimus(DB00337)|Pimozide(DB01100)|Pioglitazone(DB01132)|Posaconazole(DB01263)|Pranlukast(DB01411)|Prednisolone(DB00860)|Prednisone(DB00635)|Prochlorperazine(DB00433)|Quetiapine(DB01224)|Quinapril(DB00881)|Quinine(DB00468)|Rabeprazole(DB01129)|Ranolazine(DB00243)|Reboxetine(DB00234)|Retapamulin(DB01256)|Rifabutin(DB00615)|Rifampin(DB01045)|Rimonabant(DB06155)|Ritonavir(DB00503)|Rofecoxib(DB00533)|Roxithromycin(DB00778)|Salmeterol(DB00938)|Saquinavir(DB01232)|Sertindole(DB06144)|Sibutramine(DB01105)|Simvastatin(DB00641)|Sirolimus(DB00877)|Sitagliptin(DB01261)|Solifenacin(DB01591)|Sorafenib(DB00398)|Sunitinib(DB01268)|Tacrolimus(DB00864)|Tadalafil(DB00820)|Tamoxifen(DB00675)|Telithromycin(DB00976)|Terconazole(DB00251)|Terfenadine(DB00342)|Testosterone(DB00624)|Tiagabine(DB00906)|Ticlopidine(DB00208)|Tinidazole(DB00911)|Tiotropium(DB01409)|Tipranavir(DB00932)|Toremifene(DB00539)|Triazolam(DB00897)|Trimetrexate(DB01157)|Troglitazone(DB00197)|Valdecoxib(DB00580)|Vardenafil(DB00862)|Vinblastine(DB00570)|Vincristine(DB00541)|Vindesine(DB00309)|Vinorelbine(DB00361)|Voriconazole(DB00582)|Zaleplon(DB00962)|Zileuton(DB00744)|Ziprasidone(DB00246)|Zolpidem(DB00425)|Zonisamide(DB00909)													---	---	---	---
Unknown	0	broad.mit.edu	37	7	99482941	99482941	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:99482941delA								OR2AE1 (8285 upstream) : TRIM4 (5096 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	99641161	99641161	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:99641161delT								ZKSCAN1 (5758 upstream) : ZSCAN21 (6256 downstream)																																			---	---	---	---
MCM7	4176	broad.mit.edu	37	7	99699035	99699035	+	5'UTR	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:99699035delC	uc003usw.1	-	1					MCM7_uc003usv.1_5'Flank|MCM7_uc003usx.1_5'UTR|AP4M1_uc011kjg.1_5'Flank|AP4M1_uc010lgl.1_5'Flank|AP4M1_uc003utb.3_5'Flank|AP4M1_uc003utc.3_5'Flank|AP4M1_uc010lgm.2_5'Flank|AP4M1_uc003utd.2_5'Flank|AP4M1_uc011kjh.1_5'Flank|AP4M1_uc003ute.3_5'Flank|AP4M1_uc003utf.3_5'Flank	NM_005916	NP_005907			minichromosome maintenance complex component 7						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)													---	---	---	---
STAG3	10734	broad.mit.edu	37	7	99801910	99801910	+	Intron	DEL	T	-	-	rs143599714	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:99801910delT	uc003utx.1	+						STAG3_uc011kjk.1_Intron|GATS_uc003uty.3_Intron|GATS_uc003utz.3_Intron|GATS_uc003uua.3_Intron|GATS_uc010lgt.2_Intron|STAG3_uc003uub.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)																	---	---	---	---
ZCWPW1	55063	broad.mit.edu	37	7	100004130	100004130	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-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)																	---	---	---	---
Unknown	0	broad.mit.edu	37	7	100606333	100606340	+	Intron	DEL	TTTTTTTT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:100606333_100606340delTTTTTTTT	uc003uxk.1	+						uc003uxl.1_Intron|uc010lhn.1_5'Flank					Homo sapiens MUC3B mRNA for intestinal mucin, partial cds.																														---	---	---	---
MUC12	10071	broad.mit.edu	37	7	100647947	100647947	+	5'Flank	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:100647947delT	uc003uxo.2	+											SubName: Full=MUC12 protein; Flags: Fragment;												0																		---	---	---	---
MUC12	10071	broad.mit.edu	37	7	100657762	100657762	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:100657762delT	uc003uxo.2	+											SubName: Full=MUC12 protein; Flags: Fragment;												0																		---	---	---	---
SERPINE1	5054	broad.mit.edu	37	7	100770210	100770211	+	5'Flank	DEL	CA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:100770210_100770211delCA	uc003uxt.2	+						SERPINE1_uc011kkj.1_5'Flank|SERPINE1_uc003uxs.2_5'Flank	NM_000602	NP_000593			plasminogen activator inhibitor-1 isoform 1						angiogenesis|cellular response to chemical stimulus|cellular response to lipopolysaccharide|chronological cell aging|defense response to Gram-negative bacterium|fibrinolysis|negative regulation of apoptosis|negative regulation of cell adhesion mediated by integrin|negative regulation of fibrinolysis|negative regulation of plasminogen activation|negative regulation of smooth muscle cell migration|negative regulation of smooth muscle cell-matrix adhesion|negative regulation of vascular wound healing|platelet activation|platelet degranulation|positive regulation of angiogenesis|positive regulation of interleukin-8 production|positive regulation of leukotriene production involved in inflammatory response|positive regulation of monocyte chemotaxis|positive regulation of receptor-mediated endocytosis|regulation of receptor activity	extracellular matrix|extracellular space|plasma membrane|platelet alpha granule lumen	protease binding|serine-type endopeptidase inhibitor activity			ovary(1)|lung(1)|central_nervous_system(1)	3	Lung NSC(181;0.136)|all_lung(186;0.182)				Atorvastatin(DB01076)|Dimethyl sulfoxide(DB01093)|Drotrecogin alfa(DB00055)|Simvastatin(DB00641)|Tenecteplase(DB00031)|Troglitazone(DB00197)|Urokinase(DB00013)													---	---	---	---
Unknown	0	broad.mit.edu	37	7	100791088	100791088	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:100791088delT								SERPINE1 (8546 upstream) : AP1S1 (6598 downstream)																																			---	---	---	---
VGF	7425	broad.mit.edu	37	7	100808164	100808164	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:100808164delA	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	100983599	100983602	+	IGR	DEL	AAAA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:100983599_100983602delAAAA								RABL5 (18506 upstream) : EMID2 (22520 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	100986647	100986647	+	IGR	DEL	C	-	-	rs78956387		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:100986647delC								RABL5 (21554 upstream) : EMID2 (19475 downstream)																																			---	---	---	---
EMID2	136227	broad.mit.edu	37	7	101075980	101075980	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:101075980delT	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	101810548	101810550	+	Intron	DEL	AAA	-	-	rs79229215		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:101810548_101810550delAAA	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																		---	---	---	---
CUX1	1523	broad.mit.edu	37	7	101883014	101883014	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:101883014delT	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																		---	---	---	---
NAPEPLD	222236	broad.mit.edu	37	7	102770486	102770487	+	Intron	DEL	TC	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:102770486_102770487delTC	uc003vbc.2	-						NAPEPLD_uc003vbd.2_Intron|NAPEPLD_uc011klj.1_Intron|NAPEPLD_uc003vbe.2_Intron|NAPEPLD_uc003vbf.2_Intron	NM_198990	NP_945341			N-acyl phosphatidylethanolamine phospholipase D						phospholipid catabolic process	membrane	metal ion binding			skin(1)	1																		---	---	---	---
RELN	5649	broad.mit.edu	37	7	103115664	103115665	+	Intron	DEL	TT	-	-	rs111514895		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:103115664_103115665delTT	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)														---	---	---	---
RELN	5649	broad.mit.edu	37	7	103404342	103404342	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:103404342delA	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	103725530	103725530	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:103725530delT								RELN (95567 upstream) : ORC5L (41260 downstream)																																			---	---	---	---
LHFPL3	375612	broad.mit.edu	37	7	104322069	104322069	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:104322069delA	uc003vce.2	+						LHFPL3_uc003vcf.2_Intron	NM_199000	NP_945351			lipoma HMGIC fusion partner-like 3							integral to membrane					0																		---	---	---	---
LOC723809	723809	broad.mit.edu	37	7	104555223	104555223	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:104555223delT	uc003vch.1	-							NR_027374				Homo sapiens, clone IMAGE:5754998, mRNA.												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	7	104583455	104583456	+	Intron	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:104583455_104583456delTT	uc003vci.2	+											Homo sapiens cDNA clone IMAGE:4358995, partial cds.																														---	---	---	---
SRPK2	6733	broad.mit.edu	37	7	104770516	104770516	+	Intron	DEL	A	-	-	rs36043836		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:104770516delA	uc003vct.2	-						SRPK2_uc003vcu.2_Intron|SRPK2_uc003vcv.2_Intron|SRPK2_uc003vcs.1_Intron	NM_182691	NP_872633			serine/arginine-rich protein-specific kinase 2						angiogenesis|cell differentiation|intracellular protein kinase cascade|negative regulation of viral genome replication|nuclear speck organization|positive regulation of cell cycle|positive regulation of cell proliferation|positive regulation of gene expression|positive regulation of neuron apoptosis|positive regulation of viral genome replication|spliceosome assembly	cytoplasm|nucleolus	14-3-3 protein binding|ATP binding|magnesium ion binding|protein serine/threonine kinase activity			central_nervous_system(3)|ovary(2)|upper_aerodigestive_tract(1)	6																		---	---	---	---
SRPK2	6733	broad.mit.edu	37	7	104917532	104917532	+	Intron	DEL	T	-	-	rs35129084		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:104917532delT	uc003vcv.2	-						SRPK2_uc003vcu.2_Intron|SRPK2_uc003vcw.1_Intron	NM_182692	NP_872634			serine/arginine-rich protein-specific kinase 2						angiogenesis|cell differentiation|intracellular protein kinase cascade|negative regulation of viral genome replication|nuclear speck organization|positive regulation of cell cycle|positive regulation of cell proliferation|positive regulation of gene expression|positive regulation of neuron apoptosis|positive regulation of viral genome replication|spliceosome assembly	cytoplasm|nucleolus	14-3-3 protein binding|ATP binding|magnesium ion binding|protein serine/threonine kinase activity			central_nervous_system(3)|ovary(2)|upper_aerodigestive_tract(1)	6																		---	---	---	---
SRPK2	6733	broad.mit.edu	37	7	104997803	104997804	+	Intron	INS	-	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:104997803_104997804insA	uc003vcv.2	-						SRPK2_uc003vcw.1_Intron	NM_182692	NP_872634			serine/arginine-rich protein-specific kinase 2						angiogenesis|cell differentiation|intracellular protein kinase cascade|negative regulation of viral genome replication|nuclear speck organization|positive regulation of cell cycle|positive regulation of cell proliferation|positive regulation of gene expression|positive regulation of neuron apoptosis|positive regulation of viral genome replication|spliceosome assembly	cytoplasm|nucleolus	14-3-3 protein binding|ATP binding|magnesium ion binding|protein serine/threonine kinase activity			central_nervous_system(3)|ovary(2)|upper_aerodigestive_tract(1)	6																		---	---	---	---
PUS7	54517	broad.mit.edu	37	7	105132780	105132780	+	Intron	DEL	T	-	-	rs77485064		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:105132780delT	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																		---	---	---	---
RINT1	60561	broad.mit.edu	37	7	105203513	105203514	+	Intron	INS	-	A	A	rs149463590	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:105203513_105203514insA	uc003vda.1	+						RINT1_uc010ljj.1_Intron	NM_021930	NP_068749			RAD50 interactor 1						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																		---	---	---	---
ATXN7L1	222255	broad.mit.edu	37	7	105260777	105260777	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:105260777delA	uc003vde.2	-						ATXN7L1_uc003vdf.2_Intron|ATXN7L1_uc003vdg.3_Intron|ATXN7L1_uc003vdh.3_Intron|ATXN7L1_uc011klq.1_Intron	NM_020725	NP_065776			ataxin 7-like 1 isoform 1												0																		---	---	---	---
ATXN7L1	222255	broad.mit.edu	37	7	105285163	105285163	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:105285163delA	uc003vde.2	-						ATXN7L1_uc003vdf.2_Intron|ATXN7L1_uc003vdh.3_Intron|ATXN7L1_uc011klr.1_Intron	NM_020725	NP_065776			ataxin 7-like 1 isoform 1												0																		---	---	---	---
ATXN7L1	222255	broad.mit.edu	37	7	105516738	105516739	+	Intron	INS	-	CA	CA			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:105516738_105516739insCA	uc003vde.2	-						ATXN7L1_uc003vdi.2_Intron|CDHR3_uc003vdk.2_5'Flank|uc003vdj.1_5'Flank	NM_020725	NP_065776			ataxin 7-like 1 isoform 1												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	7	105698662	105698662	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:105698662delA								CDHR3 (21786 upstream) : SYPL1 (32291 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	106590211	106590211	+	IGR	DEL	T	-	-	rs79370463		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:106590211delT								PIK3CG (42626 upstream) : PRKAR2B (94967 downstream)																																			---	---	---	---
PRKAR2B	5577	broad.mit.edu	37	7	106692240	106692240	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:106692240delA	uc003vdx.2	+							NM_002736	NP_002727			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|G2/M transition of mitotic cell cycle|intracellular signal transduction|nerve growth factor receptor signaling pathway|regulation of insulin secretion|transmembrane transport|water transport	centrosome|cytosol|plasma membrane	cAMP binding|cAMP-dependent protein kinase regulator activity			ovary(1)	1																		---	---	---	---
PRKAR2B	5577	broad.mit.edu	37	7	106779520	106779520	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:106779520delT	uc003vdx.2	+							NM_002736	NP_002727			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|G2/M transition of mitotic cell cycle|intracellular signal transduction|nerve growth factor receptor signaling pathway|regulation of insulin secretion|transmembrane transport|water transport	centrosome|cytosol|plasma membrane	cAMP binding|cAMP-dependent protein kinase regulator activity			ovary(1)	1																		---	---	---	---
COG5	10466	broad.mit.edu	37	7	106870272	106870273	+	Intron	INS	-	T	T	rs142759073	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:106870272_106870273insT	uc003ved.2	-						COG5_uc003vec.2_Intron|COG5_uc003vee.2_Intron	NM_181733	NP_859422			component of oligomeric golgi complex 5 isoform						intra-Golgi vesicle-mediated transport|protein transport	cytosol|Golgi membrane|Golgi transport complex|nucleus	protein binding			central_nervous_system(2)|skin(2)	4																		---	---	---	---
COG5	10466	broad.mit.edu	37	7	106951370	106951371	+	Intron	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:106951370_106951371delAA	uc003ved.2	-						COG5_uc003vec.2_Intron|COG5_uc003vee.2_Intron	NM_181733	NP_859422			component of oligomeric golgi complex 5 isoform						intra-Golgi vesicle-mediated transport|protein transport	cytosol|Golgi membrane|Golgi transport complex|nucleus	protein binding			central_nervous_system(2)|skin(2)	4																		---	---	---	---
COG5	10466	broad.mit.edu	37	7	106969654	106969654	+	Intron	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:106969654delC	uc003ved.2	-						COG5_uc003vec.2_Intron|COG5_uc003vee.2_Intron	NM_181733	NP_859422			component of oligomeric golgi complex 5 isoform						intra-Golgi vesicle-mediated transport|protein transport	cytosol|Golgi membrane|Golgi transport complex|nucleus	protein binding			central_nervous_system(2)|skin(2)	4																		---	---	---	---
SLC26A4	5172	broad.mit.edu	37	7	107329832	107329832	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:107329832delT	uc003vep.2	+						SLC26A4_uc011kmb.1_5'Flank|SLC26A4_uc011kmc.1_5'Flank	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				---	---	---	---
SLC26A3	1811	broad.mit.edu	37	7	107418806	107418812	+	Intron	DEL	TTTTTTT	-	-	rs67365475		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:107418806_107418812delTTTTTTT	uc003ver.2	-						SLC26A3_uc003ves.2_Intron	NM_000111	NP_000102			solute carrier family 26, member 3						excretion	integral to membrane|membrane fraction	inorganic anion exchanger activity|secondary active sulfate transmembrane transporter activity|sequence-specific DNA binding transcription factor activity|transcription cofactor activity			ovary(3)|skin(1)	4																		---	---	---	---
LAMB1	3912	broad.mit.edu	37	7	107568669	107568669	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:107568669delA	uc003vew.2	-						LAMB1_uc003vev.2_Intron|LAMB1_uc003veu.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)													---	---	---	---
LAMB4	22798	broad.mit.edu	37	7	107698419	107698419	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:107698419delA	uc010ljo.1	-						LAMB4_uc003vey.2_Intron|LAMB4_uc010ljp.1_Intron	NM_007356	NP_031382			laminin, beta 4 precursor						cell adhesion	basement membrane				ovary(4)|breast(2)|large_intestine(1)|skin(1)	8																		---	---	---	---
PNPLA8	50640	broad.mit.edu	37	7	108138578	108138578	+	Intron	DEL	A	-	-	rs72406388		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:108138578delA	uc003vff.1	-						PNPLA8_uc003vfg.1_Intron|PNPLA8_uc003vfh.1_Intron|PNPLA8_uc003vfi.1_Intron|PNPLA8_uc003vfj.1_Intron|PNPLA8_uc003vfk.1_Intron	NM_015723	NP_056538			patatin-like phospholipase domain containing 8						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																		---	---	---	---
Unknown	0	broad.mit.edu	37	7	108266175	108266175	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:108266175delA								DNAJB9 (50883 upstream) : C7orf66 (257865 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	109187681	109187681	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:109187681delT								C7orf66 (663044 upstream) : EIF3IP1 (411603 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	109880179	109880180	+	IGR	INS	-	AA	AA	rs35850403		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:109880179_109880180insAA								EIF3IP1 (279909 upstream) : IMMP2L (422930 downstream)																																			---	---	---	---
IMMP2L	83943	broad.mit.edu	37	7	110334699	110334700	+	Intron	DEL	GA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:110334699_110334700delGA	uc003vfq.1	-						IMMP2L_uc010ljr.1_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	110543833	110543834	+	Intron	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:110543833_110543834delTT	uc003vfq.1	-						IMMP2L_uc010ljr.1_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)														---	---	---	---
LRRN3	54674	broad.mit.edu	37	7	110753443	110753445	+	Intron	DEL	TTT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:110753443_110753445delTTT	uc003vft.3	+						IMMP2L_uc003vfq.1_Intron|IMMP2L_uc010ljr.1_Intron|IMMP2L_uc003vfr.2_Intron|LRRN3_uc003vfu.3_Intron|LRRN3_uc003vfs.3_Intron	NM_001099660	NP_001093130			leucine rich repeat neuronal 3 precursor							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)														---	---	---	---
IMMP2L	83943	broad.mit.edu	37	7	111108385	111108385	+	Intron	DEL	A	-	-	rs34481882		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:111108385delA	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)														---	---	---	---
Unknown	0	broad.mit.edu	37	7	111251772	111251773	+	IGR	DEL	TT	-	-	rs77718776		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:111251772_111251773delTT								IMMP2L (49234 upstream) : DOCK4 (114392 downstream)																																			---	---	---	---
DOCK4	9732	broad.mit.edu	37	7	111396814	111396814	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:111396814delA	uc003vfx.2	-						DOCK4_uc011kml.1_Intron|DOCK4_uc011kmm.1_Intron|DOCK4_uc003vfw.2_Intron|DOCK4_uc003vfy.2_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)																---	---	---	---
DOCK4	9732	broad.mit.edu	37	7	111534278	111534278	+	Intron	DEL	A	-	-	rs67303129		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:111534278delA	uc003vfx.2	-						DOCK4_uc003vfy.2_Intron|DOCK4_uc003vga.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)																---	---	---	---
ZNF277	11179	broad.mit.edu	37	7	111856342	111856342	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:111856342delT	uc003vge.2	+						ZNF277_uc003vgd.2_Intron|ZNF277_uc003vgf.2_Intron|ZNF277_uc003vgc.2_Intron	NM_021994	NP_068834			zinc finger protein (C2H2 type) 277							nucleus	DNA binding|protein binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(2)|breast(2)	4																		---	---	---	---
ZNF277	11179	broad.mit.edu	37	7	111953338	111953340	+	Intron	DEL	TTT	-	-	rs71836432		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:111953338_111953340delTTT	uc003vge.2	+						ZNF277_uc003vgd.2_Intron|ZNF277_uc003vgf.2_Intron|ZNF277_uc003vgg.2_Intron	NM_021994	NP_068834			zinc finger protein (C2H2 type) 277							nucleus	DNA binding|protein binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(2)|breast(2)	4																		---	---	---	---
Unknown	0	broad.mit.edu	37	7	112028252	112028252	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:112028252delT								ZNF277 (44263 upstream) : IFRD1 (34974 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	112268575	112268575	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:112268575delT								C7orf53 (137640 upstream) : TMEM168 (137214 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	112613300	112613302	+	IGR	DEL	GAA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:112613300_112613302delGAA								C7orf60 (33368 upstream) : GPR85 (107166 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	113473701	113473701	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:113473701delA								LOC401397 (715064 upstream) : PPP1R3A (43181 downstream)																																			---	---	---	---
FOXP2	93986	broad.mit.edu	37	7	114039164	114039170	+	Intron	DEL	TTTTTCT	-	-	rs66789053		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:114039164_114039170delTTTTTCT	uc003vgv.1	+						FOXP2_uc003vgu.2_Intron|FOXP2_uc003vgt.1_Intron	NM_014491	NP_055306			forkhead box P2 isoform I						camera-type eye development|caudate nucleus development|cerebellum development|cerebral cortex development|embryo development|growth|lung alveolus development|negative regulation of transcription, DNA-dependent|pattern specification process|positive regulation of epithelial cell proliferation involved in lung morphogenesis|positive regulation of mesenchymal cell proliferation|post-embryonic development|putamen development|regulation of sequence-specific DNA binding transcription factor activity|righting reflex|skeletal muscle tissue development|smooth muscle tissue development|vocal learning	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(4)|pancreas(1)|lung(1)|breast(1)|skin(1)	8																		---	---	---	---
Unknown	0	broad.mit.edu	37	7	115899372	115899373	+	IGR	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:115899372_115899373delTT								TES (537 upstream) : CAV2 (28754 downstream)																																			---	---	---	---
CAV1	857	broad.mit.edu	37	7	116198944	116198944	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:116198944delT	uc003vif.1	+						CAV1_uc010lkd.1_Intron|CAV1_uc010lke.1_Intron|CAV1_uc003vig.1_Intron|CAV1_uc003vih.2_Intron|CAV1_uc010lkf.1_Intron	NM_001753	NP_001744			caveolin 1						blood coagulation|calcium ion transport|caveola assembly|cellular response to starvation|cholesterol homeostasis|cytosolic calcium ion homeostasis|inactivation of MAPK activity|interspecies interaction between organisms|leukocyte migration|lipid storage|maintenance of protein location in cell|mammary gland involution|membrane depolarization|negative regulation of BMP signaling pathway|negative regulation of canonical Wnt receptor signaling pathway|negative regulation of endothelial cell proliferation|negative regulation of epithelial cell differentiation|negative regulation of nitric oxide biosynthetic process|negative regulation of peptidyl-serine phosphorylation|negative regulation of protein binding|negative regulation of transcription from RNA polymerase II promoter|nitric oxide homeostasis|nitric oxide metabolic process|positive regulation of calcium ion transport into cytosol|positive regulation of canonical Wnt receptor signaling pathway|positive regulation of metalloenzyme activity|positive regulation of peptidyl-serine phosphorylation|positive regulation of vasoconstriction|protein homooligomerization|receptor internalization|regulation of blood coagulation|regulation of fatty acid metabolic process|regulation of nitric-oxide synthase activity|regulation of smooth muscle contraction|response to calcium ion|response to estrogen stimulus|response to hypoxia|response to progesterone stimulus|skeletal muscle tissue development|T cell costimulation|triglyceride metabolic process|vasculogenesis|vesicle organization	apical plasma membrane|basolateral plasma membrane|caveola|caveola|cytosol|endoplasmic reticulum|endosome|Golgi membrane|lipid particle|perinuclear region of cytoplasm	cholesterol binding|nitric-oxide synthase binding|peptidase activator activity|protein binding|protein complex scaffold|receptor binding				0	all_epithelial(6;1.42e-06)|Lung NSC(10;0.0056)|all_lung(10;0.00609)		STAD - Stomach adenocarcinoma(10;0.00878)															---	---	---	---
MET	4233	broad.mit.edu	37	7	116374279	116374279	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:116374279delT	uc003vij.2	+						MET_uc010lkh.2_Intron|MET_uc011knc.1_Intron|MET_uc011knd.1_Intron|MET_uc011kne.1_Intron|MET_uc011knf.1_Intron|MET_uc011kng.1_Intron|MET_uc011knh.1_Intron|MET_uc011kni.1_Intron|MET_uc011knj.1_Intron|MET_uc011kna.1_Intron|MET_uc011knb.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)				---	---	---	---
ST7	7982	broad.mit.edu	37	7	116668388	116668388	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:116668388delT	uc003vin.2	+						ST7_uc011knl.1_Intron|ST7_uc003vio.2_Intron|ST7_uc003viq.2_Intron|ST7_uc011knm.1_Intron|ST7_uc003vir.2_Intron	NM_021908	NP_068708			suppression of tumorigenicity 7 isoform b							integral to membrane	binding			central_nervous_system(1)|skin(1)	2	all_cancers(3;3.88e-07)|all_epithelial(6;3.42e-07)|Lung NSC(10;0.00072)|all_lung(10;0.000847)		STAD - Stomach adenocarcinoma(10;0.000512)	LUSC - Lung squamous cell carcinoma(290;0.133)														---	---	---	---
ST7	7982	broad.mit.edu	37	7	116778444	116778445	+	Intron	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:116778444_116778445delTT	uc003vin.2	+						ST7_uc011knl.1_Intron|ST7_uc003vio.2_Intron|ST7_uc003viq.2_Intron|ST7_uc011knm.1_Intron|ST7_uc003vir.2_Intron|ST7OT2_uc003viu.2_Intron|ST7_uc011knn.1_Intron|ST7OT2_uc003viw.2_Intron|ST7_uc003vix.1_Intron	NM_021908	NP_068708			suppression of tumorigenicity 7 isoform b							integral to membrane	binding			central_nervous_system(1)|skin(1)	2	all_cancers(3;3.88e-07)|all_epithelial(6;3.42e-07)|Lung NSC(10;0.00072)|all_lung(10;0.000847)		STAD - Stomach adenocarcinoma(10;0.000512)	LUSC - Lung squamous cell carcinoma(290;0.133)														---	---	---	---
CTTNBP2	83992	broad.mit.edu	37	7	117376495	117376496	+	Intron	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:117376495_117376496delAA	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	117703410	117703410	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:117703410delT								CTTNBP2 (189849 upstream) : NAA38 (120676 downstream)																																			---	---	---	---
ANKRD7	56311	broad.mit.edu	37	7	117875954	117875954	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:117875954delT	uc003vji.2	+							NM_019644	NP_062618			ankyrin repeat domain 7						male gonad development						0																		---	---	---	---
Unknown	0	broad.mit.edu	37	7	117938689	117938690	+	IGR	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:117938689_117938690delAA								ANKRD7 (55907 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	118184965	118184965	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:118184965delA								ANKRD7 (302183 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	118629360	118629360	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:118629360delT								ANKRD7 (746578 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	118791615	118791615	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:118791615delA								ANKRD7 (908833 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	119472435	119472435	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:119472435delT								None (None upstream) : KCND2 (441287 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	121261841	121261841	+	IGR	DEL	T	-	-	rs35197822		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:121261841delT								FAM3C (225419 upstream) : PTPRZ1 (251318 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	121424702	121424703	+	IGR	DEL	TG	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:121424702_121424703delTG								FAM3C (388280 upstream) : PTPRZ1 (88456 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	121441282	121441282	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:121441282delT								FAM3C (404860 upstream) : PTPRZ1 (71877 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	121466000	121466000	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:121466000delA								FAM3C (429578 upstream) : PTPRZ1 (47159 downstream)																																			---	---	---	---
PTPRZ1	5803	broad.mit.edu	37	7	121560032	121560032	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:121560032delA	uc003vjy.2	+						PTPRZ1_uc003vjz.2_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																		---	---	---	---
CADPS2	93664	broad.mit.edu	37	7	121994053	121994053	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:121994053delT	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	122025627	122025628	+	Intron	DEL	AA	-	-	rs76821426		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:122025627_122025628delAA	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	122067197	122067198	+	Intron	DEL	TT	-	-	rs61097528		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:122067197_122067198delTT	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	122177227	122177227	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:122177227delA	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																		---	---	---	---
IQUB	154865	broad.mit.edu	37	7	123109214	123109214	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:123109214delT	uc003vkn.2	-						IQUB_uc003vko.2_Intron|IQUB_uc010lkt.2_Intron|IQUB_uc003vkp.1_Intron	NM_178827	NP_849149			IQ motif and ubiquitin domain containing											ovary(3)|large_intestine(1)	4																		---	---	---	---
ASB15	142685	broad.mit.edu	37	7	123268248	123268249	+	Intron	DEL	CT	-	-	rs144088439		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:123268248_123268249delCT	uc003vku.1	+						ASB15_uc003vkw.1_Intron	NM_080928	NP_563616			ankyrin repeat and SOCS box-containing 15						intracellular signal transduction					skin(2)|lung(1)	3																		---	---	---	---
LMOD2	442721	broad.mit.edu	37	7	123296664	123296664	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:123296664delT	uc003vky.2	+							NM_207163	NP_997046			leiomodin 2 (cardiac)							cytoskeleton	actin binding|tropomyosin binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	7	123408897	123408897	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:123408897delT								WASL (19781 upstream) : HYALP1 (45296 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	123423761	123423761	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:123423761delA								WASL (34645 upstream) : HYALP1 (30432 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	123744089	123744089	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:123744089delT	uc011koc.1	+											Homo sapiens disrupted in Rett 1 mRNA sequence.																														---	---	---	---
Unknown	0	broad.mit.edu	37	7	124194953	124194953	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:124194953delA								TMEM229A (521430 upstream) : GPR37 (191163 downstream)																																			---	---	---	---
POT1	25913	broad.mit.edu	37	7	124514788	124514789	+	Intron	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:124514788_124514789delAA	uc003vlm.2	-						POT1_uc011koe.1_Intron|POT1_uc003vlk.2_Intron|POT1_uc003vll.2_Intron|POT1_uc003vlo.2_Intron|POT1_uc003vln.2_Intron	NM_015450	NP_056265			protection of telomeres 1 isoform 1						DNA duplex unwinding|negative regulation of telomere maintenance via telomerase|positive regulation of DNA strand elongation|positive regulation of helicase activity|positive regulation of telomerase activity|positive regulation of telomere maintenance via telomerase|telomere capping|telomere formation via telomerase|telomere maintenance via telomerase	nuclear telomere cap complex|nucleoplasm	DEAD/H-box RNA helicase binding|single-stranded telomeric DNA binding|telomerase inhibitor activity			central_nervous_system(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	7	124608445	124608445	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:124608445delA	uc010lkx.1	+						uc003vlp.2_Intron|uc003vlq.1_Intron					Homo sapiens cDNA FLJ33356 fis, clone BRACE2005160.																														---	---	---	---
Unknown	0	broad.mit.edu	37	7	124684721	124684722	+	Intron	DEL	AC	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:124684721_124684722delAC	uc010lkx.1	+						uc003vlp.2_Intron|uc003vlq.1_Intron					Homo sapiens cDNA FLJ33356 fis, clone BRACE2005160.																														---	---	---	---
Unknown	0	broad.mit.edu	37	7	125164590	125164591	+	IGR	DEL	GA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:125164590_125164591delGA								POT1 (594553 upstream) : GRM8 (914061 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	125712802	125712802	+	IGR	DEL	A	-	-	rs72389817		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:125712802delA								None (None upstream) : GRM8 (365850 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	125930409	125930410	+	IGR	DEL	CA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:125930409_125930410delCA								None (None upstream) : GRM8 (148242 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	126035333	126035334	+	IGR	DEL	AC	-	-	rs35832366		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:126035333_126035334delAC								None (None upstream) : GRM8 (43318 downstream)																																			---	---	---	---
GRM8	2918	broad.mit.edu	37	7	126405176	126405176	+	Intron	DEL	A	-	-	rs72242086		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:126405176delA	uc003vlr.2	-						GRM8_uc003vls.2_Intron|GRM8_uc011kof.1_Intron|GRM8_uc003vlt.2_Intron|GRM8_uc010lkz.1_Intron|GRM8_uc003vlu.1_Intron	NM_000845	NP_000836			glutamate receptor, metabotropic 8 isoform a						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)			---	---	---	---
GRM8	2918	broad.mit.edu	37	7	126537516	126537516	+	Intron	DEL	G	-	-	rs111865367	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:126537516delG	uc003vlr.2	-						GRM8_uc003vls.2_Intron|GRM8_uc011kof.1_Intron|GRM8_uc003vlt.2_Intron|GRM8_uc010lkz.1_Intron|GRM8_uc003vlu.1_Intron	NM_000845	NP_000836			glutamate receptor, metabotropic 8 isoform a						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)			---	---	---	---
GRM8	2918	broad.mit.edu	37	7	126662010	126662010	+	Intron	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:126662010delC	uc003vlr.2	-						GRM8_uc003vls.2_Intron|GRM8_uc011kof.1_Intron|GRM8_uc003vlt.2_Intron|GRM8_uc010lkz.1_Intron|GRM8_uc003vlu.1_Intron	NM_000845	NP_000836			glutamate receptor, metabotropic 8 isoform a						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)			---	---	---	---
GRM8	2918	broad.mit.edu	37	7	126749380	126749380	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:126749380delA	uc003vlr.2	-						GRM8_uc003vls.2_Intron|GRM8_uc011kof.1_Intron|GRM8_uc003vlt.2_Intron|GRM8_uc010lkz.1_Intron|GRM8_uc003vlu.1_Intron	NM_000845	NP_000836			glutamate receptor, metabotropic 8 isoform a						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)			---	---	---	---
GRM8	2918	broad.mit.edu	37	7	126763933	126763938	+	Intron	DEL	CCTTTC	-	-	rs142144949		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:126763933_126763938delCCTTTC	uc003vlr.2	-						GRM8_uc003vls.2_Intron|GRM8_uc011kof.1_Intron|GRM8_uc003vlt.2_Intron|GRM8_uc010lkz.1_Intron	NM_000845	NP_000836			glutamate receptor, metabotropic 8 isoform a						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)			---	---	---	---
GRM8	2918	broad.mit.edu	37	7	126871303	126871303	+	Intron	DEL	A	-	-	rs34629865		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:126871303delA	uc003vlr.2	-						GRM8_uc003vls.2_Intron|GRM8_uc011kof.1_Intron|GRM8_uc003vlt.2_Intron|GRM8_uc010lkz.1_Intron	NM_000845	NP_000836			glutamate receptor, metabotropic 8 isoform a						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)			---	---	---	---
Unknown	0	broad.mit.edu	37	7	127214375	127214375	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:127214375delT								ZNF800 (181608 upstream) : GCC1 (6308 downstream)																																			---	---	---	---
SND1	27044	broad.mit.edu	37	7	127334693	127334693	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:127334693delT	uc003vmi.2	+							NM_014390	NP_055205			staphylococcal nuclease domain containing 1						gene silencing by RNA|interspecies interaction between organisms|regulation of transcription, DNA-dependent|transcription, DNA-dependent	melanosome|nucleus|RNA-induced silencing complex	nuclease activity|nucleic acid binding|protein binding|transcription cofactor activity			ovary(2)|central_nervous_system(1)	3																		---	---	---	---
SND1	27044	broad.mit.edu	37	7	127357412	127357412	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:127357412delT	uc003vmi.2	+						SND1_uc010lle.2_5'Flank	NM_014390	NP_055205			staphylococcal nuclease domain containing 1						gene silencing by RNA|interspecies interaction between organisms|regulation of transcription, DNA-dependent|transcription, DNA-dependent	melanosome|nucleus|RNA-induced silencing complex	nuclease activity|nucleic acid binding|protein binding|transcription cofactor activity			ovary(2)|central_nervous_system(1)	3																		---	---	---	---
Unknown	0	broad.mit.edu	37	7	127870103	127870103	+	IGR	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:127870103delC								MIR129-1 (22107 upstream) : LEP (11228 downstream)																																			---	---	---	---
TNPO3	23534	broad.mit.edu	37	7	128632289	128632289	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:128632289delT	uc003vol.1	-						TNPO3_uc003vom.1_Intron|TNPO3_uc010lly.1_Intron|TNPO3_uc010llz.1_Intron	NM_012470	NP_036602			transportin 3						splicing factor protein import into nucleus	cytoplasm|nucleus	protein binding|receptor activity			ovary(2)|skin(2)|lung(1)	5																		---	---	---	---
FAM40B	57464	broad.mit.edu	37	7	129077277	129077277	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:129077277delA	uc011koy.1	+						FAM40B_uc003vow.2_Intron	NM_020704	NP_065755			hypothetical protein LOC57464 isoform a												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	7	129138712	129138713	+	IGR	INS	-	GA	GA			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:129138712_129138713insGA								FAM40B (10475 upstream) : NRF1 (112842 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	129150570	129150570	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:129150570delA	uc003voy.2	+											Homo sapiens full length insert cDNA clone ZA79C08.																														---	---	---	---
Unknown	0	broad.mit.edu	37	7	129637312	129637312	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:129637312delA								UBE2H (44523 upstream) : ZC3HC1 (20815 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	129970694	129970697	+	IGR	DEL	TTTT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:129970694_129970697delTTTT								CPA4 (6675 upstream) : CPA5 (13933 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	130378087	130378087	+	IGR	DEL	G	-	-	rs289431	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:130378087delG								TSGA13 (5819 upstream) : KLF14 (39391 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	130525845	130525850	+	IGR	DEL	TTTTTT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:130525845_130525850delTTTTTT								KLF14 (106985 upstream) : MIR29A (35656 downstream)																																			---	---	---	---
FLJ43663	378805	broad.mit.edu	37	7	130724867	130724867	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:130724867delA	uc011kpk.1	-						FLJ43663_uc003vqo.1_Intron|FLJ43663_uc003vqp.2_Intron|FLJ43663_uc003vqq.2_Intron	NR_024153				Homo sapiens cDNA FLJ43663 fis, clone SYNOV4005989.												0																		---	---	---	---
MKLN1	4289	broad.mit.edu	37	7	130947668	130947668	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:130947668delT	uc011kpl.1	+							NM_001145354	NP_001138826			muskelin 1, intracellular mediator containing						signal transduction	cytoplasm	protein binding			breast(1)	1	Melanoma(18;0.162)																	---	---	---	---
MKLN1	4289	broad.mit.edu	37	7	131095685	131095685	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:131095685delT	uc011kpm.1	+						MKLN1_uc011kpl.1_Intron|MKLN1_uc010lmh.2_Intron|MKLN1_uc003vqs.2_Intron	NM_013255	NP_037387			muskelin 1, intracellular mediator containing						signal transduction	cytoplasm	protein binding			breast(1)	1	Melanoma(18;0.162)																	---	---	---	---
Unknown	0	broad.mit.edu	37	7	131341807	131341809	+	IGR	DEL	TTT	-	-	rs71899143		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:131341807_131341809delTTT								PODXL (100431 upstream) : PLXNA4 (466283 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	131344303	131344304	+	IGR	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:131344303_131344304delTT								PODXL (102927 upstream) : PLXNA4 (463788 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	131524298	131524298	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:131524298delT								PODXL (282922 upstream) : PLXNA4 (283794 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	131602420	131602420	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:131602420delA								PODXL (361044 upstream) : PLXNA4 (205672 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	131618164	131618164	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:131618164delA								PODXL (376788 upstream) : PLXNA4 (189928 downstream)																																			---	---	---	---
PLXNA4	91584	broad.mit.edu	37	7	132011929	132011929	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:132011929delA	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	132052249	132052249	+	Intron	DEL	G	-	-	rs151291548	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:132052249delG	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	132060352	132060352	+	Intron	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:132060352delC	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	132137251	132137251	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:132137251delA	uc003vra.3	-						PLXNA4_uc003vrc.2_Intron	NM_020911	NP_065962			plexin A4 isoform 1							integral to membrane|intracellular|plasma membrane				ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	7	132410211	132410212	+	Intron	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:132410211_132410212delTT	uc003vrd.1	+											Homo sapiens cDNA FLJ40288 fis, clone TESTI2028098.																														---	---	---	---
CHCHD3	54927	broad.mit.edu	37	7	132719269	132719275	+	Intron	DEL	TTTTTTT	-	-	rs77416363		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:132719269_132719275delTTTTTTT	uc003vre.2	-						CHCHD3_uc010lmi.2_Intron|CHCHD3_uc003vrf.2_Intron|CHCHD3_uc010lmj.2_Intron|CHCHD3_uc011kpn.1_Intron	NM_017812	NP_060282			coiled-coil-helix-coiled-coil-helix domain						inner mitochondrial membrane organization|mitochondrial fusion	mitochondrial inner membrane	protein complex scaffold				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	7	132875485	132875487	+	IGR	DEL	AAA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:132875485_132875487delAAA								CHCHD3 (108657 upstream) : EXOC4 (62336 downstream)																																			---	---	---	---
EXOC4	60412	broad.mit.edu	37	7	133473253	133473253	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:133473253delT	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	134071200	134071200	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:134071200delA								SLC35B4 (69373 upstream) : AKR1B1 (55907 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	134290692	134290693	+	IGR	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:134290692_134290693delTT								AKR1B15 (26392 upstream) : BPGM (40838 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	134323564	134323564	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:134323564delT								AKR1B15 (59264 upstream) : BPGM (7967 downstream)																																			---	---	---	---
CALD1	800	broad.mit.edu	37	7	134557109	134557122	+	Intron	DEL	AAAAAAAAAAAAAA	-	-	rs35569742		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:134557109_134557122delAAAAAAAAAAAAAA	uc003vrz.2	+						CALD1_uc003vry.2_Intron|CALD1_uc003vsa.2_Intron|CALD1_uc003vsb.2_Intron|CALD1_uc010lmm.2_Intron|CALD1_uc011kpt.1_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																		---	---	---	---
AGBL3	340351	broad.mit.edu	37	7	134701791	134701791	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:134701791delT	uc011kpw.1	+							NM_178563	NP_848658			carboxypeptidase 3, cytosolic						proteolysis	cytosol	metallocarboxypeptidase activity|zinc ion binding				0																		---	---	---	---
AGBL3	340351	broad.mit.edu	37	7	134741870	134741871	+	Intron	INS	-	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:134741870_134741871insA	uc011kpw.1	+							NM_178563	NP_848658			carboxypeptidase 3, cytosolic						proteolysis	cytosol	metallocarboxypeptidase activity|zinc ion binding				0																		---	---	---	---
WDR91	29062	broad.mit.edu	37	7	134894606	134894606	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:134894606delA	uc003vsp.2	-						WDR91_uc010lmq.2_5'Flank|WDR91_uc010lmr.2_5'Flank	NM_014149	NP_054868			WD repeat domain 91											breast(2)|ovary(1)|skin(1)	4																		---	---	---	---
Unknown	0	broad.mit.edu	37	7	135016711	135016712	+	IGR	INS	-	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:135016711_135016712insA								STRA8 (73469 upstream) : CNOT4 (29841 downstream)																																			---	---	---	---
CNOT4	4850	broad.mit.edu	37	7	135134577	135134580	+	Intron	DEL	TTTT	-	-	rs35975371		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:135134577_135134580delTTTT	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	135262446	135262446	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:135262446delT	uc003vsw.2	+						NUP205_uc011kqa.1_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	135335604	135335605	+	IGR	DEL	GT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:135335604_135335605delGT								NUP205 (2115 upstream) : PL-5283 (11616 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	135467404	135467404	+	IGR	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:135467404delC								FAM180A (33810 upstream) : LUZP6 (144101 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	135695164	135695165	+	IGR	INS	-	ACAC	ACAC	rs143527129	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:135695164_135695165insACAC								LUZP6 (32960 upstream) : CHRM2 (858234 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	136250118	136250118	+	IGR	DEL	T	-	-	rs145484281		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:136250118delT								LUZP6 (587914 upstream) : CHRM2 (303281 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	136397207	136397207	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:136397207delT								LUZP6 (735003 upstream) : CHRM2 (156192 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	136426843	136426843	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:136426843delA								LUZP6 (764639 upstream) : CHRM2 (126556 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	136550249	136550250	+	IGR	INS	-	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:136550249_136550250insA								LUZP6 (888045 upstream) : CHRM2 (3149 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	136789180	136789181	+	Intron	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:136789180_136789181delTT	uc003vtp.1	-											Homo sapiens clone N1 NTera2D1 teratocarcinoma mRNA.																														---	---	---	---
PTN	5764	broad.mit.edu	37	7	136997826	136997827	+	Intron	INS	-	CT	CT	rs2060782		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:136997826_136997827insCT	uc003vtq.2	-						PTN_uc010lmx.2_Intron|PTN_uc003vtr.1_Intron	NM_002825	NP_002816			pleiotrophin						nervous system development|positive regulation of cell division|positive regulation of cell proliferation|transmembrane receptor protein tyrosine phosphatase signaling pathway	endoplasmic reticulum|extracellular space	growth factor activity|heparin binding|protein phosphatase inhibitor activity			upper_aerodigestive_tract(1)|pancreas(1)	2																		---	---	---	---
DGKI	9162	broad.mit.edu	37	7	137230229	137230230	+	Intron	DEL	AC	-	-	rs35616684		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:137230229_137230230delAC	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																		---	---	---	---
Unknown	0	broad.mit.edu	37	7	138103442	138103442	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:138103442delT								AKR1D1 (300392 upstream) : TRIM24 (41637 downstream)																																			---	---	---	---
TRIM24	8805	broad.mit.edu	37	7	138255390	138255390	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:138255390delT	uc003vuc.2	+						TRIM24_uc003vub.2_Intron	NM_015905	NP_056989			transcriptional intermediary factor 1 alpha						cellular response to estrogen stimulus|protein catabolic process|regulation of apoptosis|regulation of protein stability|transcription from RNA polymerase II promoter	cytoplasm	chromatin binding|estrogen response element binding|histone acetyl-lysine binding|p53 binding|transcription coactivator activity|ubiquitin-protein ligase activity|zinc ion binding			central_nervous_system(3)|ovary(2)|stomach(1)|breast(1)|skin(1)	8																		---	---	---	---
KIAA1549	57670	broad.mit.edu	37	7	138519718	138519720	+	3'UTR	DEL	AAA	-	-	rs66813823		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:138519718_138519720delAAA	uc011kqj.1	-	20					KIAA1549_uc011kqi.1_3'UTR|KIAA1549_uc003vuk.3_3'UTR	NM_020910	NP_065961			hypothetical protein LOC57670 isoform 1							integral to membrane			KIAA1549/BRAF(229)	central_nervous_system(229)|pancreas(1)	230								O	BRAF	pilocytic astrocytoma								---	---	---	---
ZC3HAV1L	92092	broad.mit.edu	37	7	138713748	138713749	+	Intron	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:138713748_138713749delTT	uc003vum.1	-							NM_080660	NP_542391			zinc finger CCCH-type, antiviral 1-like												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	7	138883938	138883938	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:138883938delT								TTC26 (9388 upstream) : UBN2 (32293 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	139195464	139195464	+	IGR	DEL	T	-	-	rs111854318		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:139195464delT								KLRG2 (27007 upstream) : CLEC2L (13210 downstream)																																			---	---	---	---
TBXAS1	6916	broad.mit.edu	37	7	139590698	139590698	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:139590698delT	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|TBXAS1_uc011kqx.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	139721982	139721983	+	IGR	INS	-	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:139721982_139721983insT								TBXAS1 (1859 upstream) : PARP12 (1566 downstream)																																			---	---	---	---
PARP12	64761	broad.mit.edu	37	7	139738671	139738671	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:139738671delA	uc003vvl.1	-						PARP12_uc003vvk.1_Intron|PARP12_uc010lnf.1_Intron	NM_022750	NP_073587			poly ADP-ribose polymerase 12							nucleus	NAD+ ADP-ribosyltransferase activity|nucleic acid binding|zinc ion binding			ovary(3)	3	Melanoma(164;0.0142)																	---	---	---	---
JHDM1D	80853	broad.mit.edu	37	7	139820179	139820179	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:139820179delA	uc003vvm.2	-						JHDM1D_uc010lng.2_5'Flank	NM_030647	NP_085150			jumonji C domain containing histone demethylase						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)																	---	---	---	---
Unknown	0	broad.mit.edu	37	7	140000664	140000664	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:140000664delT								LOC100134229 (121225 upstream) : SLC37A3 (32890 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	140031996	140031996	+	IGR	DEL	A	-	-	rs5887968		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:140031996delA								LOC100134229 (152557 upstream) : SLC37A3 (1558 downstream)																																			---	---	---	---
DENND2A	27147	broad.mit.edu	37	7	140218541	140218542	+	Intron	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:140218541_140218542delAA	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)																	---	---	---	---
BRAF	673	broad.mit.edu	37	7	140515110	140515110	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:140515110delT	uc003vwc.3	-							NM_004333	NP_004324			B-Raf						activation of MAPKK activity|anti-apoptosis|nerve growth factor receptor signaling pathway|organ morphogenesis|positive regulation of peptidyl-serine phosphorylation|small GTPase mediated signal transduction|synaptic transmission	cytosol|nucleus|plasma membrane	ATP binding|metal ion binding		KIAA1549/BRAF(229)|AKAP9_ENST00000356239/BRAF(10)|AGTRAP/BRAF(2)|FCHSD1/BRAF(2)|SLC45A3/BRAF(2)	thyroid(8166)|large_intestine(5052)|skin(3798)|NS(368)|central_nervous_system(284)|ovary(236)|lung(78)|eye(53)|prostate(44)|endometrium(30)|biliary_tract(28)|soft_tissue(27)|haematopoietic_and_lymphoid_tissue(22)|breast(18)|upper_aerodigestive_tract(13)|stomach(13)|pancreas(10)|small_intestine(10)|testis(7)|bone(6)|cervix(5)|genital_tract(4)|oesophagus(3)|urinary_tract(3)|adrenal_gland(3)|gastrointestinal_tract_(site_indeterminate)(2)|liver(2)|meninges(1)|kidney(1)|autonomic_ganglia(1)|pituitary(1)|salivary_gland(1)	18290	Melanoma(164;0.00956)				Sorafenib(DB00398)		61	Mis|T|O	AKAP9|KIAA1549	melanoma|colorectal|papillary thyroid|borderline ov|Non small-cell lung cancer (NSCLC)|cholangiocarcinoma|pilocytic astrocytoma		Cardio-facio-cutaneous syndrome		Cardiofaciocutaneous_syndrome				---	---	---	---
BRAF	673	broad.mit.edu	37	7	140538845	140538845	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:140538845delT	uc003vwc.3	-							NM_004333	NP_004324			B-Raf						activation of MAPKK activity|anti-apoptosis|nerve growth factor receptor signaling pathway|organ morphogenesis|positive regulation of peptidyl-serine phosphorylation|small GTPase mediated signal transduction|synaptic transmission	cytosol|nucleus|plasma membrane	ATP binding|metal ion binding		KIAA1549/BRAF(229)|AKAP9_ENST00000356239/BRAF(10)|AGTRAP/BRAF(2)|FCHSD1/BRAF(2)|SLC45A3/BRAF(2)	thyroid(8166)|large_intestine(5052)|skin(3798)|NS(368)|central_nervous_system(284)|ovary(236)|lung(78)|eye(53)|prostate(44)|endometrium(30)|biliary_tract(28)|soft_tissue(27)|haematopoietic_and_lymphoid_tissue(22)|breast(18)|upper_aerodigestive_tract(13)|stomach(13)|pancreas(10)|small_intestine(10)|testis(7)|bone(6)|cervix(5)|genital_tract(4)|oesophagus(3)|urinary_tract(3)|adrenal_gland(3)|gastrointestinal_tract_(site_indeterminate)(2)|liver(2)|meninges(1)|kidney(1)|autonomic_ganglia(1)|pituitary(1)|salivary_gland(1)	18290	Melanoma(164;0.00956)				Sorafenib(DB00398)		61	Mis|T|O	AKAP9|KIAA1549	melanoma|colorectal|papillary thyroid|borderline ov|Non small-cell lung cancer (NSCLC)|cholangiocarcinoma|pilocytic astrocytoma		Cardio-facio-cutaneous syndrome		Cardiofaciocutaneous_syndrome				---	---	---	---
Unknown	0	broad.mit.edu	37	7	140705527	140705530	+	IGR	DEL	CATC	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:140705527_140705530delCATC								BRAF (80963 upstream) : MRPS33 (432 downstream)																																			---	---	---	---
MRPS33	51650	broad.mit.edu	37	7	140707718	140707718	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:140707718delT	uc003vwd.3	-						MRPS33_uc003vwe.3_Intron	NM_016071	NP_057155			mitochondrial ribosomal protein S33						translation	mitochondrial small ribosomal subunit	structural constituent of ribosome				0	Melanoma(164;0.00956)																	---	---	---	---
Unknown	0	broad.mit.edu	37	7	140841085	140841085	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:140841085delT								MRPS33 (126304 upstream) : AGK (409993 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	140898974	140898974	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:140898974delA								MRPS33 (184193 upstream) : AGK (352104 downstream)																																			---	---	---	---
AGK	55750	broad.mit.edu	37	7	141253675	141253675	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:141253675delT	uc003vwi.2	+						AGK_uc011krg.1_Intron|AGK_uc003vwh.2_Intron	NM_018238	NP_060708			acylglycerol kinase precursor						activation of protein kinase C activity by G-protein coupled receptor protein signaling pathway	mitochondrial membrane	acylglycerol kinase activity|ATP binding|diacylglycerol kinase activity|NAD+ kinase activity			ovary(1)|breast(1)	2	Melanoma(164;0.0171)																	---	---	---	---
WEE2	494551	broad.mit.edu	37	7	141416003	141416003	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:141416003delT	uc003vwn.2	+						FLJ40852_uc011krh.1_Intron|FLJ40852_uc010lnm.2_Intron|FLJ40852_uc010lnn.2_Intron|FLJ40852_uc003vwm.3_Intron|FLJ40852_uc010lno.2_Intron	NM_001105558	NP_001099028			WEE1 homolog 2						egg activation|female meiosis|female pronucleus assembly|meiotic metaphase II|meiotic prophase I|mitosis|negative regulation of oocyte development|regulation of meiosis I	centrosome|nucleus	ATP binding|magnesium ion binding|non-membrane spanning protein tyrosine kinase activity|protein serine/threonine kinase activity			ovary(1)|stomach(1)	2	Melanoma(164;0.0171)																	---	---	---	---
Unknown	0	broad.mit.edu	37	7	141496173	141496173	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:141496173delA								TAS2R5 (5007 upstream) : PRSS37 (39913 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	141864638	141864638	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:141864638delT								LOC93432 (20863 upstream) : LOC100124692 (6332 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	143136758	143136758	+	Intron	DEL	C	-	-	rs35747219		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:143136758delC	uc003wda.2	+											Homo sapiens mRNA; cDNA DKFZp686O0656 (from clone DKFZp686O0656).																														---	---	---	---
Unknown	0	broad.mit.edu	37	7	143493856	143493856	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:143493856delA	uc011ktn.1	+						uc011kto.1_Intron|uc011ktp.1_Intron|LOC154761_uc011ktq.1_Intron|LOC154761_uc011ktr.1_Intron|LOC154761_uc011kts.1_Intron|LOC154761_uc003wdj.1_Intron	NM_001130026	NP_001123498			hypothetical protein LOC285966 isoform B																														---	---	---	---
Unknown	0	broad.mit.edu	37	7	143635163	143635163	+	IGR	DEL	T	-	-	rs112220155		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:143635163delT								OR2F2 (1885 upstream) : OR2F1 (20994 downstream)																																			---	---	---	---
TPK1	27010	broad.mit.edu	37	7	144271919	144271919	+	Intron	DEL	T	-	-	rs34081525		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:144271919delT	uc003weq.2	-						TPK1_uc003weo.2_Intron|TPK1_uc003wep.2_Intron|TPK1_uc003wer.2_Intron|TPK1_uc003wes.2_Intron	NM_022445	NP_071890			thiamin pyrophosphokinase 1 isoform a						thiamine diphosphate biosynthetic process	cytosol	ATP binding|kinase activity|thiamine diphosphokinase activity			ovary(2)	2					Thiamine(DB00152)													---	---	---	---
TPK1	27010	broad.mit.edu	37	7	144404174	144404174	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:144404174delA	uc003weq.2	-						TPK1_uc003weo.2_Intron|TPK1_uc003wep.2_Intron|TPK1_uc003wer.2_Intron|TPK1_uc003wes.2_Intron	NM_022445	NP_071890			thiamin pyrophosphokinase 1 isoform a						thiamine diphosphate biosynthetic process	cytosol	ATP binding|kinase activity|thiamine diphosphokinase activity			ovary(2)	2					Thiamine(DB00152)													---	---	---	---
TPK1	27010	broad.mit.edu	37	7	144447019	144447019	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:144447019delA	uc003weq.2	-						TPK1_uc003wer.2_Intron|TPK1_uc003wes.2_Intron	NM_022445	NP_071890			thiamin pyrophosphokinase 1 isoform a						thiamine diphosphate biosynthetic process	cytosol	ATP binding|kinase activity|thiamine diphosphokinase activity			ovary(2)	2					Thiamine(DB00152)													---	---	---	---
Unknown	0	broad.mit.edu	37	7	144793634	144793634	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:144793634delA								TPK1 (260488 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	145154419	145154422	+	IGR	DEL	AAAA	-	-	rs34081677		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:145154419_145154422delAAAA								TPK1 (621273 upstream) : CNTNAP2 (659031 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	145299839	145299839	+	IGR	DEL	G	-	-	rs145237295		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:145299839delG								TPK1 (766693 upstream) : CNTNAP2 (513614 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	145322770	145322771	+	IGR	INS	-	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:145322770_145322771insT								TPK1 (789624 upstream) : CNTNAP2 (490682 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	145544535	145544536	+	IGR	DEL	TG	-	-	rs77595842		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:145544535_145544536delTG								None (None upstream) : CNTNAP2 (268917 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	145596181	145596182	+	IGR	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:145596181_145596182delTT								None (None upstream) : CNTNAP2 (217271 downstream)																																			---	---	---	---
CNTNAP2	26047	broad.mit.edu	37	7	145938701	145938701	+	Intron	DEL	T	-	-	rs67513706		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:145938701delT	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	146141925	146141925	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:146141925delT	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	146516832	146516832	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:146516832delT	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	146558427	146558427	+	Intron	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:146558427delG	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	146879714	146879714	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:146879714delA	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	147643396	147643396	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:147643396delT	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	147926613	147926613	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:147926613delA	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	147950338	147950338	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:147950338delT	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	147951102	147951102	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:147951102delA	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	148112873	148112873	+	3'UTR	DEL	A	-	-	rs72270926		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:148112873delA	uc003weu.1	+	24					CNTNAP2_uc003wev.1_3'UTR	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)			---	---	---	---
Unknown	0	broad.mit.edu	37	7	148388260	148388261	+	IGR	DEL	TT	-	-	rs144894045		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:148388260_148388261delTT								C7orf33 (75309 upstream) : CUL1 (6745 downstream)																																			---	---	---	---
CUL1	8454	broad.mit.edu	37	7	148422314	148422315	+	Intron	DEL	CA	-	-	rs34702366	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:148422314_148422315delCA	uc010lpg.2	+						CUL1_uc003wey.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)															---	---	---	---
EZH2	2146	broad.mit.edu	37	7	148529563	148529563	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:148529563delA	uc003wfd.1	-						EZH2_uc011kug.1_Intron|EZH2_uc003wfb.1_Intron|EZH2_uc003wfc.1_Intron|EZH2_uc011kuh.1_Intron|EZH2_uc011kui.1_Intron|EZH2_uc011kuj.1_Intron	NM_004456	NP_004447			enhancer of zeste 2 isoform a						negative regulation of retinoic acid receptor signaling pathway|negative regulation of transcription, DNA-dependent|transcription, DNA-dependent	ESC/E(Z) complex	DNA binding|histone-lysine N-methyltransferase activity|protein binding			haematopoietic_and_lymphoid_tissue(180)|skin(2)|large_intestine(1)	183	Melanoma(164;0.15)		OV - Ovarian serous cystadenocarcinoma(82;0.00239)					Mis		DLBCL								---	---	---	---
Unknown	0	broad.mit.edu	37	7	148688810	148688810	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:148688810delA								MIR1975 (50156 upstream) : PDIA4 (11344 downstream)																																			---	---	---	---
ZNF282	8427	broad.mit.edu	37	7	148914656	148914656	+	Intron	DEL	A	-	-	rs74332781		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:148914656delA	uc003wfm.2	+						ZNF282_uc011kun.1_Intron|ZNF282_uc003wfo.2_Intron	NM_003575	NP_003566			zinc finger protein 282						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)														---	---	---	---
ZNF212	7988	broad.mit.edu	37	7	148948144	148948150	+	Intron	DEL	TTTTTTT	-	-	rs143562848		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:148948144_148948150delTTTTTTT	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	149839615	149839615	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:149839615delT								ATP6V0E2 (261829 upstream) : ACTR3C (104687 downstream)																																			---	---	---	---
ACTR3C	653857	broad.mit.edu	37	7	149953856	149953856	+	Intron	DEL	A	-	-	rs113978264		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:149953856delA	uc003wgu.1	-							NM_001040135	NP_001035225			actin-related protein 3-beta isoform 2						regulation of actin filament polymerization	cytoskeleton	actin binding|ATP binding				0																		---	---	---	---
GIMAP7	168537	broad.mit.edu	37	7	150216993	150216993	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:150216993delT	uc003whk.2	+							NM_153236	NP_694968			GTPase, IMAP family member 7								GTP binding			pancreas(1)|skin(1)	2			OV - Ovarian serous cystadenocarcinoma(82;0.0218)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)														---	---	---	---
LOC100128542	100128542	broad.mit.edu	37	7	150453070	150453070	+	Intron	DEL	T	-	-	rs79802427		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:150453070delT	uc011kuw.1	+							NM_001162367	NP_001155839			hypothetical protein LOC100128542												0																		---	---	---	---
LOC100128542	100128542	broad.mit.edu	37	7	150483099	150483100	+	Intron	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:150483099_150483100delAA	uc011kuw.1	+							NM_001162367	NP_001155839			hypothetical protein LOC100128542												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	7	150626469	150626469	+	IGR	DEL	A	-	-	rs67659133		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:150626469delA								ABP1 (68090 upstream) : KCNH2 (15581 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	151027560	151027560	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:151027560delA								SMARCD3 (53329 upstream) : NUB1 (11298 downstream)																																			---	---	---	---
PRKAG2	51422	broad.mit.edu	37	7	151263800	151263800	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:151263800delA	uc003wkk.2	-						PRKAG2_uc003wki.2_Intron|PRKAG2_uc011kvl.1_Intron|PRKAG2_uc003wkj.2_Intron|PRKAG2_uc003wkl.2_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	151329895	151329896	+	Intron	DEL	TT	-	-	rs113654522		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:151329895_151329896delTT	uc003wkk.2	-						PRKAG2_uc003wki.2_5'Flank|PRKAG2_uc011kvl.1_Intron|PRKAG2_uc003wkj.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	151372015	151372015	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:151372015delT	uc003wkk.2	-						PRKAG2_uc011kvl.1_Intron|PRKAG2_uc003wkj.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	151517900	151517900	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:151517900delT	uc003wkk.2	-						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)														---	---	---	---
GALNT11	63917	broad.mit.edu	37	7	151742757	151742757	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:151742757delT	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)														---	---	---	---
GALNT11	63917	broad.mit.edu	37	7	151756345	151756345	+	Intron	DEL	T	-	-	rs11340801		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:151756345delT	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)														---	---	---	---
Unknown	0	broad.mit.edu	37	7	151830826	151830829	+	IGR	DEL	TGTT	-	-	rs139450844		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:151830826_151830829delTGTT								GALNT11 (11399 upstream) : MLL3 (1183 downstream)																																			---	---	---	---
MLL3	58508	broad.mit.edu	37	7	151889637	151889638	+	Intron	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:151889637_151889638delAA	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	152026662	152026662	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:152026662delA	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								---	---	---	---
Unknown	0	broad.mit.edu	37	7	152335790	152335790	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:152335790delT								LOC100128822 (173162 upstream) : XRCC2 (7799 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	152381024	152381024	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:152381024delA								XRCC2 (7774 upstream) : ACTR3B (75827 downstream)																																			---	---	---	---
DPP6	1804	broad.mit.edu	37	7	154539365	154539366	+	Intron	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:154539365_154539366delAA	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)															---	---	---	---
DPP6	1804	broad.mit.edu	37	7	154555042	154555042	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:154555042delA	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)															---	---	---	---
DPP6	1804	broad.mit.edu	37	7	154645548	154645548	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:154645548delT	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-4200-01A-01D-1126-08	TCGA-BR-4200-11A-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	154800284	154800284	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:154800284delA								LOC202781 (2872 upstream) : HTR5A (62262 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	154849273	154849276	+	IGR	DEL	AAAC	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:154849273_154849276delAAAC								LOC202781 (51861 upstream) : HTR5A (13270 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	154883586	154883587	+	IGR	INS	-	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:154883586_154883587insA								HTR5A (6127 upstream) : INSIG1 (205899 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	154988168	154988169	+	IGR	INS	-	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:154988168_154988169insT								HTR5A (110709 upstream) : INSIG1 (101317 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	155082411	155082411	+	IGR	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:155082411delC								HTR5A (204952 upstream) : INSIG1 (7075 downstream)																																			---	---	---	---
RBM33	155435	broad.mit.edu	37	7	155473256	155473256	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:155473256delT	uc010lqk.1	+						RBM33_uc003wme.2_Intron	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	156334270	156334271	+	IGR	DEL	GT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:156334270_156334271delGT								C7orf4 (475 upstream) : C7orf13 (96791 downstream)																																			---	---	---	---
UBE3C	9690	broad.mit.edu	37	7	157046585	157046585	+	Intron	DEL	T	-	-	rs79641264		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:157046585delT	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)														---	---	---	---
Unknown	0	broad.mit.edu	37	7	157317027	157317027	+	IGR	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:157317027delC								DNAJB6 (106895 upstream) : PTPRN2 (14724 downstream)																																			---	---	---	---
PTPRN2	5799	broad.mit.edu	37	7	157620055	157620059	+	Intron	DEL	CACAA	-	-	rs72362151		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:157620055_157620059delCACAA	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	157917927	157917927	+	Intron	DEL	T	-	-	rs76194301		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:157917927delT	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	157924408	157924411	+	Intron	DEL	ACAC	-	-	rs144342358		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:157924408_157924411delACAC	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	158123999	158124003	+	Intron	DEL	ACCAT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:158123999_158124003delACCAT	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)														---	---	---	---
Unknown	0	broad.mit.edu	37	7	158510407	158510412	+	IGR	DEL	TCTTCC	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:158510407_158510412delTCTTCC								NCAPG2 (12887 upstream) : ESYT2 (13277 downstream)																																			---	---	---	---
ESYT2	57488	broad.mit.edu	37	7	158590014	158590014	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:158590014delT	uc003wob.1	-						ESYT2_uc003woc.1_Intron|ESYT2_uc003wod.1_Intron	NM_020728	NP_065779			family with sequence similarity 62 (C2 domain							integral to membrane|plasma membrane				central_nervous_system(2)|kidney(1)	3																		---	---	---	---
ESYT2	57488	broad.mit.edu	37	7	158603379	158603380	+	Intron	DEL	GA	-	-	rs142766987	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:158603379_158603380delGA	uc003wob.1	-						ESYT2_uc003woc.1_Intron|ESYT2_uc003wod.1_Intron	NM_020728	NP_065779			family with sequence similarity 62 (C2 domain							integral to membrane|plasma membrane				central_nervous_system(2)|kidney(1)	3																		---	---	---	---
VIPR2	7434	broad.mit.edu	37	7	158878408	158878409	+	Intron	DEL	TT	-	-	rs113222672		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:158878408_158878409delTT	uc003woh.2	-						VIPR2_uc010lqx.2_Intron|VIPR2_uc010lqy.2_Intron	NM_003382	NP_003373			vasoactive intestinal peptide receptor 2						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)														---	---	---	---
Unknown	0	broad.mit.edu	37	7	159024963	159024963	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:159024963delT								VIPR2 (87314 upstream) : None (None downstream)																																			---	---	---	---
RPL23AP53	644128	broad.mit.edu	37	8	176251	176251	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:176251delA	uc010lra.2	-						RPL23AP53_uc003woq.3_Intron|RPL23AP53_uc010lrb.2_Intron	NR_003572				Homo sapiens cDNA FLJ45055 fis, clone BRAWH3022900.												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	8	338371	338371	+	IGR	DEL	T	-	-	rs79886082		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:338371delT								ZNF596 (141039 upstream) : FBXO25 (18437 downstream)																																			---	---	---	---
FBXO25	26260	broad.mit.edu	37	8	363407	363407	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-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)														---	---	---	---
Unknown	0	broad.mit.edu	37	8	511289	511289	+	IGR	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:511289delC								C8orf42 (15958 upstream) : ERICH1 (53460 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	736808	736808	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:736808delT	uc003wpj.1	+											Homo sapiens cDNA clone IMAGE:4824304.																														---	---	---	---
Unknown	0	broad.mit.edu	37	8	1244552	1244552	+	IGR	DEL	C	-	-	rs11331161		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:1244552delC								ERICH1 (563326 upstream) : DLGAP2 (205017 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	1291377	1291377	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:1291377delA								ERICH1 (610151 upstream) : DLGAP2 (158192 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	1402522	1402523	+	IGR	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:1402522_1402523delTT								ERICH1 (721296 upstream) : DLGAP2 (47046 downstream)																																			---	---	---	---
DLGAP2	9228	broad.mit.edu	37	8	1478394	1478395	+	Intron	INS	-	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:1478394_1478395insG	uc003wpl.2	+							NM_004745	NP_004736			discs large-associated protein 2						neuron-neuron synaptic transmission	cell junction|neurofilament|postsynaptic density|postsynaptic membrane	protein binding				0		Ovarian(12;0.0271)|Hepatocellular(245;0.0838)|Colorectal(14;0.0846)		BRCA - Breast invasive adenocarcinoma(11;0.000169)|READ - Rectum adenocarcinoma(644;0.171)														---	---	---	---
DLGAP2	9228	broad.mit.edu	37	8	1492074	1492074	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:1492074delT	uc003wpl.2	+							NM_004745	NP_004736			discs large-associated protein 2						neuron-neuron synaptic transmission	cell junction|neurofilament|postsynaptic density|postsynaptic membrane	protein binding				0		Ovarian(12;0.0271)|Hepatocellular(245;0.0838)|Colorectal(14;0.0846)		BRCA - Breast invasive adenocarcinoma(11;0.000169)|READ - Rectum adenocarcinoma(644;0.171)														---	---	---	---
Unknown	0	broad.mit.edu	37	8	1684758	1684758	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:1684758delA								DLGAP2 (28118 upstream) : CLN8 (27112 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	1694924	1694924	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:1694924delA								DLGAP2 (38284 upstream) : CLN8 (16946 downstream)																																			---	---	---	---
ARHGEF10	9639	broad.mit.edu	37	8	1781752	1781752	+	Intron	DEL	C	-	-	rs145663936	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:1781752delC	uc003wpr.2	+						ARHGEF10_uc003wpq.1_Intron|ARHGEF10_uc003wps.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	1957413	1957413	+	IGR	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:1957413delG								KBTBD11 (2305 upstream) : MYOM2 (35745 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	2195494	2195495	+	IGR	INS	-	G	G	rs111274980		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:2195494_2195495insG								MYOM2 (102115 upstream) : CSMD1 (597381 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	2257777	2257777	+	IGR	DEL	C	-	-	rs67351628		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:2257777delC								MYOM2 (164398 upstream) : CSMD1 (535099 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	2280536	2280537	+	IGR	DEL	TG	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:2280536_2280537delTG								MYOM2 (187157 upstream) : CSMD1 (512339 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	2532747	2532747	+	IGR	DEL	A	-	-	rs72307847		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:2532747delA								MYOM2 (439368 upstream) : CSMD1 (260129 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	2630236	2630237	+	IGR	INS	-	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:2630236_2630237insA								MYOM2 (536857 upstream) : CSMD1 (162639 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	2770968	2770969	+	IGR	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:2770968_2770969delTT								MYOM2 (677589 upstream) : CSMD1 (21907 downstream)																																			---	---	---	---
CSMD1	64478	broad.mit.edu	37	8	2816070	2816070	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:2816070delT	uc011kwk.1	-						CSMD1_uc011kwj.1_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	3071688	3071689	+	Intron	DEL	GA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:3071688_3071689delGA	uc011kwk.1	-						CSMD1_uc011kwj.1_Intron|CSMD1_uc003wqe.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	3079844	3079845	+	Intron	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:3079844_3079845delTT	uc011kwk.1	-						CSMD1_uc011kwj.1_Intron|CSMD1_uc003wqe.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	3156975	3156975	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:3156975delA	uc011kwk.1	-						CSMD1_uc011kwj.1_Intron|CSMD1_uc003wqe.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	3180453	3180453	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:3180453delT	uc011kwk.1	-						CSMD1_uc011kwj.1_Intron|CSMD1_uc003wqe.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	3457649	3457650	+	Intron	DEL	AC	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:3457649_3457650delAC	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	3518908	3518908	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:3518908delT	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	3593936	3593937	+	Intron	DEL	AA	-	-	rs34615106		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:3593936_3593937delAA	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	3618484	3618484	+	Intron	DEL	T	-	-	rs72464949		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:3618484delT	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	3651724	3651724	+	Intron	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:3651724delG	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	3806414	3806414	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:3806414delT	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	3813081	3813081	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:3813081delT	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	3903385	3903385	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:3903385delT	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	4015612	4015614	+	Intron	DEL	TTT	-	-	rs140268259		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:4015612_4015614delTTT	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	4230016	4230017	+	Intron	INS	-	A	A	rs76147667	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:4230016_4230017insA	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	4253280	4253280	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:4253280delA	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	4285011	4285014	+	Intron	DEL	ACAC	-	-	rs112367601		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:4285011_4285014delACAC	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	4323927	4323927	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:4323927delA	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	4350666	4350666	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:4350666delT	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	4471236	4471236	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:4471236delA	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	4766055	4766056	+	Intron	INS	-	T	T	rs145887696	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:4766055_4766056insT	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	4791530	4791530	+	Intron	DEL	A	-	-	rs60553620	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:4791530delA	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	4829902	4829902	+	Intron	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:4829902delC	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	4848060	4848060	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:4848060delT	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	4876773	4876773	+	IGR	DEL	A	-	-	rs34169279		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:4876773delA								CSMD1 (24445 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	5118626	5118626	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:5118626delA								CSMD1 (266298 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	5204049	5204052	+	IGR	DEL	CACA	-	-	rs34340907		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:5204049_5204052delCACA								CSMD1 (351721 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	5332132	5332132	+	IGR	DEL	A	-	-	rs11346804		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:5332132delA								CSMD1 (479804 upstream) : MCPH1 (931989 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	5348618	5348618	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:5348618delT								CSMD1 (496290 upstream) : MCPH1 (915503 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	5348645	5348645	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:5348645delT								CSMD1 (496317 upstream) : MCPH1 (915476 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	5443914	5443914	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:5443914delA								CSMD1 (591586 upstream) : MCPH1 (820207 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	5594365	5594365	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:5594365delT								CSMD1 (742037 upstream) : MCPH1 (669756 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	5780831	5780831	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:5780831delA								CSMD1 (928503 upstream) : MCPH1 (483290 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	5913272	5913272	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:5913272delT								None (None upstream) : MCPH1 (350849 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	5924986	5924987	+	IGR	INS	-	CA	CA	rs35256079		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:5924986_5924987insCA								None (None upstream) : MCPH1 (339134 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	5960995	5960995	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:5960995delT								None (None upstream) : MCPH1 (303126 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	6006273	6006274	+	IGR	INS	-	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:6006273_6006274insA								None (None upstream) : MCPH1 (257847 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	6260752	6260753	+	IGR	INS	-	G	G	rs13276193	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:6260752_6260753insG								None (None upstream) : MCPH1 (3368 downstream)																																			---	---	---	---
MCPH1	79648	broad.mit.edu	37	8	6275042	6275042	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:6275042delT	uc003wqi.2	+						MCPH1_uc003wqh.2_Intron|MCPH1_uc011kwl.1_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	6468361	6468361	+	Intron	DEL	A	-	-	rs34105423		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:6468361delA	uc003wqi.2	+							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	6478733	6478733	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:6478733delT	uc003wqi.2	+						uc003wqm.2_RNA	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	6483312	6483312	+	Intron	DEL	A	-	-	rs80151198		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:6483312delA	uc003wqi.2	+						uc003wqm.2_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	6508622	6508623	+	5'Flank	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:6508622_6508623delTT	uc003wqm.2	-											full-length cDNA clone CS0DI013YC19 of Placenta Cot 25-normalized of Homo sapiens (human).																														---	---	---	---
AGPAT5	55326	broad.mit.edu	37	8	6605777	6605777	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:6605777delT	uc003wqo.2	+						AGPAT5_uc011kwm.1_Intron	NM_018361	NP_060831			1-acylglycerol-3-phosphate O-acyltransferase 5						phospholipid biosynthetic process	integral to membrane|mitochondrion	1-acylglycerol-3-phosphate O-acyltransferase activity				0			STAD - Stomach adenocarcinoma(24;0.0578)	READ - Rectum adenocarcinoma(644;0.156)|COAD - Colon adenocarcinoma(149;0.191)														---	---	---	---
Unknown	0	broad.mit.edu	37	8	6652930	6652930	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:6652930delT								AGPAT5 (33911 upstream) : XKR5 (13113 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	6665533	6665533	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:6665533delA								AGPAT5 (46514 upstream) : XKR5 (510 downstream)																																			---	---	---	---
XKR5	389610	broad.mit.edu	37	8	6673270	6673271	+	Intron	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:6673270_6673271delAA	uc003wqp.2	-						XKR5_uc003wqq.2_Intron|XKR5_uc003wqr.1_Intron	NM_207411	NP_997294			XK-related protein 5a							integral to membrane					0			STAD - Stomach adenocarcinoma(24;0.0984)	READ - Rectum adenocarcinoma(644;0.137)|COAD - Colon adenocarcinoma(149;0.166)												OREG0018511	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
Unknown	0	broad.mit.edu	37	8	7785295	7785295	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:7785295delA	uc010lro.1	+							NM_001039615	NP_001034704			zinc finger protein 705D																														---	---	---	---
Unknown	0	broad.mit.edu	37	8	8111605	8111606	+	IGR	INS	-	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:8111605_8111606insC								FLJ10661 (9219 upstream) : SGK223 (63653 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	8382948	8382948	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:8382948delT								SGK223 (143691 upstream) : CLDN23 (176718 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	8500844	8500844	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:8500844delA								SGK223 (261587 upstream) : CLDN23 (58822 downstream)																																			---	---	---	---
MFHAS1	9258	broad.mit.edu	37	8	8652241	8652241	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:8652241delT	uc003wsj.1	-							NM_004225	NP_004216			malignant fibrous histiocytoma amplified												0		Hepatocellular(245;0.217)		COAD - Colon adenocarcinoma(149;0.124)														---	---	---	---
MFHAS1	9258	broad.mit.edu	37	8	8683757	8683758	+	Intron	INS	-	GT	GT	rs138177121	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:8683757_8683758insGT	uc003wsj.1	-							NM_004225	NP_004216			malignant fibrous histiocytoma amplified												0		Hepatocellular(245;0.217)		COAD - Colon adenocarcinoma(149;0.124)														---	---	---	---
MFHAS1	9258	broad.mit.edu	37	8	8724519	8724519	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:8724519delA	uc003wsj.1	-							NM_004225	NP_004216			malignant fibrous histiocytoma amplified												0		Hepatocellular(245;0.217)		COAD - Colon adenocarcinoma(149;0.124)														---	---	---	---
Unknown	0	broad.mit.edu	37	8	9219856	9219856	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:9219856delA								PPP1R3B (210772 upstream) : TNKS (193589 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	9351625	9351626	+	IGR	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:9351625_9351626delTT								PPP1R3B (342541 upstream) : TNKS (61819 downstream)																																			---	---	---	---
TNKS	8658	broad.mit.edu	37	8	9592868	9592868	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:9592868delT	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)														---	---	---	---
TNKS	8658	broad.mit.edu	37	8	9631235	9631235	+	Intron	DEL	A	-	-	rs67728773		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:9631235delA	uc003wss.2	+						TNKS_uc011kww.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	9722437	9722437	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:9722437delT								TNKS (82582 upstream) : LOC157627 (35137 downstream)																																			---	---	---	---
LOC157627	157627	broad.mit.edu	37	8	9763121	9763121	+	5'Flank	DEL	A	-	-	rs58583211	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:9763121delA	uc003wsu.2	-						uc003wsw.1_5'Flank|MIR124-1_hsa-mir-124-1|MI0000443_5'Flank	NR_024281				Homo sapiens clone 23687 mRNA sequence.												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	8	9784375	9784375	+	IGR	DEL	C	-	-	rs10715748		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:9784375delC								MIR124-1 (23393 upstream) : MSRA (127455 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	9845296	9845296	+	IGR	DEL	T	-	-	rs111445632		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:9845296delT								MIR124-1 (84314 upstream) : MSRA (66534 downstream)																																			---	---	---	---
MSRA	4482	broad.mit.edu	37	8	9934430	9934430	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:9934430delA	uc003wsx.2	+						MSRA_uc011kwx.1_Intron	NM_012331	NP_036463			methionine sulfoxide reductase A isoform a						methionine metabolic process|protein modification process|response to oxidative stress	mitochondrion|nucleus	peptide-methionine-(S)-S-oxide reductase activity				0		Myeloproliferative disorder(644;0.178)			L-Methionine(DB00134)													---	---	---	---
MSRA	4482	broad.mit.edu	37	8	10149019	10149019	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:10149019delT	uc003wsx.2	+						MSRA_uc011kwx.1_Intron|MSRA_uc011kwy.1_Intron|MSRA_uc003wsz.2_Intron|MSRA_uc003wsy.2_Intron	NM_012331	NP_036463			methionine sulfoxide reductase A isoform a						methionine metabolic process|protein modification process|response to oxidative stress	mitochondrion|nucleus	peptide-methionine-(S)-S-oxide reductase activity				0		Myeloproliferative disorder(644;0.178)			L-Methionine(DB00134)													---	---	---	---
MSRA	4482	broad.mit.edu	37	8	10247275	10247275	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:10247275delT	uc003wsx.2	+						MSRA_uc011kwx.1_Intron|MSRA_uc003wsz.2_Intron|MSRA_uc003wsy.2_Intron	NM_012331	NP_036463			methionine sulfoxide reductase A isoform a						methionine metabolic process|protein modification process|response to oxidative stress	mitochondrion|nucleus	peptide-methionine-(S)-S-oxide reductase activity				0		Myeloproliferative disorder(644;0.178)			L-Methionine(DB00134)													---	---	---	---
Unknown	0	broad.mit.edu	37	8	10376138	10376138	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:10376138delA	uc010lru.2	-											Homo sapiens cDNA, FLJ97155.																														---	---	---	---
Unknown	0	broad.mit.edu	37	8	10576184	10576184	+	IGR	DEL	A	-	-	rs35635514		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:10576184delA								C8orf74 (18081 upstream) : SOX7 (5095 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	10702394	10702394	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:10702394delT								SOX7 (5095 upstream) : XKR6 (51263 downstream)																																			---	---	---	---
XKR6	286046	broad.mit.edu	37	8	10755310	10755310	+	3'UTR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:10755310delT	uc003wtk.1	-	3						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	10908082	10908083	+	Intron	DEL	AA	-	-	rs34111383		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:10908082_10908083delAA	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	11039363	11039363	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:11039363delT	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)														---	---	---	---
BLK	640	broad.mit.edu	37	8	11396585	11396585	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:11396585delT	uc003wty.2	+						BLK_uc003wtz.2_Intron	NM_001715	NP_001706			B lymphoid tyrosine kinase						intracellular protein kinase cascade|positive regulation of insulin secretion		ATP binding|non-membrane spanning protein tyrosine kinase activity			large_intestine(1)|stomach(1)|ovary(1)	3			STAD - Stomach adenocarcinoma(15;0.00391)	COAD - Colon adenocarcinoma(149;0.207)														---	---	---	---
GATA4	2626	broad.mit.edu	37	8	11560687	11560689	+	5'Flank	DEL	AAA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:11560687_11560689delAAA	uc003wuc.2	+						GATA4_uc011kxb.1_Intron|GATA4_uc003wub.1_Intron|GATA4_uc010lrz.1_5'Flank	NM_002052	NP_002043			GATA binding protein 4						atrial septum primum morphogenesis|atrial septum secundum morphogenesis|blood coagulation|cardiac right ventricle morphogenesis|cell-cell signaling|embryonic foregut morphogenesis|embryonic heart tube anterior/posterior pattern formation|endocardial cushion development|endoderm development|heart looping|intestinal epithelial cell differentiation|male gonad development|positive regulation of angiogenesis|positive regulation of cardioblast differentiation|positive regulation of transcription from RNA polymerase II promoter|positive regulation vascular endothelial growth factor production|response to drug|transcription from RNA polymerase II promoter|ventricular septum development	nucleoplasm	activating transcription factor binding|sequence-specific DNA binding|transcription regulatory region DNA binding|zinc ion binding			central_nervous_system(1)	1	all_epithelial(15;0.0839)		STAD - Stomach adenocarcinoma(15;0.00225)	COAD - Colon adenocarcinoma(149;0.199)														---	---	---	---
Unknown	0	broad.mit.edu	37	8	11620076	11620077	+	3'UTR	DEL	AG	-	-	rs144508804	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:11620076_11620077delAG	uc003wud.1	+	1										SubName: Full=C8orf49 protein; SubName: Full=Chromosome 8 open reading frame 49;																														---	---	---	---
CTSB	1508	broad.mit.edu	37	8	11714365	11714366	+	Intron	DEL	AA	-	-	rs145888542		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:11714365_11714366delAA	uc003wum.2	-						CTSB_uc011kxl.1_Intron|CTSB_uc003wun.2_Intron|CTSB_uc003wuo.2_Intron|CTSB_uc003wup.2_Intron|CTSB_uc003wuq.2_Intron|CTSB_uc010lsc.2_Intron|CTSB_uc003wur.2_Intron|CTSB_uc003wus.1_Intron|CTSB_uc003wut.1_Intron	NM_147780	NP_680090			cathepsin B preproprotein						proteolysis|regulation of apoptosis|regulation of catalytic activity	lysosome|melanosome	cysteine-type endopeptidase activity				0	all_epithelial(15;0.205)		STAD - Stomach adenocarcinoma(15;0.00546)	COAD - Colon adenocarcinoma(149;0.184)														---	---	---	---
Unknown	0	broad.mit.edu	37	8	11751597	11751597	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:11751597delT								CTSB (25951 upstream) : DEFB136 (79851 downstream)																																			---	---	---	---
DEFB135	613209	broad.mit.edu	37	8	11838574	11838574	+	5'Flank	DEL	A	-	-	rs12678157	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:11838574delA	uc003wuw.1	+							NM_001033017	NP_001028189			beta-defensin 135 precursor						defense response to bacterium	extracellular region					0																		---	---	---	---
DEFB134	613211	broad.mit.edu	37	8	11855801	11855801	+	5'Flank	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:11855801delA	uc011kxn.1	-							NM_001033019	NP_001028191			beta-defensin 134 precursor						defense response to bacterium	extracellular region					0			STAD - Stomach adenocarcinoma(15;0.033)	COAD - Colon adenocarcinoma(149;0.159)														---	---	---	---
FAM66D	100132923	broad.mit.edu	37	8	12359650	12359650	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:12359650delA	uc011kxp.1	+						uc003wvm.1_Intron|uc003wvv.2_Intron|uc003wvw.1_Intron|uc003wvx.1_Intron					Homo sapiens cDNA FLJ37098 fis, clone BRACE2019004.												0																		---	---	---	---
FAM66D	100132923	broad.mit.edu	37	8	12411529	12411530	+	Intron	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:12411529_12411530delAA	uc011kxp.1	+						uc003wvm.1_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	12516145	12516146	+	Intron	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:12516145_12516146delAA	uc003wvy.3	-						uc003wwc.3_Intron					Homo sapiens cDNA FLJ42906 fis, clone BRHIP3016213.																														---	---	---	---
C8orf79	57604	broad.mit.edu	37	8	12869786	12869787	+	Intron	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:12869786_12869787delAA	uc010lsq.2	+						C8orf79_uc011kxw.1_Intron|C8orf79_uc003wwj.3_5'UTR|C8orf79_uc010lsr.2_5'UTR	NM_020844	NP_065895			hypothetical protein LOC57604 isoform 1								methyltransferase activity				0																		---	---	---	---
DLC1	10395	broad.mit.edu	37	8	13093163	13093163	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:13093163delT	uc003wwm.2	-						DLC1_uc003wwl.1_Intron|DLC1_uc003wwn.2_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																		---	---	---	---
DLC1	10395	broad.mit.edu	37	8	13112209	13112209	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:13112209delA	uc003wwm.2	-						DLC1_uc003wwl.1_Intron|DLC1_uc003wwn.2_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																		---	---	---	---
DLC1	10395	broad.mit.edu	37	8	13268162	13268162	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:13268162delA	uc003wwm.2	-						DLC1_uc003wwn.2_Intron|DLC1_uc011kxy.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																		---	---	---	---
DLC1	10395	broad.mit.edu	37	8	13304452	13304453	+	Intron	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:13304452_13304453delAA	uc003wwm.2	-						DLC1_uc003wwn.2_Intron|DLC1_uc011kxy.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																		---	---	---	---
C8orf48	157773	broad.mit.edu	37	8	13425581	13425581	+	3'UTR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:13425581delT	uc003wwp.2	+	1						NM_001007090	NP_001007091			hypothetical protein LOC157773								protein binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	8	13781201	13781201	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:13781201delT								C8orf48 (355405 upstream) : SGCZ (166173 downstream)																																			---	---	---	---
SGCZ	137868	broad.mit.edu	37	8	14088275	14088276	+	Intron	INS	-	TG	TG	rs71209026		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:14088275_14088276insTG	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	14275244	14275244	+	Intron	DEL	C	-	-	rs57354962	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:14275244delC	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	14520505	14520506	+	Intron	INS	-	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:14520505_14520506insA	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)														---	---	---	---
SGCZ	137868	broad.mit.edu	37	8	14783374	14783374	+	Intron	DEL	A	-	-	rs11308398		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:14783374delA	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)														---	---	---	---
SGCZ	137868	broad.mit.edu	37	8	14812686	14812686	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:14812686delA	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)														---	---	---	---
SGCZ	137868	broad.mit.edu	37	8	14875020	14875020	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:14875020delT	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)														---	---	---	---
SGCZ	137868	broad.mit.edu	37	8	14914053	14914054	+	Intron	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:14914053_14914054delAA	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)														---	---	---	---
SGCZ	137868	broad.mit.edu	37	8	15055395	15055396	+	Intron	DEL	AC	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:15055395_15055396delAC	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	15114236	15114236	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:15114236delA								SGCZ (18444 upstream) : TUSC3 (283494 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	15143081	15143081	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:15143081delT								SGCZ (47289 upstream) : TUSC3 (254649 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	15179893	15179893	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:15179893delA								SGCZ (84101 upstream) : TUSC3 (217837 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	15269399	15269399	+	IGR	DEL	T	-	-	rs75014269		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:15269399delT								SGCZ (173607 upstream) : TUSC3 (128331 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	15310400	15310400	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:15310400delT								SGCZ (214608 upstream) : TUSC3 (87330 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	15342985	15342985	+	IGR	DEL	G	-	-	rs6530874	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:15342985delG								SGCZ (247193 upstream) : TUSC3 (54745 downstream)																																			---	---	---	---
TUSC3	7991	broad.mit.edu	37	8	15489771	15489771	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:15489771delT	uc003wwt.2	+						TUSC3_uc003wwr.2_Intron|TUSC3_uc003wws.2_Intron|TUSC3_uc003wwu.2_Intron|TUSC3_uc003wwv.2_Intron|TUSC3_uc003www.2_Intron|TUSC3_uc003wwx.2_Intron|TUSC3_uc003wwy.2_Intron	NM_006765	NP_006756			tumor suppressor candidate 3 isoform a						cell redox homeostasis|post-translational protein modification|protein N-linked glycosylation via asparagine	integral to membrane|oligosaccharyltransferase complex				ovary(2)|central_nervous_system(1)	3				Colorectal(111;0.113)														---	---	---	---
Unknown	0	broad.mit.edu	37	8	15676574	15676574	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:15676574delA								TUSC3 (54581 upstream) : MSR1 (288814 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	15684270	15684270	+	IGR	DEL	A	-	-	rs11357003		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:15684270delA								TUSC3 (62277 upstream) : MSR1 (281118 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	15707319	15707319	+	IGR	DEL	A	-	-	rs11300212		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:15707319delA								TUSC3 (85326 upstream) : MSR1 (258069 downstream)																																			---	---	---	---
MSR1	4481	broad.mit.edu	37	8	16001742	16001742	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:16001742delT	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	16161003	16161003	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:16161003delT								MSR1 (110703 upstream) : FGF20 (689331 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	16497257	16497259	+	IGR	DEL	TCT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:16497257_16497259delTCT								MSR1 (446957 upstream) : FGF20 (353075 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	16723482	16723482	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:16723482delA								MSR1 (673182 upstream) : FGF20 (126852 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	16745917	16745920	+	IGR	DEL	GTAA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:16745917_16745920delGTAA								MSR1 (695617 upstream) : FGF20 (104414 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	16797179	16797179	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:16797179delA								MSR1 (746879 upstream) : FGF20 (53155 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	16872697	16872697	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:16872697delT								FGF20 (13023 upstream) : EFHA2 (12050 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	16984375	16984375	+	IGR	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:16984375delG								EFHA2 (4227 upstream) : ZDHHC2 (29461 downstream)																																			---	---	---	---
CNOT7	29883	broad.mit.edu	37	8	17088377	17088377	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:17088377delA	uc003wxf.1	-						CNOT7_uc003wxg.1_Intron	NM_013354	NP_037486			CCR4-NOT transcription complex, subunit 7						carbohydrate metabolic process|nuclear-transcribed mRNA poly(A) tail shortening	CCR4-NOT complex|cytoplasmic mRNA processing body|cytosol	nucleic acid binding|protein binding|sequence-specific DNA binding transcription factor activity|signal transducer activity			central_nervous_system(1)	1				Colorectal(111;0.0523)|COAD - Colon adenocarcinoma(73;0.209)														---	---	---	---
VPS37A	137492	broad.mit.edu	37	8	17142557	17142557	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:17142557delA	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)														---	---	---	---
MTMR7	9108	broad.mit.edu	37	8	17200938	17200938	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:17200938delA	uc003wxm.2	-						MTMR7_uc003wxn.2_Intron	NM_004686	NP_004677			myotubularin related protein 7								protein tyrosine phosphatase activity			skin(1)	1				Colorectal(111;0.112)														---	---	---	---
MTMR7	9108	broad.mit.edu	37	8	17228370	17228371	+	Intron	INS	-	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:17228370_17228371insA	uc003wxm.2	-							NM_004686	NP_004677			myotubularin related protein 7								protein tyrosine phosphatase activity			skin(1)	1				Colorectal(111;0.112)														---	---	---	---
Unknown	0	broad.mit.edu	37	8	17305299	17305299	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:17305299delA								MTMR7 (34259 upstream) : SLC7A2 (49301 downstream)																																			---	---	---	---
SLC7A2	6542	broad.mit.edu	37	8	17392204	17392209	+	Intron	DEL	AAAAAA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:17392204_17392209delAAAAAA	uc011kyc.1	+							NM_001008539	NP_001008539			solute carrier family 7, member 2 isoform 2						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)													---	---	---	---
SLC7A2	6542	broad.mit.edu	37	8	17421309	17421309	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:17421309delT	uc011kyc.1	+						SLC7A2_uc011kyd.1_Intron|SLC7A2_uc011kye.1_Intron|SLC7A2_uc011kyf.1_Intron	NM_001008539	NP_001008539			solute carrier family 7, member 2 isoform 2						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)													---	---	---	---
PDGFRL	5157	broad.mit.edu	37	8	17458145	17458145	+	Intron	DEL	A	-	-	rs113265127		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:17458145delA	uc003wxr.2	+							NM_006207	NP_006198			platelet-derived growth factor receptor-like							extracellular region	platelet activating factor receptor activity|platelet-derived growth factor beta-receptor activity				0				Colorectal(111;0.0752)														---	---	---	---
MTUS1	57509	broad.mit.edu	37	8	17503022	17503022	+	3'UTR	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:17503022delC	uc003wxv.2	-	15					MTUS1_uc003wxt.2_3'UTR|MTUS1_uc011kyg.1_3'UTR|MTUS1_uc010lsy.2_RNA|MTUS1_uc003wxw.2_3'UTR|MTUS1_uc003wxs.2_3'UTR	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)														---	---	---	---
MTUS1	57509	broad.mit.edu	37	8	17549214	17549214	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:17549214delT	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)														---	---	---	---
MTUS1	57509	broad.mit.edu	37	8	17635656	17635656	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:17635656delT	uc003wxv.2	-						MTUS1_uc003wxw.2_Intron|MTUS1_uc010lsz.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)														---	---	---	---
MTUS1	57509	broad.mit.edu	37	8	17645631	17645631	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:17645631delA	uc003wxv.2	-						MTUS1_uc003wxw.2_Intron|MTUS1_uc010lsz.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)														---	---	---	---
MTUS1	57509	broad.mit.edu	37	8	17655848	17655848	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:17655848delT	uc003wxv.2	-						MTUS1_uc003wxw.2_Intron|MTUS1_uc010lsz.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	17843299	17843299	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:17843299delT	uc003wyi.3	+						PCM1_uc011kyh.1_Intron|PCM1_uc003wyj.3_Intron|PCM1_uc011kyi.1_Intron|PCM1_uc011kyj.1_Intron|PCM1_uc003wyk.3_Intron|PCM1_uc011kyk.1_Intron	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	17891350	17891350	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:17891350delA								PCM1 (3895 upstream) : ASAH1 (22575 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	17968930	17968930	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:17968930delT								ASAH1 (26423 upstream) : NAT1 (59041 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	18000179	18000179	+	IGR	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:18000179delG								ASAH1 (57672 upstream) : NAT1 (27792 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	18009924	18009924	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:18009924delA								ASAH1 (67417 upstream) : NAT1 (18047 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	18083044	18083045	+	IGR	INS	-	T	T	rs141082268	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:18083044_18083045insT								NAT1 (1847 upstream) : NAT2 (165710 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	18322388	18322388	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:18322388delT								NAT2 (63665 upstream) : PSD3 (62426 downstream)																																			---	---	---	---
PSD3	23362	broad.mit.edu	37	8	18432468	18432469	+	Intron	INS	-	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:18432468_18432469insT	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	18465730	18465730	+	Intron	DEL	A	-	-	rs112973048		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:18465730delA	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	18520297	18520298	+	Intron	INS	-	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:18520297_18520298insT	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	18632018	18632018	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:18632018delT	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	18893268	18893268	+	IGR	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:18893268delG								PSD3 (22072 upstream) : SH2D4A (277939 downstream)																																			---	---	---	---
CSGALNACT1	55790	broad.mit.edu	37	8	19406636	19406637	+	Intron	DEL	TT	-	-	rs11335504		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:19406636_19406637delTT	uc011kyn.1	-						CSGALNACT1_uc011kyo.1_Intron|CSGALNACT1_uc003wzg.2_Intron|CSGALNACT1_uc011kyp.1_Intron|CSGALNACT1_uc003wzh.2_Intron	NM_001130518	NP_001123990			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)														---	---	---	---
CSGALNACT1	55790	broad.mit.edu	37	8	19604770	19604770	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:19604770delA	uc011kyp.1	-							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	19647479	19647479	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:19647479delA								CSGALNACT1 (32097 upstream) : INTS10 (27439 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	19750739	19750739	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:19750739delA								INTS10 (41155 upstream) : LPL (45843 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	19761303	19761303	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:19761303delA								INTS10 (51719 upstream) : LPL (35279 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	19860231	19860231	+	IGR	DEL	T	-	-	rs112344872		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:19860231delT								LPL (35462 upstream) : SLC18A1 (142136 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	19910477	19910478	+	IGR	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:19910477_19910478delTT								LPL (85708 upstream) : SLC18A1 (91889 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	19999123	19999125	+	IGR	DEL	GAA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:19999123_19999125delGAA								LPL (174354 upstream) : SLC18A1 (3242 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	20173954	20173954	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:20173954delT								LZTS1 (61151 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	20415918	20415918	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:20415918delT								LZTS1 (303115 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	20563398	20563398	+	IGR	DEL	A	-	-	rs2597396	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:20563398delA								LZTS1 (450595 upstream) : GFRA2 (986132 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	20726119	20726119	+	IGR	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:20726119delC								LZTS1 (613316 upstream) : GFRA2 (823411 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	20957989	20957989	+	IGR	DEL	G	-	-	rs72002628		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:20957989delG								LZTS1 (845186 upstream) : GFRA2 (591541 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	21048314	21048314	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:21048314delT								LZTS1 (935511 upstream) : GFRA2 (501216 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	21053097	21053097	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:21053097delA								LZTS1 (940294 upstream) : GFRA2 (496433 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	21070050	21070050	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:21070050delA								LZTS1 (957247 upstream) : GFRA2 (479480 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	21091759	21091760	+	IGR	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:21091759_21091760delAA								LZTS1 (978956 upstream) : GFRA2 (457770 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	21145650	21145650	+	IGR	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:21145650delC								None (None upstream) : GFRA2 (403880 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	21173818	21173818	+	IGR	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:21173818delC								None (None upstream) : GFRA2 (375712 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	21224588	21224592	+	IGR	DEL	TTTTT	-	-	rs11362857		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:21224588_21224592delTTTTT								None (None upstream) : GFRA2 (324938 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	21334103	21334104	+	IGR	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:21334103_21334104delAA								None (None upstream) : GFRA2 (215426 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	21390714	21390715	+	IGR	INS	-	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:21390714_21390715insA								None (None upstream) : GFRA2 (158815 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	21528838	21528838	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:21528838delT								None (None upstream) : GFRA2 (20692 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	21531226	21531227	+	IGR	DEL	TC	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:21531226_21531227delTC								None (None upstream) : GFRA2 (18303 downstream)																																			---	---	---	---
GFRA2	2675	broad.mit.edu	37	8	21578508	21578508	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:21578508delA	uc003wzu.1	-						GFRA2_uc003wzv.1_Intron|GFRA2_uc003wzw.1_Intron|DOK2_uc003wzx.1_Intron	NM_001495	NP_001486			GDNF family receptor alpha 2 isoform a							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)														---	---	---	---
DOK2	9046	broad.mit.edu	37	8	21675949	21675949	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:21675949delA	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	21683965	21683965	+	Intron	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:21683965delC	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	21727974	21727974	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:21727974delA	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	21829688	21829689	+	Intron	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:21829688_21829689delTT	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)														---	---	---	---
Unknown	0	broad.mit.edu	37	8	21871754	21871755	+	IGR	DEL	AA	-	-	rs77996360		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:21871754_21871755delAA								XPO7 (7659 upstream) : NPM2 (9881 downstream)																																			---	---	---	---
EPB49	2039	broad.mit.edu	37	8	21910191	21910191	+	5'Flank	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:21910191delT	uc011kyt.1	+						EPB49_uc010ltl.2_5'Flank|EPB49_uc011kys.1_5'Flank|EPB49_uc010ltn.2_5'Flank	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)														---	---	---	---
Unknown	0	broad.mit.edu	37	8	22217821	22217821	+	IGR	DEL	G	-	-	rs4872477	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:22217821delG								PIWIL2 (4237 upstream) : SLC39A14 (6941 downstream)																																			---	---	---	---
SLC39A14	23516	broad.mit.edu	37	8	22232904	22232904	+	Intron	DEL	T	-	-	rs75573552		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:22232904delT	uc003xbq.3	+						SLC39A14_uc011kzg.1_Intron|SLC39A14_uc003xbp.3_Intron|SLC39A14_uc011kzh.1_Intron	NM_001128431	NP_001121903			solute carrier family 39 (zinc transporter),							endoplasmic reticulum|Golgi apparatus|integral to membrane|lamellipodium|plasma membrane	zinc ion transmembrane transporter activity				0				Colorectal(74;0.019)|COAD - Colon adenocarcinoma(73;0.0731)														---	---	---	---
PPP3CC	5533	broad.mit.edu	37	8	22327644	22327644	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:22327644delT	uc003xbs.2	+						PPP3CC_uc003xbr.1_Intron|PPP3CC_uc011kzi.1_Intron|PPP3CC_uc003xbt.2_Intron	NM_005605	NP_005596			protein phosphatase 3, catalytic subunit, gamma						activation of pro-apoptotic gene products|induction of apoptosis by intracellular signals	cytosol	calmodulin binding|metal ion binding|phosphoprotein phosphatase activity			ovary(1)	1		Prostate(55;0.104)		BRCA - Breast invasive adenocarcinoma(99;0.00756)|Colorectal(74;0.0238)|COAD - Colon adenocarcinoma(73;0.0835)														---	---	---	---
PPP3CC	5533	broad.mit.edu	37	8	22344246	22344247	+	Intron	DEL	TT	-	-	rs113567997		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:22344246_22344247delTT	uc003xbs.2	+						PPP3CC_uc003xbr.1_Intron|PPP3CC_uc011kzi.1_Intron|PPP3CC_uc003xbt.2_Intron	NM_005605	NP_005596			protein phosphatase 3, catalytic subunit, gamma						activation of pro-apoptotic gene products|induction of apoptosis by intracellular signals	cytosol	calmodulin binding|metal ion binding|phosphoprotein phosphatase activity			ovary(1)	1		Prostate(55;0.104)		BRCA - Breast invasive adenocarcinoma(99;0.00756)|Colorectal(74;0.0238)|COAD - Colon adenocarcinoma(73;0.0835)														---	---	---	---
PEBP4	157310	broad.mit.edu	37	8	22705543	22705544	+	Intron	DEL	CT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:22705543_22705544delCT	uc003xcn.1	-							NM_144962	NP_659399			phosphatidylethanolamine-binding protein 4							lysosome				ovary(1)|large_intestine(1)|breast(1)|skin(1)	4		Prostate(55;0.0453)|Breast(100;0.103)		Colorectal(74;0.0434)|COAD - Colon adenocarcinoma(73;0.124)														---	---	---	---
PEBP4	157310	broad.mit.edu	37	8	22719859	22719859	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:22719859delA	uc003xcn.1	-							NM_144962	NP_659399			phosphatidylethanolamine-binding protein 4							lysosome				ovary(1)|large_intestine(1)|breast(1)|skin(1)	4		Prostate(55;0.0453)|Breast(100;0.103)		Colorectal(74;0.0434)|COAD - Colon adenocarcinoma(73;0.124)														---	---	---	---
Unknown	0	broad.mit.edu	37	8	22789819	22789819	+	IGR	DEL	G	-	-	rs67777709		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:22789819delG								PEBP4 (4398 upstream) : RHOBTB2 (55111 downstream)																																			---	---	---	---
TNFRSF10B	8795	broad.mit.edu	37	8	22889426	22889427	+	Intron	DEL	TT	-	-	rs58469567		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:22889426_22889427delTT	uc003xcu.2	-						TNFRSF10B_uc003xct.2_Intron|TNFRSF10B_uc011kzq.1_Intron|TNFRSF10B_uc003xcv.2_Intron	NM_003842	NP_003833			tumor necrosis factor receptor superfamily,						activation of NF-kappaB-inducing kinase activity|activation of pro-apoptotic gene products|cell surface receptor linked signaling pathway|cellular response to mechanical stimulus|induction of apoptosis via death domain receptors|positive regulation of I-kappaB kinase/NF-kappaB cascade	plasma membrane	caspase activator activity|receptor activity|TRAIL binding				0		Prostate(55;0.0421)|Breast(100;0.067)		Colorectal(74;0.0179)|COAD - Colon adenocarcinoma(73;0.0703)														---	---	---	---
TNFRSF10B	8795	broad.mit.edu	37	8	22891325	22891325	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:22891325delA	uc003xcu.2	-						TNFRSF10B_uc003xct.2_Intron|TNFRSF10B_uc011kzq.1_Intron|TNFRSF10B_uc003xcv.2_Intron	NM_003842	NP_003833			tumor necrosis factor receptor superfamily,						activation of NF-kappaB-inducing kinase activity|activation of pro-apoptotic gene products|cell surface receptor linked signaling pathway|cellular response to mechanical stimulus|induction of apoptosis via death domain receptors|positive regulation of I-kappaB kinase/NF-kappaB cascade	plasma membrane	caspase activator activity|receptor activity|TRAIL binding				0		Prostate(55;0.0421)|Breast(100;0.067)		Colorectal(74;0.0179)|COAD - Colon adenocarcinoma(73;0.0703)														---	---	---	---
TNFRSF10B	8795	broad.mit.edu	37	8	22904871	22904873	+	Intron	DEL	AAA	-	-	rs111401661		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:22904871_22904873delAAA	uc003xcu.2	-						TNFRSF10B_uc003xct.2_Intron|TNFRSF10B_uc011kzq.1_Intron|TNFRSF10B_uc003xcv.2_Intron	NM_003842	NP_003833			tumor necrosis factor receptor superfamily,						activation of NF-kappaB-inducing kinase activity|activation of pro-apoptotic gene products|cell surface receptor linked signaling pathway|cellular response to mechanical stimulus|induction of apoptosis via death domain receptors|positive regulation of I-kappaB kinase/NF-kappaB cascade	plasma membrane	caspase activator activity|receptor activity|TRAIL binding				0		Prostate(55;0.0421)|Breast(100;0.067)		Colorectal(74;0.0179)|COAD - Colon adenocarcinoma(73;0.0703)														---	---	---	---
TNFRSF10B	8795	broad.mit.edu	37	8	22924959	22924959	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:22924959delA	uc003xcu.2	-						uc003xcw.1_5'Flank|TNFRSF10B_uc003xct.2_Intron|TNFRSF10B_uc011kzq.1_Intron|TNFRSF10B_uc003xcv.2_Intron	NM_003842	NP_003833			tumor necrosis factor receptor superfamily,						activation of NF-kappaB-inducing kinase activity|activation of pro-apoptotic gene products|cell surface receptor linked signaling pathway|cellular response to mechanical stimulus|induction of apoptosis via death domain receptors|positive regulation of I-kappaB kinase/NF-kappaB cascade	plasma membrane	caspase activator activity|receptor activity|TRAIL binding				0		Prostate(55;0.0421)|Breast(100;0.067)		Colorectal(74;0.0179)|COAD - Colon adenocarcinoma(73;0.0703)														---	---	---	---
Unknown	0	broad.mit.edu	37	8	22982507	22982507	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:22982507delT								TNFRSF10C (7559 upstream) : TNFRSF10D (10597 downstream)																																			---	---	---	---
ENTPD4	9583	broad.mit.edu	37	8	23292410	23292411	+	Intron	INS	-	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:23292410_23292411insT	uc003xdl.2	-						ENTPD4_uc011kzu.1_Intron|ENTPD4_uc003xdm.2_Intron|ENTPD4_uc011kzv.1_Intron	NM_004901	NP_004892			ectonucleoside triphosphate diphosphohydrolase 4						UDP catabolic process	autophagic vacuole membrane|cytoplasmic vesicle|integral to Golgi membrane	uridine-diphosphatase activity			ovary(1)|kidney(1)	2		Prostate(55;0.114)		Colorectal(74;0.0161)|COAD - Colon adenocarcinoma(73;0.0649)														---	---	---	---
Unknown	0	broad.mit.edu	37	8	23654546	23654546	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:23654546delT								NKX2-6 (90624 upstream) : STC1 (44888 downstream)																																			---	---	---	---
STC1	6781	broad.mit.edu	37	8	23711622	23711623	+	Intron	INS	-	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:23711622_23711623insC	uc003xdw.1	-							NM_003155	NP_003146			stanniocalcin 1 precursor						cell surface receptor linked signaling pathway|cell-cell signaling|cellular calcium ion homeostasis		hormone activity			skin(3)|upper_aerodigestive_tract(1)	4		Prostate(55;0.055)|Breast(100;0.116)		Colorectal(74;0.0155)|COAD - Colon adenocarcinoma(73;0.0632)														---	---	---	---
Unknown	0	broad.mit.edu	37	8	23716024	23716026	+	IGR	DEL	AAG	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:23716024_23716026delAAG								STC1 (3704 upstream) : ADAM28 (435554 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	23745389	23745390	+	IGR	DEL	TG	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:23745389_23745390delTG								STC1 (33069 upstream) : ADAM28 (406190 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	23770259	23770259	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:23770259delT								STC1 (57939 upstream) : ADAM28 (381321 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	23804497	23804497	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:23804497delA								STC1 (92177 upstream) : ADAM28 (347083 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	23821054	23821054	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:23821054delA								STC1 (108734 upstream) : ADAM28 (330526 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	23883795	23883796	+	IGR	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:23883795_23883796delAA								STC1 (171475 upstream) : ADAM28 (267784 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	24130247	24130247	+	IGR	DEL	T	-	-	rs72509143		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:24130247delT								STC1 (417927 upstream) : ADAM28 (21333 downstream)																																			---	---	---	---
ADAMDEC1	27299	broad.mit.edu	37	8	24257686	24257686	+	Frame_Shift_Del	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:24257686delA	uc003xdz.2	+	11	1235	c.1015delA	c.(1015-1017)AAAfs	p.K339fs	ADAMDEC1_uc010lub.2_Frame_Shift_Del_p.K260fs|ADAMDEC1_uc011lab.1_Frame_Shift_Del_p.K260fs	NM_014479	NP_055294	O15204	ADEC1_HUMAN	ADAM-like, decysin 1 isoform 1	339	Peptidase M12B.				integrin-mediated signaling pathway|negative regulation of cell adhesion|proteolysis	extracellular region|integral to membrane	integrin binding|metalloendopeptidase activity|zinc ion binding			skin(2)	2		Prostate(55;0.0181)		Colorectal(74;0.016)|COAD - Colon adenocarcinoma(73;0.0646)|BRCA - Breast invasive adenocarcinoma(99;0.168)														---	---	---	---
ADAM7	8756	broad.mit.edu	37	8	24300334	24300335	+	Intron	INS	-	T	T	rs147405626	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:24300334_24300335insT	uc003xeb.2	+						ADAM7_uc003xea.1_Intron	NM_003817	NP_003808			a disintegrin and metalloproteinase domain 7						proteolysis	integral to membrane	metalloendopeptidase activity|zinc ion binding			skin(3)|ovary(1)|kidney(1)	5		Prostate(55;0.0181)		Colorectal(74;0.0199)|COAD - Colon adenocarcinoma(73;0.0754)|BRCA - Breast invasive adenocarcinoma(99;0.182)														---	---	---	---
Unknown	0	broad.mit.edu	37	8	24524072	24524072	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:24524072delA								ADAM7 (139591 upstream) : NEFM (247202 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	24546695	24546696	+	IGR	DEL	TC	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:24546695_24546696delTC								ADAM7 (162214 upstream) : NEFM (224578 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	24676904	24676905	+	IGR	INS	-	AGAC	AGAC	rs146755992	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:24676904_24676905insAGAC								ADAM7 (292423 upstream) : NEFM (94369 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	24686782	24686782	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:24686782delT								ADAM7 (302301 upstream) : NEFM (84492 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	24806250	24806255	+	IGR	DEL	AAAAAA	-	-	rs72094798		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:24806250_24806255delAAAAAA								NEFM (29645 upstream) : NEFL (2216 downstream)																																			---	---	---	---
DOCK5	80005	broad.mit.edu	37	8	25050871	25050871	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:25050871delT	uc003xeg.2	+						DOCK5_uc010luf.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	25147360	25147360	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:25147360delA	uc003xeg.2	+						DOCK5_uc010luf.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	25185724	25185724	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:25185724delA	uc003xeg.2	+						DOCK5_uc010luf.1_Intron|DOCK5_uc003xeh.1_Intron|DOCK5_uc003xei.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	25545766	25545766	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:25545766delA	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)														---	---	---	---
PPP2R2A	5520	broad.mit.edu	37	8	25630964	25630964	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:25630964delA	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	25815918	25815918	+	Intron	DEL	T	-	-	rs72445411		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:25815918delT	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)														---	---	---	---
EBF2	64641	broad.mit.edu	37	8	25861634	25861635	+	Intron	DEL	AA	-	-	rs67122983		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:25861634_25861635delAA	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)														---	---	---	---
EBF2	64641	broad.mit.edu	37	8	25887427	25887427	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:25887427delT	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)														---	---	---	---
PPP2R2A	5520	broad.mit.edu	37	8	25902514	25902514	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:25902514delA	uc003xek.2	+						EBF2_uc003xes.1_5'Flank|EBF2_uc003xet.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)														---	---	---	---
PPP2R2A	5520	broad.mit.edu	37	8	25904950	25904950	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:25904950delT	uc003xek.2	+						EBF2_uc003xes.1_5'Flank|EBF2_uc003xet.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)														---	---	---	---
PPP2R2A	5520	broad.mit.edu	37	8	25951669	25951669	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:25951669delA	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)														---	---	---	---
PPP2R2A	5520	broad.mit.edu	37	8	26056182	26056184	+	Intron	DEL	TCT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:26056182_26056184delTCT	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)														---	---	---	---
BNIP3L	665	broad.mit.edu	37	8	26265015	26265015	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:26265015delT	uc003xex.1	+						BNIP3L_uc010luh.1_Intron|BNIP3L_uc010lui.1_Intron|BNIP3L_uc003xey.2_Intron	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)														---	---	---	---
DPYSL2	1808	broad.mit.edu	37	8	26406235	26406235	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:26406235delA	uc003xfa.2	+							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	26422415	26422415	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:26422415delT	uc003xfa.2	+							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	26438823	26438823	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:26438823delT	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	26499591	26499591	+	Intron	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:26499591delG	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	26516366	26516366	+	IGR	DEL	T	-	-	rs113316672		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:26516366delT								DPYSL2 (673 upstream) : ADRA1A (89301 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	26538330	26538335	+	IGR	DEL	CTTCCT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:26538330_26538335delCTTCCT								DPYSL2 (22637 upstream) : ADRA1A (67332 downstream)																																			---	---	---	---
ADRA1A	148	broad.mit.edu	37	8	26636774	26636774	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:26636774delT	uc003xfh.1	-						ADRA1A_uc003xfc.1_Intron|ADRA1A_uc010lul.1_Intron|ADRA1A_uc003xfd.1_Intron|ADRA1A_uc003xfe.1_Intron|ADRA1A_uc010lum.1_Intron|ADRA1A_uc003xff.1_Intron|ADRA1A_uc003xfg.1_Intron	NM_000680	NP_000671			alpha-1A-adrenergic receptor isoform 1						activation of phospholipase C activity|aging|apoptosis|calcium ion transport into cytosol|cell-cell signaling|intracellular protein kinase cascade|negative regulation of cell proliferation|negative regulation of Rho protein signal transduction|negative regulation of synaptic transmission, GABAergic|positive regulation of action potential|positive regulation of cardiac muscle contraction|positive regulation of ERK1 and ERK2 cascade|positive regulation of protein kinase C signaling cascade|positive regulation of vasoconstriction|response to drug|response to hormone stimulus|response to stress|smooth muscle contraction	integral to plasma membrane	alpha1-adrenergic receptor activity			breast(2)|ovary(1)|lung(1)|skin(1)	5		all_cancers(63;0.122)|Ovarian(32;2.61e-05)|all_epithelial(46;0.118)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0228)|Epithelial(17;4.92e-10)|Colorectal(74;0.0132)|READ - Rectum adenocarcinoma(644;0.115)	Alfuzosin(DB00346)|Amiodarone(DB01118)|Amphetamine(DB00182)|Benzphetamine(DB00865)|Bethanidine(DB00217)|Carvedilol(DB01136)|Dapiprazole(DB00298)|Debrisoquin(DB04840)|Dextroamphetamine(DB01576)|Doxazosin(DB00590)|Epinastine(DB00751)|Epinephrine(DB00668)|Ergotamine(DB00696)|Flupenthixol(DB00875)|Guanadrel Sulfate(DB00226)|Guanethidine(DB01170)|Labetalol(DB00598)|Lisdexamfetamine(DB01255)|Maprotiline(DB00934)|Mephentermine(DB01365)|Metaraminol(DB00610)|Methamphetamine(DB01577)|Methotrimeprazine(DB01403)|Methoxamine(DB00723)|Midodrine(DB00211)|Nefazodone(DB01149)|Nicergoline(DB00699)|Nilutamide(DB00665)|Norepinephrine(DB00368)|Norgestrel(DB00506)|Oxymetazoline(DB00935)|Perphenazine(DB00850)|Phendimetrazine(DB01579)|Phenoxybenzamine(DB00925)|Phenylephrine(DB00388)|Phenylpropanolamine(DB00397)|Prazosin(DB00457)|Promazine(DB00420)|Promethazine(DB01069)|Propericiazine(DB01608)|Propiomazine(DB00777)|Pseudoephedrine(DB00852)|Risperidone(DB00734)|Sertindole(DB06144)|Tamsulosin(DB00706)|Terazosin(DB01162)|Thioridazine(DB00679)|Tolazoline(DB00797)|Trazodone(DB00656)|Trifluoperazine(DB00831)|Ziprasidone(DB00246)													---	---	---	---
Unknown	0	broad.mit.edu	37	8	26764744	26764745	+	IGR	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:26764744_26764745delTT								ADRA1A (41822 upstream) : MIR548H-4 (141625 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	26814321	26814321	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:26814321delA								ADRA1A (91399 upstream) : MIR548H-4 (92049 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	26846001	26846001	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:26846001delA								ADRA1A (123079 upstream) : MIR548H-4 (60369 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	26864160	26864160	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:26864160delT								ADRA1A (141238 upstream) : MIR548H-4 (42210 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	26904584	26904584	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:26904584delA								ADRA1A (181662 upstream) : MIR548H-4 (1786 downstream)																																			---	---	---	---
PTK2B	2185	broad.mit.edu	37	8	27173150	27173150	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:27173150delT	uc003xfn.1	+						PTK2B_uc003xfo.1_Intron	NM_173174	NP_775266			PTK2B protein tyrosine kinase 2 beta isoform a						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)														---	---	---	---
Unknown	0	broad.mit.edu	37	8	27447737	27447737	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:27447737delA								EPHX2 (45253 upstream) : CLU (6714 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	27475554	27475554	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:27475554delT								CLU (3227 upstream) : SCARA3 (16023 downstream)																																			---	---	---	---
SCARA5	286133	broad.mit.edu	37	8	27734593	27734593	+	Intron	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:27734593delC	uc003xgj.2	-						SCARA5_uc010luz.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	27909451	27909451	+	Intron	DEL	C	-	-	rs13253013	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:27909451delC	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	28073406	28073406	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:28073406delT								ELP3 (24739 upstream) : PNOC (101243 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	28074061	28074061	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:28074061delT								ELP3 (25394 upstream) : PNOC (100588 downstream)																																			---	---	---	---
ZNF395	55893	broad.mit.edu	37	8	28259089	28259090	+	Intron	INS	-	GC	GC	rs141287627	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:28259089_28259090insGC	uc003xgt.2	-							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)														---	---	---	---
Unknown	0	broad.mit.edu	37	8	28436921	28436921	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:28436921delA								FZD3 (14962 upstream) : EXTL3 (122232 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	28620498	28620498	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:28620498delT								EXTL3 (9296 upstream) : INTS9 (4682 downstream)																																			---	---	---	---
HMBOX1	79618	broad.mit.edu	37	8	28777489	28777490	+	Intron	DEL	TG	-	-	rs148345782		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:28777489_28777490delTG	uc003xhd.3	+						HMBOX1_uc010lvd.2_Intron|HMBOX1_uc003xhc.3_Intron|HMBOX1_uc010lve.2_Intron|HMBOX1_uc003xhe.2_Intron	NM_001135726	NP_001129198			homeobox containing 1						negative regulation of transcription, DNA-dependent|positive regulation of transcription, DNA-dependent	cytoplasm|nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			ovary(1)	1		Ovarian(32;0.0192)		KIRC - Kidney renal clear cell carcinoma(542;0.135)|Kidney(114;0.161)														---	---	---	---
KIF13B	23303	broad.mit.edu	37	8	28928382	28928382	+	Intron	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:28928382delC	uc003xhh.3	-						KIF13B_uc011laz.1_Intron	NM_015254	NP_056069			kinesin family member 13B						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)														---	---	---	---
KIF13B	23303	broad.mit.edu	37	8	28956895	28956895	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:28956895delT	uc003xhh.3	-						KIF13B_uc011laz.1_5'Flank	NM_015254	NP_056069			kinesin family member 13B						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)														---	---	---	---
KIF13B	23303	broad.mit.edu	37	8	29005918	29005919	+	Intron	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:29005918_29005919delTT	uc003xhh.3	-						KIF13B_uc003xhj.2_Intron	NM_015254	NP_056069			kinesin family member 13B						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)														---	---	---	---
Unknown	0	broad.mit.edu	37	8	29302293	29302293	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:29302293delT								DUSP4 (94108 upstream) : C8orf75 (276485 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	29304716	29304716	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:29304716delT								DUSP4 (96531 upstream) : C8orf75 (274062 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	29708485	29708486	+	IGR	INS	-	TG	TG			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:29708485_29708486insTG								C8orf75 (102860 upstream) : LOC286135 (70543 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	29826884	29826885	+	IGR	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:29826884_29826885delTT								LOC286135 (15763 upstream) : TMEM66 (93747 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	29919008	29919008	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:29919008delT								LOC286135 (107887 upstream) : TMEM66 (1624 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	30092442	30092443	+	IGR	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:30092442_30092443delTT								DCTN6 (51383 upstream) : RBPMS (149501 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	30106987	30106988	+	IGR	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:30106987_30106988delAA								DCTN6 (65928 upstream) : RBPMS (134956 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	30166328	30166328	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:30166328delT								DCTN6 (125269 upstream) : RBPMS (75616 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	30231041	30231041	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:30231041delA								DCTN6 (189982 upstream) : RBPMS (10903 downstream)																																			---	---	---	---
GSR	2936	broad.mit.edu	37	8	30539225	30539225	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-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)													---	---	---	---
UBXN8	7993	broad.mit.edu	37	8	30600408	30600408	+	5'Flank	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:30600408delT	uc003xii.2	+						UBXN8_uc010lvi.2_5'Flank|UBXN8_uc011lbb.1_5'Flank	NM_005671	NP_005662			reproduction 8						single fertilization						0																		---	---	---	---
Unknown	0	broad.mit.edu	37	8	30786182	30786182	+	IGR	DEL	T	-	-	rs111459064		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:30786182delT								TEX15 (39960 upstream) : PURG (67139 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	30797497	30797497	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:30797497delA								TEX15 (51275 upstream) : PURG (55824 downstream)																																			---	---	---	---
WRN	7486	broad.mit.edu	37	8	30957063	30957063	+	Intron	DEL	T	-	-	rs114173587	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:30957063delT	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				---	---	---	---
WRN	7486	broad.mit.edu	37	8	30995619	30995619	+	Intron	DEL	A	-	-	rs79484796		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:30995619delA	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				---	---	---	---
Unknown	0	broad.mit.edu	37	8	31042075	31042076	+	IGR	DEL	GT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:31042075_31042076delGT								WRN (10799 upstream) : NRG1 (455192 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	31193451	31193452	+	IGR	INS	-	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:31193451_31193452insT								WRN (162175 upstream) : NRG1 (303816 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	31368588	31368588	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:31368588delT								WRN (337312 upstream) : NRG1 (128680 downstream)																																			---	---	---	---
NRG1	3084	broad.mit.edu	37	8	31826245	31826246	+	Intron	INS	-	T	T	rs138075202	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:31826245_31826246insT	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	32045264	32045264	+	Intron	DEL	A	-	-	rs79691535		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:32045264delA	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	32069504	32069504	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:32069504delT	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	32143392	32143392	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:32143392delA	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	32165378	32165379	+	Intron	DEL	TG	-	-	rs142575544		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:32165378_32165379delTG	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)														---	---	---	---
Unknown	0	broad.mit.edu	37	8	32725268	32725268	+	IGR	DEL	A	-	-	rs71910222		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:32725268delA								NRG1 (102710 upstream) : FUT10 (503078 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	32882592	32882592	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:32882592delT	uc003xjb.2	+											Homo sapiens cDNA clone IMAGE:4837650.																														---	---	---	---
Unknown	0	broad.mit.edu	37	8	33023117	33023117	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:33023117delA								NRG1 (400559 upstream) : FUT10 (205229 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	33169796	33169797	+	IGR	DEL	AG	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:33169796_33169797delAG								NRG1 (547238 upstream) : FUT10 (58549 downstream)																																			---	---	---	---
FUT10	84750	broad.mit.edu	37	8	33234750	33234750	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:33234750delA	uc003xje.2	-						FUT10_uc003xjc.2_Intron|FUT10_uc003xjd.2_Intron|FUT10_uc011lbi.1_Intron	NM_032664	NP_116053			fucosyltransferase 10						embryo development|fertilization|hemopoiesis|L-fucose catabolic process|nervous system development|protein folding|protein glycosylation|protein targeting|wound healing	Golgi cisterna membrane|integral to membrane	alpha(1,3)-fucosyltransferase activity			ovary(1)|pancreas(1)	2				KIRC - Kidney renal clear cell carcinoma(67;0.129)|Kidney(114;0.154)														---	---	---	---
FUT10	84750	broad.mit.edu	37	8	33308549	33308549	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:33308549delA	uc003xje.2	-						FUT10_uc003xjc.2_Intron|FUT10_uc003xjd.2_Intron|FUT10_uc011lbi.1_Intron|FUT10_uc003xjf.2_Intron|FUT10_uc003xjg.2_Intron|FUT10_uc003xjh.2_Intron	NM_032664	NP_116053			fucosyltransferase 10						embryo development|fertilization|hemopoiesis|L-fucose catabolic process|nervous system development|protein folding|protein glycosylation|protein targeting|wound healing	Golgi cisterna membrane|integral to membrane	alpha(1,3)-fucosyltransferase activity			ovary(1)|pancreas(1)	2				KIRC - Kidney renal clear cell carcinoma(67;0.129)|Kidney(114;0.154)														---	---	---	---
FUT10	84750	broad.mit.edu	37	8	33315781	33315781	+	Intron	DEL	A	-	-	rs11362213		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:33315781delA	uc003xje.2	-						FUT10_uc003xjc.2_5'Flank|FUT10_uc003xjd.2_Intron|FUT10_uc011lbi.1_Intron|FUT10_uc003xjf.2_Intron|FUT10_uc003xjg.2_Intron|FUT10_uc003xjh.2_Intron|FUT10_uc003xji.1_Intron	NM_032664	NP_116053			fucosyltransferase 10						embryo development|fertilization|hemopoiesis|L-fucose catabolic process|nervous system development|protein folding|protein glycosylation|protein targeting|wound healing	Golgi cisterna membrane|integral to membrane	alpha(1,3)-fucosyltransferase activity			ovary(1)|pancreas(1)	2				KIRC - Kidney renal clear cell carcinoma(67;0.129)|Kidney(114;0.154)														---	---	---	---
Unknown	0	broad.mit.edu	37	8	33430981	33430982	+	IGR	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:33430981_33430982delAA								RNF122 (6338 upstream) : DUSP26 (17874 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	33462535	33462535	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:33462535delT								DUSP26 (5096 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	33516778	33516781	+	IGR	DEL	TTTT	-	-	rs35851314		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:33516778_33516781delTTTT								DUSP26 (59339 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	33541639	33541639	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:33541639delA								DUSP26 (84200 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	33741498	33741498	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:33741498delA								DUSP26 (284059 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	33771747	33771748	+	IGR	INS	-	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:33771747_33771748insT								DUSP26 (314308 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	33869703	33869703	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:33869703delT								DUSP26 (412264 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	34013217	34013217	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:34013217delA								DUSP26 (555778 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	34057098	34057098	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:34057098delT								DUSP26 (599659 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	34274681	34274682	+	IGR	INS	-	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:34274681_34274682insT								DUSP26 (817242 upstream) : UNC5D (818293 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	34277321	34277321	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:34277321delT								DUSP26 (819882 upstream) : UNC5D (815654 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	34345539	34345539	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:34345539delT								DUSP26 (888100 upstream) : UNC5D (747436 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	34585302	34585303	+	IGR	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:34585302_34585303delTT								None (None upstream) : UNC5D (507672 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	34637529	34637531	+	IGR	DEL	CAA	-	-	rs34807123		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:34637529_34637531delCAA								None (None upstream) : UNC5D (455444 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	34732162	34732162	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:34732162delA								None (None upstream) : UNC5D (360813 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	34734598	34734598	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:34734598delT								None (None upstream) : UNC5D (358377 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	34854109	34854110	+	IGR	DEL	AA	-	-	rs34260461		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:34854109_34854110delAA								None (None upstream) : UNC5D (238865 downstream)																																			---	---	---	---
UNC5D	137970	broad.mit.edu	37	8	35102370	35102370	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:35102370delT	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)														---	---	---	---
UNC5D	137970	broad.mit.edu	37	8	35153943	35153943	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:35153943delT	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)														---	---	---	---
UNC5D	137970	broad.mit.edu	37	8	35380604	35380604	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:35380604delT	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)														---	---	---	---
UNC5D	137970	broad.mit.edu	37	8	35649347	35649347	+	3'UTR	DEL	T	-	-	rs77074972		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:35649347delT	uc003xjr.1	+	17					UNC5D_uc003xjs.1_3'UTR|UNC5D_uc003xju.1_3'UTR	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	35803885	35803885	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:35803885delT								UNC5D (151705 upstream) : KCNU1 (837957 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	35868964	35868964	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:35868964delA								UNC5D (216784 upstream) : KCNU1 (772878 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	36181846	36181847	+	IGR	DEL	GT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:36181846_36181847delGT								UNC5D (529666 upstream) : KCNU1 (459995 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	36186386	36186387	+	IGR	INS	-	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:36186386_36186387insT								UNC5D (534206 upstream) : KCNU1 (455455 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	36191661	36191661	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:36191661delT								UNC5D (539481 upstream) : KCNU1 (450181 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	36221514	36221515	+	IGR	DEL	AA	-	-	rs141641351		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:36221514_36221515delAA								UNC5D (569334 upstream) : KCNU1 (420327 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	36227090	36227090	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:36227090delT								UNC5D (574910 upstream) : KCNU1 (414752 downstream)																																			---	---	---	---
KCNU1	157855	broad.mit.edu	37	8	36760726	36760726	+	Intron	DEL	A	-	-	rs146364992		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:36760726delA	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)														---	---	---	---
KCNU1	157855	broad.mit.edu	37	8	36779849	36779849	+	Intron	DEL	A	-	-	rs68098747		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:36779849delA	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	36867869	36867869	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:36867869delT								KCNU1 (74228 upstream) : ZNF703 (685432 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	36875965	36875965	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:36875965delT								KCNU1 (82324 upstream) : ZNF703 (677336 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	37058188	37058188	+	IGR	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:37058188delG								KCNU1 (264547 upstream) : ZNF703 (495113 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	37090510	37090521	+	IGR	DEL	TCTCTCTCTCTC	-	-	rs66726423		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:37090510_37090521delTCTCTCTCTCTC								KCNU1 (296869 upstream) : ZNF703 (462780 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	37227530	37227530	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:37227530delT								KCNU1 (433889 upstream) : ZNF703 (325771 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	37421236	37421236	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:37421236delA								KCNU1 (627595 upstream) : ZNF703 (132065 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	37527480	37527480	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:37527480delA								KCNU1 (733839 upstream) : ZNF703 (25821 downstream)																																			---	---	---	---
GPR124	25960	broad.mit.edu	37	8	37686567	37686567	+	Intron	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:37686567delC	uc003xkj.2	+						GPR124_uc003xki.2_Intron|GPR124_uc010lvy.2_Intron	NM_032777	NP_116166			G protein-coupled receptor 124 precursor						central nervous system development|endothelial cell migration|neuropeptide signaling pathway|regulation of angiogenesis|regulation of chemotaxis|sprouting angiogenesis	integral to membrane|plasma membrane	G-protein coupled receptor activity			large_intestine(2)|ovary(2)|skin(1)	5			BRCA - Breast invasive adenocarcinoma(5;2.75e-24)|LUSC - Lung squamous cell carcinoma(8;3.5e-10)															---	---	---	---
GPR124	25960	broad.mit.edu	37	8	37686680	37686680	+	Intron	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:37686680delC	uc003xkj.2	+						GPR124_uc003xki.2_Intron|GPR124_uc010lvy.2_Intron	NM_032777	NP_116166			G protein-coupled receptor 124 precursor						central nervous system development|endothelial cell migration|neuropeptide signaling pathway|regulation of angiogenesis|regulation of chemotaxis|sprouting angiogenesis	integral to membrane|plasma membrane	G-protein coupled receptor activity			large_intestine(2)|ovary(2)|skin(1)	5			BRCA - Breast invasive adenocarcinoma(5;2.75e-24)|LUSC - Lung squamous cell carcinoma(8;3.5e-10)															---	---	---	---
Unknown	0	broad.mit.edu	37	8	37867127	37867128	+	IGR	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:37867127_37867128delTT								ADRB3 (42943 upstream) : EIF4EBP1 (20892 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	37920564	37920565	+	IGR	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:37920564_37920565delAA								EIF4EBP1 (2682 upstream) : ASH2L (42446 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	38018137	38018137	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:38018137delA								STAR (9537 upstream) : LSM1 (2724 downstream)																																			---	---	---	---
BAG4	9530	broad.mit.edu	37	8	38058829	38058829	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:38058829delT	uc003xky.1	+						BAG4_uc003xkz.1_Intron	NM_004874	NP_004865			BCL2-associated athanogene 4						anti-apoptosis|apoptosis|protein folding	cytoplasm|nucleus	receptor signaling protein activity			ovary(1)	1	Colorectal(12;0.000442)	all_lung(54;0.00787)|Lung NSC(58;0.0295)|Hepatocellular(245;0.121)																---	---	---	---
Unknown	0	broad.mit.edu	37	8	38078090	38078090	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:38078090delT								BAG4 (9553 upstream) : DDHD2 (10919 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	38082470	38082471	+	IGR	DEL	GT	-	-	rs113588753		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:38082470_38082471delGT								BAG4 (13933 upstream) : DDHD2 (6538 downstream)																																			---	---	---	---
DDHD2	23259	broad.mit.edu	37	8	38088428	38088428	+	5'Flank	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:38088428delA	uc003xlb.2	+						DDHD2_uc003xla.2_5'Flank|DDHD2_uc003xlc.2_5'Flank|DDHD2_uc011lbl.1_5'Flank	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)															---	---	---	---
WHSC1L1	54904	broad.mit.edu	37	8	38175280	38175280	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:38175280delA	uc003xli.2	-						WHSC1L1_uc011lbm.1_Intron|WHSC1L1_uc010lwe.2_Intron|WHSC1L1_uc003xlj.2_3'UTR	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								---	---	---	---
FGFR1	2260	broad.mit.edu	37	8	38291845	38291851	+	Intron	DEL	TGCTTTT	-	-	rs151115715	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:38291845_38291851delTGCTTTT	uc003xlp.2	-						FGFR1_uc011lbo.1_Intron|FGFR1_uc011lbp.1_Intron|FGFR1_uc011lbq.1_Intron|FGFR1_uc010lwk.2_Intron|FGFR1_uc011lbs.1_Intron|FGFR1_uc011lbt.1_Intron|FGFR1_uc011lbu.1_Intron|FGFR1_uc011lbv.1_Intron|FGFR1_uc011lbw.1_Intron|FGFR1_uc011lbx.1_Intron|FGFR1_uc003xlv.2_Intron|FGFR1_uc003xlu.2_Intron|FGFR1_uc003xlw.1_Intron	NM_023110	NP_075598			fibroblast growth factor receptor 1 isoform 1						axon guidance|cell growth|insulin receptor signaling pathway|MAPKKK cascade|positive regulation of cell proliferation|skeletal system development	extracellular region|integral to plasma membrane|membrane fraction	ATP binding|fibroblast growth factor receptor activity|heparin binding|protein homodimerization activity			lung(5)|central_nervous_system(5)|stomach(2)|breast(2)|ovary(1)	15	all_cancers(2;9.05e-47)|all_epithelial(2;2.64e-50)|all_lung(3;1.71e-23)|Lung NSC(2;3.61e-23)|Colorectal(12;0.000442)	Breast(189;1.48e-05)|all_lung(54;0.00354)|Lung NSC(58;0.0138)|Hepatocellular(245;0.065)	Epithelial(3;3.96e-34)|all cancers(3;3.06e-30)|BRCA - Breast invasive adenocarcinoma(5;2.28e-21)|COAD - Colon adenocarcinoma(9;0.24)		Palifermin(DB00039)		1	T	BCR|FOP|ZNF198|CEP1	MPD|NHL		Pfeiffer syndrome|Kallman syndrome						---	---	---	---
Unknown	0	broad.mit.edu	37	8	38456394	38456395	+	IGR	DEL	AC	-	-	rs71916195		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:38456394_38456395delAC								C8orf86 (70214 upstream) : RNF5P1 (1300 downstream)																																			---	---	---	---
TACC1	6867	broad.mit.edu	37	8	38596184	38596185	+	Intron	DEL	TT	-	-	rs112889333		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:38596184_38596185delTT	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)															---	---	---	---
TACC1	6867	broad.mit.edu	37	8	38606405	38606405	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:38606405delA	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)															---	---	---	---
TACC1	6867	broad.mit.edu	37	8	38640944	38640944	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:38640944delT	uc011lbz.1	+						TACC1_uc011lby.1_Intron|TACC1_uc003xma.2_Intron|TACC1_uc003xlz.2_Intron|TACC1_uc003xmc.3_Intron|TACC1_uc003xmb.3_Intron|TACC1_uc003xme.1_Intron|TACC1_uc003xmd.1_Intron|TACC1_uc010lwo.1_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)															---	---	---	---
TACC1	6867	broad.mit.edu	37	8	38678721	38678721	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:38678721delA	uc010lwp.2	+						TACC1_uc011lby.1_Intron|TACC1_uc003xma.2_Intron|TACC1_uc003xlz.2_Intron|TACC1_uc003xmc.3_Intron|TACC1_uc011lbz.1_Intron|TACC1_uc003xmb.3_Intron|TACC1_uc003xme.1_Intron|TACC1_uc003xmd.1_Intron|TACC1_uc010lwo.1_Intron|TACC1_uc003xmf.3_Intron|TACC1_uc011lca.1_Intron|TACC1_uc011lcb.1_Intron|TACC1_uc011lcc.1_Intron|TACC1_uc011lcd.1_Intron|TACC1_uc003xmh.3_Intron|TACC1_uc010lwq.2_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)															---	---	---	---
Unknown	0	broad.mit.edu	37	8	38749155	38749155	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:38749155delA								TACC1 (38610 upstream) : PLEKHA2 (9598 downstream)																																			---	---	---	---
ADAM9	8754	broad.mit.edu	37	8	38959364	38959364	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:38959364delT	uc003xmr.2	+						ADAM9_uc011lcf.1_Intron|ADAM9_uc011lcg.1_Intron|ADAM9_uc010lwr.2_Intron|ADAM9_uc003xms.2_Intron	NM_003816	NP_003807			ADAM metallopeptidase domain 9 isoform 1						activation of MAPKK activity|cell-cell adhesion mediated by integrin|cell-matrix adhesion|keratinocyte differentiation|monocyte activation|PMA-inducible membrane protein ectodomain proteolysis|PMA-inducible membrane protein ectodomain proteolysis|positive regulation of cell adhesion mediated by integrin|positive regulation of keratinocyte migration|positive regulation of macrophage fusion|positive regulation of membrane protein ectodomain proteolysis|positive regulation of protein secretion|response to calcium ion|response to glucocorticoid stimulus|response to hydrogen peroxide|response to manganese ion|response to tumor necrosis factor|transforming growth factor beta receptor signaling pathway	extracellular space|extracellular space|integral to membrane|intrinsic to external side of plasma membrane	collagen binding|integrin binding|laminin binding|metalloendopeptidase activity|protein kinase C binding|SH3 domain binding|zinc ion binding			ovary(1)|central_nervous_system(1)	2		all_lung(54;0.00292)|Lung NSC(58;0.0115)|Hepatocellular(245;0.0153)	LUSC - Lung squamous cell carcinoma(45;2.74e-07)															---	---	---	---
ADAM32	203102	broad.mit.edu	37	8	39110177	39110177	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:39110177delA	uc003xmt.3	+						ADAM32_uc011lch.1_Intron|ADAM32_uc003xmu.3_Intron|ADAM32_uc003xmv.2_Intron	NM_145004	NP_659441			a disintegrin and metalloprotease domain 32						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)															---	---	---	---
ADAM5P	255926	broad.mit.edu	37	8	39196327	39196327	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:39196327delA	uc003xmx.1	+						ADAM5P_uc003xmy.1_Intron|ADAM5P_uc003xmz.1_Intron|ADAM5P_uc010lwt.1_Intron|ADAM5P_uc003xna.2_Intron|ADAM5P_uc003xnb.2_Intron|ADAM5P_uc003xnc.2_Intron	NR_001448				Homo sapiens mRNA for tMDC II, isoform [a].												0																		---	---	---	---
ADAM5P	255926	broad.mit.edu	37	8	39223097	39223097	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:39223097delA	uc003xmx.1	+						ADAM5P_uc003xmy.1_Intron|ADAM5P_uc003xmz.1_Intron|ADAM5P_uc010lwt.1_Intron|ADAM5P_uc003xna.2_Intron|ADAM5P_uc003xnb.2_Intron|ADAM5P_uc003xnc.2_Intron	NR_001448				Homo sapiens mRNA for tMDC II, isoform [a].												0																		---	---	---	---
ADAM18	8749	broad.mit.edu	37	8	39452207	39452207	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:39452207delT	uc003xni.2	+						ADAM18_uc003xnh.2_Intron|ADAM18_uc010lww.2_Intron|ADAM18_uc010lwx.2_Intron	NM_014237	NP_055052			a disintegrin and metalloprotease domain 18						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)															---	---	---	---
ADAM18	8749	broad.mit.edu	37	8	39477093	39477093	+	Intron	DEL	C	-	-	rs141643159		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:39477093delC	uc003xni.2	+						ADAM18_uc010lww.2_Intron|ADAM18_uc010lwx.2_Intron	NM_014237	NP_055052			a disintegrin and metalloprotease domain 18						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)															---	---	---	---
ADAM18	8749	broad.mit.edu	37	8	39498387	39498387	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:39498387delT	uc003xni.2	+						ADAM18_uc010lww.2_Intron|ADAM18_uc010lwx.2_Intron	NM_014237	NP_055052			a disintegrin and metalloprotease domain 18						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)															---	---	---	---
Unknown	0	broad.mit.edu	37	8	39595797	39595798	+	IGR	INS	-	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:39595797_39595798insG								ADAM18 (8312 upstream) : ADAM2 (5458 downstream)																																			---	---	---	---
ADAM2	2515	broad.mit.edu	37	8	39649750	39649750	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:39649750delA	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	39653601	39653601	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:39653601delA	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)														---	---	---	---
Unknown	0	broad.mit.edu	37	8	39702653	39702653	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:39702653delT								ADAM2 (6874 upstream) : IDO1 (68675 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	39751783	39751783	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:39751783delT								ADAM2 (56004 upstream) : IDO1 (19545 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	39755915	39755915	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:39755915delT								ADAM2 (60136 upstream) : IDO1 (15413 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	39880426	39880427	+	IGR	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:39880426_39880427delTT								IDO2 (6516 upstream) : C8orf4 (130562 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	40302986	40302987	+	IGR	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:40302986_40302987delTT								C8orf4 (290165 upstream) : ZMAT4 (85129 downstream)																																			---	---	---	---
ZMAT4	79698	broad.mit.edu	37	8	40405811	40405811	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:40405811delA	uc003xnr.2	-						ZMAT4_uc003xns.2_Intron	NM_024645	NP_078921			zinc finger, matrin type 4 isoform a							nucleus	DNA binding|zinc ion binding			pancreas(1)|central_nervous_system(1)|skin(1)	3	Ovarian(28;0.00724)|Colorectal(14;0.0468)	all_cancers(7;0.00936)|all_epithelial(6;3.53e-06)|all_lung(54;0.0318)|Lung NSC(58;0.0919)|Esophageal squamous(32;0.15)|Hepatocellular(245;0.152)	LUSC - Lung squamous cell carcinoma(45;0.00722)															---	---	---	---
ZMAT4	79698	broad.mit.edu	37	8	40447251	40447252	+	Intron	INS	-	TTT	TTT	rs141826061	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:40447251_40447252insTTT	uc003xnr.2	-						ZMAT4_uc003xns.2_Intron	NM_024645	NP_078921			zinc finger, matrin type 4 isoform a							nucleus	DNA binding|zinc ion binding			pancreas(1)|central_nervous_system(1)|skin(1)	3	Ovarian(28;0.00724)|Colorectal(14;0.0468)	all_cancers(7;0.00936)|all_epithelial(6;3.53e-06)|all_lung(54;0.0318)|Lung NSC(58;0.0919)|Esophageal squamous(32;0.15)|Hepatocellular(245;0.152)	LUSC - Lung squamous cell carcinoma(45;0.00722)															---	---	---	---
ZMAT4	79698	broad.mit.edu	37	8	40543988	40543989	+	Intron	INS	-	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:40543988_40543989insA	uc003xnr.2	-						ZMAT4_uc003xns.2_Intron	NM_024645	NP_078921			zinc finger, matrin type 4 isoform a							nucleus	DNA binding|zinc ion binding			pancreas(1)|central_nervous_system(1)|skin(1)	3	Ovarian(28;0.00724)|Colorectal(14;0.0468)	all_cancers(7;0.00936)|all_epithelial(6;3.53e-06)|all_lung(54;0.0318)|Lung NSC(58;0.0919)|Esophageal squamous(32;0.15)|Hepatocellular(245;0.152)	LUSC - Lung squamous cell carcinoma(45;0.00722)															---	---	---	---
ZMAT4	79698	broad.mit.edu	37	8	40752295	40752296	+	Intron	INS	-	AA	AA	rs148635231	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:40752295_40752296insAA	uc003xnr.2	-						ZMAT4_uc003xns.2_Intron	NM_024645	NP_078921			zinc finger, matrin type 4 isoform a							nucleus	DNA binding|zinc ion binding			pancreas(1)|central_nervous_system(1)|skin(1)	3	Ovarian(28;0.00724)|Colorectal(14;0.0468)	all_cancers(7;0.00936)|all_epithelial(6;3.53e-06)|all_lung(54;0.0318)|Lung NSC(58;0.0919)|Esophageal squamous(32;0.15)|Hepatocellular(245;0.152)	LUSC - Lung squamous cell carcinoma(45;0.00722)															---	---	---	---
ZMAT4	79698	broad.mit.edu	37	8	40753582	40753582	+	Intron	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:40753582delC	uc003xnr.2	-						ZMAT4_uc003xns.2_Intron	NM_024645	NP_078921			zinc finger, matrin type 4 isoform a							nucleus	DNA binding|zinc ion binding			pancreas(1)|central_nervous_system(1)|skin(1)	3	Ovarian(28;0.00724)|Colorectal(14;0.0468)	all_cancers(7;0.00936)|all_epithelial(6;3.53e-06)|all_lung(54;0.0318)|Lung NSC(58;0.0919)|Esophageal squamous(32;0.15)|Hepatocellular(245;0.152)	LUSC - Lung squamous cell carcinoma(45;0.00722)															---	---	---	---
Unknown	0	broad.mit.edu	37	8	40807552	40807552	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:40807552delT								ZMAT4 (52209 upstream) : SFRP1 (311927 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	40812682	40812683	+	IGR	INS	-	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-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	40896527	40896529	+	IGR	DEL	TTT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:40896527_40896529delTTT								ZMAT4 (141184 upstream) : SFRP1 (222950 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	40900679	40900679	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:40900679delT								ZMAT4 (145336 upstream) : SFRP1 (218800 downstream)																																			---	---	---	---
SFRP1	6422	broad.mit.edu	37	8	41121168	41121168	+	3'UTR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:41121168delT	uc003xnt.2	-	3						NM_003012	NP_003003			secreted frizzled-related protein 1 precursor						brain development|canonical Wnt receptor signaling pathway|cellular response to BMP stimulus|cellular response to estradiol stimulus|cellular response to fibroblast growth factor stimulus|cellular response to heparin|cellular response to hypoxia|cellular response to interleukin-1|cellular response to prostaglandin E stimulus|cellular response to starvation|cellular response to transforming growth factor beta stimulus|cellular response to tumor necrosis factor|cellular response to vitamin D|DNA fragmentation involved in apoptotic nuclear change|dorsal/ventral axis specification|hemopoietic progenitor cell differentiation|hemopoietic stem cell differentiation|menstrual cycle phase|negative regulation of androgen receptor signaling pathway|negative regulation of B cell differentiation|negative regulation of bone remodeling|negative regulation of canonical Wnt receptor signaling pathway involved in controlling type B pancreatic cell proliferation|negative regulation of cell growth|negative regulation of cell migration|negative regulation of cysteine-type endopeptidase activity|negative regulation of epithelial cell proliferation|negative regulation of epithelial to mesenchymal transition|negative regulation of fibroblast apoptosis|negative regulation of fibroblast proliferation|negative regulation of insulin secretion|negative regulation of ossification|negative regulation of osteoblast proliferation|negative regulation of peptidyl-tyrosine phosphorylation|negative regulation of transcription, DNA-dependent|negative regulation of Wnt receptor signaling pathway involved in dorsal/ventral axis specification|osteoblast differentiation|positive regulation of canonical Wnt receptor signaling pathway|positive regulation of cell growth|positive regulation of epithelial cell proliferation|positive regulation of fat cell differentiation|positive regulation of fibroblast apoptosis|positive regulation of focal adhesion assembly|positive regulation of non-canonical Wnt receptor signaling pathway|positive regulation of Rac GTPase activity|positive regulation of smoothened signaling pathway|positive regulation of stress fiber assembly|positive regulation of transcription, DNA-dependent|regulation of angiogenesis|regulation of cell cycle process|response to drug|response to organic cyclic compound|vasculature development	cell surface|cytosol|extracellular space|plasma membrane|proteinaceous extracellular matrix	cysteine-type endopeptidase activity|drug binding|frizzled binding|heparin binding|identical protein binding|PDZ domain binding|Wnt receptor activity|Wnt-protein binding			central_nervous_system(1)	1	Breast(1;9.19e-13)|Ovarian(28;0.00769)|Colorectal(14;0.0305)|Lung SC(25;0.211)	all_lung(54;0.0034)|Lung NSC(58;0.0134)|Hepatocellular(245;0.023)|Esophageal squamous(32;0.0559)	BRCA - Breast invasive adenocarcinoma(1;1.11e-10)|LUSC - Lung squamous cell carcinoma(45;0.00894)|COAD - Colon adenocarcinoma(11;0.0174)															---	---	---	---
Unknown	0	broad.mit.edu	37	8	41334474	41334476	+	IGR	DEL	CTT	-	-	rs56142483	by1000genomes;by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:41334474_41334476delCTT								SFRP1 (167494 upstream) : GOLGA7 (13605 downstream)																																			---	---	---	---
ANK1	286	broad.mit.edu	37	8	41589191	41589191	+	Intron	DEL	T	-	-	rs72060110		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:41589191delT	uc003xok.2	-						NKX6-3_uc010lxa.1_Intron|ANK1_uc003xoi.2_Intron|ANK1_uc003xoj.2_Intron|ANK1_uc003xol.2_Intron|ANK1_uc003xom.2_Intron	NM_020476	NP_065209			ankyrin 1 isoform 1						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	41650913	41650913	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:41650913delA	uc003xok.2	-						ANK1_uc003xoi.2_Intron|ANK1_uc003xoj.2_Intron|ANK1_uc003xol.2_Intron|ANK1_uc003xom.2_Intron	NM_020476	NP_065209			ankyrin 1 isoform 1						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	41748802	41748802	+	Intron	DEL	T	-	-	rs111612663		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:41748802delT	uc003xom.2	-							NM_001142446	NP_001135918			ankyrin 1 isoform 9						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)															---	---	---	---
Unknown	0	broad.mit.edu	37	8	41770735	41770735	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:41770735delT								ANK1 (16455 upstream) : MYST3 (16263 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	41779987	41779987	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:41779987delA								ANK1 (25707 upstream) : MYST3 (7011 downstream)																																			---	---	---	---
MYST3	7994	broad.mit.edu	37	8	41801617	41801617	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-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)															---	---	---	---
MYST3	7994	broad.mit.edu	37	8	41830368	41830368	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:41830368delA	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)															---	---	---	---
POLB	5423	broad.mit.edu	37	8	42210592	42210593	+	Intron	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:42210592_42210593delAA	uc003xoz.1	+						POLB_uc003xpa.1_Intron|POLB_uc011lcs.1_Intron	NM_002690	NP_002681			DNA-directed DNA polymerase beta						DNA-dependent DNA replication	cytoplasm|nucleoplasm|spindle microtubule	DNA-(apurinic or apyrimidinic site) lyase activity|DNA-directed DNA polymerase activity|enzyme binding|metal ion binding|microtubule binding			ovary(1)|breast(1)	2	all_cancers(6;1.42e-24)|all_epithelial(6;1.02e-25)|all_lung(13;2.58e-12)|Lung NSC(13;4.24e-11)|Ovarian(28;0.00769)|Prostate(17;0.0119)|Colorectal(14;0.1)|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;3.18e-11)|Lung(22;0.00467)|OV - Ovarian serous cystadenocarcinoma(14;0.00523)|LUSC - Lung squamous cell carcinoma(45;0.024)		Cytarabine(DB00987)								DNA_polymerases_(catalytic_subunits)					---	---	---	---
POLB	5423	broad.mit.edu	37	8	42217310	42217310	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:42217310delT	uc003xoz.1	+						POLB_uc003xpa.1_Intron|POLB_uc011lcs.1_Intron	NM_002690	NP_002681			DNA-directed DNA polymerase beta						DNA-dependent DNA replication	cytoplasm|nucleoplasm|spindle microtubule	DNA-(apurinic or apyrimidinic site) lyase activity|DNA-directed DNA polymerase activity|enzyme binding|metal ion binding|microtubule binding			ovary(1)|breast(1)	2	all_cancers(6;1.42e-24)|all_epithelial(6;1.02e-25)|all_lung(13;2.58e-12)|Lung NSC(13;4.24e-11)|Ovarian(28;0.00769)|Prostate(17;0.0119)|Colorectal(14;0.1)|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;3.18e-11)|Lung(22;0.00467)|OV - Ovarian serous cystadenocarcinoma(14;0.00523)|LUSC - Lung squamous cell carcinoma(45;0.024)		Cytarabine(DB00987)								DNA_polymerases_(catalytic_subunits)					---	---	---	---
SLC20A2	6575	broad.mit.edu	37	8	42381496	42381498	+	Intron	DEL	AAA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:42381496_42381498delAAA	uc010lxm.2	-						SLC20A2_uc003xpe.2_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	42390513	42390513	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:42390513delA	uc010lxm.2	-						SLC20A2_uc003xpe.2_Intron|uc003xpf.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	42442929	42442929	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:42442929delA								C8orf40 (34790 upstream) : CHRNB3 (109633 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	42477409	42477409	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:42477409delT								C8orf40 (69270 upstream) : CHRNB3 (75153 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	42513187	42513187	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:42513187delT								C8orf40 (105048 upstream) : CHRNB3 (39375 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	42664204	42664204	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:42664204delT								CHRNA6 (40585 upstream) : THAP1 (27614 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	42665700	42665700	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:42665700delA								CHRNA6 (42081 upstream) : THAP1 (26118 downstream)																																			---	---	---	---
RNF170	81790	broad.mit.edu	37	8	42716472	42716472	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:42716472delT	uc003xpo.2	-						RNF170_uc011lcx.1_Intron|RNF170_uc010lxp.2_Intron|RNF170_uc003xpm.2_Intron|RNF170_uc003xpp.2_Intron|RNF170_uc003xpn.2_Intron	NM_001160223	NP_001153695			ring finger protein 170 isoform a							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)															---	---	---	---
RNF170	81790	broad.mit.edu	37	8	42740824	42740824	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:42740824delT	uc003xpo.2	-						RNF170_uc011lcx.1_Intron|RNF170_uc010lxp.2_Intron|RNF170_uc003xpm.2_Intron|RNF170_uc003xpp.2_Intron|RNF170_uc003xpn.2_Intron|RNF170_uc003xpq.3_Intron	NM_001160223	NP_001153695			ring finger protein 170 isoform a							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	42829374	42829374	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:42829374delT	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								---	---	---	---
HOOK3	84376	broad.mit.edu	37	8	42834932	42834932	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:42834932delT	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	42954420	42954420	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:42954420delT	uc003xpw.2	+							NM_032237	NP_115613			protein kinase-like protein SgK196							integral to membrane	ATP binding|protein kinase activity				0																		---	---	---	---
HGSNAT	138050	broad.mit.edu	37	8	42993725	42993725	+	5'Flank	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:42993725delT	uc003xpx.3	+							NM_152419	NP_689632			heparan-alpha-glucosaminide N-acetyltransferase						lysosomal transport|protein oligomerization	integral to membrane|lysosomal membrane	heparan-alpha-glucosaminide N-acetyltransferase activity				0	Prostate(17;0.0119)|Ovarian(28;0.0172)|Lung SC(25;0.184)	all_cancers(86;0.000223)|all_epithelial(80;1.61e-07)|all_lung(54;0.00021)|Lung NSC(58;0.000778)|Hepatocellular(245;0.0524)|Renal(179;0.0822)|Esophageal squamous(32;0.129)	Lung(22;0.0777)|LUSC - Lung squamous cell carcinoma(45;0.17)															---	---	---	---
HGSNAT	138050	broad.mit.edu	37	8	43050809	43050814	+	Intron	DEL	GAGGGT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:43050809_43050814delGAGGGT	uc003xpx.3	+							NM_152419	NP_689632			heparan-alpha-glucosaminide N-acetyltransferase						lysosomal transport|protein oligomerization	integral to membrane|lysosomal membrane	heparan-alpha-glucosaminide N-acetyltransferase activity				0	Prostate(17;0.0119)|Ovarian(28;0.0172)|Lung SC(25;0.184)	all_cancers(86;0.000223)|all_epithelial(80;1.61e-07)|all_lung(54;0.00021)|Lung NSC(58;0.000778)|Hepatocellular(245;0.0524)|Renal(179;0.0822)|Esophageal squamous(32;0.129)	Lung(22;0.0777)|LUSC - Lung squamous cell carcinoma(45;0.17)															---	---	---	---
Unknown	0	broad.mit.edu	37	8	43579140	43579140	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:43579140delT								POTEA (360812 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	43613270	43613270	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:43613270delA								POTEA (394942 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	43629424	43629424	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:43629424delA								POTEA (411096 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	43770321	43770321	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:43770321delT								POTEA (551993 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	46868969	46868969	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:46868969delA								None (None upstream) : BEYLA (883539 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	46944517	46944517	+	IGR	DEL	A	-	-	rs138170455		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:46944517delA								None (None upstream) : BEYLA (807991 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	47423498	47423498	+	IGR	DEL	T	-	-	rs113989769		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:47423498delT								None (None upstream) : BEYLA (329010 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	47466565	47466565	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:47466565delA								None (None upstream) : BEYLA (285943 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	47596411	47596411	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:47596411delT								None (None upstream) : BEYLA (156097 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	47879214	47879214	+	IGR	DEL	C	-	-	rs68193308		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:47879214delC								BEYLA (111807 upstream) : KIAA0146 (294328 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	47952416	47952416	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:47952416delT								BEYLA (185009 upstream) : KIAA0146 (221126 downstream)																																			---	---	---	---
KIAA0146	23514	broad.mit.edu	37	8	48241497	48241497	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:48241497delT	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	48631068	48631069	+	Intron	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:48631068_48631069delTT	uc003xqd.2	+						KIAA0146_uc011ldc.1_Intron|KIAA0146_uc011ldd.1_Intron|KIAA0146_uc003xqe.2_Intron|KIAA0146_uc003xqf.2_Intron|KIAA0146_uc010lxt.2_Intron|KIAA0146_uc011ldf.1_Intron|KIAA0146_uc011ldg.1_Intron|KIAA0146_uc003xqg.1_Intron	NM_001080394	NP_001073863			hypothetical protein LOC23514												0		Lung NSC(58;0.175)																---	---	---	---
UBE2V2	7336	broad.mit.edu	37	8	48966368	48966368	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:48966368delT	uc003xqm.2	+							NM_003350	NP_003341			ubiquitin-conjugating enzyme E2v2						cell proliferation|DNA double-strand break processing|protein polyubiquitination|regulation of DNA repair	cytoplasm|nucleus|UBC13-MMS2 complex	acid-amino acid ligase activity|protein binding				0		all_cancers(86;0.026)|all_epithelial(80;0.000748)|Lung NSC(129;0.00171)|all_lung(136;0.00196)											Direct_reversal_of_damage|Rad6_pathway					---	---	---	---
Unknown	0	broad.mit.edu	37	8	49055170	49055170	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:49055170delA								UBE2V2 (80718 upstream) : EFCAB1 (568181 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	49086511	49086512	+	IGR	DEL	GT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:49086511_49086512delGT								UBE2V2 (112059 upstream) : EFCAB1 (536839 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	49450886	49450887	+	IGR	DEL	TC	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:49450886_49450887delTC								UBE2V2 (476434 upstream) : EFCAB1 (172464 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	49777109	49777110	+	IGR	DEL	TG	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:49777109_49777110delTG								EFCAB1 (129239 upstream) : SNAI2 (53129 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	49787385	49787387	+	IGR	DEL	AAA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:49787385_49787387delAAA								EFCAB1 (139515 upstream) : SNAI2 (42852 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	50006056	50006056	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:50006056delT								C8orf22 (17415 upstream) : SNTG1 (816293 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	50069871	50069872	+	IGR	INS	-	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:50069871_50069872insT								C8orf22 (81230 upstream) : SNTG1 (752477 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	50146926	50146926	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:50146926delT								C8orf22 (158285 upstream) : SNTG1 (675423 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	50158938	50158943	+	IGR	DEL	AAAAAA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:50158938_50158943delAAAAAA								C8orf22 (170297 upstream) : SNTG1 (663406 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	50389828	50389828	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:50389828delA								C8orf22 (401187 upstream) : SNTG1 (432521 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	50394681	50394681	+	IGR	DEL	T	-	-	rs34910479		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:50394681delT								C8orf22 (406040 upstream) : SNTG1 (427668 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	50765657	50765658	+	IGR	DEL	AG	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:50765657_50765658delAG								C8orf22 (777016 upstream) : SNTG1 (56691 downstream)																																			---	---	---	---
SNTG1	54212	broad.mit.edu	37	8	50958105	50958106	+	Intron	INS	-	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:50958105_50958106insG	uc010lxy.1	+						SNTG1_uc003xqs.1_Intron|SNTG1_uc010lxz.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)																---	---	---	---
SNTG1	54212	broad.mit.edu	37	8	51116854	51116854	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:51116854delT	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	51706693	51706695	+	IGR	DEL	AAT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:51706693_51706695delAAT								SNTG1 (1266 upstream) : PXDNL (525449 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	51720127	51720127	+	IGR	DEL	T	-	-	rs35967636		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:51720127delT								SNTG1 (14700 upstream) : PXDNL (512017 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	51729188	51729188	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:51729188delA								SNTG1 (23761 upstream) : PXDNL (502956 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	51744546	51744546	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:51744546delT								SNTG1 (39119 upstream) : PXDNL (487598 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	51961426	51961427	+	IGR	INS	-	GT	GT	rs147485594	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:51961426_51961427insGT								SNTG1 (255999 upstream) : PXDNL (270717 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	52005578	52005578	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:52005578delT								SNTG1 (300151 upstream) : PXDNL (226566 downstream)																																			---	---	---	---
PXDNL	137902	broad.mit.edu	37	8	52432093	52432093	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:52432093delA	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	52527863	52527863	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:52527863delT	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	52613665	52613666	+	Intron	INS	-	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:52613665_52613666insT	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	52651493	52651493	+	Intron	DEL	A	-	-	rs72054429		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:52651493delA	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	52714012	52714012	+	Intron	DEL	G	-	-	rs146024479		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:52714012delG	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)																---	---	---	---
Unknown	0	broad.mit.edu	37	8	53404883	53404884	+	IGR	INS	-	C	C	rs2582608	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:53404883_53404884insC								ST18 (82444 upstream) : FAM150A (41714 downstream)																																			---	---	---	---
FAM150A	389658	broad.mit.edu	37	8	53457320	53457320	+	Intron	DEL	A	-	-	rs34453161		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:53457320delA	uc003xrd.2	-						FAM150A_uc011ldt.1_Intron	NM_207413	NP_997296			hypothetical protein LOC389658 precursor							extracellular region					0		Lung NSC(129;0.0919)|all_epithelial(80;0.125)|all_lung(136;0.17)																---	---	---	---
Unknown	0	broad.mit.edu	37	8	53485128	53485128	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:53485128delT								FAM150A (7107 upstream) : RB1CC1 (49891 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	53494596	53494596	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:53494596delT								FAM150A (16575 upstream) : RB1CC1 (40423 downstream)																																			---	---	---	---
RB1CC1	9821	broad.mit.edu	37	8	53579853	53579853	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:53579853delA	uc003xre.3	-						RB1CC1_uc003xrf.3_Intron	NM_014781	NP_055596			Rb1-inducible coiled coil protein 1 isoform 1						autophagy|cell cycle|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytosol|nucleus|pre-autophagosomal structure|ULK1-ATG13-FIP200 complex	protein binding			ovary(8)|upper_aerodigestive_tract(1)|large_intestine(1)|skin(1)	11		all_cancers(86;0.137)|all_epithelial(80;0.00494)|Lung NSC(129;0.011)|all_lung(136;0.023)																---	---	---	---
Unknown	0	broad.mit.edu	37	8	53733548	53733548	+	IGR	DEL	T	-	-	rs34255713		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:53733548delT								RB1CC1 (106522 upstream) : NPBWR1 (118920 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	53741857	53741857	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:53741857delT								RB1CC1 (114831 upstream) : NPBWR1 (110611 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	53767042	53767042	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:53767042delT								RB1CC1 (140016 upstream) : NPBWR1 (85426 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	53785013	53785013	+	IGR	DEL	T	-	-	rs112834162		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:53785013delT								RB1CC1 (157987 upstream) : NPBWR1 (67455 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	54070288	54070289	+	IGR	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:54070288_54070289delTT								NPBWR1 (216835 upstream) : OPRK1 (67987 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	54089651	54089651	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:54089651delA								NPBWR1 (236198 upstream) : OPRK1 (48625 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	54130463	54130463	+	IGR	DEL	T	-	-	rs141382867	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:54130463delT								NPBWR1 (277010 upstream) : OPRK1 (7813 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	54384635	54384635	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:54384635delT								OPRK1 (220441 upstream) : ATP6V1H (243481 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	54479585	54479587	+	IGR	DEL	TTT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:54479585_54479587delTTT								OPRK1 (315391 upstream) : ATP6V1H (148529 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	54510581	54510581	+	IGR	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:54510581delC								OPRK1 (346387 upstream) : ATP6V1H (117535 downstream)																																			---	---	---	---
ATP6V1H	51606	broad.mit.edu	37	8	54651838	54651838	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:54651838delT	uc003xrl.2	-						ATP6V1H_uc003xrk.2_Intron|ATP6V1H_uc003xrm.2_Intron|ATP6V1H_uc003xrn.2_Intron|ATP6V1H_uc011ldv.1_Intron|ATP6V1H_uc010lyd.2_Intron	NM_213620	NP_998785			ATPase, H+ transporting, lysosomal 50/57kDa, V1						ATP hydrolysis coupled proton transport|cellular iron ion homeostasis|endocytosis|insulin receptor signaling pathway|interspecies interaction between organisms|regulation of defense response to virus by virus|transferrin transport|vacuolar acidification|viral reproduction	cytosol|plasma membrane|vacuolar proton-transporting V-type ATPase, V1 domain	enzyme regulator activity|protein binding|proton-transporting ATPase activity, rotational mechanism				0		all_epithelial(80;0.0487)|Lung NSC(129;0.109)|all_lung(136;0.181)	OV - Ovarian serous cystadenocarcinoma(7;2.79e-06)|Epithelial(17;0.000629)|all cancers(17;0.00359)															---	---	---	---
ATP6V1H	51606	broad.mit.edu	37	8	54711080	54711080	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:54711080delA	uc003xrl.2	-						ATP6V1H_uc003xrk.2_Intron|ATP6V1H_uc003xrm.2_Intron|ATP6V1H_uc003xrn.2_Intron|ATP6V1H_uc011ldv.1_Intron|ATP6V1H_uc010lyd.2_Intron	NM_213620	NP_998785			ATPase, H+ transporting, lysosomal 50/57kDa, V1						ATP hydrolysis coupled proton transport|cellular iron ion homeostasis|endocytosis|insulin receptor signaling pathway|interspecies interaction between organisms|regulation of defense response to virus by virus|transferrin transport|vacuolar acidification|viral reproduction	cytosol|plasma membrane|vacuolar proton-transporting V-type ATPase, V1 domain	enzyme regulator activity|protein binding|proton-transporting ATPase activity, rotational mechanism				0		all_epithelial(80;0.0487)|Lung NSC(129;0.109)|all_lung(136;0.181)	OV - Ovarian serous cystadenocarcinoma(7;2.79e-06)|Epithelial(17;0.000629)|all cancers(17;0.00359)															---	---	---	---
RGS20	8601	broad.mit.edu	37	8	54786956	54786963	+	Intron	DEL	GTGTGTGC	-	-	rs144334152	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:54786956_54786963delGTGTGTGC	uc003xrp.2	+						RGS20_uc003xrq.2_Intron|RGS20_uc010lye.2_Intron|RGS20_uc010lyf.2_Intron	NM_170587	NP_733466			regulator of G-protein signaling 20 isoform a						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)															---	---	---	---
TCEA1	6917	broad.mit.edu	37	8	54907431	54907431	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:54907431delA	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								---	---	---	---
TCEA1	6917	broad.mit.edu	37	8	54935291	54935291	+	5'Flank	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:54935291delT	uc003xru.2	-						TCEA1_uc003xrv.2_5'Flank|TCEA1_uc011ldw.1_5'Flank|TCEA1_uc003xrw.1_5'Flank	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								---	---	---	---
LYPLA1	10434	broad.mit.edu	37	8	54973647	54973647	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:54973647delT	uc003xry.2	-						LYPLA1_uc011ldx.1_Intron|LYPLA1_uc003xrz.2_Intron	NM_006330	NP_006321			lysophospholipase 1						fatty acid metabolic process|nitric oxide metabolic process|regulation of nitric-oxide synthase activity	cytosol	lysophospholipase activity|palmitoyl-(protein) hydrolase activity			central_nervous_system(1)	1		Lung NSC(129;0.109)|all_epithelial(80;0.11)|all_lung(136;0.181)	OV - Ovarian serous cystadenocarcinoma(7;8.48e-07)|Epithelial(17;9.29e-05)|all cancers(17;0.000689)															---	---	---	---
LYPLA1	10434	broad.mit.edu	37	8	55011085	55011085	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:55011085delA	uc003xry.2	-						LYPLA1_uc011ldx.1_Intron|LYPLA1_uc003xrz.2_Intron	NM_006330	NP_006321			lysophospholipase 1						fatty acid metabolic process|nitric oxide metabolic process|regulation of nitric-oxide synthase activity	cytosol	lysophospholipase activity|palmitoyl-(protein) hydrolase activity			central_nervous_system(1)	1		Lung NSC(129;0.109)|all_epithelial(80;0.11)|all_lung(136;0.181)	OV - Ovarian serous cystadenocarcinoma(7;8.48e-07)|Epithelial(17;9.29e-05)|all cancers(17;0.000689)															---	---	---	---
MRPL15	29088	broad.mit.edu	37	8	55050511	55050511	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:55050511delT	uc003xsa.2	+							NM_014175	NP_054894			mitochondrial ribosomal protein L15 precursor						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)															---	---	---	---
Unknown	0	broad.mit.edu	37	8	55107941	55107941	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:55107941delT								MRPL15 (46867 upstream) : SOX17 (262554 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	55125554	55125554	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:55125554delT								MRPL15 (64480 upstream) : SOX17 (244941 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	55357703	55357703	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:55357703delA								MRPL15 (296629 upstream) : SOX17 (12792 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	55484358	55484358	+	IGR	DEL	T	-	-	rs75659305		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:55484358delT								SOX17 (110903 upstream) : RP1 (44269 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	55489587	55489587	+	IGR	DEL	T	-	-	rs147837035		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:55489587delT								SOX17 (116132 upstream) : RP1 (39040 downstream)																																			---	---	---	---
RP1	6101	broad.mit.edu	37	8	55544101	55544102	+	Intron	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:55544101_55544102delTT	uc011ldy.1	+											SubName: Full=cDNA, FLJ79410, moderately similar to Oxygen-regulated protein 1;						axoneme assembly|intracellular signal transduction|photoreceptor cell maintenance|photoreceptor cell outer segment organization|phototransduction, visible light|retinal cone cell development|retinal rod cell development	cilium axoneme|cytoplasm|microtubule|microtubule associated complex|photoreceptor connecting cilium|photoreceptor inner segment|photoreceptor outer segment	microtubule binding			skin(7)|ovary(4)|pancreas(1)	12		all_lung(136;0.0831)|Lung NSC(129;0.109)|all_epithelial(80;0.123)	OV - Ovarian serous cystadenocarcinoma(7;4.4e-07)|Epithelial(17;3.37e-05)|all cancers(17;0.000285)															---	---	---	---
RP1	6101	broad.mit.edu	37	8	55565864	55565864	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:55565864delA	uc011ldy.1	+											SubName: Full=cDNA, FLJ79410, moderately similar to Oxygen-regulated protein 1;						axoneme assembly|intracellular signal transduction|photoreceptor cell maintenance|photoreceptor cell outer segment organization|phototransduction, visible light|retinal cone cell development|retinal rod cell development	cilium axoneme|cytoplasm|microtubule|microtubule associated complex|photoreceptor connecting cilium|photoreceptor inner segment|photoreceptor outer segment	microtubule binding			skin(7)|ovary(4)|pancreas(1)	12		all_lung(136;0.0831)|Lung NSC(129;0.109)|all_epithelial(80;0.123)	OV - Ovarian serous cystadenocarcinoma(7;4.4e-07)|Epithelial(17;3.37e-05)|all cancers(17;0.000285)															---	---	---	---
Unknown	0	broad.mit.edu	37	8	55701031	55701031	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:55701031delT								RP1 (18500 upstream) : XKR4 (313986 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	55759757	55759757	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:55759757delA								RP1 (77226 upstream) : XKR4 (255260 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	55898073	55898073	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:55898073delA								RP1 (215542 upstream) : XKR4 (116944 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	55903968	55903968	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:55903968delT								RP1 (221437 upstream) : XKR4 (111049 downstream)																																			---	---	---	---
XKR4	114786	broad.mit.edu	37	8	56181926	56181926	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:56181926delT	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	56183651	56183651	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:56183651delT	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	56272362	56272362	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:56272362delA	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	56310146	56310147	+	Intron	DEL	TT	-	-	rs11444857		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:56310146_56310147delTT	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	56443419	56443419	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:56443419delT								XKR4 (4711 upstream) : TMEM68 (207901 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	56466905	56466905	+	IGR	DEL	A	-	-	rs34241961		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:56466905delA								XKR4 (28197 upstream) : TMEM68 (184415 downstream)																																			---	---	---	---
TMEM68	137695	broad.mit.edu	37	8	56657760	56657761	+	Intron	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:56657760_56657761delTT	uc003xsg.1	-						TMEM68_uc003xsh.1_Intron	NM_152417	NP_689630			transmembrane protein 68							integral to membrane	acyltransferase activity			skin(1)	1			Epithelial(17;0.000361)|all cancers(17;0.00326)															---	---	---	---
TMEM68	137695	broad.mit.edu	37	8	56661142	56661143	+	Intron	DEL	GA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:56661142_56661143delGA	uc003xsg.1	-						TMEM68_uc003xsh.1_Intron	NM_152417	NP_689630			transmembrane protein 68							integral to membrane	acyltransferase activity			skin(1)	1			Epithelial(17;0.000361)|all cancers(17;0.00326)															---	---	---	---
Unknown	0	broad.mit.edu	37	8	56751003	56751003	+	IGR	DEL	A	-	-	rs34227949		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:56751003delA								TGS1 (13000 upstream) : LYN (41383 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	56760465	56760465	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:56760465delT								TGS1 (22462 upstream) : LYN (31921 downstream)																																			---	---	---	---
LYN	4067	broad.mit.edu	37	8	56808188	56808188	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:56808188delT	uc003xsk.3	+						LYN_uc003xsl.3_Intron	NM_002350	NP_002341			Yamaguchi sarcoma viral (v-yes-1) oncogene						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)															---	---	---	---
Unknown	0	broad.mit.edu	37	8	56964194	56964196	+	IGR	DEL	AAC	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:56964194_56964196delAAC								LYN (40258 upstream) : RPS20 (16543 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	56979639	56979639	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:56979639delA								LYN (55703 upstream) : RPS20 (1100 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	57001605	57001605	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:57001605delT								RPS20 (14465 upstream) : MOS (23897 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	57146712	57146714	+	IGR	DEL	TTT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:57146712_57146714delTTT								CHCHD7 (15538 upstream) : SDR16C5 (65856 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	57281223	57281223	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:57281223delA								SDR16C5 (47982 upstream) : PENK (72290 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	57442690	57442690	+	Intron	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:57442690delG	uc003xtb.1	+						uc003xtc.1_Intron					Homo sapiens cDNA FLJ34244 fis, clone FCBBF3028794.																														---	---	---	---
Unknown	0	broad.mit.edu	37	8	57535333	57535335	+	IGR	DEL	AAA	-	-	rs35619698		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:57535333_57535335delAAA								PENK (176051 upstream) : IMPAD1 (335156 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	57660935	57660935	+	IGR	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:57660935delC								PENK (301653 upstream) : IMPAD1 (209556 downstream)																																			---	---	---	---
IMPAD1	54928	broad.mit.edu	37	8	57896594	57896595	+	Intron	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:57896594_57896595delAA	uc003xte.3	-							NM_017813	NP_060283			inositol monophosphatase domain containing 1							Golgi apparatus|integral to membrane	inositol-1(or 4)-monophosphatase activity|metal ion binding			ovary(1)	1		all_cancers(86;0.175)|all_lung(136;0.0321)|Lung NSC(129;0.0417)|all_epithelial(80;0.0448)																---	---	---	---
Unknown	0	broad.mit.edu	37	8	57973878	57973878	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:57973878delT								IMPAD1 (67451 upstream) : C8orf71 (218224 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	57986793	57986794	+	IGR	INS	-	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:57986793_57986794insC								IMPAD1 (80366 upstream) : C8orf71 (205308 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	58462021	58462022	+	IGR	INS	-	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:58462021_58462022insA								C8orf71 (264733 upstream) : FAM110B (445091 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	58625220	58625222	+	IGR	DEL	AAA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:58625220_58625222delAAA								C8orf71 (427932 upstream) : FAM110B (281891 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	58731561	58731561	+	IGR	DEL	A	-	-	rs143864666		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:58731561delA								C8orf71 (534273 upstream) : FAM110B (175552 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	59096369	59096369	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:59096369delA								FAM110B (34092 upstream) : UBXN2B (227454 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	59219877	59219877	+	IGR	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:59219877delG								FAM110B (157600 upstream) : UBXN2B (103946 downstream)																																			---	---	---	---
UBXN2B	137886	broad.mit.edu	37	8	59336303	59336305	+	Intron	DEL	TTT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:59336303_59336305delTTT	uc003xtl.2	+							NM_001077619	NP_001071087			UBX domain protein 2B							cytosol|endoplasmic reticulum|Golgi apparatus|nucleus				ovary(2)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	8	59461778	59461781	+	IGR	DEL	TATA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:59461778_59461781delTATA								CYP7A1 (49058 upstream) : SDCBP (3947 downstream)																																			---	---	---	---
NSMAF	8439	broad.mit.edu	37	8	59500894	59500895	+	Intron	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-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	59510913	59510913	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:59510913delA	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-4200-01A-01D-1126-08	TCGA-BR-4200-11A-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)																---	---	---	---
NSMAF	8439	broad.mit.edu	37	8	59572659	59572659	+	5'Flank	DEL	A	-	-	rs35599436		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:59572659delA	uc011lee.1	-						NSMAF_uc003xtt.2_5'Flank|NSMAF_uc003xtu.2_5'Flank|uc003xtv.1_3'UTR	NM_001144772	NP_001138244			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	59599373	59599373	+	IGR	DEL	A	-	-	rs34765672		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:59599373delA								NSMAF (26969 upstream) : TOX (118604 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	59650764	59650765	+	IGR	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:59650764_59650765delAA								NSMAF (78360 upstream) : TOX (67212 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	59653871	59653871	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:59653871delA								NSMAF (81467 upstream) : TOX (64106 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	59714239	59714242	+	IGR	DEL	AAGT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:59714239_59714242delAAGT								NSMAF (141835 upstream) : TOX (3735 downstream)																																			---	---	---	---
TOX	9760	broad.mit.edu	37	8	60011521	60011522	+	Intron	INS	-	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:60011521_60011522insA	uc003xtw.1	-							NM_014729	NP_055544			thymus high mobility group box protein TOX							nucleus	DNA binding			kidney(2)|lung(1)|skin(1)	4		all_cancers(86;0.165)|Myeloproliferative disorder(644;0.00452)|all_lung(136;0.036)|Lung NSC(129;0.0464)|all_epithelial(80;0.0607)																---	---	---	---
Unknown	0	broad.mit.edu	37	8	60192665	60192665	+	IGR	DEL	T	-	-	rs111745971		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:60192665delT								TOX (160898 upstream) : CA8 (908758 downstream)																																			---	---	---	---
RAB2A	5862	broad.mit.edu	37	8	61447475	61447475	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:61447475delT	uc003xud.1	+						RAB2A_uc011lef.1_Intron	NM_002865	NP_002856			RAB2A, member RAS oncogene family						ER to Golgi vesicle-mediated transport|protein transport|small GTPase mediated signal transduction	endoplasmic reticulum membrane|ER-Golgi intermediate compartment membrane|Golgi membrane|melanosome	GDP binding|GTP binding|GTPase activity				0			BRCA - Breast invasive adenocarcinoma(89;0.0805)															---	---	---	---
RAB2A	5862	broad.mit.edu	37	8	61470289	61470290	+	Intron	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:61470289_61470290delTT	uc003xud.1	+						RAB2A_uc011lef.1_Intron	NM_002865	NP_002856			RAB2A, member RAS oncogene family						ER to Golgi vesicle-mediated transport|protein transport|small GTPase mediated signal transduction	endoplasmic reticulum membrane|ER-Golgi intermediate compartment membrane|Golgi membrane|melanosome	GDP binding|GTP binding|GTPase activity				0			BRCA - Breast invasive adenocarcinoma(89;0.0805)															---	---	---	---
RAB2A	5862	broad.mit.edu	37	8	61520872	61520872	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:61520872delT	uc003xud.1	+						RAB2A_uc011lef.1_Intron	NM_002865	NP_002856			RAB2A, member RAS oncogene family						ER to Golgi vesicle-mediated transport|protein transport|small GTPase mediated signal transduction	endoplasmic reticulum membrane|ER-Golgi intermediate compartment membrane|Golgi membrane|melanosome	GDP binding|GTP binding|GTPase activity				0			BRCA - Breast invasive adenocarcinoma(89;0.0805)															---	---	---	---
CHD7	55636	broad.mit.edu	37	8	61658074	61658076	+	Intron	DEL	CTT	-	-	rs34063122		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:61658074_61658076delCTT	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	61714076	61714076	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:61714076delT	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	p.556_871dup(1)		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	61771697	61771697	+	Intron	DEL	T	-	-	rs34162663		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:61771697delT	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)															---	---	---	---
Unknown	0	broad.mit.edu	37	8	61819160	61819161	+	IGR	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:61819160_61819161delAA								CHD7 (39697 upstream) : CLVS1 (381364 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	61823183	61823183	+	IGR	DEL	A	-	-	rs71559314		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:61823183delA								CHD7 (43720 upstream) : CLVS1 (377342 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	62190221	62190222	+	IGR	INS	-	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:62190221_62190222insG								CHD7 (410758 upstream) : CLVS1 (10303 downstream)																																			---	---	---	---
CLVS1	157807	broad.mit.edu	37	8	62358167	62358167	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:62358167delT	uc003xuh.2	+						CLVS1_uc003xui.2_Intron|CLVS1_uc010lyp.2_Intron	NM_173519	NP_775790			retinaldehyde binding protein 1-like 1						lysosome organization	clathrin-coated vesicle|early endosome membrane|trans-Golgi network	phosphatidylinositol-3,5-bisphosphate binding|transporter activity			skin(4)|ovary(1)	5																		---	---	---	---
Unknown	0	broad.mit.edu	37	8	62646102	62646103	+	IGR	INS	-	A	A	rs140058907	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:62646102_62646103insA								ASPH (18903 upstream) : NKAIN3 (515398 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	62777653	62777653	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:62777653delA								ASPH (150454 upstream) : NKAIN3 (383848 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	62958659	62958660	+	IGR	INS	-	TG	TG	rs140895064	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:62958659_62958660insTG								ASPH (331460 upstream) : NKAIN3 (202841 downstream)																																			---	---	---	---
NKAIN3	286183	broad.mit.edu	37	8	63197342	63197342	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:63197342delA	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	63312075	63312075	+	Intron	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:63312075delG	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	63322405	63322405	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:63322405delT	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	63323189	63323189	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:63323189delA	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	63334204	63334205	+	Intron	INS	-	AT	AT			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:63334204_63334205insAT	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	63337010	63337010	+	Intron	DEL	A	-	-	rs5891855		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:63337010delA	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	63398969	63398969	+	Intron	DEL	A	-	-	rs147115278		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:63398969delA	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	63438831	63438831	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:63438831delA	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	63601884	63601885	+	Intron	INS	-	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:63601884_63601885insC	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	64077654	64077654	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:64077654delT								TTPA (79042 upstream) : YTHDF3 (3467 downstream)																																			---	---	---	---
YTHDF3	253943	broad.mit.edu	37	8	64081982	64081982	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:64081982delT	uc003xuy.2	+						YTHDF3_uc010lys.2_Intron|YTHDF3_uc003xuz.2_Intron|YTHDF3_uc003xva.2_Intron|YTHDF3_uc011len.1_Intron	NM_152758	NP_689971			YTH domain family, member 3												0	Breast(64;0.0716)	all_cancers(86;0.169)|Lung NSC(129;0.0324)|all_lung(136;0.0593)|all_epithelial(80;0.146)	BRCA - Breast invasive adenocarcinoma(89;0.161)															---	---	---	---
Unknown	0	broad.mit.edu	37	8	64177733	64177733	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:64177733delT								YTHDF3 (52388 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	64269097	64269097	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:64269097delT								YTHDF3 (143752 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	64404835	64404835	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:64404835delT								YTHDF3 (279490 upstream) : MIR124-2 (886871 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	64459789	64459790	+	IGR	DEL	TC	-	-	rs3030423		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:64459789_64459790delTC								YTHDF3 (334444 upstream) : MIR124-2 (831916 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	65068688	65068688	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:65068688delA								YTHDF3 (943343 upstream) : MIR124-2 (223018 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	65204064	65204065	+	IGR	INS	-	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:65204064_65204065insT								None (None upstream) : MIR124-2 (87641 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	65275539	65275539	+	IGR	DEL	T	-	-	rs35376000		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:65275539delT								None (None upstream) : MIR124-2 (16167 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	65291908	65291909	+	Intron	INS	-	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:65291908_65291909insC	uc003xvd.2	+						uc003xve.2_Intron|uc003xvf.2_RNA					Homo sapiens cDNA FLJ42262 fis, clone TKIDN2013134.																														---	---	---	---
Unknown	0	broad.mit.edu	37	8	65343001	65343001	+	IGR	DEL	T	-	-	rs74980123		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:65343001delT								MIR124-2 (51187 upstream) : LOC401463 (143867 downstream)																																			---	---	---	---
LOC401463	401463	broad.mit.edu	37	8	65496560	65496560	+	5'Flank	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:65496560delA	uc003xvh.2	-											Homo sapiens cDNA FLJ39831 fis, clone SPLEN2012961.												0																		---	---	---	---
CYP7B1	9420	broad.mit.edu	37	8	65544458	65544458	+	Intron	DEL	A	-	-	rs35942788		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:65544458delA	uc003xvj.2	-							NM_004820	NP_004811			cytochrome P450, family 7, subfamily B,						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)																---	---	---	---
Unknown	0	broad.mit.edu	37	8	65803666	65803666	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:65803666delT								CYP7B1 (92318 upstream) : ARMC1 (711406 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	66013388	66013388	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:66013388delT								CYP7B1 (302040 upstream) : ARMC1 (501684 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	66194390	66194393	+	IGR	DEL	ACAC	-	-	rs34058018		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:66194390_66194393delACAC								CYP7B1 (483042 upstream) : ARMC1 (320679 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	66261108	66261109	+	IGR	INS	-	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:66261108_66261109insT								CYP7B1 (549760 upstream) : ARMC1 (253963 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	66330503	66330503	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:66330503delT								CYP7B1 (619155 upstream) : ARMC1 (184569 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	66347188	66347188	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:66347188delA								CYP7B1 (635840 upstream) : ARMC1 (167884 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	66392569	66392569	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:66392569delT								CYP7B1 (681221 upstream) : ARMC1 (122503 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	66454168	66454168	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:66454168delA	uc003xvk.1	-											Homo sapiens cDNA FLJ37641 fis, clone BRHIP2000087.																														---	---	---	---
Unknown	0	broad.mit.edu	37	8	66483955	66483955	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:66483955delT								CYP7B1 (772607 upstream) : ARMC1 (31117 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	66493463	66493463	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:66493463delA								CYP7B1 (782115 upstream) : ARMC1 (21609 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	66550308	66550308	+	IGR	DEL	T	-	-	rs112854275		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:66550308delT								ARMC1 (3876 upstream) : MTFR1 (6580 downstream)																																			---	---	---	---
PDE7A	5150	broad.mit.edu	37	8	66636440	66636440	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:66636440delA	uc003xvq.2	-						PDE7A_uc003xvr.2_Intron|PDE7A_uc003xvp.2_Intron	NM_002604	NP_002595			phosphodiesterase 7A isoform b							cell fraction|cytosol	3',5'-cyclic-AMP phosphodiesterase activity|metal ion binding				0			Epithelial(68;0.0509)|BRCA - Breast invasive adenocarcinoma(89;0.111)|all cancers(69;0.168)|OV - Ovarian serous cystadenocarcinoma(28;0.238)		Dyphylline(DB00651)|Ketotifen(DB00920)													---	---	---	---
Unknown	0	broad.mit.edu	37	8	66783104	66783104	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:66783104delT								PDE7A (29349 upstream) : DNAJC5B (150687 downstream)																																			---	---	---	---
DNAJC5B	85479	broad.mit.edu	37	8	66955795	66955796	+	Translation_Start_Site	INS	-	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:66955795_66955796insG	uc003xvs.1	+	2	223_224	c.-68_-67insG	c.(-70--65)CATGGG>CATGGGG		DNAJC5B_uc003xvt.1_RNA	NM_033105	NP_149096			DnaJ (Hsp40) homolog, subfamily C, member 5						protein folding	membrane	heat shock protein binding|unfolded protein binding				0		Lung NSC(129;0.114)|all_lung(136;0.188)	Epithelial(68;0.0213)|all cancers(69;0.0839)|BRCA - Breast invasive adenocarcinoma(89;0.0886)|OV - Ovarian serous cystadenocarcinoma(28;0.112)															---	---	---	---
DNAJC5B	85479	broad.mit.edu	37	8	66964201	66964201	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:66964201delT	uc003xvs.1	+						DNAJC5B_uc003xvt.1_Intron	NM_033105	NP_149096			DnaJ (Hsp40) homolog, subfamily C, member 5						protein folding	membrane	heat shock protein binding|unfolded protein binding				0		Lung NSC(129;0.114)|all_lung(136;0.188)	Epithelial(68;0.0213)|all cancers(69;0.0839)|BRCA - Breast invasive adenocarcinoma(89;0.0886)|OV - Ovarian serous cystadenocarcinoma(28;0.112)															---	---	---	---
DNAJC5B	85479	broad.mit.edu	37	8	67002519	67002520	+	Intron	DEL	AG	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:67002519_67002520delAG	uc003xvs.1	+						DNAJC5B_uc003xvt.1_Intron	NM_033105	NP_149096			DnaJ (Hsp40) homolog, subfamily C, member 5						protein folding	membrane	heat shock protein binding|unfolded protein binding				0		Lung NSC(129;0.114)|all_lung(136;0.188)	Epithelial(68;0.0213)|all cancers(69;0.0839)|BRCA - Breast invasive adenocarcinoma(89;0.0886)|OV - Ovarian serous cystadenocarcinoma(28;0.112)															---	---	---	---
Unknown	0	broad.mit.edu	37	8	67035794	67035794	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:67035794delA								DNAJC5B (23039 upstream) : TRIM55 (3484 downstream)																																			---	---	---	---
TRIM55	84675	broad.mit.edu	37	8	67062909	67062911	+	Intron	DEL	TTT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:67062909_67062911delTTT	uc003xvv.2	+						TRIM55_uc003xvu.2_Intron|TRIM55_uc003xvw.2_Intron|TRIM55_uc003xvx.2_Intron	NM_184085	NP_908973			tripartite motif-containing 55 isoform 1							cytoplasm|microtubule|nucleus	signal transducer activity|zinc ion binding			skin(3)|ovary(1)|central_nervous_system(1)	5		Lung NSC(129;0.138)|all_lung(136;0.221)	Epithelial(68;0.0136)|all cancers(69;0.0582)|BRCA - Breast invasive adenocarcinoma(89;0.0628)|OV - Ovarian serous cystadenocarcinoma(28;0.0904)															---	---	---	---
Unknown	0	broad.mit.edu	37	8	67240710	67240710	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:67240710delT								CRH (150012 upstream) : RRS1 (100553 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	67258388	67258388	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:67258388delT								CRH (167690 upstream) : RRS1 (82875 downstream)																																			---	---	---	---
SGK3	23678	broad.mit.edu	37	8	67657041	67657042	+	Intron	DEL	TT	-	-	rs111235370		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:67657041_67657042delTT	uc003xwr.2	+						SGK3_uc003xwp.2_Intron	NM_001033578	NP_001028750			serum/glucocorticoid regulated kinase 3 isoform						cell communication|response to stress	cytoplasmic membrane-bounded vesicle|early endosome	ATP binding|phosphatidylinositol binding|protein serine/threonine kinase activity			ovary(1)|large_intestine(1)|lung(1)|breast(1)	4	Breast(64;0.186)	Lung NSC(129;0.0908)|all_lung(136;0.152)	Epithelial(68;0.0046)|OV - Ovarian serous cystadenocarcinoma(28;0.0112)|all cancers(69;0.0141)|BRCA - Breast invasive adenocarcinoma(89;0.206)															---	---	---	---
SGK3	23678	broad.mit.edu	37	8	67750019	67750019	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:67750019delA	uc003xwr.2	+						SGK3_uc003xwp.2_Intron|SGK3_uc003xwt.2_Intron|SGK3_uc003xwu.2_Intron	NM_001033578	NP_001028750			serum/glucocorticoid regulated kinase 3 isoform						cell communication|response to stress	cytoplasmic membrane-bounded vesicle|early endosome	ATP binding|phosphatidylinositol binding|protein serine/threonine kinase activity			ovary(1)|large_intestine(1)|lung(1)|breast(1)	4	Breast(64;0.186)	Lung NSC(129;0.0908)|all_lung(136;0.152)	Epithelial(68;0.0046)|OV - Ovarian serous cystadenocarcinoma(28;0.0112)|all cancers(69;0.0141)|BRCA - Breast invasive adenocarcinoma(89;0.206)															---	---	---	---
Unknown	0	broad.mit.edu	37	8	67879021	67879022	+	IGR	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:67879021_67879022delAA								SNHG6 (41244 upstream) : LRRC67 (21346 downstream)																																			---	---	---	---
COPS5	10987	broad.mit.edu	37	8	67971240	67971242	+	Intron	DEL	AAA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:67971240_67971242delAAA	uc003xxe.2	-						COPS5_uc003xxd.2_Intron|COPS5_uc003xxf.2_Intron|COPS5_uc010lyu.1_5'Flank|COPS5_uc010lyv.1_Intron	NM_006837	NP_006828			COP9 signalosome subunit 5						cullin deneddylation|transcription from RNA polymerase II promoter	eukaryotic translation initiation factor 3 complex|signalosome	metal ion binding|metallopeptidase activity|protein binding|transcription coactivator activity|translation initiation factor activity			ovary(1)|skin(1)	2	Breast(64;0.214)	Lung NSC(129;0.0908)|all_lung(136;0.152)	Epithelial(68;0.00389)|OV - Ovarian serous cystadenocarcinoma(28;0.00691)|all cancers(69;0.0205)|BRCA - Breast invasive adenocarcinoma(89;0.153)															---	---	---	---
CSPP1	79848	broad.mit.edu	37	8	68057756	68057756	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:68057756delT	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)															---	---	---	---
ARFGEF1	10565	broad.mit.edu	37	8	68161191	68161191	+	Intron	DEL	T	-	-	rs112367908		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:68161191delT	uc003xxo.1	-						ARFGEF1_uc003xxl.1_Intron	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	68185639	68185641	+	Intron	DEL	TTT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:68185639_68185641delTTT	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	68243970	68243970	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:68243970delA	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)															---	---	---	---
Unknown	0	broad.mit.edu	37	8	68330707	68330708	+	IGR	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:68330707_68330708delAA								ARFGEF1 (74795 upstream) : CPA6 (3698 downstream)																																			---	---	---	---
CPA6	57094	broad.mit.edu	37	8	68409715	68409715	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:68409715delA	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	68494131	68494131	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:68494131delA	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	68649680	68649680	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:68649680delT	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	68650261	68650261	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:68650261delA	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)															---	---	---	---
Unknown	0	broad.mit.edu	37	8	68784707	68784707	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:68784707delA								CPA6 (126087 upstream) : PREX2 (79641 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	68823131	68823132	+	IGR	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:68823131_68823132delTT								CPA6 (164511 upstream) : PREX2 (41216 downstream)																																			---	---	---	---
PREX2	80243	broad.mit.edu	37	8	68884932	68884932	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:68884932delT	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																		---	---	---	---
PREX2	80243	broad.mit.edu	37	8	69055504	69055504	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:69055504delT	uc003xxv.1	+							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																		---	---	---	---
Unknown	0	broad.mit.edu	37	8	69753623	69753628	+	IGR	DEL	GTGTGT	-	-	rs34634691		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:69753623_69753628delGTGTGT								C8orf34 (22367 upstream) : SULF1 (625231 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	69763476	69763476	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:69763476delT								C8orf34 (32220 upstream) : SULF1 (615383 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	69790919	69790919	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:69790919delT								C8orf34 (59663 upstream) : SULF1 (587940 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	69883872	69883873	+	Intron	DEL	CT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:69883872_69883873delCT	uc003xyc.1	-											Homo sapiens cDNA FLJ30952 fis, clone HCASM1000130.																														---	---	---	---
Unknown	0	broad.mit.edu	37	8	69940719	69940719	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:69940719delA	uc003xyc.1	-											Homo sapiens cDNA FLJ30952 fis, clone HCASM1000130.																														---	---	---	---
Unknown	0	broad.mit.edu	37	8	70027194	70027194	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:70027194delA								C8orf34 (295938 upstream) : SULF1 (351665 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	70278597	70278597	+	IGR	DEL	T	-	-	rs68071506		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:70278597delT								C8orf34 (547341 upstream) : SULF1 (100262 downstream)																																			---	---	---	---
SULF1	23213	broad.mit.edu	37	8	70482114	70482115	+	Intron	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:70482114_70482115delTT	uc010lza.1	+						SULF1_uc003xyd.2_Intron|SULF1_uc003xye.2_Intron|SULF1_uc003xyf.2_Intron|SULF1_uc003xyg.2_Intron	NM_015170	NP_055985			sulfatase 1 precursor						apoptosis|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			central_nervous_system(3)|ovary(2)|pancreas(1)|skin(1)	7	Breast(64;0.0654)		Epithelial(68;0.0124)|OV - Ovarian serous cystadenocarcinoma(28;0.0265)|all cancers(69;0.0534)															---	---	---	---
SLCO5A1	81796	broad.mit.edu	37	8	70661987	70661988	+	Intron	DEL	AC	-	-	rs147742972	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:70661987_70661988delAC	uc003xyl.2	-						SLCO5A1_uc010lzb.2_Intron|SLCO5A1_uc011lfa.1_Intron|SLCO5A1_uc003xyk.2_Intron|SLCO5A1_uc010lzc.2_Intron	NM_030958	NP_112220			solute carrier organic anion transporter family,							integral to membrane|plasma membrane	transporter activity			ovary(3)|upper_aerodigestive_tract(1)	4	Breast(64;0.0654)		Epithelial(68;0.0141)|OV - Ovarian serous cystadenocarcinoma(28;0.0315)|all cancers(69;0.0594)															---	---	---	---
Unknown	0	broad.mit.edu	37	8	70849110	70849115	+	IGR	DEL	TTTTTT	-	-	rs34687723		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:70849110_70849115delTTTTTT								SLCO5A1 (101811 upstream) : PRDM14 (114910 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	71385185	71385186	+	IGR	INS	-	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:71385185_71385186insA								NCOA2 (69165 upstream) : TRAM1 (100487 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	71418493	71418493	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:71418493delT								NCOA2 (102473 upstream) : TRAM1 (67180 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	71485261	71485261	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:71485261delT								NCOA2 (169241 upstream) : TRAM1 (412 downstream)																																			---	---	---	---
EYA1	2138	broad.mit.edu	37	8	72178246	72178246	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:72178246delT	uc003xys.3	-						EYA1_uc003xyr.3_Intron|EYA1_uc003xyt.3_Intron|EYA1_uc010lzf.2_Intron|EYA1_uc003xyu.2_Intron|EYA1_uc011lfe.1_Intron|EYA1_uc003xyv.2_Intron	NM_172058	NP_742055			eyes absent 1 isoform b						double-strand break repair|histone dephosphorylation|positive regulation of DNA repair|protein sumoylation|regulation of transcription, DNA-dependent|response to ionizing radiation|sensory perception of sound|transcription, DNA-dependent	cytoplasm|nucleus	metal ion binding|protein tyrosine phosphatase activity			ovary(2)|central_nervous_system(2)|upper_aerodigestive_tract(1)	5	Breast(64;0.046)		Epithelial(68;0.0837)|all cancers(69;0.247)															---	---	---	---
Unknown	0	broad.mit.edu	37	8	72513139	72513139	+	IGR	DEL	T	-	-	rs67274080		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:72513139delT								EYA1 (238672 upstream) : MSC (240638 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	72777375	72777375	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:72777375delA	uc011lff.1	+						uc003xyy.2_Intron					Homo sapiens cDNA FLJ41321 fis, clone BRAMY2045299.																														---	---	---	---
Unknown	0	broad.mit.edu	37	8	72868670	72868670	+	Intron	DEL	T	-	-	rs148731898		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:72868670delT	uc011lff.1	+						uc003xyy.2_Intron					Homo sapiens cDNA FLJ41321 fis, clone BRAMY2045299.																														---	---	---	---
Unknown	0	broad.mit.edu	37	8	73068619	73068620	+	IGR	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:73068619_73068620delTT								TRPA1 (80800 upstream) : KCNB2 (381006 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	73154017	73154036	+	Intron	DEL	AGGAAGGAAGGAAGGAGGGA	-	-	rs11276636		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:73154017_73154036delAGGAAGGAAGGAAGGAGGGA	uc010lzg.2	-											Homo sapiens cDNA, FLJ99767.																														---	---	---	---
KCNB2	9312	broad.mit.edu	37	8	73482806	73482806	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:73482806delT	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)															---	---	---	---
KCNB2	9312	broad.mit.edu	37	8	73492117	73492117	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:73492117delA	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)															---	---	---	---
KCNB2	9312	broad.mit.edu	37	8	73645226	73645226	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:73645226delA	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)															---	---	---	---
Unknown	0	broad.mit.edu	37	8	74044871	74044872	+	IGR	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:74044871_74044872delTT								C8orf84 (39364 upstream) : RPL7 (158003 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	74669843	74669844	+	IGR	DEL	AC	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:74669843_74669844delAC								STAU2 (9900 upstream) : UBE2W (22488 downstream)																																			---	---	---	---
UBE2W	55284	broad.mit.edu	37	8	74737352	74737352	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:74737352delA	uc003xzv.2	-						UBE2W_uc003xzt.2_Intron|UBE2W_uc003xzu.2_Intron|UBE2W_uc003xzw.2_Intron	NM_018299	NP_060769			ubiquitin-conjugating enzyme E2W (putative)						protein K11-linked ubiquitination|protein monoubiquitination		ATP binding|protein binding|ubiquitin-protein ligase activity				0	Breast(64;0.0311)		Epithelial(68;0.0235)|all cancers(69;0.0687)|BRCA - Breast invasive adenocarcinoma(89;0.069)															---	---	---	---
UBE2W	55284	broad.mit.edu	37	8	74782628	74782629	+	Intron	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:74782628_74782629delAA	uc003xzv.2	-						UBE2W_uc003xzt.2_Intron|UBE2W_uc003xzu.2_Intron|UBE2W_uc003xzw.2_Intron	NM_018299	NP_060769			ubiquitin-conjugating enzyme E2W (putative)						protein K11-linked ubiquitination|protein monoubiquitination		ATP binding|protein binding|ubiquitin-protein ligase activity				0	Breast(64;0.0311)		Epithelial(68;0.0235)|all cancers(69;0.0687)|BRCA - Breast invasive adenocarcinoma(89;0.069)															---	---	---	---
Unknown	0	broad.mit.edu	37	8	74970413	74970413	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:74970413delA								LY96 (29108 upstream) : JPH1 (176528 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	74983918	74983918	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:74983918delT								LY96 (42613 upstream) : JPH1 (163023 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	75385319	75385320	+	IGR	DEL	TT	-	-	rs34633437		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:75385319_75385320delTT								GDAP1 (105986 upstream) : MIR2052 (232608 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	75585323	75585324	+	Intron	INS	-	AA	AA			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:75585323_75585324insAA	uc003yaj.1	+											Homo sapiens cDNA FLJ39080 fis, clone NT2RP7018197.																														---	---	---	---
Unknown	0	broad.mit.edu	37	8	75637090	75637090	+	Intron	DEL	T	-	-	rs112503330		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:75637090delT	uc003yaj.1	+											Homo sapiens cDNA FLJ39080 fis, clone NT2RP7018197.																														---	---	---	---
PI15	51050	broad.mit.edu	37	8	75748793	75748793	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:75748793delA	uc003yal.2	+						uc003yak.1_Intron|PI15_uc003yam.2_Intron	NM_015886	NP_056970			protease inhibitor 15 preproprotein							extracellular region	peptidase inhibitor activity			central_nervous_system(2)|ovary(1)	3	Breast(64;0.137)		BRCA - Breast invasive adenocarcinoma(89;0.104)|Epithelial(68;0.118)															---	---	---	---
CRISPLD1	83690	broad.mit.edu	37	8	75928137	75928137	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:75928137delT	uc003yan.2	+						CRISPLD1_uc011lfk.1_Intron|CRISPLD1_uc011lfl.1_Intron	NM_031461	NP_113649			cysteine-rich secretory protein LCCL domain							extracellular region				ovary(1)|central_nervous_system(1)	2	Breast(64;0.0799)		Epithelial(68;0.155)|BRCA - Breast invasive adenocarcinoma(89;0.161)															---	---	---	---
Unknown	0	broad.mit.edu	37	8	75978346	75978347	+	IGR	DEL	AA	-	-	rs16919372		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:75978346_75978347delAA								CRISPLD1 (31555 upstream) : HNF4G (341836 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	76002964	76002965	+	IGR	INS	-	CA	CA	rs139900242	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:76002964_76002965insCA								CRISPLD1 (56173 upstream) : HNF4G (317218 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	76266550	76266550	+	IGR	DEL	T	-	-	rs113339022		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:76266550delT								CRISPLD1 (319759 upstream) : HNF4G (53633 downstream)																																			---	---	---	---
HNF4G	3174	broad.mit.edu	37	8	76324955	76324955	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:76324955delT	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	76621404	76621404	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:76621404delA								HNF4G (142345 upstream) : LOC100192378 (901711 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	76826363	76826367	+	IGR	DEL	TTTTG	-	-	rs113404851		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:76826363_76826367delTTTTG								HNF4G (347304 upstream) : LOC100192378 (696748 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	76849158	76849158	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:76849158delA								HNF4G (370099 upstream) : LOC100192378 (673957 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	76896160	76896161	+	IGR	DEL	AC	-	-	rs35653232		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:76896160_76896161delAC								HNF4G (417101 upstream) : LOC100192378 (626954 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	76902615	76902615	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:76902615delA								HNF4G (423556 upstream) : LOC100192378 (620500 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	77300845	77300845	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:77300845delA								HNF4G (821786 upstream) : LOC100192378 (222270 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	77806773	77806776	+	IGR	DEL	TTTT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:77806773_77806776delTTTT								ZFHX4 (27253 upstream) : PEX2 (85720 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	78063359	78063360	+	IGR	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:78063359_78063360delAA								PEX2 (150835 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	78068057	78068057	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:78068057delT								PEX2 (155533 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	78271073	78271073	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:78271073delT								PEX2 (358549 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	78445373	78445374	+	IGR	DEL	TC	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:78445373_78445374delTC								PEX2 (532849 upstream) : PKIA (982962 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	78566357	78566357	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:78566357delT								PEX2 (653833 upstream) : PKIA (861979 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	78639966	78639966	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:78639966delA								PEX2 (727442 upstream) : PKIA (788370 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	78795183	78795183	+	IGR	DEL	A	-	-	rs67759245		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:78795183delA								PEX2 (882659 upstream) : PKIA (633153 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	78942084	78942085	+	IGR	DEL	AA	-	-	rs9657044	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:78942084_78942085delAA								None (None upstream) : PKIA (486251 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	79014451	79014451	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:79014451delT								None (None upstream) : PKIA (413885 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	79027678	79027679	+	IGR	INS	-	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:79027678_79027679insA								None (None upstream) : PKIA (400657 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	79206201	79206202	+	IGR	INS	-	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:79206201_79206202insA								None (None upstream) : PKIA (222134 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	79227967	79227967	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:79227967delA								None (None upstream) : PKIA (200369 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	79331405	79331405	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:79331405delT								None (None upstream) : PKIA (96931 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	79423472	79423473	+	IGR	DEL	AC	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:79423472_79423473delAC								None (None upstream) : PKIA (4863 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	79782913	79782913	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:79782913delT								IL7 (65155 upstream) : STMN2 (740467 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	79824265	79824265	+	IGR	DEL	T	-	-	rs66498119		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:79824265delT								IL7 (106507 upstream) : STMN2 (699115 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	79930426	79930426	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:79930426delT								IL7 (212668 upstream) : STMN2 (592954 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	79975682	79975682	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:79975682delA								IL7 (257924 upstream) : STMN2 (547698 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	80161171	80161172	+	IGR	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:80161171_80161172delAA								IL7 (443413 upstream) : STMN2 (362208 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	80202775	80202776	+	IGR	DEL	TG	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:80202775_80202776delTG								IL7 (485017 upstream) : STMN2 (320604 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	80473805	80473805	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:80473805delT								IL7 (756047 upstream) : STMN2 (49575 downstream)																																			---	---	---	---
STMN2	11075	broad.mit.edu	37	8	80564273	80564273	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:80564273delT	uc003ybj.2	+						STMN2_uc010lzp.2_Intron|STMN2_uc011lfn.1_Intron	NM_007029	NP_008960			superiorcervical ganglia, neural specific 10						intracellular signal transduction|negative regulation of microtubule depolymerization|negative regulation of microtubule polymerization|negative regulation of neuron projection development|neuron differentiation|positive regulation of microtubule depolymerization|positive regulation of neuron projection development	axon|growth cone|membrane|membrane fraction|perinuclear region of cytoplasm|soluble fraction	protein binding			ovary(1)|central_nervous_system(1)	2	all_lung(9;8.34e-05)		Epithelial(68;0.0229)|all cancers(69;0.0874)															---	---	---	---
STMN2	11075	broad.mit.edu	37	8	80576217	80576217	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:80576217delA	uc003ybj.2	+						STMN2_uc010lzp.2_Intron|STMN2_uc011lfn.1_Intron|STMN2_uc003ybk.2_5'Flank	NM_007029	NP_008960			superiorcervical ganglia, neural specific 10						intracellular signal transduction|negative regulation of microtubule depolymerization|negative regulation of microtubule polymerization|negative regulation of neuron projection development|neuron differentiation|positive regulation of microtubule depolymerization|positive regulation of neuron projection development	axon|growth cone|membrane|membrane fraction|perinuclear region of cytoplasm|soluble fraction	protein binding			ovary(1)|central_nervous_system(1)	2	all_lung(9;8.34e-05)		Epithelial(68;0.0229)|all cancers(69;0.0874)															---	---	---	---
Unknown	0	broad.mit.edu	37	8	80631492	80631492	+	IGR	DEL	T	-	-	rs72493832		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:80631492delT								STMN2 (53098 upstream) : HEY1 (44754 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	80687404	80687405	+	Intron	INS	-	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:80687404_80687405insT	uc003ybn.2	-											Homo sapiens cDNA FLJ30770 fis, clone FEBRA2000734.																														---	---	---	---
Unknown	0	broad.mit.edu	37	8	80735027	80735027	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:80735027delT	uc003ybn.2	-											Homo sapiens cDNA FLJ30770 fis, clone FEBRA2000734.																														---	---	---	---
MRPS28	28957	broad.mit.edu	37	8	80928174	80928174	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:80928174delA	uc003ybp.2	-						MRPS28_uc003ybo.2_Intron|TPD52_uc010lzr.2_Intron	NM_014018	NP_054737			mitochondrial ribosomal protein S28							mitochondrial small ribosomal subunit					0	Lung NSC(7;1.86e-06)|all_lung(9;6.91e-06)		BRCA - Breast invasive adenocarcinoma(6;0.00769)|Epithelial(68;0.0208)|all cancers(69;0.0805)															---	---	---	---
Unknown	0	broad.mit.edu	37	8	81239953	81239953	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:81239953delA								TPD52 (156117 upstream) : ZBTB10 (157901 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	81308981	81308981	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:81308981delA								TPD52 (225145 upstream) : ZBTB10 (88873 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	81374646	81374648	+	IGR	DEL	AAA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:81374646_81374648delAAA								TPD52 (290810 upstream) : ZBTB10 (23206 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	81448493	81448493	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:81448493delT								ZBTB10 (13885 upstream) : ZNF704 (102276 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	81472059	81472059	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:81472059delA								ZBTB10 (37451 upstream) : ZNF704 (78710 downstream)																																			---	---	---	---
ZNF704	619279	broad.mit.edu	37	8	81583372	81583372	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:81583372delT	uc003yby.1	-							NM_001033723	NP_001028895			zinc finger protein 704							intracellular	zinc ion binding				0	all_cancers(3;8.53e-08)|all_epithelial(4;4.59e-10)|Breast(3;2.56e-06)|Lung NSC(7;2.58e-06)|all_lung(9;9.4e-06)		BRCA - Breast invasive adenocarcinoma(6;0.00401)|Epithelial(68;0.00448)|all cancers(69;0.0277)															---	---	---	---
ZNF704	619279	broad.mit.edu	37	8	81621077	81621078	+	Intron	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:81621077_81621078delTT	uc003yby.1	-							NM_001033723	NP_001028895			zinc finger protein 704							intracellular	zinc ion binding				0	all_cancers(3;8.53e-08)|all_epithelial(4;4.59e-10)|Breast(3;2.56e-06)|Lung NSC(7;2.58e-06)|all_lung(9;9.4e-06)		BRCA - Breast invasive adenocarcinoma(6;0.00401)|Epithelial(68;0.00448)|all cancers(69;0.0277)															---	---	---	---
Unknown	0	broad.mit.edu	37	8	81800820	81800821	+	IGR	DEL	CC	-	-	rs73692272	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:81800820_81800821delCC								ZNF704 (13804 upstream) : PAG1 (79227 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	81856483	81856483	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:81856483delT								ZNF704 (69467 upstream) : PAG1 (23565 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	82365938	82365938	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:82365938delA								PMP2 (6219 upstream) : FABP9 (4681 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	82383327	82383330	+	IGR	DEL	TTTT	-	-	rs141732903		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:82383327_82383330delTTTT								FABP9 (9569 upstream) : FABP4 (7402 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	82414597	82414598	+	IGR	DEL	AA	-	-	rs35242812		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:82414597_82414598delAA								FABP4 (19124 upstream) : FABP12 (22685 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	82468118	82468118	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:82468118delT								FABP12 (24568 upstream) : IMPA1 (101033 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	82559733	82559733	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:82559733delT								FABP12 (116183 upstream) : IMPA1 (9418 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	82849952	82849953	+	IGR	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:82849952_82849953delTT								SNX16 (95431 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	83109390	83109390	+	IGR	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:83109390delC								SNX16 (354869 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	83498824	83498827	+	IGR	DEL	AAAA	-	-	rs111971033		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:83498824_83498827delAAAA								SNX16 (744303 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	83558721	83558721	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:83558721delA								SNX16 (804200 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	83627117	83627118	+	IGR	INS	-	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:83627117_83627118insA								SNX16 (872596 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	83898639	83898639	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:83898639delT								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	83907236	83907236	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:83907236delA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	84045205	84045205	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:84045205delA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	84063926	84063926	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:84063926delT								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	84170279	84170279	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:84170279delT								None (None upstream) : RALYL (925174 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	84412008	84412008	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:84412008delT								None (None upstream) : RALYL (683445 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	84471433	84471434	+	IGR	DEL	TT	-	-	rs11431876		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:84471433_84471434delTT								None (None upstream) : RALYL (624019 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	84862647	84862647	+	IGR	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:84862647delG								None (None upstream) : RALYL (232806 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	84890563	84890564	+	IGR	DEL	AC	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:84890563_84890564delAC								None (None upstream) : RALYL (204889 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	84971440	84971440	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:84971440delA								None (None upstream) : RALYL (124013 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	85032798	85032801	+	IGR	DEL	TTTT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:85032798_85032801delTTTT								None (None upstream) : RALYL (62652 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	85061446	85061446	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:85061446delA								None (None upstream) : RALYL (34007 downstream)																																			---	---	---	---
RALYL	138046	broad.mit.edu	37	8	85199868	85199868	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-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	85351182	85351182	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:85351182delT	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	85458376	85458376	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:85458376delT	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	85483825	85483825	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:85483825delT	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	85776436	85776437	+	Intron	INS	-	TG	TG	rs138257189	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:85776436_85776437insTG	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																		---	---	---	---
Unknown	0	broad.mit.edu	37	8	85837300	85837301	+	IGR	INS	-	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:85837300_85837301insT								RALYL (3229 upstream) : LRRCC1 (182076 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	85919980	85919980	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:85919980delT								RALYL (85909 upstream) : LRRCC1 (99397 downstream)																																			---	---	---	---
E2F5	1875	broad.mit.edu	37	8	86102568	86102568	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:86102568delT	uc003ycz.3	+						E2F5_uc003yda.3_Intron|E2F5_uc010mab.2_Intron	NM_001951	NP_001942			E2F transcription factor 5 isoform 1						G1 phase of mitotic cell cycle	transcription factor complex	DNA binding|sequence-specific DNA binding transcription factor activity|transcription factor binding			ovary(1)	1																		---	---	---	---
CA2	760	broad.mit.edu	37	8	86389131	86389135	+	Intron	DEL	TTTTT	-	-	rs111230295		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:86389131_86389135delTTTTT	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	86970475	86970475	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:86970475delT								REXO1L1 (395207 upstream) : PSKH2 (90218 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	87107039	87107040	+	IGR	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:87107039_87107040delAA								PSKH2 (25188 upstream) : ATP6V0D2 (4099 downstream)																																			---	---	---	---
ATP6V0D2	245972	broad.mit.edu	37	8	87108605	87108605	+	5'Flank	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:87108605delT	uc003ydp.1	+							NM_152565	NP_689778			ATPase, H+ transporting, lysosomal 38kDa, V0						ATP hydrolysis coupled proton transport|cellular iron ion homeostasis|insulin receptor signaling pathway|transferrin transport	apical plasma membrane|endosome membrane|proton-transporting V-type ATPase, V0 domain|vacuolar proton-transporting V-type ATPase complex	hydrogen ion transmembrane transporter activity|protein binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	8	87246016	87246016	+	IGR	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:87246016delC								SLC7A13 (3407 upstream) : WWP1 (108978 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	87250879	87250879	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:87250879delT								SLC7A13 (8270 upstream) : WWP1 (104115 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	87342875	87342876	+	IGR	INS	-	G	G	rs71275846		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:87342875_87342876insG								SLC7A13 (100266 upstream) : WWP1 (12118 downstream)																																			---	---	---	---
WWP1	11059	broad.mit.edu	37	8	87357639	87357639	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:87357639delT	uc003ydt.2	+						uc003yds.2_5'Flank	NM_007013	NP_008944			WW domain containing E3 ubiquitin protein ligase						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																		---	---	---	---
WWP1	11059	broad.mit.edu	37	8	87393192	87393192	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:87393192delT	uc003ydt.2	+						WWP1_uc010mai.2_Intron	NM_007013	NP_008944			WW domain containing E3 ubiquitin protein ligase						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																		---	---	---	---
Unknown	0	broad.mit.edu	37	8	87793051	87793051	+	IGR	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:87793051delC								CNGB3 (37150 upstream) : CNBD1 (85625 downstream)																																			---	---	---	---
CNBD1	168975	broad.mit.edu	37	8	88185893	88185893	+	Intron	DEL	T	-	-	rs111945368		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:88185893delT	uc003ydy.2	+							NM_173538	NP_775809			cyclic nucleotide binding domain containing 1											ovary(3)	3																		---	---	---	---
Unknown	0	broad.mit.edu	37	8	88422251	88422251	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:88422251delA								CNBD1 (27296 upstream) : DCAF4L2 (460722 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	88618225	88618225	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:88618225delA								CNBD1 (223270 upstream) : DCAF4L2 (264748 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	88682534	88682534	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:88682534delT								CNBD1 (287579 upstream) : DCAF4L2 (200439 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	88805028	88805028	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:88805028delT								CNBD1 (410073 upstream) : DCAF4L2 (77945 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	88904406	88904408	+	IGR	DEL	TTT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:88904406_88904408delTTT								DCAF4L2 (18110 upstream) : MMP16 (145054 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	88910978	88910978	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:88910978delT								DCAF4L2 (24682 upstream) : MMP16 (138484 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	88912139	88912140	+	IGR	INS	-	AA	AA			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:88912139_88912140insAA								DCAF4L2 (25843 upstream) : MMP16 (137322 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	88960153	88960153	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:88960153delT								DCAF4L2 (73857 upstream) : MMP16 (89309 downstream)																																			---	---	---	---
MMP16	4325	broad.mit.edu	37	8	89237213	89237213	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:89237213delT	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																		---	---	---	---
MMP16	4325	broad.mit.edu	37	8	89258900	89258900	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:89258900delT	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																		---	---	---	---
MMP16	4325	broad.mit.edu	37	8	89284750	89284750	+	Intron	DEL	A	-	-	rs35509129		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:89284750delA	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																		---	---	---	---
MMP16	4325	broad.mit.edu	37	8	89286202	89286204	+	Intron	DEL	CAT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:89286202_89286204delCAT	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	89346335	89346336	+	IGR	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:89346335_89346336delTT								MMP16 (6618 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	89441055	89441055	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:89441055delT								MMP16 (101338 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	89467040	89467040	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:89467040delA								MMP16 (127323 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	90126461	90126461	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:90126461delA								MMP16 (786744 upstream) : RIPK2 (643514 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	90307297	90307297	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:90307297delT								MMP16 (967580 upstream) : RIPK2 (462678 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	90562649	90562650	+	IGR	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:90562649_90562650delTT								None (None upstream) : RIPK2 (207325 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	90602845	90602845	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:90602845delA								None (None upstream) : RIPK2 (167130 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	90721142	90721142	+	IGR	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:90721142delC								None (None upstream) : RIPK2 (48833 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	90748634	90748634	+	Intron	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:90748634delG	uc003yed.2	-											full-length cDNA clone CS0DL001YK24 of B cells (Ramos cell line) Cot 25-normalized of Homo sapiens (human).																														---	---	---	---
RIPK2	8767	broad.mit.edu	37	8	90798702	90798702	+	Intron	DEL	A	-	-	rs112047259		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:90798702delA	uc003yee.2	+						RIPK2_uc003yef.2_Intron	NM_003821	NP_003812			receptor-interacting serine-threonine kinase 2						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)															---	---	---	---
OSGIN2	734	broad.mit.edu	37	8	90936586	90936586	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:90936586delT	uc003yeg.2	+						OSGIN2_uc003yeh.2_Intron	NM_004337	NP_004328			oxidative stress induced growth inhibitor family						germ cell development|meiosis						0			BRCA - Breast invasive adenocarcinoma(11;0.0344)															---	---	---	---
NBN	4683	broad.mit.edu	37	8	90962508	90962508	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:90962508delA	uc003yej.1	-						NBN_uc003yei.1_Intron|NBN_uc011lgb.1_Intron	NM_002485	NP_002476			nibrin						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				---	---	---	---
NBN	4683	broad.mit.edu	37	8	90992883	90992883	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:90992883delA	uc003yej.1	-						NBN_uc003yei.1_Intron|NBN_uc011lgb.1_Intron	NM_002485	NP_002476			nibrin						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				---	---	---	---
DECR1	1666	broad.mit.edu	37	8	91056917	91056917	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:91056917delT	uc003yek.1	+						DECR1_uc011lgc.1_Intron|DECR1_uc011lgd.1_Intron	NM_001359	NP_001350			2,4-dienoyl CoA reductase 1 precursor						fatty acid beta-oxidation|protein homotetramerization	mitochondrial matrix|nucleus|plasma membrane	2,4-dienoyl-CoA reductase (NADPH) activity|NADPH binding|oxidoreductase activity, acting on NADH or NADPH				0			BRCA - Breast invasive adenocarcinoma(11;0.00953)															---	---	---	---
Unknown	0	broad.mit.edu	37	8	91248610	91248611	+	IGR	INS	-	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:91248610_91248611insT								CALB1 (140923 upstream) : TMEM64 (385612 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	91507270	91507270	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:91507270delA								CALB1 (399583 upstream) : TMEM64 (126953 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	91515123	91515123	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:91515123delA								CALB1 (407436 upstream) : TMEM64 (119100 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	91565637	91565637	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:91565637delT								CALB1 (457950 upstream) : TMEM64 (68586 downstream)																																			---	---	---	---
TMEM64	169200	broad.mit.edu	37	8	91637754	91637755	+	3'UTR	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:91637754_91637755delAA	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)															---	---	---	---
TMEM64	169200	broad.mit.edu	37	8	91801255	91801255	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:91801255delT	uc003yeo.2	-						NECAB1_uc011lgg.1_5'Flank	NM_001008495	NP_001008495			transmembrane protein 64 isoform 1							integral to membrane					0			BRCA - Breast invasive adenocarcinoma(11;0.0598)															---	---	---	---
NECAB1	64168	broad.mit.edu	37	8	91852877	91852877	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:91852877delA	uc011lgg.1	+							NM_022351	NP_071746			N-terminal EF-hand calcium binding protein 1						antibiotic biosynthetic process	cytoplasm	calcium ion binding|oxidoreductase activity			central_nervous_system(1)	1			BRCA - Breast invasive adenocarcinoma(11;0.0499)															---	---	---	---
NECAB1	64168	broad.mit.edu	37	8	91876506	91876506	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:91876506delA	uc011lgg.1	+							NM_022351	NP_071746			N-terminal EF-hand calcium binding protein 1						antibiotic biosynthetic process	cytoplasm	calcium ion binding|oxidoreductase activity			central_nervous_system(1)	1			BRCA - Breast invasive adenocarcinoma(11;0.0499)															---	---	---	---
TMEM55A	55529	broad.mit.edu	37	8	92055807	92055807	+	5'Flank	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:92055807delT	uc003yes.2	-							NM_018710	NP_061180			transmembrane protein 55A							integral to membrane|late endosome membrane|lysosomal membrane	hydrolase activity				0			BRCA - Breast invasive adenocarcinoma(11;0.033)															---	---	---	---
SLC26A7	115111	broad.mit.edu	37	8	92256713	92256714	+	Intron	DEL	TT	-	-	rs111564622		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:92256713_92256714delTT	uc003yex.2	+						SLC26A7_uc003yey.2_Intron	NM_052832	NP_439897			solute carrier family 26, member 7 isoform a							basolateral plasma membrane|integral to membrane|recycling endosome membrane	anion:anion antiporter activity|bicarbonate transmembrane transporter activity|chloride channel activity|oxalate transmembrane transporter activity|sulfate transmembrane transporter activity			ovary(2)	2			BRCA - Breast invasive adenocarcinoma(11;0.00802)															---	---	---	---
SLC26A7	115111	broad.mit.edu	37	8	92301876	92301877	+	Intron	DEL	AA	-	-	rs111279250		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:92301876_92301877delAA	uc003yex.2	+						SLC26A7_uc003yey.2_Intron|SLC26A7_uc003yez.2_Intron|SLC26A7_uc003yfa.2_Intron	NM_052832	NP_439897			solute carrier family 26, member 7 isoform a							basolateral plasma membrane|integral to membrane|recycling endosome membrane	anion:anion antiporter activity|bicarbonate transmembrane transporter activity|chloride channel activity|oxalate transmembrane transporter activity|sulfate transmembrane transporter activity			ovary(2)	2			BRCA - Breast invasive adenocarcinoma(11;0.00802)															---	---	---	---
Unknown	0	broad.mit.edu	37	8	92461362	92461362	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:92461362delT								SLC26A7 (50982 upstream) : RUNX1T1 (509790 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	92701214	92701214	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:92701214delA								SLC26A7 (290834 upstream) : RUNX1T1 (269938 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	92799972	92799973	+	IGR	INS	-	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:92799972_92799973insT								SLC26A7 (389592 upstream) : RUNX1T1 (171179 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	92838326	92838329	+	IGR	DEL	TGTG	-	-	rs35222977		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:92838326_92838329delTGTG								SLC26A7 (427946 upstream) : RUNX1T1 (132823 downstream)																																			---	---	---	---
RUNX1T1	862	broad.mit.edu	37	8	93066354	93066357	+	Intron	DEL	AAAA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:93066354_93066357delAAAA	uc003yfd.2	-						RUNX1T1_uc003yfc.1_Intron|RUNX1T1_uc003yfe.1_Intron|RUNX1T1_uc010mao.2_Intron|RUNX1T1_uc011lgi.1_Intron|RUNX1T1_uc003yfh.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	93076849	93076849	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:93076849delT	uc003yfd.2	-						RUNX1T1_uc003yfc.1_5'Flank|RUNX1T1_uc003yfe.1_Intron|RUNX1T1_uc010mao.2_Intron|RUNX1T1_uc011lgi.1_Intron|RUNX1T1_uc003yfh.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	93165362	93165371	+	IGR	DEL	TTTTTTTTTT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:93165362_93165371delTTTTTTTTTT								RUNX1T1 (57656 upstream) : C8orf83 (730494 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	93736914	93736914	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:93736914delT	uc003yfj.1	-											Homo sapiens cDNA FLJ46284 fis, clone TESTI4031818.																														---	---	---	---
Unknown	0	broad.mit.edu	37	8	93766381	93766382	+	Intron	DEL	CA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:93766381_93766382delCA	uc003yfj.1	-											Homo sapiens cDNA FLJ46284 fis, clone TESTI4031818.																														---	---	---	---
C8orf83	286144	broad.mit.edu	37	8	93957871	93957871	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:93957871delT	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	94203752	94203752	+	IGR	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:94203752delG								C8orf83 (173851 upstream) : FAM92A1 (509021 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	94230541	94230541	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:94230541delT								C8orf83 (200640 upstream) : FAM92A1 (482232 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	94462035	94462035	+	IGR	DEL	A	-	-	rs77531634		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:94462035delA								C8orf83 (432134 upstream) : FAM92A1 (250738 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	94492917	94492920	+	IGR	DEL	AAAA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:94492917_94492920delAAAA								C8orf83 (463016 upstream) : FAM92A1 (219853 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	94580971	94580971	+	IGR	DEL	A	-	-	rs76284534		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:94580971delA								C8orf83 (551070 upstream) : FAM92A1 (131802 downstream)																																			---	---	---	---
RBM12B	389677	broad.mit.edu	37	8	94749438	94749438	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:94749438delA	uc003yfz.2	-						C8orf39_uc011lgj.1_5'Flank	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)															---	---	---	---
TMEM67	91147	broad.mit.edu	37	8	94794155	94794155	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:94794155delT	uc011lgk.1	+						TMEM67_uc010mat.1_Intron|TMEM67_uc010maw.2_Intron|TMEM67_uc003yga.3_Intron	NM_153704	NP_714915			meckelin isoform 1						cilium assembly|ER-associated protein catabolic process|negative regulation of centrosome duplication	centrosome|cilium membrane|cytoplasmic vesicle membrane|endoplasmic reticulum membrane|integral to membrane|microtubule basal body	unfolded protein binding			ovary(2)	2	Breast(36;4.14e-07)		BRCA - Breast invasive adenocarcinoma(8;0.00896)															---	---	---	---
TMEM67	91147	broad.mit.edu	37	8	94817178	94817178	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:94817178delA	uc011lgk.1	+						TMEM67_uc010maw.2_Intron|TMEM67_uc003yga.3_Intron|TMEM67_uc011lgl.1_Intron	NM_153704	NP_714915			meckelin isoform 1						cilium assembly|ER-associated protein catabolic process|negative regulation of centrosome duplication	centrosome|cilium membrane|cytoplasmic vesicle membrane|endoplasmic reticulum membrane|integral to membrane|microtubule basal body	unfolded protein binding			ovary(2)	2	Breast(36;4.14e-07)		BRCA - Breast invasive adenocarcinoma(8;0.00896)															---	---	---	---
Unknown	0	broad.mit.edu	37	8	94896430	94896430	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:94896430delT								TMEM67 (66084 upstream) : PDP1 (32653 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	94911814	94911814	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:94911814delT								TMEM67 (81468 upstream) : PDP1 (17269 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	94921283	94921284	+	IGR	DEL	TT	-	-	rs112659325		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:94921283_94921284delTT								TMEM67 (90937 upstream) : PDP1 (7799 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	94969529	94969529	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:94969529delT								PDP1 (31235 upstream) : CDH17 (169865 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	95091634	95091634	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:95091634delA								PDP1 (153340 upstream) : CDH17 (47760 downstream)																																	OREG0018867	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
CDH17	1015	broad.mit.edu	37	8	95214102	95214102	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:95214102delT	uc003ygh.2	-						CDH17_uc011lgo.1_Intron|CDH17_uc011lgp.1_Intron	NM_004063	NP_004054			cadherin 17 precursor							integral to membrane	calcium ion binding			ovary(5)|skin(1)	6	Breast(36;4.65e-06)		BRCA - Breast invasive adenocarcinoma(8;0.00691)															---	---	---	---
RAD54B	25788	broad.mit.edu	37	8	95464092	95464092	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:95464092delA	uc003ygk.2	-						RAD54B_uc003ygl.1_Intron|RAD54B_uc003ygn.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					---	---	---	---
KIAA1429	25962	broad.mit.edu	37	8	95536229	95536230	+	Intron	INS	-	TTTA	TTTA	rs144503026	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:95536229_95536230insTTTA	uc003ygo.1	-						KIAA1429_uc003ygp.2_Intron|KIAA1429_uc010maz.1_Intron	NM_015496	NP_056311			hypothetical protein LOC25962 isoform 1						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	95550837	95550837	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:95550837delT	uc003ygo.1	-						KIAA1429_uc003ygp.2_Intron	NM_015496	NP_056311			hypothetical protein LOC25962 isoform 1						mRNA processing|RNA splicing	nucleus				ovary(1)|skin(1)	2	Breast(36;3.29e-05)		BRCA - Breast invasive adenocarcinoma(8;0.00185)															---	---	---	---
Unknown	0	broad.mit.edu	37	8	95615711	95615711	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:95615711delA								KIAA1429 (50023 upstream) : ESRP1 (37653 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	95829559	95829560	+	IGR	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:95829559_95829560delAA								DPY19L4 (23483 upstream) : INTS8 (5974 downstream)																																			---	---	---	---
INTS8	55656	broad.mit.edu	37	8	95886162	95886162	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:95886162delT	uc003yhb.2	+						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)																	---	---	---	---
C8orf38	137682	broad.mit.edu	37	8	96002752	96002753	+	Intron	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:96002752_96002753delAA	uc003yhi.2	+						C8orf38_uc003yhe.1_Intron|C8orf38_uc003yhf.2_Intron	NM_152416	NP_689629			hypothetical protein LOC137682 precursor						biosynthetic process	mitochondrion	transferase activity				0	Breast(36;3.32e-06)																	---	---	---	---
C8orf38	137682	broad.mit.edu	37	8	96006763	96006766	+	Intron	DEL	AAAA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:96006763_96006766delAAAA	uc003yhi.2	+						C8orf38_uc003yhe.1_Intron|C8orf38_uc003yhf.2_Intron	NM_152416	NP_689629			hypothetical protein LOC137682 precursor						biosynthetic process	mitochondrion	transferase activity				0	Breast(36;3.32e-06)																	---	---	---	---
C8orf38	137682	broad.mit.edu	37	8	96025335	96025335	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:96025335delT	uc003yhi.2	+						C8orf38_uc003yhe.1_Intron|C8orf38_uc003yhf.2_Intron	NM_152416	NP_689629			hypothetical protein LOC137682 precursor						biosynthetic process	mitochondrion	transferase activity				0	Breast(36;3.32e-06)																	---	---	---	---
Unknown	0	broad.mit.edu	37	8	96442837	96442838	+	IGR	INS	-	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:96442837_96442838insG								C8orf37 (161400 upstream) : GDF6 (711722 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	96530405	96530406	+	IGR	INS	-	T	T	rs141674282	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:96530405_96530406insT								C8orf37 (248968 upstream) : GDF6 (624154 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	96540458	96540458	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:96540458delA								C8orf37 (259021 upstream) : GDF6 (614102 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	96743189	96743189	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:96743189delA								C8orf37 (461752 upstream) : GDF6 (411371 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	97220202	97220202	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:97220202delA								GDF6 (47182 upstream) : UQCRB (19108 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	97642345	97642345	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:97642345delA								SDC2 (18308 upstream) : PGCP (15154 downstream)																																			---	---	---	---
PGCP	10404	broad.mit.edu	37	8	97791980	97791980	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:97791980delT	uc003yhw.2	+							NM_016134	NP_057218			plasma glutamate carboxypeptidase precursor						peptide metabolic process|proteolysis	cytoplasm|extracellular space	metal ion binding|metallocarboxypeptidase activity			upper_aerodigestive_tract(1)	1	Breast(36;1.86e-05)																	---	---	---	---
PGCP	10404	broad.mit.edu	37	8	97829841	97829842	+	Intron	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:97829841_97829842delTT	uc003yhw.2	+						PGCP_uc010mbe.2_Intron	NM_016134	NP_057218			plasma glutamate carboxypeptidase precursor						peptide metabolic process|proteolysis	cytoplasm|extracellular space	metal ion binding|metallocarboxypeptidase activity			upper_aerodigestive_tract(1)	1	Breast(36;1.86e-05)																	---	---	---	---
PGCP	10404	broad.mit.edu	37	8	97912184	97912184	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:97912184delA	uc003yhw.2	+						PGCP_uc010mbe.2_Intron	NM_016134	NP_057218			plasma glutamate carboxypeptidase precursor						peptide metabolic process|proteolysis	cytoplasm|extracellular space	metal ion binding|metallocarboxypeptidase activity			upper_aerodigestive_tract(1)	1	Breast(36;1.86e-05)																	---	---	---	---
PGCP	10404	broad.mit.edu	37	8	97914256	97914256	+	Intron	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:97914256delG	uc003yhw.2	+						PGCP_uc010mbe.2_Intron	NM_016134	NP_057218			plasma glutamate carboxypeptidase precursor						peptide metabolic process|proteolysis	cytoplasm|extracellular space	metal ion binding|metallocarboxypeptidase activity			upper_aerodigestive_tract(1)	1	Breast(36;1.86e-05)																	---	---	---	---
PGCP	10404	broad.mit.edu	37	8	97991279	97991280	+	Intron	DEL	AA	-	-	rs35073062		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:97991279_97991280delAA	uc003yhw.2	+							NM_016134	NP_057218			plasma glutamate carboxypeptidase precursor						peptide metabolic process|proteolysis	cytoplasm|extracellular space	metal ion binding|metallocarboxypeptidase activity			upper_aerodigestive_tract(1)	1	Breast(36;1.86e-05)																	---	---	---	---
PGCP	10404	broad.mit.edu	37	8	98111779	98111780	+	Intron	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:98111779_98111780delTT	uc003yhw.2	+							NM_016134	NP_057218			plasma glutamate carboxypeptidase precursor						peptide metabolic process|proteolysis	cytoplasm|extracellular space	metal ion binding|metallocarboxypeptidase activity			upper_aerodigestive_tract(1)	1	Breast(36;1.86e-05)																	---	---	---	---
PGCP	10404	broad.mit.edu	37	8	98121875	98121875	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:98121875delT	uc003yhw.2	+							NM_016134	NP_057218			plasma glutamate carboxypeptidase precursor						peptide metabolic process|proteolysis	cytoplasm|extracellular space	metal ion binding|metallocarboxypeptidase activity			upper_aerodigestive_tract(1)	1	Breast(36;1.86e-05)																	---	---	---	---
Unknown	0	broad.mit.edu	37	8	98449163	98449164	+	IGR	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:98449163_98449164delAA								TSPYL5 (158987 upstream) : MTDH (207243 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	98459294	98459297	+	IGR	DEL	TTTT	-	-	rs72408932		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:98459294_98459297delTTTT								TSPYL5 (169118 upstream) : MTDH (197110 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	98549125	98549125	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:98549125delT								TSPYL5 (258949 upstream) : MTDH (107282 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	98618748	98618748	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:98618748delT								TSPYL5 (328572 upstream) : MTDH (37659 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	98642341	98642343	+	IGR	DEL	AGG	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:98642341_98642343delAGG								TSPYL5 (352165 upstream) : MTDH (14064 downstream)																																			---	---	---	---
MTDH	92140	broad.mit.edu	37	8	98723801	98723801	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:98723801delA	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)															---	---	---	---
Unknown	0	broad.mit.edu	37	8	98746925	98746925	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:98746925delA								MTDH (4438 upstream) : LAPTM4B (40884 downstream)																																			---	---	---	---
LAPTM4B	55353	broad.mit.edu	37	8	98787753	98787754	+	5'Flank	DEL	AA	-	-	rs112936102		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:98787753_98787754delAA	uc003yia.2	+						LAPTM4B_uc010mbg.2_5'Flank	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)															---	---	---	---
LAPTM4B	55353	broad.mit.edu	37	8	98796648	98796648	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:98796648delT	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)															---	---	---	---
Unknown	0	broad.mit.edu	37	8	98876473	98876476	+	IGR	DEL	TTTT	-	-	rs35727614		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:98876473_98876476delTTTT								LAPTM4B (11644 upstream) : MATN2 (4835 downstream)																																			---	---	---	---
MATN2	4147	broad.mit.edu	37	8	98945384	98945384	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:98945384delA	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)															---	---	---	---
MATN2	4147	broad.mit.edu	37	8	98981850	98981851	+	Intron	DEL	AA	-	-	rs2512041	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:98981850_98981851delAA	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)															---	---	---	---
MATN2	4147	broad.mit.edu	37	8	98999070	98999070	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:98999070delT	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)															---	---	---	---
MATN2	4147	broad.mit.edu	37	8	99026335	99026336	+	Intron	INS	-	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:99026335_99026336insA	uc003yic.2	+						MATN2_uc010mbh.1_Intron|MATN2_uc003yid.2_Intron|MATN2_uc003yie.1_Intron|MATN2_uc010mbi.1_Intron|MATN2_uc010mbj.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)															---	---	---	---
Unknown	0	broad.mit.edu	37	8	99181583	99181583	+	IGR	DEL	T	-	-	rs111539653		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:99181583delT								POP1 (9515 upstream) : NIPAL2 (22804 downstream)																																			---	---	---	---
STK3	6788	broad.mit.edu	37	8	99467038	99467038	+	3'UTR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:99467038delT	uc003yip.2	-	11					STK3_uc003yio.2_3'UTR	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	99697193	99697194	+	Intron	INS	-	TG	TG	rs143370118	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:99697193_99697194insTG	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	99771869	99771869	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:99771869delA	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	99773094	99773094	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:99773094delA	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	99889699	99889699	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:99889699delT	uc003yio.2	-							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)														---	---	---	---
Unknown	0	broad.mit.edu	37	8	99996720	99996721	+	IGR	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:99996720_99996721delAA								OSR2 (32396 upstream) : VPS13B (28773 downstream)																																			---	---	---	---
VPS13B	157680	broad.mit.edu	37	8	100046124	100046124	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:100046124delA	uc003yiv.2	+						VPS13B_uc003yiw.2_Intron|VPS13B_uc003yit.2_Intron|VPS13B_uc003yiu.1_Intron|VPS13B_uc003yis.2_Intron|VPS13B_uc011lgy.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	100089408	100089408	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:100089408delT	uc003yiv.2	+						VPS13B_uc003yiw.2_Intron|VPS13B_uc003yit.2_Intron|VPS13B_uc003yiu.1_Intron|VPS13B_uc003yis.2_Intron|VPS13B_uc011lgy.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	100255707	100255707	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:100255707delT	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	100676543	100676546	+	Intron	DEL	TTTT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:100676543_100676546delTTTT	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	100730293	100730294	+	Intron	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:100730293_100730294delTT	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)															---	---	---	---
RGS22	26166	broad.mit.edu	37	8	101105392	101105392	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:101105392delA	uc003yjb.1	-						RGS22_uc003yja.1_Intron|RGS22_uc003yjc.1_Intron|RGS22_uc010mbo.1_Intron	NM_015668	NP_056483			regulator of G-protein signaling 22						negative regulation of signal transduction	cytoplasm|plasma membrane	GTPase activator activity|signal transducer activity			ovary(3)|skin(2)|breast(1)|central_nervous_system(1)	7			Epithelial(11;6.71e-08)|all cancers(13;4.19e-06)|OV - Ovarian serous cystadenocarcinoma(57;0.000469)|STAD - Stomach adenocarcinoma(118;0.169)															---	---	---	---
SPAG1	6674	broad.mit.edu	37	8	101184863	101184870	+	Intron	DEL	TGTGTGTG	-	-	rs33985708		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:101184863_101184870delTGTGTGTG	uc003yjh.1	+						SPAG1_uc003yjg.1_Intron|SPAG1_uc003yji.1_Intron	NM_172218	NP_757367			sperm associated antigen 1						single fertilization	cytoplasm	GTP binding|hydrolase activity			ovary(2)|central_nervous_system(1)	3	all_cancers(14;2.35e-05)|all_epithelial(15;5.2e-08)|Lung NSC(17;0.000283)|all_lung(17;0.000823)	Breast(495;0.195)	Epithelial(11;1.12e-09)|all cancers(13;1.26e-07)|OV - Ovarian serous cystadenocarcinoma(57;4.37e-05)|STAD - Stomach adenocarcinoma(118;0.0525)	KIRC - Kidney renal clear cell carcinoma(542;0.00178)|READ - Rectum adenocarcinoma(644;0.236)														---	---	---	---
Unknown	0	broad.mit.edu	37	8	101355682	101355683	+	IGR	INS	-	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:101355682_101355683insT								RNF19A (33355 upstream) : ANKRD46 (166304 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	101714843	101714843	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:101714843delA								SNX31 (52950 upstream) : PABPC1 (301 downstream)																																			---	---	---	---
PABPC1	26986	broad.mit.edu	37	8	101728028	101728028	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:101728028delA	uc003yjs.1	-						PABPC1_uc011lhc.1_Intron|PABPC1_uc011lhd.1_Intron|PABPC1_uc003yjt.1_Intron|PABPC1_uc003yju.2_Intron	NM_002568	NP_002559			poly(A) binding protein, cytoplasmic 1						mRNA polyadenylation|mRNA stabilization|negative regulation of nuclear-transcribed mRNA catabolic process, nonsense-mediated decay|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay|nuclear-transcribed mRNA poly(A) tail shortening|translation	catalytic step 2 spliceosome|cytosol	nucleotide binding|poly(A) RNA binding|protein C-terminus binding|translation activator activity				0	all_cancers(14;6.8e-05)|all_epithelial(15;3.16e-07)|Lung NSC(17;0.000453)|all_lung(17;0.00125)		Epithelial(11;6.37e-11)|all cancers(13;1.11e-08)|OV - Ovarian serous cystadenocarcinoma(57;3.91e-05)|STAD - Stomach adenocarcinoma(118;0.206)															---	---	---	---
YWHAZ	7534	broad.mit.edu	37	8	101936665	101936666	+	Intron	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:101936665_101936666delTT	uc011lhe.1	-						YWHAZ_uc003yjv.2_Intron|YWHAZ_uc011lhf.1_Intron|YWHAZ_uc003yjw.2_Intron|YWHAZ_uc010mbq.2_Intron|YWHAZ_uc011lhg.1_Intron|YWHAZ_uc010mbr.2_Intron|YWHAZ_uc003yjx.2_Intron|YWHAZ_uc003yjy.2_Intron	NM_001135702	NP_001129174			tyrosine 3/tryptophan 5 -monooxygenase						anti-apoptosis|mRNA metabolic process|platelet activation|signal transduction	cytosol|melanosome	transcription factor binding				0	all_cancers(14;7.43e-06)|all_epithelial(15;2.77e-08)|Lung NSC(17;6.08e-05)|all_lung(17;0.000197)		Epithelial(11;2.79e-11)|all cancers(13;5.45e-09)|OV - Ovarian serous cystadenocarcinoma(57;4.75e-05)		Ginkgo biloba(DB01381)													---	---	---	---
Unknown	0	broad.mit.edu	37	8	101979901	101979901	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:101979901delT								YWHAZ (14278 upstream) : ZNF706 (229367 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	102165852	102165852	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:102165852delA								YWHAZ (200229 upstream) : ZNF706 (43416 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	102230755	102230755	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:102230755delA								ZNF706 (12795 upstream) : NACAP1 (143267 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	102390787	102390787	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:102390787delT								NACAP1 (5852 upstream) : GRHL2 (113881 downstream)																																			---	---	---	---
GRHL2	79977	broad.mit.edu	37	8	102615302	102615303	+	Intron	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:102615302_102615303delAA	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)															---	---	---	---
GRHL2	79977	broad.mit.edu	37	8	102659979	102659979	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:102659979delT	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)															---	---	---	---
NCALD	83988	broad.mit.edu	37	8	102769894	102769894	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:102769894delT	uc003yke.2	-						NCALD_uc003ykf.2_Intron|NCALD_uc003ykg.2_Intron|NCALD_uc003ykh.2_Intron|NCALD_uc003yki.2_Intron|NCALD_uc003ykj.2_Intron|NCALD_uc003ykk.2_Intron|NCALD_uc003ykl.2_Intron	NM_032041	NP_114430			neurocalcin delta						synaptic transmission|vesicle-mediated transport	clathrin coat of trans-Golgi network vesicle|cytosol	actin binding|calcium ion binding|clathrin binding|tubulin binding				0	all_cancers(14;8.94e-08)|all_epithelial(15;7.03e-10)|Lung NSC(17;1.36e-05)|all_lung(17;2.7e-05)		all cancers(13;1.09e-06)|OV - Ovarian serous cystadenocarcinoma(57;0.000699)															---	---	---	---
NCALD	83988	broad.mit.edu	37	8	102829200	102829200	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:102829200delA	uc003ykf.2	-						NCALD_uc003ykg.2_Intron|NCALD_uc003ykh.2_Intron|NCALD_uc003yki.2_Intron|NCALD_uc003ykj.2_Intron|NCALD_uc003ykk.2_Intron|NCALD_uc003ykl.2_Intron	NM_001040628	NP_001035718			neurocalcin delta						synaptic transmission|vesicle-mediated transport	clathrin coat of trans-Golgi network vesicle|cytosol	actin binding|calcium ion binding|clathrin binding|tubulin binding				0	all_cancers(14;8.94e-08)|all_epithelial(15;7.03e-10)|Lung NSC(17;1.36e-05)|all_lung(17;2.7e-05)		all cancers(13;1.09e-06)|OV - Ovarian serous cystadenocarcinoma(57;0.000699)															---	---	---	---
RRM2B	50484	broad.mit.edu	37	8	103238407	103238407	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:103238407delA	uc003ykn.2	-						RRM2B_uc003yko.2_Intron|RRM2B_uc010mbv.1_Intron|RRM2B_uc010mbw.1_Intron|RRM2B_uc010mbx.1_Intron|RRM2B_uc010mby.1_Intron	NM_015713	NP_056528			ribonucleotide reductase M2 B (TP53 inducible)						deoxyribonucleoside diphosphate metabolic process|DNA repair|nucleobase, nucleoside and nucleotide interconversion	nucleoplasm	ribonucleoside-diphosphate reductase activity|transition metal ion binding			ovary(2)	2	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;0.000728)										Direct_reversal_of_damage|Modulation_of_nucleotide_pools					---	---	---	---
UBR5	51366	broad.mit.edu	37	8	103276945	103276945	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:103276945delA	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)															---	---	---	---
UBR5	51366	broad.mit.edu	37	8	103289349	103289349	+	Frame_Shift_Del	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:103289349delT	uc003ykr.1	-	45	6393	c.6360delA	c.(6358-6360)AAAfs	p.K2120fs	UBR5_uc003yks.1_Frame_Shift_Del_p.K2120fs	NM_015902	NP_056986	O95071	UBR5_HUMAN	ubiquitin protein ligase E3 component n-recognin	2120					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	103413005	103413006	+	Intron	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:103413005_103413006delAA	uc003ykr.1	-						UBR5_uc003yks.1_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)															---	---	---	---
KLF10	7071	broad.mit.edu	37	8	103665676	103665676	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:103665676delA	uc011lhk.1	-						KLF10_uc011lhj.1_Intron	NM_005655	NP_005646			Kruppel-like factor 10 isoform a						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)															---	---	---	---
Unknown	0	broad.mit.edu	37	8	103810555	103810555	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:103810555delA								KLF10 (142572 upstream) : AZIN1 (27982 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	103948727	103948727	+	IGR	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:103948727delC								AZIN1 (72330 upstream) : ATP6V1C1 (84521 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	103963545	103963545	+	IGR	DEL	A	-	-	rs72222713		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:103963545delA								AZIN1 (87148 upstream) : ATP6V1C1 (69703 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	103966330	103966332	+	IGR	DEL	TTT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:103966330_103966332delTTT								AZIN1 (89933 upstream) : ATP6V1C1 (66916 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	103988133	103988136	+	IGR	DEL	AAAA	-	-	rs11364478		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:103988133_103988136delAAAA								AZIN1 (111736 upstream) : ATP6V1C1 (45112 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	104009402	104009403	+	IGR	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:104009402_104009403delAA								AZIN1 (133005 upstream) : ATP6V1C1 (23845 downstream)																																			---	---	---	---
ATP6V1C1	528	broad.mit.edu	37	8	104032070	104032070	+	5'Flank	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:104032070delA	uc003ykz.3	+						ATP6V1C1_uc010mbz.2_5'Flank|ATP6V1C1_uc003yla.2_5'Flank|ATP6V1C1_uc011lhl.1_5'Flank	NM_001695	NP_001686			ATPase, H+ transporting, lysosomal V1 subunit						ATP hydrolysis coupled proton transport|cellular iron ion homeostasis|insulin receptor signaling pathway|transferrin transport	cytosol|plasma membrane|proton-transporting V-type ATPase, V1 domain	protein binding|proton-transporting ATPase activity, rotational mechanism				0	Lung NSC(17;0.000427)|all_lung(17;0.000533)		OV - Ovarian serous cystadenocarcinoma(57;3.57e-05)|STAD - Stomach adenocarcinoma(118;0.133)															---	---	---	---
Unknown	0	broad.mit.edu	37	8	104105920	104105921	+	IGR	DEL	TA	-	-	rs10100696	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:104105920_104105921delTA								ATP6V1C1 (20636 upstream) : C8orf56 (39271 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	104296205	104296205	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:104296205delT	uc003ylf.2	-											Homo sapiens cDNA FLJ43745 fis, clone TESTI2019648.																														---	---	---	---
RIMS2	9699	broad.mit.edu	37	8	104591570	104591570	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:104591570delA	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)			---	---	---	---
RIMS2	9699	broad.mit.edu	37	8	104647073	104647073	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:104647073delT	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)			---	---	---	---
RIMS2	9699	broad.mit.edu	37	8	104710212	104710213	+	Intron	INS	-	G	G	rs142428540	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:104710212_104710213insG	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)			---	---	---	---
RIMS2	9699	broad.mit.edu	37	8	104785162	104785163	+	Intron	INS	-	A	A	rs137890647	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:104785162_104785163insA	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)			---	---	---	---
RIMS2	9699	broad.mit.edu	37	8	104832598	104832598	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:104832598delA	uc003ylp.2	+						RIMS2_uc003ylw.2_Intron|RIMS2_uc003ylq.2_Intron|RIMS2_uc003ylr.2_Intron	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)			---	---	---	---
RIMS2	9699	broad.mit.edu	37	8	104945721	104945721	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:104945721delA	uc003yls.2	+						RIMS2_uc003ylp.2_Intron|RIMS2_uc003ylw.2_Intron|RIMS2_uc003ylq.2_Intron|RIMS2_uc003ylr.2_Intron|RIMS2_uc003ylt.2_Intron	NM_014677	NP_055492			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)			---	---	---	---
RIMS2	9699	broad.mit.edu	37	8	105016746	105016746	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:105016746delA	uc003yls.2	+						RIMS2_uc003ylp.2_Intron|RIMS2_uc003ylw.2_Intron|RIMS2_uc003ylq.2_Intron|RIMS2_uc003ylr.2_Intron	NM_014677	NP_055492			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)			---	---	---	---
Unknown	0	broad.mit.edu	37	8	105266432	105266433	+	IGR	INS	-	TT	TT	rs145076961	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:105266432_105266433insTT								RIMS2 (981 upstream) : TM7SF4 (85621 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	105384320	105384321	+	IGR	DEL	CT	-	-	rs147064189		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:105384320_105384321delCT								TM7SF4 (15404 upstream) : DPYS (7332 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	105384651	105384651	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:105384651delT								TM7SF4 (15735 upstream) : DPYS (7002 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	105492984	105492984	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:105492984delT								DPYS (13707 upstream) : MIR548A3 (3613 downstream)																																			---	---	---	---
LRP12	29967	broad.mit.edu	37	8	105562299	105562299	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:105562299delT	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	105576859	105576859	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:105576859delA	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	105587839	105587839	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:105587839delA	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	105679998	105679998	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:105679998delA								LRP12 (78778 upstream) : ZFPM2 (651149 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	105779233	105779238	+	IGR	DEL	GTGTGT	-	-	rs34403551		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:105779233_105779238delGTGTGT								LRP12 (178013 upstream) : ZFPM2 (551909 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	105891897	105891897	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:105891897delT								LRP12 (290677 upstream) : ZFPM2 (439250 downstream)																																			---	---	---	---
ZFPM2	23414	broad.mit.edu	37	8	106364816	106364817	+	Intron	DEL	TT	-	-	rs72068796		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:106364816_106364817delTT	uc003ymd.2	+							NM_012082	NP_036214			zinc finger protein, multitype 2						blood coagulation|negative regulation of fat cell differentiation|outflow tract septum morphogenesis|right ventricular cardiac muscle tissue morphogenesis|ventricular septum morphogenesis	nucleoplasm	DNA binding|RNA polymerase II transcription coactivator activity|transcription corepressor activity|transcription factor binding|zinc ion binding			ovary(4)|large_intestine(1)	5			OV - Ovarian serous cystadenocarcinoma(57;8.28e-08)															---	---	---	---
ZFPM2	23414	broad.mit.edu	37	8	106495982	106495984	+	Intron	DEL	TTT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:106495982_106495984delTTT	uc003ymd.2	+							NM_012082	NP_036214			zinc finger protein, multitype 2						blood coagulation|negative regulation of fat cell differentiation|outflow tract septum morphogenesis|right ventricular cardiac muscle tissue morphogenesis|ventricular septum morphogenesis	nucleoplasm	DNA binding|RNA polymerase II transcription coactivator activity|transcription corepressor activity|transcription factor binding|zinc ion binding			ovary(4)|large_intestine(1)	5			OV - Ovarian serous cystadenocarcinoma(57;8.28e-08)															---	---	---	---
Unknown	0	broad.mit.edu	37	8	106928386	106928387	+	IGR	INS	-	C	C	rs144108463	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:106928386_106928387insC								ZFPM2 (111621 upstream) : OXR1 (354086 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	107067405	107067405	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:107067405delT								ZFPM2 (250640 upstream) : OXR1 (215068 downstream)																																			---	---	---	---
OXR1	55074	broad.mit.edu	37	8	107299885	107299885	+	Intron	DEL	A	-	-	rs35486315		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:107299885delA	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	107314511	107314511	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:107314511delA	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	107488120	107488120	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:107488120delT	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)															---	---	---	---
OXR1	55074	broad.mit.edu	37	8	107584063	107584064	+	Intron	INS	-	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:107584063_107584064insA	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)															---	---	---	---
OXR1	55074	broad.mit.edu	37	8	107620559	107620559	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:107620559delA	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)															---	---	---	---
OXR1	55074	broad.mit.edu	37	8	107722696	107722696	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:107722696delA	uc011lht.1	+						OXR1_uc003ymf.2_Intron|OXR1_uc011lhu.1_Intron|OXR1_uc010mcg.2_Intron|OXR1_uc010mch.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	107856991	107856991	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:107856991delA								ABRA (74519 upstream) : ANGPT1 (404720 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	107938347	107938347	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:107938347delT								ABRA (155875 upstream) : ANGPT1 (323364 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	108685554	108685555	+	IGR	INS	-	ACAC	ACAC	rs148313172	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:108685554_108685555insACAC								ANGPT1 (175300 upstream) : RSPO2 (225990 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	108716576	108716579	+	IGR	DEL	AGAG	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:108716576_108716579delAGAG								ANGPT1 (206322 upstream) : RSPO2 (194966 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	108838311	108838313	+	IGR	DEL	AAA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:108838311_108838313delAAA								ANGPT1 (328057 upstream) : RSPO2 (73232 downstream)																																			---	---	---	---
RSPO2	340419	broad.mit.edu	37	8	108912256	108912256	+	3'UTR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:108912256delA	uc003yms.2	-	6					RSPO2_uc003ymq.2_3'UTR|RSPO2_uc003ymr.2_3'UTR	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)															---	---	---	---
RSPO2	340419	broad.mit.edu	37	8	109029199	109029199	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:109029199delA	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)															---	---	---	---
RSPO2	340419	broad.mit.edu	37	8	109087709	109087713	+	Intron	DEL	AAAAA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:109087709_109087713delAAAAA	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	109108316	109108319	+	IGR	DEL	AGGA	-	-	rs1799713	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:109108316_109108319delAGGA								RSPO2 (12403 upstream) : EIF3E (105654 downstream)																																			---	---	---	---
EIF3E	3646	broad.mit.edu	37	8	109234404	109234405	+	Intron	INS	-	G	G	rs143079793	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:109234404_109234405insG	uc003ymu.2	-						EIF3E_uc003ymt.2_Intron|EIF3E_uc003ymv.2_Intron|EIF3E_uc010mci.1_Intron	NM_001568	NP_001559			eukaryotic translation initiation factor 3,						negative regulation of translational initiation|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay	cytosol|eukaryotic translation initiation factor 3 complex|PML body	protein N-terminus binding			ovary(2)|kidney(1)	3			OV - Ovarian serous cystadenocarcinoma(57;6.84e-10)															---	---	---	---
EIF3E	3646	broad.mit.edu	37	8	109245907	109245907	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:109245907delA	uc003ymu.2	-						EIF3E_uc003ymt.2_Intron|EIF3E_uc003ymv.2_Intron|EIF3E_uc010mci.1_Intron	NM_001568	NP_001559			eukaryotic translation initiation factor 3,						negative regulation of translational initiation|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay	cytosol|eukaryotic translation initiation factor 3 complex|PML body	protein N-terminus binding			ovary(2)|kidney(1)	3			OV - Ovarian serous cystadenocarcinoma(57;6.84e-10)															---	---	---	---
Unknown	0	broad.mit.edu	37	8	109556063	109556063	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:109556063delT								TTC35 (56927 upstream) : TMEM74 (63017 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	109857734	109857735	+	IGR	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:109857734_109857735delTT								TMEM74 (57964 upstream) : TRHR (242004 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	109867985	109867985	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:109867985delA								TMEM74 (68215 upstream) : TRHR (231754 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	110196351	110196351	+	IGR	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:110196351delC								TRHR (64541 upstream) : NUDCD1 (56798 downstream)																																			---	---	---	---
NUDCD1	84955	broad.mit.edu	37	8	110274248	110274248	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:110274248delA	uc003ynb.3	-						NUDCD1_uc003yna.2_Intron|NUDCD1_uc010mcl.2_Intron	NM_032869	NP_116258			NudC domain containing 1 isoform 1											ovary(1)|breast(1)	2	all_neural(195;0.219)		OV - Ovarian serous cystadenocarcinoma(57;1.56e-12)															---	---	---	---
ENY2	56943	broad.mit.edu	37	8	110350129	110350129	+	Intron	DEL	A	-	-	rs113480072		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:110350129delA	uc003ynd.2	+						ENY2_uc003ync.2_Intron	NM_020189	NP_064574			enhancer of yellow 2 homolog						histone deubiquitination|mRNA transport|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	SAGA complex	ligand-dependent nuclear receptor transcription coactivator activity				0	all_neural(195;0.219)		OV - Ovarian serous cystadenocarcinoma(57;9.05e-13)															---	---	---	---
PKHD1L1	93035	broad.mit.edu	37	8	110473965	110473965	+	Intron	DEL	A	-	-	rs144083788	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:110473965delA	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)			---	---	---	---
Unknown	0	broad.mit.edu	37	8	110546016	110546016	+	IGR	DEL	A	-	-	rs76484491		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:110546016delA								PKHD1L1 (2517 upstream) : EBAG9 (5913 downstream)																																			---	---	---	---
SYBU	55638	broad.mit.edu	37	8	110683464	110683464	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:110683464delT	uc010mct.2	-						SYBU_uc010mcs.2_Intron|SYBU_uc010mcu.2_Intron|SYBU_uc003ynp.3_Intron|SYBU_uc010mcv.2_Intron	NM_001099745	NP_001093215			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	110741416	110741416	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:110741416delT								SYBU (37396 upstream) : KCNV1 (237819 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	110745182	110745182	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:110745182delT								SYBU (41162 upstream) : KCNV1 (234053 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	110760496	110760496	+	IGR	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:110760496delG								SYBU (56476 upstream) : KCNV1 (218739 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	110806862	110806862	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:110806862delA								SYBU (102842 upstream) : KCNV1 (172373 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	110993675	110993680	+	IGR	DEL	AAAAAA	-	-	rs79723542		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:110993675_110993680delAAAAAA								KCNV1 (5599 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	111097341	111097341	+	IGR	DEL	T	-	-	rs34607393		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:111097341delT								KCNV1 (109265 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	111119257	111119257	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:111119257delA								KCNV1 (131181 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	111402247	111402247	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:111402247delT								KCNV1 (414171 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	111638960	111638960	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:111638960delT								KCNV1 (650884 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	111648236	111648236	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:111648236delA								KCNV1 (660160 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	111794856	111794856	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:111794856delT								KCNV1 (806780 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	112045122	112045122	+	IGR	DEL	A	-	-	rs73318801	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:112045122delA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	112364661	112364661	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:112364661delA								None (None upstream) : CSMD3 (870500 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	112603662	112603663	+	IGR	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:112603662_112603663delAA								None (None upstream) : CSMD3 (631498 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	112997093	112997093	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:112997093delT								None (None upstream) : CSMD3 (238068 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	113203597	113203597	+	IGR	DEL	A	-	-	rs6469407	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:113203597delA								None (None upstream) : CSMD3 (31564 downstream)																																			---	---	---	---
CSMD3	114788	broad.mit.edu	37	8	113243713	113243713	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:113243713delT	uc003ynu.2	-						CSMD3_uc003yns.2_Intron|CSMD3_uc003ynt.2_Intron|CSMD3_uc011lhx.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)			---	---	---	---
CSMD3	114788	broad.mit.edu	37	8	113333278	113333278	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:113333278delA	uc003ynu.2	-						CSMD3_uc003yns.2_Intron|CSMD3_uc003ynt.2_Intron|CSMD3_uc011lhx.1_Intron|CSMD3_uc003ynw.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)			---	---	---	---
CSMD3	114788	broad.mit.edu	37	8	113435369	113435369	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:113435369delT	uc003ynu.2	-						CSMD3_uc003yns.2_Intron|CSMD3_uc003ynt.2_Intron|CSMD3_uc011lhx.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)			---	---	---	---
CSMD3	114788	broad.mit.edu	37	8	113683477	113683478	+	Intron	INS	-	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:113683477_113683478insT	uc003ynu.2	-						CSMD3_uc003yns.2_Intron|CSMD3_uc003ynt.2_Intron|CSMD3_uc011lhx.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)			---	---	---	---
CSMD3	114788	broad.mit.edu	37	8	113742962	113742962	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:113742962delT	uc003ynu.2	-						CSMD3_uc003ynt.2_Intron|CSMD3_uc011lhx.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)			---	---	---	---
CSMD3	114788	broad.mit.edu	37	8	113863558	113863558	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:113863558delA	uc003ynu.2	-						CSMD3_uc003ynt.2_Intron|CSMD3_uc011lhx.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)			---	---	---	---
CSMD3	114788	broad.mit.edu	37	8	113945803	113945803	+	Intron	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:113945803delG	uc003ynu.2	-						CSMD3_uc003ynt.2_Intron|CSMD3_uc011lhx.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)			---	---	---	---
CSMD3	114788	broad.mit.edu	37	8	114183506	114183506	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:114183506delA	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)			---	---	---	---
CSMD3	114788	broad.mit.edu	37	8	114240808	114240808	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:114240808delA	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)			---	---	---	---
CSMD3	114788	broad.mit.edu	37	8	114283215	114283215	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:114283215delA	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)			---	---	---	---
CSMD3	114788	broad.mit.edu	37	8	114351672	114351672	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:114351672delA	uc003ynu.2	-						CSMD3_uc003ynt.2_Intron|CSMD3_uc011lhx.1_Intron|CSMD3_uc010mcx.1_Intron|CSMD3_uc003ynx.3_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)			---	---	---	---
CSMD3	114788	broad.mit.edu	37	8	114443945	114443945	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:114443945delT	uc003ynu.2	-						CSMD3_uc011lhx.1_Intron|CSMD3_uc010mcx.1_Intron|CSMD3_uc003ynx.3_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	114704345	114704345	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:114704345delT								CSMD3 (255103 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	115111548	115111548	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:115111548delA								CSMD3 (662306 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	115342489	115342490	+	IGR	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:115342489_115342490delTT								CSMD3 (893247 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	115765824	115765825	+	IGR	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:115765824_115765825delTT								None (None upstream) : TRPS1 (654900 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	115814953	115814953	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:115814953delT								None (None upstream) : TRPS1 (605772 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	115827164	115827164	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:115827164delA								None (None upstream) : TRPS1 (593561 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	116140916	116140916	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:116140916delA								None (None upstream) : TRPS1 (279809 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	116171979	116171979	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:116171979delT								None (None upstream) : TRPS1 (248746 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	116249210	116249211	+	IGR	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:116249210_116249211delAA								None (None upstream) : TRPS1 (171514 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	116252988	116252988	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:116252988delA								None (None upstream) : TRPS1 (167737 downstream)																																			---	---	---	---
TRPS1	7227	broad.mit.edu	37	8	116524753	116524753	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:116524753delT	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	116578760	116578760	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:116578760delT	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	116675477	116675477	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:116675477delT	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	116680306	116680306	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:116680306delT	uc003ynz.2	-						TRPS1_uc011lhy.1_5'Flank|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	116683468	116683468	+	5'Flank	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:116683468delA	uc003ynz.2	-						TRPS1_uc003yny.2_5'Flank|TRPS1_uc010mcy.2_5'Flank	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	116696348	116696348	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:116696348delA								TRPS1 (15120 upstream) : EIF3H (960708 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	116700597	116700598	+	IGR	DEL	TT	-	-	rs11350250		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:116700597_116700598delTT								TRPS1 (19369 upstream) : EIF3H (956458 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	116778984	116778984	+	IGR	DEL	A	-	-	rs71706620		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:116778984delA								TRPS1 (97756 upstream) : EIF3H (878072 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	116872029	116872029	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:116872029delT								TRPS1 (190801 upstream) : EIF3H (785027 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	116912978	116912978	+	IGR	DEL	C	-	-	rs67444394		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:116912978delC								TRPS1 (231750 upstream) : EIF3H (744078 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	116936357	116936357	+	IGR	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:116936357delC								TRPS1 (255129 upstream) : EIF3H (720699 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	117169889	117169889	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:117169889delA								TRPS1 (488661 upstream) : EIF3H (487167 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	117225204	117225204	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:117225204delA								TRPS1 (543976 upstream) : EIF3H (431852 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	117314218	117314218	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:117314218delA								TRPS1 (632990 upstream) : EIF3H (342838 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	117333999	117333999	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:117333999delT								TRPS1 (652771 upstream) : EIF3H (323057 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	117446285	117446285	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:117446285delA								TRPS1 (765057 upstream) : EIF3H (210771 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	117499338	117499338	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:117499338delT								TRPS1 (818110 upstream) : EIF3H (157718 downstream)																																			---	---	---	---
UTP23	84294	broad.mit.edu	37	8	117784420	117784421	+	3'UTR	INS	-	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:117784420_117784421insA	uc003yoc.2	+	3						NM_032334	NP_115710			UTP23, small subunit (SSU) processome component,						rRNA processing	nucleolus					0																		---	---	---	---
Unknown	0	broad.mit.edu	37	8	117810495	117810495	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:117810495delT								UTP23 (23576 upstream) : RAD21 (47679 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	117927876	117927876	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:117927876delT								RAD21 (40771 upstream) : C8orf85 (22588 downstream)																																			---	---	---	---
SLC30A8	169026	broad.mit.edu	37	8	117974030	117974031	+	Intron	INS	-	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:117974030_117974031insT	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)															---	---	---	---
Unknown	0	broad.mit.edu	37	8	118330792	118330792	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:118330792delT								SLC30A8 (141840 upstream) : MED30 (202173 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	118472143	118472143	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:118472143delT								SLC30A8 (283191 upstream) : MED30 (60822 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	118478352	118478352	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:118478352delA								SLC30A8 (289400 upstream) : MED30 (54613 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	118647969	118647969	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:118647969delT								MED30 (95470 upstream) : EXT1 (163633 downstream)																																			---	---	---	---
EXT1	2131	broad.mit.edu	37	8	118993947	118993947	+	Intron	DEL	A	-	-	rs71569753		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:118993947delA	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				---	---	---	---
EXT1	2131	broad.mit.edu	37	8	119002089	119002091	+	Intron	DEL	AAC	-	-	rs147685109	by1000genomes;by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:119002089_119002091delAAC	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				---	---	---	---
EXT1	2131	broad.mit.edu	37	8	119013732	119013732	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:119013732delT	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				---	---	---	---
Unknown	0	broad.mit.edu	37	8	119160183	119160183	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:119160183delT								EXT1 (36125 upstream) : SAMD12 (41512 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	119193292	119193292	+	IGR	DEL	T	-	-	rs76232999	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:119193292delT								EXT1 (69234 upstream) : SAMD12 (8403 downstream)																																			---	---	---	---
SAMD12	401474	broad.mit.edu	37	8	119239764	119239764	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:119239764delA	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	119297342	119297342	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:119297342delT	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	119373633	119373633	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:119373633delA	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	119559579	119559580	+	Intron	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:119559579_119559580delTT	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)															---	---	---	---
SAMD12	401474	broad.mit.edu	37	8	119628324	119628324	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:119628324delA	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)															---	---	---	---
Unknown	0	broad.mit.edu	37	8	120054247	120054248	+	IGR	INS	-	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:120054247_120054248insT								TNFRSF11B (89864 upstream) : COLEC10 (25176 downstream)																																			---	---	---	---
MAL2	114569	broad.mit.edu	37	8	120238650	120238650	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:120238650delT	uc003yop.2	+							NM_052886	NP_443118			MAL2 proteolipid protein							apical plasma membrane|endomembrane system|integral to membrane|perinuclear region of cytoplasm	protein binding				0	all_cancers(13;1.91e-26)|Lung NSC(37;8.61e-08)|Ovarian(258;0.018)|Hepatocellular(40;0.161)		STAD - Stomach adenocarcinoma(47;0.000967)															---	---	---	---
Unknown	0	broad.mit.edu	37	8	120359986	120359986	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:120359986delT								MAL2 (102075 upstream) : NOV (68566 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	120499426	120499427	+	IGR	DEL	GA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:120499426_120499427delGA								NOV (62748 upstream) : ENPP2 (69892 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	120523248	120523248	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:120523248delT								NOV (86570 upstream) : ENPP2 (46071 downstream)																																			---	---	---	---
ENPP2	5168	broad.mit.edu	37	8	120590298	120590298	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:120590298delT	uc003yot.1	-						ENPP2_uc011lic.1_Intron|ENPP2_uc003yor.1_Intron|ENPP2_uc003yos.1_Intron|ENPP2_uc010mdd.1_Intron	NM_001040092	NP_001035181			autotaxin isoform 2 preproprotein						cellular component movement|chemotaxis|G-protein coupled receptor protein signaling pathway|immune response|phosphate metabolic process|phosphatidylcholine catabolic process|regulation of cell migration	extracellular space|integral to plasma membrane	alkylglycerophosphoethanolamine phosphodiesterase activity|calcium ion binding|lysophospholipase activity|nucleic acid binding|nucleotide diphosphatase activity|phosphodiesterase I activity|polysaccharide binding|scavenger receptor activity|transcription factor binding|zinc ion binding			ovary(2)|central_nervous_system(2)|upper_aerodigestive_tract(1)|large_intestine(1)|kidney(1)	7	Lung NSC(37;5.03e-06)|Ovarian(258;0.0249)|Hepatocellular(40;0.161)		STAD - Stomach adenocarcinoma(47;0.00185)															---	---	---	---
ENPP2	5168	broad.mit.edu	37	8	120601658	120601658	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:120601658delT	uc003yot.1	-						ENPP2_uc003yor.1_Intron|ENPP2_uc003yos.1_Intron|ENPP2_uc010mdd.1_Intron	NM_001040092	NP_001035181			autotaxin isoform 2 preproprotein						cellular component movement|chemotaxis|G-protein coupled receptor protein signaling pathway|immune response|phosphate metabolic process|phosphatidylcholine catabolic process|regulation of cell migration	extracellular space|integral to plasma membrane	alkylglycerophosphoethanolamine phosphodiesterase activity|calcium ion binding|lysophospholipase activity|nucleic acid binding|nucleotide diphosphatase activity|phosphodiesterase I activity|polysaccharide binding|scavenger receptor activity|transcription factor binding|zinc ion binding			ovary(2)|central_nervous_system(2)|upper_aerodigestive_tract(1)|large_intestine(1)|kidney(1)	7	Lung NSC(37;5.03e-06)|Ovarian(258;0.0249)|Hepatocellular(40;0.161)		STAD - Stomach adenocarcinoma(47;0.00185)															---	---	---	---
ENPP2	5168	broad.mit.edu	37	8	120623144	120623148	+	Intron	DEL	AAAAA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:120623144_120623148delAAAAA	uc003yot.1	-						ENPP2_uc003yos.1_Intron|ENPP2_uc010mdd.1_Intron	NM_001040092	NP_001035181			autotaxin isoform 2 preproprotein						cellular component movement|chemotaxis|G-protein coupled receptor protein signaling pathway|immune response|phosphate metabolic process|phosphatidylcholine catabolic process|regulation of cell migration	extracellular space|integral to plasma membrane	alkylglycerophosphoethanolamine phosphodiesterase activity|calcium ion binding|lysophospholipase activity|nucleic acid binding|nucleotide diphosphatase activity|phosphodiesterase I activity|polysaccharide binding|scavenger receptor activity|transcription factor binding|zinc ion binding			ovary(2)|central_nervous_system(2)|upper_aerodigestive_tract(1)|large_intestine(1)|kidney(1)	7	Lung NSC(37;5.03e-06)|Ovarian(258;0.0249)|Hepatocellular(40;0.161)		STAD - Stomach adenocarcinoma(47;0.00185)															---	---	---	---
TAF2	6873	broad.mit.edu	37	8	120770136	120770136	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:120770136delA	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)															---	---	---	---
DSCC1	79075	broad.mit.edu	37	8	120866474	120866474	+	Intron	DEL	A	-	-	rs35384749		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:120866474delA	uc003yov.2	-							NM_024094	NP_076999			defective in sister chromatid cohesion 1						DNA replication|maintenance of mitotic sister chromatid cohesion|post-translational protein acetylation|regulation of DNA replication	chromatin|chromosome, centromeric region|nucleoplasm	DNA binding|protein binding			pancreas(1)	1	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	120890182	120890183	+	Intron	INS	-	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:120890182_120890183insT	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)															---	---	---	---
DEPDC6	64798	broad.mit.edu	37	8	120943457	120943457	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:120943457delA	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)															---	---	---	---
DEPDC6	64798	broad.mit.edu	37	8	120967713	120967714	+	Intron	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:120967713_120967714delTT	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)															---	---	---	---
DEPDC6	64798	broad.mit.edu	37	8	121026767	121026767	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:121026767delT	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)															---	---	---	---
DEPDC6	64798	broad.mit.edu	37	8	121038588	121038588	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:121038588delT	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)															---	---	---	---
Unknown	0	broad.mit.edu	37	8	121132994	121132995	+	IGR	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:121132994_121132995delTT								DEPDC6 (69838 upstream) : COL14A1 (4357 downstream)																																			---	---	---	---
MRPL13	28998	broad.mit.edu	37	8	121424028	121424028	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:121424028delA	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)															---	---	---	---
SNTB1	6641	broad.mit.edu	37	8	121648291	121648291	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:121648291delT	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	121885100	121885100	+	IGR	DEL	T	-	-	rs78853437		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:121885100delT								SNTB1 (60791 upstream) : HAS2 (740171 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	122336117	122336118	+	IGR	INS	-	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:122336117_122336118insT								SNTB1 (511808 upstream) : HAS2 (289153 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	122336350	122336350	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:122336350delA								SNTB1 (512041 upstream) : HAS2 (288921 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	122525895	122525899	+	IGR	DEL	AAAAA	-	-	rs145455496		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:122525895_122525899delAAAAA								SNTB1 (701586 upstream) : HAS2 (99372 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	122776956	122776956	+	IGR	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:122776956delC								HAS2AS (120023 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	122779995	122779995	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:122779995delT								HAS2AS (123062 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	122899379	122899379	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:122899379delT								HAS2AS (242446 upstream) : ZHX2 (894522 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	123009172	123009172	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:123009172delT	uc003ypj.2	-											Homo sapiens, clone IMAGE:5466006, mRNA.																														---	---	---	---
Unknown	0	broad.mit.edu	37	8	123105701	123105704	+	Intron	DEL	TGTG	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:123105701_123105704delTGTG	uc003ypj.2	-											Homo sapiens, clone IMAGE:5466006, mRNA.																														---	---	---	---
Unknown	0	broad.mit.edu	37	8	123482245	123482245	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:123482245delA								HAS2AS (825312 upstream) : ZHX2 (311656 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	123540244	123540245	+	IGR	DEL	AA	-	-	rs77721660		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:123540244_123540245delAA								HAS2AS (883311 upstream) : ZHX2 (253656 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	123593575	123593575	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:123593575delT								HAS2AS (936642 upstream) : ZHX2 (200326 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	123651835	123651835	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:123651835delA								HAS2AS (994902 upstream) : ZHX2 (142066 downstream)																																	OREG0018950	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
Unknown	0	broad.mit.edu	37	8	123682766	123682766	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:123682766delA								None (None upstream) : ZHX2 (111135 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	123708743	123708743	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:123708743delA								None (None upstream) : ZHX2 (85158 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	123709167	123709167	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:123709167delA								None (None upstream) : ZHX2 (84734 downstream)																																			---	---	---	---
ZHX2	22882	broad.mit.edu	37	8	123942634	123942634	+	Intron	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:123942634delC	uc003ypk.1	+							NM_014943	NP_055758			zinc fingers and homeoboxes 2							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)															---	---	---	---
WDR67	93594	broad.mit.edu	37	8	124097015	124097015	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:124097015delT	uc003ypp.1	+						WDR67_uc011lig.1_Intron|WDR67_uc011lih.1_Intron|WDR67_uc003ypq.1_Intron|WDR67_uc003ypo.1_Intron	NM_145647	NP_663622			WD repeat domain 67 isoform 1							centrosome	Rab GTPase activator activity			skin(1)	1	Lung NSC(37;7e-10)|Ovarian(258;0.0205)		STAD - Stomach adenocarcinoma(47;0.00527)															---	---	---	---
WDR67	93594	broad.mit.edu	37	8	124146769	124146769	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:124146769delA	uc003ypp.1	+						WDR67_uc011lig.1_Intron|WDR67_uc011lih.1_Intron|WDR67_uc003ypq.1_Intron|WDR67_uc003yps.1_Intron|WDR67_uc003ypt.1_Intron|WDR67_uc003ypu.1_Intron	NM_145647	NP_663622			WD repeat domain 67 isoform 1							centrosome	Rab GTPase activator activity			skin(1)	1	Lung NSC(37;7e-10)|Ovarian(258;0.0205)		STAD - Stomach adenocarcinoma(47;0.00527)															---	---	---	---
Unknown	0	broad.mit.edu	37	8	124298992	124298992	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:124298992delT								ZHX1 (11211 upstream) : ATAD2 (33101 downstream)																																			---	---	---	---
ATAD2	29028	broad.mit.edu	37	8	124353188	124353191	+	Intron	DEL	TTTT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:124353188_124353191delTTTT	uc003yqh.3	-						ATAD2_uc011lii.1_Intron|ATAD2_uc003yqi.3_Intron	NM_014109	NP_054828			ATPase family, AAA domain containing 2						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)															---	---	---	---
ATAD2	29028	broad.mit.edu	37	8	124388646	124388646	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:124388646delA	uc003yqh.3	-						ATAD2_uc011lii.1_Intron|ATAD2_uc003yqi.3_Intron|ATAD2_uc003yqj.2_Intron	NM_014109	NP_054828			ATPase family, AAA domain containing 2						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)															---	---	---	---
ATAD2	29028	broad.mit.edu	37	8	124424071	124424071	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:124424071delA	uc003yqi.3	-											Homo sapiens PRO2000 mRNA, complete cds.						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)															---	---	---	---
Unknown	0	broad.mit.edu	37	8	124483159	124483159	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:124483159delT								WDYHV1 (28899 upstream) : FBXO32 (32200 downstream)																																			---	---	---	---
FBXO32	114907	broad.mit.edu	37	8	124547489	124547489	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:124547489delA	uc003yqr.2	-						FBXO32_uc010mdk.2_Intron	NM_058229	NP_478136			F-box only protein 32 isoform 1											skin(3)|breast(2)|lung(1)	6	Lung NSC(37;1.13e-13)|Ovarian(258;0.00838)		STAD - Stomach adenocarcinoma(47;0.00288)															---	---	---	---
Unknown	0	broad.mit.edu	37	8	124561444	124561444	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:124561444delT								FBXO32 (7998 upstream) : KLHL38 (96471 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	124574055	124574055	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:124574055delT								FBXO32 (20609 upstream) : KLHL38 (83860 downstream)																																			---	---	---	---
ANXA13	312	broad.mit.edu	37	8	124708346	124708347	+	Intron	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:124708346_124708347delTT	uc003yqu.2	-						ANXA13_uc003yqt.2_Intron	NM_004306	NP_004297			annexin A13 isoform a						cell differentiation	plasma membrane	calcium ion binding|calcium-dependent phospholipid binding			ovary(1)|pancreas(1)|skin(1)	3	Lung NSC(37;2.06e-11)|Ovarian(258;0.00579)|all_neural(195;0.0741)		STAD - Stomach adenocarcinoma(47;0.00288)															---	---	---	---
ANXA13	312	broad.mit.edu	37	8	124750342	124750342	+	5'Flank	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:124750342delT	uc003yqu.2	-						ANXA13_uc003yqt.2_5'Flank	NM_004306	NP_004297			annexin A13 isoform a						cell differentiation	plasma membrane	calcium ion binding|calcium-dependent phospholipid binding			ovary(1)|pancreas(1)|skin(1)	3	Lung NSC(37;2.06e-11)|Ovarian(258;0.00579)|all_neural(195;0.0741)		STAD - Stomach adenocarcinoma(47;0.00288)															---	---	---	---
Unknown	0	broad.mit.edu	37	8	125303096	125303096	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:125303096delA								FER1L6 (170795 upstream) : TMEM65 (20065 downstream)																																			---	---	---	---
TMEM65	157378	broad.mit.edu	37	8	125362719	125362720	+	Intron	DEL	CA	-	-	rs34348469		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:125362719_125362720delCA	uc010mdl.2	-							NM_194291	NP_919267			transmembrane protein 65							integral to membrane					0	Lung NSC(37;1.18e-11)|Ovarian(258;0.00438)|all_neural(195;0.0779)|Hepatocellular(40;0.108)		STAD - Stomach adenocarcinoma(47;0.00288)															---	---	---	---
TMEM65	157378	broad.mit.edu	37	8	125369058	125369059	+	Intron	INS	-	A	A	rs150250749	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:125369058_125369059insA	uc010mdl.2	-							NM_194291	NP_919267			transmembrane protein 65							integral to membrane					0	Lung NSC(37;1.18e-11)|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	125441525	125441527	+	IGR	DEL	AGG	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:125441525_125441527delAGG								TMEM65 (56585 upstream) : TRMT12 (21521 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	125445687	125445688	+	IGR	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:125445687_125445688delAA								TMEM65 (60747 upstream) : TRMT12 (17360 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	125483931	125483931	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:125483931delT	uc003yrb.2	-											Homo sapiens mRNA; cDNA DKFZp781F0756 (from clone DKFZp781F0756).																														---	---	---	---
TATDN1	83940	broad.mit.edu	37	8	125512995	125512997	+	Intron	DEL	AAA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:125512995_125512997delAAA	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)															---	---	---	---
MTSS1	9788	broad.mit.edu	37	8	125633795	125633795	+	Intron	DEL	T	-	-	rs66470911		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:125633795delT	uc003yrk.2	-						MTSS1_uc003yrj.2_Intron|MTSS1_uc003yrl.2_Intron	NM_014751	NP_055566			metastasis suppressor 1						actin cytoskeleton organization|cell adhesion|cellular component movement|filopodium assembly|transmembrane receptor protein tyrosine kinase signaling pathway	actin cytoskeleton|endocytic vesicle|ruffle	actin monomer binding|cytoskeletal adaptor activity|receptor binding|SH3 domain binding			ovary(1)	1	Ovarian(258;0.00438)|all_neural(195;0.00459)|Hepatocellular(40;0.108)		STAD - Stomach adenocarcinoma(47;0.00288)															---	---	---	---
MTSS1	9788	broad.mit.edu	37	8	125639617	125639619	+	Intron	DEL	CTT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:125639617_125639619delCTT	uc003yrk.2	-						MTSS1_uc003yrj.2_Intron|MTSS1_uc003yrl.2_Intron	NM_014751	NP_055566			metastasis suppressor 1						actin cytoskeleton organization|cell adhesion|cellular component movement|filopodium assembly|transmembrane receptor protein tyrosine kinase signaling pathway	actin cytoskeleton|endocytic vesicle|ruffle	actin monomer binding|cytoskeletal adaptor activity|receptor binding|SH3 domain binding			ovary(1)	1	Ovarian(258;0.00438)|all_neural(195;0.00459)|Hepatocellular(40;0.108)		STAD - Stomach adenocarcinoma(47;0.00288)															---	---	---	---
MTSS1	9788	broad.mit.edu	37	8	125660951	125660951	+	Intron	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:125660951delC	uc003yrk.2	-						MTSS1_uc003yrj.2_Intron|MTSS1_uc003yrl.2_Intron	NM_014751	NP_055566			metastasis suppressor 1						actin cytoskeleton organization|cell adhesion|cellular component movement|filopodium assembly|transmembrane receptor protein tyrosine kinase signaling pathway	actin cytoskeleton|endocytic vesicle|ruffle	actin monomer binding|cytoskeletal adaptor activity|receptor binding|SH3 domain binding			ovary(1)	1	Ovarian(258;0.00438)|all_neural(195;0.00459)|Hepatocellular(40;0.108)		STAD - Stomach adenocarcinoma(47;0.00288)															---	---	---	---
MTSS1	9788	broad.mit.edu	37	8	125689435	125689435	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:125689435delT	uc003yrk.2	-						MTSS1_uc003yrj.2_Intron|MTSS1_uc003yrl.2_Intron	NM_014751	NP_055566			metastasis suppressor 1						actin cytoskeleton organization|cell adhesion|cellular component movement|filopodium assembly|transmembrane receptor protein tyrosine kinase signaling pathway	actin cytoskeleton|endocytic vesicle|ruffle	actin monomer binding|cytoskeletal adaptor activity|receptor binding|SH3 domain binding			ovary(1)	1	Ovarian(258;0.00438)|all_neural(195;0.00459)|Hepatocellular(40;0.108)		STAD - Stomach adenocarcinoma(47;0.00288)															---	---	---	---
MTSS1	9788	broad.mit.edu	37	8	125727927	125727927	+	Intron	DEL	T	-	-	rs34773142		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:125727927delT	uc003yrk.2	-						MTSS1_uc003yrj.2_Intron|MTSS1_uc003yrl.2_Intron	NM_014751	NP_055566			metastasis suppressor 1						actin cytoskeleton organization|cell adhesion|cellular component movement|filopodium assembly|transmembrane receptor protein tyrosine kinase signaling pathway	actin cytoskeleton|endocytic vesicle|ruffle	actin monomer binding|cytoskeletal adaptor activity|receptor binding|SH3 domain binding			ovary(1)	1	Ovarian(258;0.00438)|all_neural(195;0.00459)|Hepatocellular(40;0.108)		STAD - Stomach adenocarcinoma(47;0.00288)															---	---	---	---
Unknown	0	broad.mit.edu	37	8	125943268	125943269	+	IGR	DEL	TG	-	-	rs141482010		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:125943268_125943269delTG								MTSS1 (202538 upstream) : LOC157381 (8615 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	125977978	125977978	+	IGR	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:125977978delC								LOC157381 (14641 upstream) : ZNF572 (7561 downstream)																																			---	---	---	---
SQLE	6713	broad.mit.edu	37	8	126019615	126019615	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:126019615delT	uc011liq.1	+							NM_003129	NP_003120			squalene epoxidase						cholesterol biosynthetic process	endoplasmic reticulum membrane|integral to membrane|microsome	flavin adenine dinucleotide binding|squalene monooxygenase activity			ovary(1)|breast(1)	2	Ovarian(258;0.0028)|all_neural(195;0.00294)|Hepatocellular(40;0.108)		STAD - Stomach adenocarcinoma(47;0.000918)|COAD - Colon adenocarcinoma(160;0.205)		Butenafine(DB01091)|Naftifine(DB00735)|Terbinafine(DB00857)													---	---	---	---
NSMCE2	286053	broad.mit.edu	37	8	126143849	126143849	+	Intron	DEL	A	-	-	rs34646266		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:126143849delA	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	126174034	126174039	+	Intron	DEL	AAAAAA	-	-	rs66512067		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:126174034_126174039delAAAAAA	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	126282351	126282351	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:126282351delA	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	126304463	126304464	+	Intron	DEL	AA	-	-	rs34130712		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:126304463_126304464delAA	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	126490902	126490902	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:126490902delA								TRIB1 (40260 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	126749077	126749077	+	IGR	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:126749077delG								TRIB1 (298435 upstream) : FAM84B (815610 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	126776904	126776904	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:126776904delA								TRIB1 (326262 upstream) : FAM84B (787783 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	126785654	126785654	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:126785654delA								TRIB1 (335012 upstream) : FAM84B (779033 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	126865693	126865694	+	IGR	INS	-	CATGGTAGTAAA	CATGGTAGTAAA	rs149904650	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:126865693_126865694insCATGGTAGTAAA								TRIB1 (415051 upstream) : FAM84B (698993 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	126935886	126935886	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:126935886delA								TRIB1 (485244 upstream) : FAM84B (628801 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	127028738	127028738	+	IGR	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:127028738delC								TRIB1 (578096 upstream) : FAM84B (535949 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	127057113	127057113	+	IGR	DEL	T	-	-	rs78375706		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:127057113delT								TRIB1 (606471 upstream) : FAM84B (507574 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	127260584	127260584	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:127260584delT								TRIB1 (809942 upstream) : FAM84B (304103 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	127366494	127366494	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:127366494delT								TRIB1 (915852 upstream) : FAM84B (198193 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	127489110	127489110	+	IGR	DEL	A	-	-	rs34277531		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:127489110delA								None (None upstream) : FAM84B (75577 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	127580142	127580142	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:127580142delT								FAM84B (9676 upstream) : LOC727677 (721920 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	127586697	127586697	+	IGR	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:127586697delC								FAM84B (16231 upstream) : LOC727677 (715365 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	127595688	127595689	+	IGR	DEL	AC	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:127595688_127595689delAC								FAM84B (25222 upstream) : LOC727677 (706373 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	127619475	127619475	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:127619475delA								FAM84B (49009 upstream) : LOC727677 (682587 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	127672078	127672078	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:127672078delT								FAM84B (101612 upstream) : LOC727677 (629984 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	127716341	127716341	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:127716341delA								FAM84B (145875 upstream) : LOC727677 (585721 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	127754901	127754902	+	IGR	DEL	TT	-	-	rs147902007		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:127754901_127754902delTT								FAM84B (184435 upstream) : LOC727677 (547160 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	127801810	127801810	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:127801810delT								FAM84B (231344 upstream) : LOC727677 (500252 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	127934263	127934263	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:127934263delT								FAM84B (363797 upstream) : LOC727677 (367799 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	128098496	128098496	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:128098496delA								FAM84B (528030 upstream) : LOC727677 (203566 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	128221570	128221570	+	RNA	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:128221570delA	uc003ysa.1	-	2		c.672delT								Homo sapiens cDNA FLJ43320 fis, clone NT2RI2024935.																														---	---	---	---
Unknown	0	broad.mit.edu	37	8	128618266	128618267	+	IGR	DEL	GA	-	-	rs147544748		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:128618266_128618267delGA								LOC727677 (123882 upstream) : MYC (129498 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	128632894	128632894	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:128632894delA								LOC727677 (138510 upstream) : MYC (114871 downstream)																																			---	---	---	---
PVT1	5820	broad.mit.edu	37	8	128810551	128810551	+	Intron	DEL	A	-	-	rs78369020		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:128810551delA	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	128918856	128918856	+	Intron	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:128918856delG	uc010mdq.2	+						PVT1_uc003ysl.2_Intron|PVT1_uc010mdp.1_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	129015214	129015215	+	Intron	INS	-	CTTC	CTTC			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:129015214_129015215insCTTC	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	129093084	129093084	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:129093084delT	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	129714399	129714399	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:129714399delA								MIR1208 (551965 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	129903584	129903584	+	IGR	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:129903584delG								MIR1208 (741150 upstream) : GSDMC (856859 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	129997310	129997310	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:129997310delT								MIR1208 (834876 upstream) : GSDMC (763133 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	130009514	130009514	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:130009514delA								MIR1208 (847080 upstream) : GSDMC (750929 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	130426915	130426915	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:130426915delT								None (None upstream) : GSDMC (333528 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	130433002	130433002	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:130433002delT								None (None upstream) : GSDMC (327441 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	130628324	130628324	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:130628324delA								None (None upstream) : GSDMC (132119 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	130634456	130634457	+	IGR	INS	-	G	G	rs151263405	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:130634456_130634457insG								None (None upstream) : GSDMC (125986 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	130675068	130675068	+	IGR	DEL	T	-	-	rs72326930		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:130675068delT								None (None upstream) : GSDMC (85375 downstream)																																			---	---	---	---
GSDMC	56169	broad.mit.edu	37	8	130768314	130768314	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:130768314delA	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	130872878	130872878	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:130872878delT	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)															---	---	---	---
ASAP1	50807	broad.mit.edu	37	8	131088777	131088777	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:131088777delT	uc003yta.1	-						ASAP1_uc003ysz.1_Intron|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																		---	---	---	---
ASAP1	50807	broad.mit.edu	37	8	131105355	131105355	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:131105355delA	uc003yta.1	-						ASAP1_uc003ysz.1_Intron|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																		---	---	---	---
ASAP1	50807	broad.mit.edu	37	8	131140419	131140420	+	Intron	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:131140419_131140420delAA	uc003yta.1	-						ASAP1_uc003ysz.1_Intron|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																		---	---	---	---
ASAP1	50807	broad.mit.edu	37	8	131203991	131203991	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:131203991delA	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																		---	---	---	---
ASAP1	50807	broad.mit.edu	37	8	131228012	131228013	+	Intron	INS	-	A	A	rs75341478	byFrequency;by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:131228012_131228013insA	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																		---	---	---	---
ASAP1	50807	broad.mit.edu	37	8	131304975	131304975	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:131304975delA	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																		---	---	---	---
ASAP1	50807	broad.mit.edu	37	8	131331136	131331136	+	Intron	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:131331136delG	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																		---	---	---	---
ASAP1	50807	broad.mit.edu	37	8	131411895	131411895	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:131411895delA	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	131636686	131636687	+	IGR	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:131636686_131636687delAA								ASAP1 (222470 upstream) : ADCY8 (155861 downstream)																																			---	---	---	---
ADCY8	114	broad.mit.edu	37	8	131808027	131808028	+	Intron	DEL	GT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:131808027_131808028delGT	uc003ytd.3	-						ADCY8_uc010mds.2_Intron	NM_001115	NP_001106			adenylate cyclase 8						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)			---	---	---	---
ADCY8	114	broad.mit.edu	37	8	131960272	131960272	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:131960272delA	uc003ytd.3	-						ADCY8_uc010mds.2_Intron	NM_001115	NP_001106			adenylate cyclase 8						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)			---	---	---	---
ADCY8	114	broad.mit.edu	37	8	132029319	132029320	+	Intron	DEL	TT	-	-	rs111610879		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:132029319_132029320delTT	uc003ytd.3	-						ADCY8_uc010mds.2_Intron	NM_001115	NP_001106			adenylate cyclase 8						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)			---	---	---	---
Unknown	0	broad.mit.edu	37	8	132157457	132157458	+	IGR	INS	-	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:132157457_132157458insA								ADCY8 (104622 upstream) : EFR3A (758901 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	132444137	132444139	+	IGR	DEL	ATC	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:132444137_132444139delATC								ADCY8 (391302 upstream) : EFR3A (472220 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	132513027	132513027	+	IGR	DEL	A	-	-	rs72221691		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:132513027delA								ADCY8 (460192 upstream) : EFR3A (403332 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	132826426	132826426	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:132826426delT								ADCY8 (773591 upstream) : EFR3A (89933 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	132869012	132869012	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:132869012delA								ADCY8 (816177 upstream) : EFR3A (47347 downstream)																																			---	---	---	---
EFR3A	23167	broad.mit.edu	37	8	132953236	132953236	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:132953236delA	uc003yte.2	+							NM_015137	NP_055952			EFR3 homolog A							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)															---	---	---	---
KCNQ3	3786	broad.mit.edu	37	8	133240236	133240237	+	Intron	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:133240236_133240237delAA	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)															---	---	---	---
KCNQ3	3786	broad.mit.edu	37	8	133323191	133323194	+	Intron	DEL	TTTC	-	-	rs79830223	byFrequency;by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:133323191_133323194delTTTC	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)															---	---	---	---
KCNQ3	3786	broad.mit.edu	37	8	133408674	133408677	+	Intron	DEL	AAAA	-	-	rs75974913		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:133408674_133408677delAAAA	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	133555115	133555115	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:133555115delT								KCNQ3 (62111 upstream) : HPYR1 (17630 downstream)																																			---	---	---	---
TMEM71	137835	broad.mit.edu	37	8	133770855	133770855	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:133770855delA	uc003ytp.2	-						TMEM71_uc003ytn.2_Intron|TMEM71_uc003yto.2_Intron	NM_144649	NP_653250			transmembrane protein 71 isoform 1							integral to membrane				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	133788155	133788155	+	Intron	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:133788155delC	uc003ytt.2	+						PHF20L1_uc003ytr.2_Intron|PHF20L1_uc010mdv.2_Intron|PHF20L1_uc003yts.2_Intron|PHF20L1_uc011lja.1_Intron|PHF20L1_uc003ytu.1_5'Flank|PHF20L1_uc003ytq.2_Intron	NM_016018	NP_057102			PHD finger protein 20-like 1 isoform 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)															---	---	---	---
WISP1	8840	broad.mit.edu	37	8	134214747	134214747	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:134214747delA	uc003yub.2	+						WISP1_uc003yuc.2_Intron|WISP1_uc010meb.2_Intron|WISP1_uc010mec.2_Intron|WISP1_uc010med.2_Intron	NM_003882	NP_003873			WNT1 inducible signaling pathway protein 1						cell adhesion|cell-cell signaling|regulation of cell growth|Wnt receptor signaling pathway	extracellular region|soluble fraction	insulin-like growth factor binding			central_nervous_system(1)|kidney(1)	2	all_epithelial(106;5.39e-23)|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)															---	---	---	---
Unknown	0	broad.mit.edu	37	8	134318649	134318649	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:134318649delA								NDRG1 (9102 upstream) : ST3GAL1 (148442 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	134328551	134328552	+	IGR	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:134328551_134328552delTT								NDRG1 (19004 upstream) : ST3GAL1 (138539 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	134419168	134419168	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:134419168delA								NDRG1 (109621 upstream) : ST3GAL1 (47923 downstream)																																			---	---	---	---
ST3GAL1	6482	broad.mit.edu	37	8	134540426	134540426	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:134540426delA	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	134860605	134860606	+	IGR	INS	-	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:134860605_134860606insT								ST3GAL1 (276422 upstream) : ZFAT (629427 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	135095619	135095631	+	IGR	DEL	TTTTTTTTTTTTT	-	-	rs36072972		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:135095619_135095631delTTTTTTTTTTTTT								ST3GAL1 (511436 upstream) : ZFAT (394402 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	135188272	135188272	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:135188272delT								ST3GAL1 (604089 upstream) : ZFAT (301761 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	135216985	135216986	+	IGR	INS	-	T	T	rs78009327		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:135216985_135216986insT								ST3GAL1 (632802 upstream) : ZFAT (273047 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	135480413	135480414	+	IGR	INS	-	T	T	rs146901216	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:135480413_135480414insT								ST3GAL1 (896230 upstream) : ZFAT (9619 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	135488629	135488629	+	IGR	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:135488629delC								ST3GAL1 (904446 upstream) : ZFAT (1404 downstream)																																			---	---	---	---
ZFAT	57623	broad.mit.edu	37	8	135563152	135563152	+	Intron	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:135563152delG	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	135779967	135779967	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:135779967delT								ZFAT (54686 upstream) : MIR30B (32796 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	135907566	135907566	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:135907566delA								MIR30D (90378 upstream) : LOC286094 (338808 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	135939106	135939106	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:135939106delT								MIR30D (121918 upstream) : LOC286094 (307268 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	136037368	136037368	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:136037368delT								MIR30D (220180 upstream) : LOC286094 (209006 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	136339685	136339685	+	IGR	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:136339685delG								LOC286094 (27726 upstream) : KHDRBS3 (130031 downstream)																																			---	---	---	---
KHDRBS3	10656	broad.mit.edu	37	8	136536267	136536267	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:136536267delT	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)															---	---	---	---
KHDRBS3	10656	broad.mit.edu	37	8	136593191	136593191	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:136593191delT	uc003yuv.2	+						KHDRBS3_uc003yuw.2_Intron|KHDRBS3_uc010mek.2_5'Flank	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)															---	---	---	---
KHDRBS3	10656	broad.mit.edu	37	8	136632314	136632316	+	Intron	DEL	TTT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:136632314_136632316delTTT	uc003yuv.2	+						KHDRBS3_uc003yuw.2_Intron|KHDRBS3_uc010mek.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	136864682	136864682	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:136864682delT								KHDRBS3 (204836 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	137355795	137355795	+	IGR	DEL	A	-	-	rs79272116		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:137355795delA								KHDRBS3 (695949 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	137365951	137365951	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:137365951delT								KHDRBS3 (706105 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	137745445	137745446	+	IGR	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:137745445_137745446delTT								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	137784165	137784166	+	IGR	INS	-	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:137784165_137784166insA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	137990481	137990483	+	IGR	DEL	AAA	-	-	rs111947836		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:137990481_137990483delAAA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	138116393	138116393	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:138116393delA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	138176087	138176087	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-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	138235957	138235958	+	IGR	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:138235957_138235958delAA								None (None upstream) : FAM135B (906310 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	138332094	138332095	+	IGR	DEL	GT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:138332094_138332095delGT								None (None upstream) : FAM135B (810173 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	138344718	138344718	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:138344718delT								None (None upstream) : FAM135B (797550 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	138857123	138857123	+	IGR	DEL	T	-	-	rs34793131		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:138857123delT								None (None upstream) : FAM135B (285145 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	138913235	138913235	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:138913235delA								None (None upstream) : FAM135B (229033 downstream)																																			---	---	---	---
FAM135B	51059	broad.mit.edu	37	8	139240495	139240495	+	Intron	DEL	T	-	-	rs66594804		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:139240495delT	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)			---	---	---	---
FAM135B	51059	broad.mit.edu	37	8	139284245	139284246	+	Intron	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:139284245_139284246delTT	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)			---	---	---	---
FAM135B	51059	broad.mit.edu	37	8	139286020	139286021	+	Intron	INS	-	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:139286020_139286021insT	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)			---	---	---	---
FAM135B	51059	broad.mit.edu	37	8	139385036	139385036	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:139385036delA	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)			---	---	---	---
FAM135B	51059	broad.mit.edu	37	8	139434941	139434942	+	Intron	INS	-	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:139434941_139434942insA	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	139601386	139601386	+	3'UTR	DEL	A	-	-	rs72284088		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:139601386delA	uc003yvd.2	-	65					COL22A1_uc011ljo.1_3'UTR	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	139614125	139614125	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:139614125delA	uc003yvd.2	-						COL22A1_uc011ljo.1_Intron	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	139685860	139685860	+	Intron	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:139685860delG	uc003yvd.2	-						COL22A1_uc011ljo.1_Intron	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	139705494	139705495	+	Intron	DEL	TG	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:139705494_139705495delTG	uc003yvd.2	-						COL22A1_uc011ljo.1_Intron	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	139825456	139825457	+	Intron	INS	-	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:139825456_139825457insC	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	139986791	139986792	+	IGR	INS	-	C	C	rs141801654	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:139986791_139986792insC								COL22A1 (60555 upstream) : KCNK9 (626290 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	140005454	140005455	+	IGR	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:140005454_140005455delAA								COL22A1 (79218 upstream) : KCNK9 (607627 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	140018626	140018626	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:140018626delA								COL22A1 (92390 upstream) : KCNK9 (594456 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	140110500	140110500	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:140110500delA								COL22A1 (184264 upstream) : KCNK9 (502582 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	140441552	140441554	+	IGR	DEL	AAA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:140441552_140441554delAAA								COL22A1 (515316 upstream) : KCNK9 (171528 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	140574683	140574684	+	IGR	INS	-	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:140574683_140574684insA								COL22A1 (648447 upstream) : KCNK9 (38398 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	140606137	140606165	+	IGR	DEL	GAGGCACAGAGGGCTGTCATCAGTGAGGT	-	-	rs9720159		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:140606137_140606165delGAGGCACAGAGGGCTGTCATCAGTGAGGT								COL22A1 (679901 upstream) : KCNK9 (6917 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	140606756	140606756	+	IGR	DEL	G	-	-	rs5895612		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:140606756delG								COL22A1 (680520 upstream) : KCNK9 (6326 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	140734119	140734119	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:140734119delA								KCNK9 (18820 upstream) : TRAPPC9 (8467 downstream)																																			---	---	---	---
TRAPPC9	83696	broad.mit.edu	37	8	141102176	141102179	+	Intron	DEL	AAAA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:141102176_141102179delAAAA	uc003yvj.2	-						TRAPPC9_uc003yvh.2_Intron|TRAPPC9_uc010mel.1_Intron|TRAPPC9_uc003yvi.1_Intron	NM_001160372	NP_001153844			trafficking protein particle complex 9 isoform						cell differentiation	endoplasmic reticulum|Golgi apparatus				skin(2)	2																		---	---	---	---
TRAPPC9	83696	broad.mit.edu	37	8	141361475	141361475	+	Intron	DEL	T	-	-	rs34577924		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:141361475delT	uc003yvj.2	-						TRAPPC9_uc003yvh.2_Intron|TRAPPC9_uc003yvi.1_Intron	NM_001160372	NP_001153844			trafficking protein particle complex 9 isoform						cell differentiation	endoplasmic reticulum|Golgi apparatus				skin(2)	2																		---	---	---	---
TRAPPC9	83696	broad.mit.edu	37	8	141424843	141424843	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:141424843delT	uc003yvj.2	-						TRAPPC9_uc003yvh.2_Intron|TRAPPC9_uc003yvi.1_Intron	NM_001160372	NP_001153844			trafficking protein particle complex 9 isoform						cell differentiation	endoplasmic reticulum|Golgi apparatus				skin(2)	2																		---	---	---	---
TRAPPC9	83696	broad.mit.edu	37	8	141454967	141454968	+	Intron	DEL	AA	-	-	rs71902242		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:141454967_141454968delAA	uc003yvj.2	-						TRAPPC9_uc003yvh.2_Intron|TRAPPC9_uc003yvi.1_Intron	NM_001160372	NP_001153844			trafficking protein particle complex 9 isoform						cell differentiation	endoplasmic reticulum|Golgi apparatus				skin(2)	2																		---	---	---	---
EIF2C2	27161	broad.mit.edu	37	8	141628106	141628107	+	Intron	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:141628106_141628107delAA	uc003yvn.2	-						EIF2C2_uc010men.2_Intron|EIF2C2_uc010meo.2_Intron	NM_012154	NP_036286			argonaute 2 isoform 1						mRNA cleavage involved in gene silencing by miRNA|negative regulation of translation involved in gene silencing by miRNA|negative regulation of translational initiation|pre-miRNA processing|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasmic mRNA processing body|cytosol|micro-ribonucleoprotein complex|mRNA cap binding complex|nucleus|polysome|RNA-induced silencing complex	endoribonuclease activity, cleaving siRNA-paired mRNA|metal ion binding|protein binding|RNA 7-methylguanosine cap binding|siRNA binding|translation initiation factor activity				0	all_cancers(97;2.54e-14)|all_epithelial(106;5.99e-13)|Lung NSC(106;1.45e-05)|all_lung(105;2.07e-05)|Ovarian(258;0.0154)|Acute lymphoblastic leukemia(118;0.155)	Breast(495;0.159)	BRCA - Breast invasive adenocarcinoma(115;0.158)															---	---	---	---
EIF2C2	27161	broad.mit.edu	37	8	141643006	141643006	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:141643006delT	uc003yvn.2	-						EIF2C2_uc010men.2_Intron|EIF2C2_uc010meo.2_Intron	NM_012154	NP_036286			argonaute 2 isoform 1						mRNA cleavage involved in gene silencing by miRNA|negative regulation of translation involved in gene silencing by miRNA|negative regulation of translational initiation|pre-miRNA processing|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasmic mRNA processing body|cytosol|micro-ribonucleoprotein complex|mRNA cap binding complex|nucleus|polysome|RNA-induced silencing complex	endoribonuclease activity, cleaving siRNA-paired mRNA|metal ion binding|protein binding|RNA 7-methylguanosine cap binding|siRNA binding|translation initiation factor activity				0	all_cancers(97;2.54e-14)|all_epithelial(106;5.99e-13)|Lung NSC(106;1.45e-05)|all_lung(105;2.07e-05)|Ovarian(258;0.0154)|Acute lymphoblastic leukemia(118;0.155)	Breast(495;0.159)	BRCA - Breast invasive adenocarcinoma(115;0.158)															---	---	---	---
PTK2	5747	broad.mit.edu	37	8	141772872	141772872	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:141772872delT	uc003yvu.2	-						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_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)															---	---	---	---
PTK2	5747	broad.mit.edu	37	8	141785584	141785584	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:141785584delA	uc003yvu.2	-						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_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)															---	---	---	---
PTK2	5747	broad.mit.edu	37	8	141810338	141810338	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:141810338delT	uc003yvu.2	-						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_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)															---	---	---	---
PTK2	5747	broad.mit.edu	37	8	141822811	141822811	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:141822811delA	uc003yvu.2	-						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)															---	---	---	---
PTK2	5747	broad.mit.edu	37	8	141827996	141827997	+	Intron	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:141827996_141827997delTT	uc003yvu.2	-						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)															---	---	---	---
PTK2	5747	broad.mit.edu	37	8	141859129	141859129	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:141859129delA	uc003yvu.2	-						PTK2_uc003yvq.2_5'Flank|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)															---	---	---	---
PTK2	5747	broad.mit.edu	37	8	141907470	141907470	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:141907470delA	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)															---	---	---	---
PTK2	5747	broad.mit.edu	37	8	141972973	141972974	+	Intron	DEL	CC	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:141972973_141972974delCC	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	142022603	142022603	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:142022603delT								PTK2 (11271 upstream) : DENND3 (116117 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	142044157	142044157	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:142044157delT								PTK2 (32825 upstream) : DENND3 (94563 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	142104408	142104409	+	IGR	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:142104408_142104409delAA								PTK2 (93076 upstream) : DENND3 (34311 downstream)																																			---	---	---	---
DENND3	22898	broad.mit.edu	37	8	142199715	142199715	+	Intron	DEL	T	-	-	rs56255500		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:142199715delT	uc003yvy.2	+						DENND3_uc010mep.2_Intron|DENND3_uc003ywa.1_Intron|DENND3_uc003ywb.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	142490161	142490161	+	Intron	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:142490161delC	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	142681374	142681374	+	IGR	DEL	T	-	-	rs4907393	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:142681374delT								FLJ43860 (164044 upstream) : MIR1302-7 (186229 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	143118302	143118302	+	IGR	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:143118302delC								MIR1302-7 (250628 upstream) : NCRNA00051 (161415 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	143154699	143154699	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:143154699delA								MIR1302-7 (287025 upstream) : NCRNA00051 (125018 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	143204166	143204167	+	IGR	DEL	CA	-	-	rs138942627		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:143204166_143204167delCA								MIR1302-7 (336492 upstream) : NCRNA00051 (75550 downstream)																																			---	---	---	---
TSNARE1	203062	broad.mit.edu	37	8	143447415	143447415	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:143447415delT	uc003ywk.2	-						TSNARE1_uc003ywl.3_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)																	---	---	---	---
BAI1	575	broad.mit.edu	37	8	143610702	143610703	+	Intron	DEL	TG	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:143610702_143610703delTG	uc003ywm.2	+							NM_001702	NP_001693			brain-specific angiogenesis inhibitor 1						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)																	---	---	---	---
Unknown	0	broad.mit.edu	37	8	143734924	143734924	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:143734924delT								ARC (39091 upstream) : JRK (3951 downstream)																																			---	---	---	---
LY6K	54742	broad.mit.edu	37	8	143780077	143780077	+	5'Flank	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:143780077delA	uc011ljv.1	+						LY6K_uc011ljw.1_5'Flank|LY6K_uc011ljx.1_5'Flank	NM_017527	NP_059997			lymphocyte antigen 6 complex, locus K isoform 1							anchored to membrane|cytoplasm|extracellular region|nucleolus|plasma membrane				central_nervous_system(1)	1	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)																	---	---	---	---
Unknown	0	broad.mit.edu	37	8	143791497	143791498	+	IGR	INS	-	GAGA	GAGA			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:143791497_143791498insGAGA								LY6K (5915 upstream) : C8orf55 (17123 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	143946313	143946313	+	IGR	DEL	T	-	-	rs13282460		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:143946313delT								GML (18052 upstream) : CYP11B1 (7461 downstream)																																			---	---	---	---
ZC3H3	23144	broad.mit.edu	37	8	144534285	144534285	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:144534285delA	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)															---	---	---	---
EEF1D	1936	broad.mit.edu	37	8	144668488	144668488	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:144668488delT	uc011lki.1	-						EEF1D_uc003yyp.1_Intron|EEF1D_uc003yyq.1_Intron|EEF1D_uc011lkj.1_Intron|EEF1D_uc003yyr.2_Intron|EEF1D_uc003yyt.2_Intron|EEF1D_uc011lkk.1_Intron|EEF1D_uc003yys.2_Intron|EEF1D_uc003yyv.2_Intron|EEF1D_uc003yyu.2_Intron|EEF1D_uc011lkl.1_Intron	NM_001130057	NP_001123529			eukaryotic translation elongation factor 1 delta						positive regulation of I-kappaB kinase/NF-kappaB cascade	cytosol|eukaryotic translation elongation factor 1 complex	protein binding|signal transducer activity|translation elongation factor activity			ovary(1)|kidney(1)|skin(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)		Colorectal(110;0.134)|BRCA - Breast invasive adenocarcinoma(115;0.239)															---	---	---	---
OPLAH	26873	broad.mit.edu	37	8	145113788	145113788	+	Frame_Shift_Del	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:145113788delC	uc003zar.3	-	5	557	c.475delG	c.(475-477)GACfs	p.D159fs	OPLAH_uc003zat.1_5'Flank	NM_017570	NP_060040	O14841	OPLA_HUMAN	5-oxoprolinase (ATP-hydrolysing)	159							5-oxoprolinase (ATP-hydrolyzing) activity|ATP binding				0	all_cancers(97;1.06e-10)|all_epithelial(106;1.5e-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;2.24e-35)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.105)		L-Glutamic Acid(DB00142)													---	---	---	---
HEATR7A	727957	broad.mit.edu	37	8	145217629	145217629	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:145217629delT	uc003zbk.3	+						HEATR7A_uc003zbg.2_Intron|HEATR7A_uc003zbh.3_Intron|HEATR7A_uc003zbi.3_Intron|HEATR7A_uc011lla.1_Intron|HEATR7A_uc010mft.2_Intron	NM_032450	NP_115826			HEAT repeat containing 7A isoform 1								binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	8	145572448	145572448	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:145572448delT								SCRT1 (12505 upstream) : C8ORFK29 (4439 downstream)																																			---	---	---	---
CPSF1	29894	broad.mit.edu	37	8	145628160	145628160	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:145628160delA	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	145801059	145801059	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:145801059delT	uc003zdt.1	-						ARHGAP39_uc011llk.1_Intron|ARHGAP39_uc003zds.1_Intron	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																		---	---	---	---
ARHGAP39	80728	broad.mit.edu	37	8	145827186	145827187	+	Intron	DEL	TG	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:145827186_145827187delTG	uc003zdt.1	-						ARHGAP39_uc011llk.1_Intron|ARHGAP39_uc003zds.1_Intron	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																		---	---	---	---
ARHGAP39	80728	broad.mit.edu	37	8	145865047	145865047	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:145865047delA	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																		---	---	---	---
ZNF517	340385	broad.mit.edu	37	8	146031018	146031018	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:146031018delT	uc003zed.1	+						ZNF517_uc010mgd.1_Intron|ZNF517_uc003zee.1_Intron|ZNF517_uc011llm.1_Intron|ZNF517_uc003zef.1_Intron	NM_213605	NP_998770			zinc finger protein 517						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0	all_cancers(97;1.03e-11)|all_epithelial(106;6.69e-11)|Lung NSC(106;4.08e-05)|all_lung(105;0.000125)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		Epithelial(56;5.47e-39)|OV - Ovarian serous cystadenocarcinoma(54;6.38e-39)|all cancers(56;5.47e-34)|BRCA - Breast invasive adenocarcinoma(115;0.0355)|Colorectal(110;0.055)															---	---	---	---
ZNF7	7553	broad.mit.edu	37	8	146057399	146057399	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:146057399delA	uc003zeg.3	+						ZNF7_uc010mge.2_Intron|ZNF7_uc011lln.1_Intron|ZNF7_uc003zeh.2_Intron|ZNF7_uc003zej.2_Intron|ZNF7_uc003zek.3_5'Flank	NM_003416	NP_003407			zinc finger protein 7						multicellular organismal development|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(4)	4	all_cancers(97;1.03e-11)|all_epithelial(106;6.69e-11)|Lung NSC(106;4.08e-05)|all_lung(105;0.000125)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)	Breast(495;0.0812)|Ovarian(118;0.0822)|Acute lymphoblastic leukemia(644;0.143)	Epithelial(56;8.75e-39)|OV - Ovarian serous cystadenocarcinoma(54;1.13e-38)|all cancers(56;8.48e-34)|BRCA - Breast invasive adenocarcinoma(115;0.0355)|Colorectal(110;0.055)	GBM - Glioblastoma multiforme(99;2.11e-07)														---	---	---	---
COMMD5	28991	broad.mit.edu	37	8	146091976	146091976	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:146091976delT	uc010mgf.2	-							NM_014066	NP_054785			COMM domain containing 5							nucleus	protein binding			ovary(1)	1	all_cancers(97;1.14e-11)|all_epithelial(106;7.74e-11)|Lung NSC(106;4.08e-05)|all_lung(105;0.000125)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		Epithelial(56;8.75e-39)|OV - Ovarian serous cystadenocarcinoma(54;1.13e-38)|all cancers(56;8.48e-34)|BRCA - Breast invasive adenocarcinoma(115;0.0355)|Colorectal(110;0.055)															---	---	---	---
Unknown	0	broad.mit.edu	37	8	146152004	146152004	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:146152004delA								COMMD5 (25158 upstream) : ZNF16 (3742 downstream)																																			---	---	---	---
ZNF252	286101	broad.mit.edu	37	8	146227846	146227847	+	Intron	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:146227846_146227847delAA	uc011llo.1	-						ZNF252_uc003zew.3_Intron|C8orf77_uc003zfb.3_5'Flank					SubName: Full=cDNA FLJ52642, weakly similar to Zinc finger protein 3;												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	9	104023	104023	+	5'Flank	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:104023delA	uc003zfy.2	-											Homo sapiens chromosome 2 mRNA sequence.																														---	---	---	---
KANK1	23189	broad.mit.edu	37	9	488912	488912	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:488912delA	uc003zgl.1	+							NM_015158	NP_055973			KN motif and ankyrin repeat domains 1 isoform a						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)														---	---	---	---
Unknown	0	broad.mit.edu	37	9	1142432	1142433	+	IGR	DEL	TG	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:1142432_1142433delTG								DMRT2 (84879 upstream) : SMARCA2 (872909 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	1642280	1642281	+	IGR	INS	-	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:1642280_1642281insT								DMRT2 (584727 upstream) : SMARCA2 (373061 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	1813006	1813007	+	IGR	INS	-	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:1813006_1813007insA								DMRT2 (755453 upstream) : SMARCA2 (202335 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	1944769	1944769	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:1944769delA								DMRT2 (887216 upstream) : SMARCA2 (70573 downstream)																																			---	---	---	---
SMARCA2	6595	broad.mit.edu	37	9	2032819	2032819	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:2032819delT	uc003zhc.2	+						SMARCA2_uc003zhd.2_Intron|SMARCA2_uc010mha.2_Intron	NM_003070	NP_003061			SWI/SNF-related matrix-associated						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	2050323	2050323	+	Intron	DEL	T	-	-	rs33981080		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:2050323delT	uc003zhc.2	+						SMARCA2_uc003zhd.2_Intron|SMARCA2_uc010mha.2_Intron	NM_003070	NP_003061			SWI/SNF-related matrix-associated						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	2068723	2068723	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:2068723delT	uc003zhc.2	+						SMARCA2_uc003zhd.2_Intron|SMARCA2_uc010mha.2_Intron	NM_003070	NP_003061			SWI/SNF-related matrix-associated						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)														---	---	---	---
Unknown	0	broad.mit.edu	37	9	2253846	2253847	+	IGR	INS	-	A	A	rs140014943	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:2253846_2253847insA								SMARCA2 (60225 upstream) : FLJ35024 (168855 downstream)																																			---	---	---	---
FLJ35024	401491	broad.mit.edu	37	9	2552176	2552176	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:2552176delT	uc003zhh.1	-						FLJ35024_uc003zhi.2_Intron|FLJ35024_uc003zhj.3_Intron					Homo sapiens cDNA FLJ35024 fis, clone OCBBF2015233.												0																		---	---	---	---
FLJ35024	401491	broad.mit.edu	37	9	2580335	2580335	+	Intron	DEL	A	-	-	rs148660548		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:2580335delA	uc003zhh.1	-						FLJ35024_uc003zhi.2_Intron|FLJ35024_uc003zhj.3_Intron					Homo sapiens cDNA FLJ35024 fis, clone OCBBF2015233.												0																		---	---	---	---
KIAA0020	9933	broad.mit.edu	37	9	2807208	2807208	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:2807208delA	uc003zhp.1	-						KIAA0020_uc010mhc.1_Intron|KIAA0020_uc003zhq.1_Intron	NM_014878	NP_055693			KIAA0020 protein							endoplasmic reticulum|nucleolus	RNA binding			ovary(1)	1				GBM - Glioblastoma multiforme(50;0.0319)														---	---	---	---
RLN2	6019	broad.mit.edu	37	9	5300456	5300456	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:5300456delA	uc003zja.1	-						RLN2_uc003ziz.1_Intron	NM_134441	NP_604390			relaxin 2 isoform 1 preproprotein						female pregnancy	extracellular region	hormone activity				0	all_hematologic(13;0.137)	Acute lymphoblastic leukemia(23;0.158)		GBM - Glioblastoma multiforme(50;0.0201)|Lung(218;0.0987)														---	---	---	---
Unknown	0	broad.mit.edu	37	9	5347813	5347814	+	IGR	DEL	TG	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:5347813_5347814delTG								RLN1 (7940 upstream) : C9orf46 (10159 downstream)																																			---	---	---	---
KIAA1432	57589	broad.mit.edu	37	9	5753519	5753520	+	Intron	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:5753519_5753520delTT	uc003zji.2	+						KIAA1432_uc003zjh.2_Intron|KIAA1432_uc003zjl.3_Intron|KIAA1432_uc003zjj.1_Intron	NM_020829	NP_065880			connexin 43-interacting protein 150 isoform a							integral to membrane					0		Acute lymphoblastic leukemia(23;0.154)		GBM - Glioblastoma multiforme(50;0.000525)|Lung(218;0.122)														---	---	---	---
ERMP1	79956	broad.mit.edu	37	9	5779063	5779063	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:5779063delA	uc011lme.1	-							NM_024896				aminopeptidase Fxna						proteolysis	endoplasmic reticulum membrane|integral to membrane	metal ion binding|metallopeptidase activity			ovary(1)	1		Acute lymphoblastic leukemia(23;0.158)		GBM - Glioblastoma multiforme(50;0.00115)|Lung(218;0.111)														---	---	---	---
UHRF2	115426	broad.mit.edu	37	9	6477576	6477576	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:6477576delA	uc003zjy.2	+						UHRF2_uc003zjz.2_Intron|UHRF2_uc003zka.1_Intron	NM_152896	NP_690856			ubiquitin-like with PHD and ring finger domains						cell cycle|cell differentiation|cell proliferation|protein autoubiquitination|regulation of cell cycle|ubiquitin-dependent protein catabolic process	nucleus	DNA binding|histone binding|ubiquitin-protein ligase activity|zinc ion binding			large_intestine(2)|ovary(1)	3		Acute lymphoblastic leukemia(23;0.158)		GBM - Glioblastoma multiforme(50;0.0392)|Lung(218;0.129)														---	---	---	---
GLDC	2731	broad.mit.edu	37	9	6556794	6556794	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:6556794delA	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)													---	---	---	---
GLDC	2731	broad.mit.edu	37	9	6600696	6600696	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:6600696delA	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	6653823	6653824	+	IGR	INS	-	AGAA	AGAA	rs146691434	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:6653823_6653824insAGAA								GLDC (8131 upstream) : KDM4C (62671 downstream)																																			---	---	---	---
KDM4C	23081	broad.mit.edu	37	9	6715376	6715376	+	5'Flank	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:6715376delA	uc003zkd.2	+						KDM4C_uc003zke.2_5'Flank					Homo sapiens cDNA FLJ25668 fis, clone TST03551.						positive regulation of cell proliferation|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor|transcription, DNA-dependent	nuclear chromatin	androgen receptor binding|enzyme binding|histone demethylase activity (H3-K9 specific)|nucleic acid binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|zinc ion binding			ovary(1)	1																		---	---	---	---
KDM4C	23081	broad.mit.edu	37	9	6793347	6793348	+	Intron	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:6793347_6793348delAA	uc003zkh.2	+						KDM4C_uc010mhu.2_Intron|KDM4C_uc010mhw.2_Intron|KDM4C_uc011lmi.1_Intron|KDM4C_uc011lmj.1_Intron|KDM4C_uc003zkg.2_Intron|KDM4C_uc011lmk.1_Intron|KDM4C_uc010mhv.2_Intron	NM_015061	NP_055876			jumonji domain containing 2C isoform 1						positive regulation of cell proliferation|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor|transcription, DNA-dependent	nuclear chromatin	androgen receptor binding|enzyme binding|histone demethylase activity (H3-K9 specific)|nucleic acid binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|zinc ion binding			ovary(1)	1																		---	---	---	---
KDM4C	23081	broad.mit.edu	37	9	7080037	7080037	+	Intron	DEL	A	-	-	rs77549139		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:7080037delA	uc003zkh.2	+						KDM4C_uc011lmj.1_Intron|KDM4C_uc003zkg.2_Intron|KDM4C_uc011lmk.1_Intron|KDM4C_uc011lml.1_Intron	NM_015061	NP_055876			jumonji domain containing 2C isoform 1						positive regulation of cell proliferation|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor|transcription, DNA-dependent	nuclear chromatin	androgen receptor binding|enzyme binding|histone demethylase activity (H3-K9 specific)|nucleic acid binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|zinc ion binding			ovary(1)	1																		---	---	---	---
KDM4C	23081	broad.mit.edu	37	9	7128278	7128279	+	Intron	DEL	AA	-	-	rs73403349	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:7128278_7128279delAA	uc003zkh.2	+						KDM4C_uc011lmj.1_Intron|KDM4C_uc003zkg.2_Intron|KDM4C_uc011lmk.1_Intron|KDM4C_uc011lml.1_Intron	NM_015061	NP_055876			jumonji domain containing 2C isoform 1						positive regulation of cell proliferation|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor|transcription, DNA-dependent	nuclear chromatin	androgen receptor binding|enzyme binding|histone demethylase activity (H3-K9 specific)|nucleic acid binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|zinc ion binding			ovary(1)	1																		---	---	---	---
KDM4C	23081	broad.mit.edu	37	9	7141364	7141365	+	Intron	INS	-	AAC	AAC			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:7141364_7141365insAAC	uc003zkh.2	+						KDM4C_uc011lmj.1_Intron|KDM4C_uc003zkg.2_Intron|KDM4C_uc011lmk.1_Intron|KDM4C_uc011lml.1_Intron	NM_015061	NP_055876			jumonji domain containing 2C isoform 1						positive regulation of cell proliferation|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor|transcription, DNA-dependent	nuclear chromatin	androgen receptor binding|enzyme binding|histone demethylase activity (H3-K9 specific)|nucleic acid binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|zinc ion binding			ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	9	7329483	7329483	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:7329483delT								KDM4C (153836 upstream) : C9orf123 (467010 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	7342087	7342088	+	IGR	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:7342087_7342088delAA								KDM4C (166440 upstream) : C9orf123 (454405 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	7502527	7502527	+	IGR	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:7502527delG								KDM4C (326880 upstream) : C9orf123 (293966 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	7613897	7613897	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:7613897delT								KDM4C (438250 upstream) : C9orf123 (182596 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	7748171	7748172	+	IGR	DEL	AA	-	-	rs78350460		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:7748171_7748172delAA								KDM4C (572524 upstream) : C9orf123 (48321 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	7856516	7856518	+	IGR	DEL	AAA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:7856516_7856518delAAA								C9orf123 (56717 upstream) : PTPRD (457729 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	7891420	7891421	+	IGR	DEL	AG	-	-	rs114829434	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:7891420_7891421delAG								C9orf123 (91621 upstream) : PTPRD (422826 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	8106328	8106328	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:8106328delA								C9orf123 (306529 upstream) : PTPRD (207919 downstream)																																			---	---	---	---
PTPRD	5789	broad.mit.edu	37	9	8395633	8395633	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:8395633delT	uc003zkk.2	-						PTPRD_uc003zkp.2_Intron|PTPRD_uc003zkq.2_Intron|PTPRD_uc003zkr.2_Intron|PTPRD_uc003zks.2_Intron|PTPRD_uc003zkl.2_Intron|PTPRD_uc003zkm.2_Intron|PTPRD_uc003zkn.2_Intron|PTPRD_uc003zko.2_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	8501114	8501114	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:8501114delA	uc003zkk.2	-						PTPRD_uc003zkp.2_Intron|PTPRD_uc003zkq.2_Intron|PTPRD_uc003zkr.2_Intron|PTPRD_uc003zks.2_Intron|PTPRD_uc003zkl.2_Intron|PTPRD_uc003zkm.2_Intron|PTPRD_uc003zkn.2_Intron|PTPRD_uc003zko.2_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	8719117	8719118	+	Intron	INS	-	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:8719117_8719118insT	uc003zkk.2	-						PTPRD_uc003zkp.2_Intron|PTPRD_uc003zkq.2_Intron|PTPRD_uc003zkr.2_Intron|PTPRD_uc003zks.2_Intron|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	8852749	8852749	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:8852749delA	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	8898260	8898260	+	Intron	DEL	T	-	-	rs33926117		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:8898260delT	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	9275820	9275821	+	Intron	DEL	TG	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:9275820_9275821delTG	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	9575169	9575170	+	Intron	DEL	AC	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:9575169_9575170delAC	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	10420556	10420556	+	Intron	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:10420556delG	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	10575752	10575753	+	Intron	INS	-	TC	TC			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:10575752_10575753insTC	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	10830824	10830824	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:10830824delT								PTPRD (218101 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	11464009	11464010	+	IGR	DEL	TG	-	-	rs141145640	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:11464009_11464010delTG								PTPRD (851286 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	11721833	11721833	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-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	11730350	11730350	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:11730350delA								None (None upstream) : TYRP1 (963036 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	11763746	11763747	+	IGR	DEL	TG	-	-	rs140297985		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:11763746_11763747delTG								None (None upstream) : TYRP1 (929639 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	12636605	12636607	+	IGR	DEL	AAA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:12636605_12636607delAAA								None (None upstream) : TYRP1 (56779 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	12824739	12824739	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:12824739delA								C9orf150 (1681 upstream) : MPDZ (280970 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	12838095	12838095	+	IGR	DEL	A	-	-	rs112251490		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:12838095delA								C9orf150 (15037 upstream) : MPDZ (267614 downstream)																																			---	---	---	---
NFIB	4781	broad.mit.edu	37	9	14266042	14266042	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:14266042delA	uc003zle.2	-						NFIB_uc003zlf.2_Intron|NFIB_uc011lmo.1_Intron	NM_005596	NP_005587			nuclear factor I/B						anterior commissure morphogenesis|chondrocyte differentiation|Clara cell differentiation|commissural neuron axon guidance|DNA replication|glial cell differentiation|lung ciliated cell differentiation|negative regulation of DNA binding|negative regulation of epithelial cell proliferation involved in lung morphogenesis|negative regulation of mesenchymal cell proliferation involved in lung development|positive regulation of transcription from RNA polymerase II promoter|principal sensory nucleus of trigeminal nerve development|Type I pneumocyte differentiation|Type II pneumocyte differentiation	cerebellar mossy fiber|nucleolus|nucleus	RNA polymerase II transcription corepressor activity|sequence-specific DNA binding RNA polymerase II transcription factor activity				0				GBM - Glioblastoma multiforme(50;4.4e-08)|LUAD - Lung adenocarcinoma(58;0.119)|Lung(218;0.164)				T	MYB|HGMA2	adenoid cystic carcinoma|lipoma								---	---	---	---
FREM1	158326	broad.mit.edu	37	9	14865660	14865663	+	Intron	DEL	TGTG	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:14865660_14865663delTGTG	uc003zlm.2	-						FREM1_uc010mic.2_Intron	NM_144966	NP_659403			FRAS1 related extracellular matrix 1 precursor						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	14881400	14881400	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:14881400delA	uc003zlm.2	-						FREM1_uc010mic.2_Intron	NM_144966	NP_659403			FRAS1 related extracellular matrix 1 precursor						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)														---	---	---	---
Unknown	0	broad.mit.edu	37	9	14927731	14927731	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:14927731delT								FREM1 (16738 upstream) : LOC389705 (65594 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	15036070	15036070	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:15036070delA	uc003zln.1	-											Homo sapiens cDNA FLJ46077 fis, clone TESTI2003768, weakly  similar to Chloride channel protein 3.																														---	---	---	---
PSIP1	11168	broad.mit.edu	37	9	15472612	15472612	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:15472612delA	uc003zlv.3	-						PSIP1_uc003zlw.3_Intron|PSIP1_uc003zlz.3_Intron|PSIP1_uc003zma.3_Intron|PSIP1_uc003zly.2_Intron	NM_033222	NP_150091			PC4 and SFRS1 interacting protein 1 isoform 2						initiation of viral infection|interspecies interaction between organisms|nuclear mRNA 5'-splice site recognition|provirus integration|regulation of transcription, DNA-dependent|response to heat|response to oxidative stress|transcription, DNA-dependent	cytosol|nuclear heterochromatin|nuclear periphery|nucleoplasm|nucleoplasm|transcriptionally active chromatin	activating transcription factor binding|chromatin binding|DNA secondary structure binding|RNA polymerase II transcription coactivator activity			breast(1)	1				GBM - Glioblastoma multiforme(50;2.38e-06)														---	---	---	---
PSIP1	11168	broad.mit.edu	37	9	15487004	15487004	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:15487004delT	uc003zlv.3	-						PSIP1_uc003zlw.3_Intron|PSIP1_uc003zlz.3_Intron|PSIP1_uc003zma.3_Intron|PSIP1_uc003zly.2_Intron	NM_033222	NP_150091			PC4 and SFRS1 interacting protein 1 isoform 2						initiation of viral infection|interspecies interaction between organisms|nuclear mRNA 5'-splice site recognition|provirus integration|regulation of transcription, DNA-dependent|response to heat|response to oxidative stress|transcription, DNA-dependent	cytosol|nuclear heterochromatin|nuclear periphery|nucleoplasm|nucleoplasm|transcriptionally active chromatin	activating transcription factor binding|chromatin binding|DNA secondary structure binding|RNA polymerase II transcription coactivator activity			breast(1)	1				GBM - Glioblastoma multiforme(50;2.38e-06)														---	---	---	---
C9orf93	203238	broad.mit.edu	37	9	15559559	15559559	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:15559559delT	uc003zmd.2	+						C9orf93_uc010mih.1_Intron|C9orf93_uc003zme.2_Intron|C9orf93_uc003zmc.2_Intron	NM_173550	NP_775821			hypothetical protein LOC203238												0				GBM - Glioblastoma multiforme(50;4.84e-07)														---	---	---	---
C9orf93	203238	broad.mit.edu	37	9	15562001	15562001	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:15562001delT	uc003zmd.2	+						C9orf93_uc010mih.1_Intron|C9orf93_uc003zme.2_Intron|C9orf93_uc011lmu.1_5'Flank|C9orf93_uc003zmc.2_Intron	NM_173550	NP_775821			hypothetical protein LOC203238												0				GBM - Glioblastoma multiforme(50;4.84e-07)														---	---	---	---
Unknown	0	broad.mit.edu	37	9	16040879	16040879	+	IGR	DEL	C	-	-	rs1359955	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:16040879delC								C9orf93 (68984 upstream) : BNC2 (368623 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	16374147	16374147	+	IGR	DEL	T	-	-	rs79537523		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:16374147delT								C9orf93 (402252 upstream) : BNC2 (35355 downstream)																																			---	---	---	---
BNC2	54796	broad.mit.edu	37	9	16805712	16805715	+	Intron	DEL	CACA	-	-	rs113858353		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:16805712_16805715delCACA	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	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	16885059	16885061	+	IGR	DEL	AAA	-	-	rs144472903		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:16885059_16885061delAAA								BNC2 (14273 upstream) : CNTLN (249977 downstream)																																			---	---	---	---
CNTLN	54875	broad.mit.edu	37	9	17219256	17219257	+	Intron	DEL	TT	-	-	rs112815886		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:17219256_17219257delTT	uc003zmz.2	+						CNTLN_uc003zmx.3_Intron|CNTLN_uc003zmy.2_Intron	NM_017738	NP_060208			centlein isoform 1							centriole|membrane	two-component sensor activity			pancreas(1)	1				GBM - Glioblastoma multiforme(50;6.14e-10)														---	---	---	---
CNTLN	54875	broad.mit.edu	37	9	17317039	17317039	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:17317039delT	uc003zmz.2	+						CNTLN_uc003zmy.2_Intron|CNTLN_uc010mio.2_Intron	NM_017738	NP_060208			centlein isoform 1							centriole|membrane	two-component sensor activity			pancreas(1)	1				GBM - Glioblastoma multiforme(50;6.14e-10)														---	---	---	---
CNTLN	54875	broad.mit.edu	37	9	17338168	17338168	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:17338168delT	uc003zmz.2	+						CNTLN_uc003zmy.2_Intron|CNTLN_uc010mio.2_Intron	NM_017738	NP_060208			centlein isoform 1							centriole|membrane	two-component sensor activity			pancreas(1)	1				GBM - Glioblastoma multiforme(50;6.14e-10)														---	---	---	---
Unknown	0	broad.mit.edu	37	9	18007789	18007789	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:18007789delA								SH3GL2 (210669 upstream) : ADAMTSL1 (466315 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	18221541	18221541	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:18221541delT								SH3GL2 (424421 upstream) : ADAMTSL1 (252563 downstream)																																			---	---	---	---
ADAMTSL1	92949	broad.mit.edu	37	9	18777687	18777687	+	Frame_Shift_Del	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:18777687delG	uc003zne.3	+	19	3587	c.3460delG	c.(3460-3462)GGGfs	p.G1154fs		NM_001040272	NP_001035362	Q8N6G6	ATL1_HUMAN	ADAMTS-like 1 isoform 4 precursor	1154						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	18890720	18890720	+	Intron	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:18890720delC	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)														---	---	---	---
HAUS6	54801	broad.mit.edu	37	9	19078313	19078313	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:19078313delA	uc003znk.2	-						HAUS6_uc011lmz.1_Intron|HAUS6_uc003znl.1_Intron|HAUS6_uc003znm.1_Intron	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																		---	---	---	---
DENND4C	55667	broad.mit.edu	37	9	19298041	19298041	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:19298041delT	uc003znq.2	+						DENND4C_uc011lnc.1_Intron	NM_017925	NP_060395			DENN/MADD domain containing 4C							integral to membrane				ovary(1)|skin(1)	2																		---	---	---	---
DENND4C	55667	broad.mit.edu	37	9	19350680	19350680	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:19350680delT	uc003znq.2	+						DENND4C_uc011lnc.1_Intron|DENND4C_uc011lnd.1_Intron|DENND4C_uc003znr.2_Intron|DENND4C_uc003zns.2_Intron|DENND4C_uc003znt.2_Intron	NM_017925	NP_060395			DENN/MADD domain containing 4C							integral to membrane				ovary(1)|skin(1)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	9	19375707	19375708	+	IGR	DEL	TG	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:19375707_19375708delTG								DENND4C (1569 upstream) : RPS6 (546 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	19383903	19383904	+	IGR	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:19383903_19383904delAA								RPS6 (3668 upstream) : ACER2 (13903 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	19393643	19393644	+	IGR	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:19393643_19393644delAA								RPS6 (13408 upstream) : ACER2 (4163 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	19469979	19469979	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:19469979delT								ACER2 (17479 upstream) : SLC24A2 (45999 downstream)																																			---	---	---	---
MLLT3	4300	broad.mit.edu	37	9	20352780	20352780	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:20352780delA	uc003zoe.2	-						MLLT3_uc011lne.1_Intron|MLLT3_uc011lnf.1_Intron	NM_004529	NP_004520			myeloid/lymphoid or mixed-lineage leukemia						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	protein binding			lung(2)|ovary(1)	3				GBM - Glioblastoma multiforme(3;4.35e-105)|Lung(42;3.48e-06)|LUSC - Lung squamous cell carcinoma(42;7.92e-05)				T	MLL	ALL								---	---	---	---
MLLT3	4300	broad.mit.edu	37	9	20448401	20448401	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:20448401delA	uc003zoe.2	-						MLLT3_uc011lne.1_Intron|MLLT3_uc011lnf.1_Intron|MLLT3_uc003zof.2_Intron|MLLT3_uc011lng.1_Intron	NM_004529	NP_004520			myeloid/lymphoid or mixed-lineage leukemia						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	protein binding			lung(2)|ovary(1)	3				GBM - Glioblastoma multiforme(3;4.35e-105)|Lung(42;3.48e-06)|LUSC - Lung squamous cell carcinoma(42;7.92e-05)				T	MLL	ALL								---	---	---	---
MLLT3	4300	broad.mit.edu	37	9	20621999	20621999	+	Intron	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:20621999delG	uc003zoe.2	-						MLLT3_uc011lne.1_5'Flank|MLLT3_uc011lnf.1_5'Flank|MLLT3_uc003zof.2_Intron|MLLT3_uc011lng.1_5'Flank	NM_004529	NP_004520			myeloid/lymphoid or mixed-lineage leukemia						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	protein binding			lung(2)|ovary(1)	3				GBM - Glioblastoma multiforme(3;4.35e-105)|Lung(42;3.48e-06)|LUSC - Lung squamous cell carcinoma(42;7.92e-05)				T	MLL	ALL								---	---	---	---
KIAA1797	54914	broad.mit.edu	37	9	20898321	20898321	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:20898321delT	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)														---	---	---	---
KIAA1797	54914	broad.mit.edu	37	9	20992960	20992962	+	Intron	DEL	AAA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:20992960_20992962delAAA	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)														---	---	---	---
Unknown	0	broad.mit.edu	37	9	21118016	21118016	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:21118016delT								IFNB1 (40073 upstream) : IFNW1 (22615 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	22150990	22150990	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:22150990delT								CDKN2BAS (29899 upstream) : DMRTA1 (295850 downstream)																																			---	---	---	---
DMRTA1	63951	broad.mit.edu	37	9	22451039	22451039	+	Intron	DEL	T	-	-	rs41270141	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:22451039delT	uc003zpp.1	+							NM_022160	NP_071443			DMRT-like family A1						cell differentiation|sex differentiation	nucleus	DNA binding|metal ion binding|sequence-specific DNA binding transcription factor activity			large_intestine(1)|skin(1)	2		all_cancers(5;4.09e-243)|Acute lymphoblastic leukemia(3;8.25e-150)|all_hematologic(3;4.25e-147)|Esophageal squamous(3;2.32e-09)|Renal(3;1.71e-07)|Breast(3;2.07e-06)|Hepatocellular(5;0.00563)		GBM - Glioblastoma multiforme(1;5.12e-278)|Lung(24;8.2e-52)|LUSC - Lung squamous cell carcinoma(38;1.46e-37)|OV - Ovarian serous cystadenocarcinoma(39;0.0517)														---	---	---	---
Unknown	0	broad.mit.edu	37	9	23200763	23200764	+	IGR	INS	-	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:23200763_23200764insA								DMRTA1 (748291 upstream) : ELAVL2 (489341 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	23510510	23510511	+	Intron	INS	-	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:23510510_23510511insT	uc003zpr.2	-											Homo sapiens mRNA; cDNA DKFZp781D1719 (from clone DKFZp781D1719).																														---	---	---	---
ELAVL2	1993	broad.mit.edu	37	9	23739555	23739555	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:23739555delA	uc003zpu.2	-						ELAVL2_uc003zps.2_Intron|ELAVL2_uc003zpt.2_Intron|ELAVL2_uc003zpv.2_Intron|ELAVL2_uc003zpw.2_Intron	NM_004432	NP_004423			ELAV (embryonic lethal, abnormal vision,						regulation of transcription, DNA-dependent		mRNA 3'-UTR binding|nucleotide binding|protein binding			ovary(2)|central_nervous_system(1)	3				GBM - Glioblastoma multiforme(1;2.18e-156)|Lung(42;2.15e-28)|LUSC - Lung squamous cell carcinoma(38;1.02e-19)														---	---	---	---
ELAVL2	1993	broad.mit.edu	37	9	23790066	23790069	+	Intron	DEL	GAAA	-	-	rs58171802	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:23790066_23790069delGAAA	uc003zpu.2	-						ELAVL2_uc003zps.2_Intron|ELAVL2_uc003zpt.2_Intron|ELAVL2_uc003zpv.2_Intron|ELAVL2_uc003zpw.2_Intron	NM_004432	NP_004423			ELAV (embryonic lethal, abnormal vision,						regulation of transcription, DNA-dependent		mRNA 3'-UTR binding|nucleotide binding|protein binding			ovary(2)|central_nervous_system(1)	3				GBM - Glioblastoma multiforme(1;2.18e-156)|Lung(42;2.15e-28)|LUSC - Lung squamous cell carcinoma(38;1.02e-19)														---	---	---	---
ELAVL2	1993	broad.mit.edu	37	9	23812121	23812121	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:23812121delT	uc003zpu.2	-						ELAVL2_uc003zps.2_Intron|ELAVL2_uc003zpt.2_Intron|ELAVL2_uc003zpv.2_Intron|ELAVL2_uc003zpw.2_Intron	NM_004432	NP_004423			ELAV (embryonic lethal, abnormal vision,						regulation of transcription, DNA-dependent		mRNA 3'-UTR binding|nucleotide binding|protein binding			ovary(2)|central_nervous_system(1)	3				GBM - Glioblastoma multiforme(1;2.18e-156)|Lung(42;2.15e-28)|LUSC - Lung squamous cell carcinoma(38;1.02e-19)														---	---	---	---
Unknown	0	broad.mit.edu	37	9	24047274	24047277	+	IGR	DEL	GTGT	-	-	rs72318396		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:24047274_24047277delGTGT								ELAVL2 (221211 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	24445601	24445601	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:24445601delT								ELAVL2 (619538 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	24953242	24953242	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:24953242delT								None (None upstream) : TUSC1 (723152 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	25002500	25002500	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:25002500delT								None (None upstream) : TUSC1 (673894 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	25036327	25036328	+	IGR	INS	-	CT	CT	rs141309092	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:25036327_25036328insCT								None (None upstream) : TUSC1 (640066 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	25246620	25246620	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:25246620delT								None (None upstream) : TUSC1 (429774 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	25459825	25459825	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:25459825delT								None (None upstream) : TUSC1 (216569 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	26272680	26272682	+	IGR	DEL	TCT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:26272680_26272682delTCT								TUSC1 (593824 upstream) : C9orf82 (568002 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	26284453	26284453	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:26284453delT								TUSC1 (605597 upstream) : C9orf82 (556231 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	26563650	26563651	+	IGR	DEL	CA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:26563650_26563651delCA								TUSC1 (884794 upstream) : C9orf82 (277033 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	26640262	26640263	+	IGR	INS	-	CT	CT			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:26640262_26640263insCT								TUSC1 (961406 upstream) : C9orf82 (200421 downstream)																																			---	---	---	---
IFT74	80173	broad.mit.edu	37	9	26980558	26980558	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:26980558delT	uc010mja.2	+						IFT74_uc010mjb.2_Intron|IFT74_uc003zqf.3_Intron|IFT74_uc003zqg.3_Intron	NM_001099223	NP_001092693			coiled-coil domain containing 2 isoform a							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	27011886	27011887	+	Intron	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:27011886_27011887delTT	uc010mja.2	+						IFT74_uc010mjb.2_Intron|IFT74_uc003zqf.3_Intron|IFT74_uc003zqg.3_Intron	NM_001099223	NP_001092693			coiled-coil domain containing 2 isoform a							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	27032568	27032568	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:27032568delA	uc010mja.2	+						IFT74_uc010mjb.2_Intron|IFT74_uc003zqf.3_Intron|IFT74_uc003zqg.3_Intron	NM_001099223	NP_001092693			coiled-coil domain containing 2 isoform a							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)														---	---	---	---
TEK	7010	broad.mit.edu	37	9	27116858	27116865	+	Intron	DEL	TTTTTTTT	-	-	rs67266240		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:27116858_27116865delTTTTTTTT	uc003zqi.3	+						TEK_uc010mjc.1_Intron|TEK_uc011lnn.1_Intron|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	27406844	27406844	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:27406844delT	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)														---	---	---	---
MOBKL2B	79817	broad.mit.edu	37	9	27524103	27524103	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:27524103delA	uc003zqn.2	-						IFNK_uc003zqp.2_5'Flank	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	27820328	27820328	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:27820328delT								C9orf72 (246486 upstream) : LINGO2 (128200 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	27923446	27923446	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:27923446delA								C9orf72 (349604 upstream) : LINGO2 (25082 downstream)																																			---	---	---	---
LINGO2	158038	broad.mit.edu	37	9	28430746	28430746	+	Intron	DEL	T	-	-	rs149304501	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:28430746delT	uc010mjf.1	-						LINGO2_uc003zqv.1_Intron	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	28704395	28704395	+	Intron	DEL	T	-	-	rs76982779		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:28704395delT	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	28830786	28830787	+	IGR	DEL	AC	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:28830786_28830787delAC								LINGO2 (111483 upstream) : MIR876 (32837 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	29059625	29059625	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:29059625delA								MIR873 (170672 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	29612998	29612998	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:29612998delT								MIR873 (724045 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	29710964	29710964	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:29710964delA								MIR873 (822011 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	29956335	29956335	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:29956335delT								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	30079574	30079574	+	IGR	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:30079574delG								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	30409191	30409192	+	IGR	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:30409191_30409192delTT								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	30610067	30610068	+	IGR	DEL	AA	-	-	rs145779170	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:30610067_30610068delAA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	30670923	30670923	+	IGR	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:30670923delC								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	31009936	31009937	+	IGR	INS	-	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:31009936_31009937insA								None (None upstream) : None (None downstream)																																			---	---	---	---
NDUFB6	4712	broad.mit.edu	37	9	32558116	32558117	+	Intron	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:32558116_32558117delTT	uc003zre.1	-						NDUFB6_uc003zrf.1_Intron	NM_002493	NP_002484			NADH dehydrogenase (ubiquinone) 1 beta						mitochondrial electron transport, NADH to ubiquinone|transport	integral to membrane|mitochondrial respiratory chain complex I	NADH dehydrogenase (ubiquinone) activity				0			LUSC - Lung squamous cell carcinoma(29;0.0181)	GBM - Glioblastoma multiforme(74;0.00199)	NADH(DB00157)													---	---	---	---
Unknown	0	broad.mit.edu	37	9	32673656	32673656	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:32673656delA								TAF1L (37989 upstream) : TMEM215 (109841 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	32769952	32769953	+	IGR	INS	-	G	G	rs72268038		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:32769952_32769953insG								TAF1L (134285 upstream) : TMEM215 (13544 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	32884112	32884112	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:32884112delT								TMEM215 (94915 upstream) : APTX (88497 downstream)																																			---	---	---	---
APTX	54840	broad.mit.edu	37	9	33005602	33005602	+	Intron	DEL	T	-	-	rs112284588		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:33005602delT	uc003zrz.2	-							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					---	---	---	---
DNAJA1	3301	broad.mit.edu	37	9	33027152	33027155	+	Intron	DEL	TTTT	-	-	rs77003798		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:33027152_33027155delTTTT	uc003zsd.1	+						DNAJA1_uc011lnt.1_Intron|DNAJA1_uc003zse.1_Intron|APTX_uc003zrz.2_5'Flank	NM_001539	NP_001530			DnaJ (Hsp40) homolog, subfamily A, member 1						protein folding|response to heat|response to unfolded protein	membrane	ATP binding|heat shock protein binding|low-density lipoprotein particle receptor binding|metal ion binding|unfolded protein binding				0			LUSC - Lung squamous cell carcinoma(29;0.0227)	GBM - Glioblastoma multiforme(74;0.102)														---	---	---	---
SMU1	55234	broad.mit.edu	37	9	33077609	33077609	+	5'Flank	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:33077609delT	uc003zsf.1	-						SMU1_uc010mjo.1_5'Flank|SMU1_uc010mjp.1_5'Flank|SMU1_uc011lnu.1_5'Flank	NM_018225	NP_060695			smu-1 suppressor of mec-8 and unc-52 homolog							cytoplasm|nucleus				ovary(1)	1			LUSC - Lung squamous cell carcinoma(29;0.0227)	GBM - Glioblastoma multiforme(74;0.11)														---	---	---	---
B4GALT1	2683	broad.mit.edu	37	9	33111981	33111981	+	3'UTR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:33111981delA	uc003zsg.2	-	6						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)													---	---	---	---
SUGT1P1	441394	broad.mit.edu	37	9	33227209	33227210	+	Intron	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:33227209_33227210delTT	uc010mjq.1	-							NR_003667				Homo sapiens suppressor of G2 allele of SKP1 pseudogene (S. cerevisiae) (SUGT1P), non-coding RNA.												0																		---	---	---	---
NFX1	4799	broad.mit.edu	37	9	33313426	33313426	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:33313426delA	uc003zsq.2	+						SUGT1P1_uc010mjq.1_Intron|NFX1_uc011lnw.1_Intron|NFX1_uc003zso.2_Intron|NFX1_uc003zsp.1_Intron|NFX1_uc010mjr.1_Intron|NFX1_uc003zsr.2_Intron	NM_002504	NP_002495			nuclear transcription factor, X-box binding 1						inflammatory response|interspecies interaction between organisms|negative regulation of transcription from RNA polymerase II promoter|transcription from RNA polymerase II promoter	nucleus	DNA binding|ligase activity|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(1)	1			LUSC - Lung squamous cell carcinoma(29;0.00506)	GBM - Glioblastoma multiforme(74;0.224)														---	---	---	---
NFX1	4799	broad.mit.edu	37	9	33348909	33348909	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:33348909delT	uc003zsq.2	+						SUGT1P1_uc010mjq.1_Intron|NFX1_uc003zsp.1_Intron|NFX1_uc010mjr.1_Intron|NFX1_uc003zsr.2_Intron	NM_002504	NP_002495			nuclear transcription factor, X-box binding 1						inflammatory response|interspecies interaction between organisms|negative regulation of transcription from RNA polymerase II promoter|transcription from RNA polymerase II promoter	nucleus	DNA binding|ligase activity|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(1)	1			LUSC - Lung squamous cell carcinoma(29;0.00506)	GBM - Glioblastoma multiforme(74;0.224)														---	---	---	---
SUGT1P1	441394	broad.mit.edu	37	9	33408539	33408540	+	Intron	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:33408539_33408540delTT	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	33457290	33457290	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:33457290delT	uc010mjq.1	-							NR_003667				Homo sapiens suppressor of G2 allele of SKP1 pseudogene (S. cerevisiae) (SUGT1P), non-coding RNA.												0																		---	---	---	---
NOL6	65083	broad.mit.edu	37	9	33464277	33464277	+	Intron	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:33464277delC	uc003zsz.2	-						SUGT1P1_uc010mjq.1_Intron|NOL6_uc003zsy.2_Intron|NOL6_uc003zta.2_Intron|NOL6_uc010mjv.2_Intron|NOL6_uc011lob.1_Intron|NOL6_uc003ztb.1_Intron	NM_022917	NP_075068			nucleolar protein family 6 alpha isoform						rRNA processing	condensed nuclear chromosome|nucleolus	RNA binding			ovary(2)	2			LUSC - Lung squamous cell carcinoma(29;0.00788)	GBM - Glioblastoma multiforme(74;0.152)														---	---	---	---
Unknown	0	broad.mit.edu	37	9	33648735	33648735	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:33648735delA								ANXA2P2 (23205 upstream) : PTENP1 (24772 downstream)																																			---	---	---	---
UBE2R2	54926	broad.mit.edu	37	9	33886045	33886045	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:33886045delA	uc003ztm.2	+							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	34029525	34029525	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:34029525delA	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)														---	---	---	---
Unknown	0	broad.mit.edu	37	9	34351708	34351709	+	IGR	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:34351708_34351709delAA								NUDT2 (8013 upstream) : KIAA1161 (17199 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	34900231	34900232	+	IGR	INS	-	AGA	AGA	rs141859455	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:34900231_34900232insAGA								C9orf144 (61648 upstream) : KIAA1045 (57289 downstream)																																			---	---	---	---
KIAA1045	23349	broad.mit.edu	37	9	34966911	34966911	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:34966911delT	uc003zvq.2	+						KIAA1045_uc003zvr.2_Intron	NM_015297	NP_056112			hypothetical protein LOC23349								calcium ion binding			skin(1)	1			LUSC - Lung squamous cell carcinoma(32;0.00575)															---	---	---	---
Unknown	0	broad.mit.edu	37	9	34986533	34986533	+	IGR	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:34986533delC								KIAA1045 (3991 upstream) : DNAJB5 (3192 downstream)																																			---	---	---	---
DNAJB5	25822	broad.mit.edu	37	9	34997369	34997369	+	3'UTR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:34997369delA	uc003zvt.2	+	4					DNAJB5_uc003zvs.2_3'UTR|DNAJB5_uc011los.1_3'UTR	NM_012266	NP_036398			DnaJ (Hsp40) homolog, subfamily B, member 5						protein folding|response to unfolded protein		heat shock protein binding|unfolded protein binding				0			LUSC - Lung squamous cell carcinoma(32;0.00575)															---	---	---	---
Unknown	0	broad.mit.edu	37	9	35013175	35013175	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:35013175delT								DNAJB5 (14747 upstream) : C9orf131 (27927 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	35158002	35158002	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:35158002delT								KIAA1539 (42109 upstream) : UNC13B (3987 downstream)																																			---	---	---	---
ATP8B5P	158381	broad.mit.edu	37	9	35450411	35450411	+	RNA	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-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																		---	---	---	---
CD72	971	broad.mit.edu	37	9	35612582	35612582	+	Intron	DEL	A	-	-	rs147554742		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:35612582delA	uc003zxb.2	-						CD72_uc003zxc.1_Intron|CD72_uc010mkt.1_Intron	NM_001782	NP_001773			CD72 molecule						axon guidance|cell adhesion	integral to plasma membrane	receptor binding|sugar binding|transmembrane receptor activity				0			Lung(28;0.00276)|LUSC - Lung squamous cell carcinoma(32;0.00418)|STAD - Stomach adenocarcinoma(86;0.194)															---	---	---	---
TMEM8B	51754	broad.mit.edu	37	9	35849521	35849521	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:35849521delT	uc003zym.2	+						TMEM8B_uc003zyo.2_Intron	NM_001042589	NP_001036054			transmembrane protein 8B isoform a						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																		---	---	---	---
Unknown	0	broad.mit.edu	37	9	36181608	36181608	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:36181608delA								CCIN (10279 upstream) : CLTA (9284 downstream)																																			---	---	---	---
GNE	10020	broad.mit.edu	37	9	36246658	36246665	+	Intron	DEL	TTTTTTTT	-	-	rs71821983		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:36246658_36246665delTTTTTTTT	uc010mlh.2	-						CLTA_uc003zzf.1_Intron|GNE_uc010mlg.2_Intron|GNE_uc011lpl.1_Intron|GNE_uc010mli.2_Intron|GNE_uc010mlj.2_Intron	NM_005476	NP_005467			UDP-N-acetylglucosamine-2-epimerase/N-						cell adhesion|lipopolysaccharide biosynthetic process|N-acetylneuraminate metabolic process|UDP-N-acetylglucosamine metabolic process		ATP binding|N-acylmannosamine kinase activity|UDP-N-acetylglucosamine 2-epimerase activity				0			STAD - Stomach adenocarcinoma(86;0.228)															---	---	---	---
RNF38	152006	broad.mit.edu	37	9	36353341	36353341	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:36353341delA	uc003zzh.2	-						RNF38_uc003zzi.2_Intron|RNF38_uc003zzj.2_Intron|RNF38_uc003zzk.2_Intron|RNF38_uc003zzl.2_Intron|RNF38_uc003zzm.2_Intron	NM_022781	NP_073618			ring finger protein 38 isoform 1								zinc ion binding			central_nervous_system(1)	1			STAD - Stomach adenocarcinoma(86;0.228)															---	---	---	---
Unknown	0	broad.mit.edu	37	9	36718404	36718404	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:36718404delA								MELK (40726 upstream) : PAX5 (120127 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	36780342	36780342	+	IGR	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:36780342delC								MELK (102664 upstream) : PAX5 (58189 downstream)																																			---	---	---	---
PAX5	5079	broad.mit.edu	37	9	36949045	36949045	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:36949045delT	uc003zzo.1	-						PAX5_uc011lpt.1_Intron|PAX5_uc011lpu.1_Intron|PAX5_uc011lpv.1_Intron|PAX5_uc011lpw.1_Intron|PAX5_uc011lpx.1_Intron|PAX5_uc011lpy.1_Intron|PAX5_uc010mls.1_Intron|PAX5_uc011lpz.1_Intron|PAX5_uc011lqa.1_Intron|PAX5_uc010mlq.1_Intron|PAX5_uc011lqb.1_Intron|PAX5_uc010mlo.1_Intron|PAX5_uc010mlp.1_Intron|PAX5_uc011lqc.1_Intron|PAX5_uc010mlr.1_Intron	NM_016734	NP_057953			paired box 5						cell differentiation|humoral immune response|nervous system development|organ morphogenesis|spermatogenesis|transcription from RNA polymerase II promoter	nucleus	DNA binding	p.?(19)	PAX5/JAK2(18)	haematopoietic_and_lymphoid_tissue(142)|lung(3)|central_nervous_system(2)	147		all_cancers(2;3.46e-10)|Acute lymphoblastic leukemia(2;7.09e-56)|all_hematologic(2;6.65e-44)		GBM - Glioblastoma multiforme(29;0.0108)				T|Mis|D|F|S	IGH@|ETV6|PML|FOXP1|ZNF521|ELN	NHL|ALL|B-ALL								---	---	---	---
Unknown	0	broad.mit.edu	37	9	37050100	37050101	+	IGR	DEL	TG	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:37050100_37050101delTG								PAX5 (15624 upstream) : ZCCHC7 (70368 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	37086286	37086287	+	Intron	DEL	CT	-	-	rs141471339		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:37086286_37086287delCT	uc003zzp.1	+											Homo sapiens cDNA FLJ13634 fis, clone PLACE1011133.																														---	---	---	---
ZCCHC7	84186	broad.mit.edu	37	9	37189687	37189688	+	Intron	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:37189687_37189688delTT	uc003zzq.2	+						ZCCHC7_uc011lqh.1_Intron|ZCCHC7_uc011lqi.1_Intron|ZCCHC7_uc010mlt.2_Intron	NM_032226	NP_115602			zinc finger, CCHC domain containing 7								nucleic acid binding|zinc ion binding			ovary(1)|central_nervous_system(1)|skin(1)	3				GBM - Glioblastoma multiforme(29;0.0137)														---	---	---	---
Unknown	0	broad.mit.edu	37	9	38160961	38160961	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:38160961delA								SHB (91751 upstream) : ALDH1B1 (231741 downstream)																																	OREG0019200	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	38169024	38169024	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:38169024delT								SHB (99814 upstream) : ALDH1B1 (223678 downstream)																																			---	---	---	---
IGFBPL1	347252	broad.mit.edu	37	9	38411307	38411307	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:38411307delT	uc004aba.2	-							NM_001007563	NP_001007564			insulin-like growth factor binding protein-like						regulation of cell growth	extracellular region	insulin-like growth factor binding				0				GBM - Glioblastoma multiforme(29;0.0437)|Lung(182;0.116)														---	---	---	---
Unknown	0	broad.mit.edu	37	9	39817161	39817161	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:39817161delA								LOC653501 (308273 upstream) : FAM74A1 (83039 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	44759534	44759534	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:44759534delA								None (None upstream) : FAM27C (230702 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	66330377	66330377	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:66330377delT								FAM74A4 (835991 upstream) : LOC442421 (166093 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	66462285	66462286	+	Intron	INS	-	TG	TG	rs12685769		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:66462285_66462286insTG	uc004aec.2	+											Homo sapiens, clone IMAGE:5213378, mRNA.																														---	---	---	---
Unknown	0	broad.mit.edu	37	9	66713785	66713786	+	IGR	INS	-	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:66713785_66713786insA								LOC442421 (210758 upstream) : AQP7P1 (540481 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	67339358	67339358	+	IGR	DEL	C	-	-	rs112612032		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:67339358delC								AQP7P1 (49866 upstream) : FAM27B (453572 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	68408397	68408397	+	5'Flank	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:68408397delC	uc004aew.1	+											Homo sapiens cDNA, FLJ98602.																														---	---	---	---
Unknown	0	broad.mit.edu	37	9	68411860	68411861	+	Intron	DEL	TC	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:68411860_68411861delTC	uc004aew.1	+						uc004aex.2_5'Flank					Homo sapiens cDNA, FLJ98602.																														---	---	---	---
Unknown	0	broad.mit.edu	37	9	68422794	68422794	+	IGR	DEL	T	-	-	rs140577179		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:68422794delT								FAM27B (628605 upstream) : MIR1299 (579445 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	68450734	68450735	+	IGR	INS	-	AAA	AAA	rs111991274		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:68450734_68450735insAAA								FAM27B (656545 upstream) : MIR1299 (551504 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	68991335	68991335	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:68991335delA								None (None upstream) : MIR1299 (10904 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	69430249	69430249	+	Intron	DEL	A	-	-	rs115788493	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:69430249delA	uc010mnx.1	+							NM_001098806	NP_001092276			coiled-coil domain containing 29																														---	---	---	---
Unknown	0	broad.mit.edu	37	9	69521172	69521173	+	IGR	INS	-	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:69521172_69521173insT								ANKRD20A4 (96064 upstream) : LOC100133920 (130188 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	69811095	69811095	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:69811095delA								LOC100133920 (146146 upstream) : FOXD4L5 (364614 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	69821801	69821801	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:69821801delT								LOC100133920 (156852 upstream) : FOXD4L5 (353908 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	69873658	69873658	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:69873658delT								LOC100133920 (208709 upstream) : FOXD4L5 (302051 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	69966788	69966788	+	IGR	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:69966788delC								LOC100133920 (301839 upstream) : FOXD4L5 (208921 downstream)																																			---	---	---	---
PIP5K1B	8395	broad.mit.edu	37	9	71472141	71472141	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:71472141delT	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)														---	---	---	---
TJP2	9414	broad.mit.edu	37	9	71836486	71836487	+	Intron	DEL	TC	-	-	rs28625301		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:71836486_71836487delTC	uc004ahe.2	+						TJP2_uc011lrs.1_Intron|TJP2_uc011lrt.1_Intron|TJP2_uc004ahd.2_Intron|TJP2_uc004ahf.2_Intron|TJP2_uc011lru.1_Intron|TJP2_uc011lrv.1_Intron	NM_004817	NP_004808			tight junction protein 2 (zona occludens 2)						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	72155039	72155041	+	Intron	DEL	CAA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:72155039_72155041delCAA	uc004ahh.2	-							NM_001163	NP_001154			amyloid beta A4 precursor protein-binding,						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	72754943	72754944	+	Intron	INS	-	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:72754943_72754944insT	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																		---	---	---	---
TRPM3	80036	broad.mit.edu	37	9	73253937	73253937	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:73253937delA	uc004aid.2	-						TRPM3_uc004ahu.2_Intron|TRPM3_uc004ahv.2_Intron|TRPM3_uc004ahw.2_Intron|TRPM3_uc004ahx.2_Intron|TRPM3_uc004ahy.2_Intron|TRPM3_uc004ahz.2_Intron|TRPM3_uc004aia.2_Intron|TRPM3_uc004aib.2_Intron|TRPM3_uc004aic.2_Intron|TRPM3_uc010mor.2_3'UTR	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	73517552	73517552	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:73517552delA	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																		---	---	---	---
Unknown	0	broad.mit.edu	37	9	74096590	74096591	+	IGR	INS	-	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:74096590_74096591insA								TRPM3 (34770 upstream) : TMEM2 (201691 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	74154766	74154766	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:74154766delA								TRPM3 (92946 upstream) : TMEM2 (143516 downstream)																																			---	---	---	---
TMEM2	23670	broad.mit.edu	37	9	74332801	74332801	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:74332801delA	uc011lsa.1	-						TMEM2_uc010mos.2_Intron|TMEM2_uc011lsb.1_Intron	NM_013390	NP_037522			transmembrane protein 2 isoform a							integral to membrane				ovary(2)	2		all_epithelial(88;4.56e-14)|Myeloproliferative disorder(762;0.0255)		GBM - Glioblastoma multiforme(74;7.45e-21)|OV - Ovarian serous cystadenocarcinoma(323;1.02e-16)														---	---	---	---
Unknown	0	broad.mit.edu	37	9	74600273	74600273	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:74600273delT								C9orf85 (883 upstream) : C9orf57 (66025 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	74993956	74993956	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:74993956delT								ZFAND5 (13793 upstream) : TMC1 (142761 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	75095994	75095994	+	IGR	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:75095994delG								ZFAND5 (115831 upstream) : TMC1 (40723 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	75117925	75117926	+	IGR	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:75117925_75117926delTT								ZFAND5 (137762 upstream) : TMC1 (18791 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	76487342	76487343	+	IGR	INS	-	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:76487342_76487343insA								ANXA1 (702035 upstream) : RORB (624909 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	76518443	76518443	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:76518443delT								ANXA1 (733136 upstream) : RORB (593809 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	76656946	76656946	+	IGR	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:76656946delC								ANXA1 (871639 upstream) : RORB (455306 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	76796127	76796128	+	IGR	INS	-	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:76796127_76796128insA								None (None upstream) : RORB (316124 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	77050611	77050611	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:77050611delA								None (None upstream) : RORB (61641 downstream)																																			---	---	---	---
TRPM6	140803	broad.mit.edu	37	9	77395082	77395082	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:77395082delA	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																		---	---	---	---
TRPM6	140803	broad.mit.edu	37	9	77415536	77415538	+	Intron	DEL	AAA	-	-	rs35092699		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:77415536_77415538delAAA	uc004ajl.1	-						TRPM6_uc004ajk.1_Intron|TRPM6_uc010mpb.1_Intron|TRPM6_uc010mpc.1_Intron|TRPM6_uc010mpd.1_Intron|TRPM6_uc010mpe.1_Intron|TRPM6_uc004ajm.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																		---	---	---	---
C9orf41	138199	broad.mit.edu	37	9	77609636	77609637	+	Intron	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:77609636_77609637delTT	uc004ajq.2	-						uc004ajp.2_Intron|C9orf41_uc011lsi.1_Intron	NM_152420	NP_689633			hypothetical protein LOC138199											ovary(1)|skin(1)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	9	77676054	77676055	+	IGR	DEL	CA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:77676054_77676055delCA								C9orf41 (32744 upstream) : C9orf95 (63 downstream)																																			---	---	---	---
C9orf95	54981	broad.mit.edu	37	9	77691372	77691372	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:77691372delA	uc004aju.2	-						C9orf95_uc004ajs.3_Intron|C9orf95_uc004ajr.3_Intron|C9orf95_uc004ajt.3_Intron	NM_017881	NP_060351			nicotinamide riboside kinase 1 isoform 1						pyridine nucleotide biosynthetic process		ATP binding|metal ion binding|ribosylnicotinamide kinase activity				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	9	77792340	77792340	+	IGR	DEL	T	-	-	rs78618122		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:77792340delT								OSTF1 (30227 upstream) : PCSK5 (713220 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	78010535	78010535	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:78010535delA								OSTF1 (248422 upstream) : PCSK5 (495025 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	78194508	78194508	+	IGR	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:78194508delC								OSTF1 (432395 upstream) : PCSK5 (311052 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	78397262	78397262	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:78397262delA								OSTF1 (635149 upstream) : PCSK5 (108298 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	78498292	78498292	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:78498292delT								OSTF1 (736179 upstream) : PCSK5 (7268 downstream)																																			---	---	---	---
GCNT1	2650	broad.mit.edu	37	9	79068250	79068250	+	Intron	DEL	C	-	-	rs11144908	byFrequency;by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:79068250delC	uc010mpf.2	+						GCNT1_uc010mpg.2_Intron	NM_001490	NP_001481			beta-1,3-galactosyl-O-glycosyl-glycoprotein						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	79332593	79332593	+	Intron	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:79332593delC	uc010mpk.2	-							NM_015225	NP_056040			prune homolog 2						apoptosis|G1 phase|induction of apoptosis	cytoplasm	metal ion binding|pyrophosphatase activity				0																		---	---	---	---
PRUNE2	158471	broad.mit.edu	37	9	79357533	79357533	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:79357533delA	uc010mpk.2	-							NM_015225	NP_056040			prune homolog 2						apoptosis|G1 phase|induction of apoptosis	cytoplasm	metal ion binding|pyrophosphatase activity				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	9	80286974	80286975	+	IGR	DEL	AT	-	-	rs35523054		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:80286974_80286975delAT								GNA14 (23742 upstream) : GNAQ (44664 downstream)																																			---	---	---	---
GNAQ	2776	broad.mit.edu	37	9	80387856	80387856	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:80387856delA	uc004akw.2	-						GNAQ_uc011lso.1_Intron	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								---	---	---	---
GNAQ	2776	broad.mit.edu	37	9	80472700	80472700	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:80472700delT	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								---	---	---	---
GNAQ	2776	broad.mit.edu	37	9	80503388	80503388	+	Intron	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:80503388delG	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								---	---	---	---
CEP78	84131	broad.mit.edu	37	9	80860316	80860317	+	Intron	INS	-	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:80860316_80860317insT	uc004akx.2	+						CEP78_uc004aky.3_Intron|CEP78_uc010mpp.2_Intron|CEP78_uc011lsp.1_Intron	NM_032171	NP_115547			centrosomal protein 78kDa isoform b						G2/M transition of mitotic cell cycle	centrosome|cytosol				ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	9	81516582	81516582	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:81516582delA								PSAT1 (571575 upstream) : TLE4 (670296 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	81551136	81551139	+	IGR	DEL	GTGT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:81551136_81551139delGTGT								PSAT1 (606129 upstream) : TLE4 (635739 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	81568802	81568803	+	IGR	DEL	AA	-	-	rs72040499		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:81568802_81568803delAA								PSAT1 (623795 upstream) : TLE4 (618075 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	81817684	81817686	+	IGR	DEL	TTT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:81817684_81817686delTTT								PSAT1 (872677 upstream) : TLE4 (369192 downstream)																																			---	---	---	---
TLE4	7091	broad.mit.edu	37	9	82228352	82228352	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:82228352delT	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																		---	---	---	---
Unknown	0	broad.mit.edu	37	9	82359959	82359960	+	IGR	DEL	CA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:82359959_82359960delCA								TLE4 (18302 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	82391170	82391170	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:82391170delT								TLE4 (49513 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	82459844	82459844	+	IGR	DEL	T	-	-	rs77488975		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:82459844delT								TLE4 (118187 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	82509972	82509972	+	IGR	DEL	A	-	-	rs67611935		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:82509972delA								TLE4 (168315 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	82597132	82597132	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:82597132delA								TLE4 (255475 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	82960527	82960527	+	IGR	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:82960527delC								TLE4 (618870 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	82986798	82986798	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:82986798delT								TLE4 (645141 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	83492062	83492062	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:83492062delA								None (None upstream) : TLE1 (706538 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	83578125	83578125	+	IGR	DEL	A	-	-	rs76230929		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:83578125delA								None (None upstream) : TLE1 (620475 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	83634137	83634137	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:83634137delA								None (None upstream) : TLE1 (564463 downstream)																																			---	---	---	---
TLE1	7088	broad.mit.edu	37	9	84231237	84231237	+	Intron	DEL	A	-	-	rs113282087	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:84231237delA	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	84459891	84459891	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:84459891delT								TLE1 (156295 upstream) : FLJ43950 (68461 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	84503514	84503515	+	IGR	INS	-	C	C	rs149634428	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:84503514_84503515insC								TLE1 (199918 upstream) : FLJ43950 (24837 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	84645587	84645587	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:84645587delT								FLJ46321 (35417 upstream) : RASEF (951730 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	85010619	85010619	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:85010619delT								FLJ46321 (400449 upstream) : RASEF (586698 downstream)																																			---	---	---	---
FRMD3	257019	broad.mit.edu	37	9	85977807	85977807	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:85977807delT	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																		---	---	---	---
FRMD3	257019	broad.mit.edu	37	9	86084602	86084602	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:86084602delA	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																		---	---	---	---
GKAP1	80318	broad.mit.edu	37	9	86380688	86380688	+	Intron	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:86380688delG	uc004amy.2	-						GKAP1_uc004amz.2_Intron	NM_025211	NP_079487			G kinase anchoring protein 1 isoform a						signal transduction	Golgi apparatus					0																		---	---	---	---
KIF27	55582	broad.mit.edu	37	9	86533239	86533239	+	Intron	DEL	G	-	-	rs66698705		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:86533239delG	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																		---	---	---	---
C9orf64	84267	broad.mit.edu	37	9	86559614	86559615	+	Intron	INS	-	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:86559614_86559615insT	uc004anb.2	-						C9orf64_uc004anc.2_Intron	NM_032307	NP_115683			hypothetical protein LOC84267												0																		---	---	---	---
SLC28A3	64078	broad.mit.edu	37	9	86946988	86946989	+	Intron	DEL	TA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:86946988_86946989delTA	uc010mpz.2	-						SLC28A3_uc011lsy.1_Intron|SLC28A3_uc004anu.1_Intron|SLC28A3_uc010mqb.2_Intron	NM_022127	NP_071410			concentrative Na+-nucleoside cotransporter						nucleobase, nucleoside and nucleotide metabolic process	integral to membrane|plasma membrane	nucleoside binding			upper_aerodigestive_tract(1)|ovary(1)|pancreas(1)|skin(1)	4																		---	---	---	---
Unknown	0	broad.mit.edu	37	9	87043096	87043096	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:87043096delA								SLC28A3 (59683 upstream) : NTRK2 (240370 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	87251727	87251728	+	IGR	INS	-	TCTTTC	TCTTTC	rs143690281		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:87251727_87251728insTCTTTC								SLC28A3 (268314 upstream) : NTRK2 (31738 downstream)																																			---	---	---	---
NTRK2	4915	broad.mit.edu	37	9	87446339	87446340	+	Intron	DEL	GA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:87446339_87446340delGA	uc004aoa.1	+						NTRK2_uc004any.1_Intron|NTRK2_uc004anz.1_Intron|NTRK2_uc011lsz.1_Intron|NTRK2_uc011lta.1_Intron|NTRK2_uc004aoc.2_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)			---	---	---	---
NTRK2	4915	broad.mit.edu	37	9	87524400	87524400	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:87524400delT	uc004aoa.1	+						NTRK2_uc004any.1_Intron|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)			---	---	---	---
NTRK2	4915	broad.mit.edu	37	9	87573116	87573116	+	Intron	DEL	A	-	-	rs111847110		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:87573116delA	uc004aoa.1	+						NTRK2_uc004any.1_3'UTR|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)			---	---	---	---
NTRK2	4915	broad.mit.edu	37	9	87577404	87577404	+	Intron	DEL	T	-	-	rs35672627		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:87577404delT	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	87707604	87707604	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:87707604delT								NTRK2 (69099 upstream) : AGTPBP1 (453851 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	87961578	87961583	+	IGR	DEL	AAAAAA	-	-	rs72054847		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:87961578_87961583delAAAAAA								NTRK2 (323073 upstream) : AGTPBP1 (199872 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	88028756	88028757	+	IGR	INS	-	AC	AC	rs142184863	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:88028756_88028757insAC								NTRK2 (390251 upstream) : AGTPBP1 (132698 downstream)																																			---	---	---	---
GOLM1	51280	broad.mit.edu	37	9	88675245	88675246	+	Intron	DEL	GA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:88675245_88675246delGA	uc004aol.2	-						GOLM1_uc010mqd.1_Intron|GOLM1_uc004aom.2_Intron	NM_016548	NP_057632			golgi membrane protein 1							Golgi apparatus|integral to plasma membrane					0																		---	---	---	---
GOLM1	51280	broad.mit.edu	37	9	88701231	88701231	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:88701231delT	uc004aol.2	-						GOLM1_uc010mqd.1_Intron|GOLM1_uc004aom.2_Intron	NM_016548	NP_057632			golgi membrane protein 1							Golgi apparatus|integral to plasma membrane					0																		---	---	---	---
GOLM1	51280	broad.mit.edu	37	9	88812453	88812454	+	Intron	INS	-	AC	AC			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:88812453_88812454insAC	uc010mqd.1	-											Homo sapiens golgi membrane protein GP73 mRNA, complete cds.							Golgi apparatus|integral to plasma membrane					0																		---	---	---	---
ZCCHC6	79670	broad.mit.edu	37	9	88957837	88957838	+	Intron	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:88957837_88957838delAA	uc004aoq.2	-						ZCCHC6_uc011ltf.1_Intron|ZCCHC6_uc004aor.2_Intron|ZCCHC6_uc004aos.2_Intron|ZCCHC6_uc004aot.2_Intron|ZCCHC6_uc004aou.2_Intron|ZCCHC6_uc004aov.2_Intron|ZCCHC6_uc004aow.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	89029709	89029710	+	IGR	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:89029709_89029710delTT								ZCCHC6 (60331 upstream) : GAS1 (529569 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	89030053	89030053	+	IGR	DEL	T	-	-	rs72750628	byFrequency;by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:89030053delT								ZCCHC6 (60675 upstream) : GAS1 (529226 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	89239578	89239578	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:89239578delT								ZCCHC6 (270200 upstream) : GAS1 (319701 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	89336109	89336109	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:89336109delT								ZCCHC6 (366731 upstream) : GAS1 (223170 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	89387822	89387822	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:89387822delT								ZCCHC6 (418444 upstream) : GAS1 (171457 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	89469634	89469634	+	IGR	DEL	A	-	-	rs111768138		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:89469634delA								ZCCHC6 (500256 upstream) : GAS1 (89645 downstream)																																			---	---	---	---
DAPK1	1612	broad.mit.edu	37	9	90317786	90317786	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:90317786delA	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	90840401	90840402	+	IGR	DEL	CT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:90840401_90840402delCT								CDK20 (250734 upstream) : SPIN1 (162438 downstream)																																			---	---	---	---
SPIN1	10927	broad.mit.edu	37	9	91089963	91089971	+	Intron	DEL	TTTTTTTTT	-	-	rs11320023		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:91089963_91089971delTTTTTTTTT	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	91143821	91143821	+	IGR	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:91143821delG								SPIN1 (50201 upstream) : NXNL2 (6195 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	91248286	91248286	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:91248286delT								NXNL2 (57583 upstream) : LOC286238 (13808 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	91393161	91393161	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:91393161delT								LOC286238 (126086 upstream) : C9orf47 (212617 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	91539534	91539534	+	IGR	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:91539534delG								LOC286238 (272459 upstream) : C9orf47 (66244 downstream)																																			---	---	---	---
SECISBP2	79048	broad.mit.edu	37	9	91954659	91954659	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:91954659delT	uc004aqj.1	+						SECISBP2_uc011ltk.1_Intron|SECISBP2_uc004aqk.1_Intron|SECISBP2_uc010mqo.1_Intron|SECISBP2_uc011ltl.1_Intron	NM_024077	NP_076982			SECIS binding protein 2						translation	nucleus	mRNA 3'-UTR binding			ovary(2)|skin(1)	3																		---	---	---	---
SEMA4D	10507	broad.mit.edu	37	9	92018592	92018592	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:92018592delT	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	92453586	92453586	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:92453586delT								LOC100129066 (118912 upstream) : DIRAS2 (918528 downstream)																																			---	---	---	---
SYK	6850	broad.mit.edu	37	9	93572779	93572779	+	Intron	DEL	G	-	-	rs113649013		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:93572779delG	uc004aqz.2	+						SYK_uc004aqy.2_Intron|SYK_uc004ara.2_Intron|SYK_uc004arb.2_Intron	NM_003177	NP_003168			spleen tyrosine kinase isoform 1						cell proliferation|integrin-mediated signaling pathway|interspecies interaction between organisms|leukocyte cell-cell adhesion|neutrophil chemotaxis|organ morphogenesis|platelet activation|protein complex assembly	cytosol|T cell receptor complex	ATP binding|integrin binding|non-membrane spanning protein tyrosine kinase activity			lung(2)|stomach(1)|ovary(1)|skin(1)	5								T	ETV6|ITK	MDS|peripheral T-cell lymphoma								---	---	---	---
Unknown	0	broad.mit.edu	37	9	93700104	93700104	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:93700104delA								SYK (39271 upstream) : AUH (275995 downstream)																																			---	---	---	---
AUH	549	broad.mit.edu	37	9	93981025	93981026	+	Intron	DEL	AT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:93981025_93981026delAT	uc004arf.3	-						AUH_uc004arg.3_Intron	NM_001698	NP_001689			AU RNA binding protein/enoyl-Coenzyme A						branched chain family amino acid catabolic process|mRNA catabolic process	mitochondrial matrix	enoyl-CoA hydratase activity|methylglutaconyl-CoA hydratase activity|mRNA 3'-UTR binding				0																		---	---	---	---
NFIL3	4783	broad.mit.edu	37	9	94184099	94184099	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:94184099delA	uc004arh.2	-							NM_005384	NP_005375			nuclear factor, interleukin 3 regulated						circadian rhythm|immune response|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																		---	---	---	---
ROR2	4920	broad.mit.edu	37	9	94592975	94592976	+	Intron	INS	-	G	G	rs143254992	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:94592975_94592976insG	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	94931387	94931387	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:94931387delA								C9orf44 (9497 upstream) : IARS (41238 downstream)																																			---	---	---	---
IARS	3376	broad.mit.edu	37	9	94973632	94973633	+	Intron	DEL	TC	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:94973632_94973633delTC	uc004art.1	-						IARS_uc004ars.1_Intron|IARS_uc004aru.3_Intron|IARS_uc010mqr.2_Intron|IARS_uc004arr.1_RNA	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	95003101	95003101	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:95003101delA	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	95078518	95078519	+	Intron	INS	-	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:95078518_95078519insC	uc004arv.2	-						NOL8_uc010mqw.2_5'Flank|NOL8_uc004arw.2_Intron|NOL8_uc011ltw.1_Intron	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	95372013	95372014	+	Intron	DEL	TG	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:95372013_95372014delTG	uc004arz.2	+						CENPP_uc010mqx.2_Intron|CENPP_uc004asj.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																		---	---	---	---
IPPK	64768	broad.mit.edu	37	9	95381894	95381895	+	Intron	INS	-	C	C	rs79475441		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:95381894_95381895insC	uc004asl.1	-						IPPK_uc004ask.1_Intron|uc004asm.2_3'UTR	NM_022755	NP_073592			inositol 1,3,4,5,6-pentakisphosphate 2-kinase						inositol or phosphatidylinositol phosphorylation	cytoplasm|nucleus	ATP binding|inositol pentakisphosphate 2-kinase activity			ovary(2)	2																		---	---	---	---
IPPK	64768	broad.mit.edu	37	9	95414581	95414582	+	Intron	INS	-	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:95414581_95414582insG	uc004asl.1	-							NM_022755	NP_073592			inositol 1,3,4,5,6-pentakisphosphate 2-kinase						inositol or phosphatidylinositol phosphorylation	cytoplasm|nucleus	ATP binding|inositol pentakisphosphate 2-kinase activity			ovary(2)	2																		---	---	---	---
WNK2	65268	broad.mit.edu	37	9	96056225	96056226	+	Intron	DEL	TC	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:96056225_96056226delTC	uc004ati.1	+						WNK2_uc011lud.1_Intron|WNK2_uc004atj.2_Intron|WNK2_uc004atk.2_Intron|WNK2_uc004atl.1_Intron	NM_006648	NP_006639			WNK lysine deficient protein kinase 2						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																		---	---	---	---
FAM120AOS	158293	broad.mit.edu	37	9	96205552	96205552	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:96205552delT	uc004atm.2	-											Homo sapiens chromosome 9 open reading frame 10 opposite strand, mRNA (cDNA clone IMAGE:5214118), partial cds.												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	9	96332043	96332043	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:96332043delA								FAM120A (3647 upstream) : PHF2 (6866 downstream)																																			---	---	---	---
FBP2	8789	broad.mit.edu	37	9	97328019	97328022	+	Intron	DEL	GATA	-	-	rs34525238		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:97328019_97328022delGATA	uc004auv.2	-						uc004aus.1_Intron|uc004aut.1_Intron|uc004auu.2_Intron	NM_003837	NP_003828			fructose-1,6-bisphosphatase 2						fructose metabolic process|gluconeogenesis	cytosol	fructose 1,6-bisphosphate 1-phosphatase activity|fructose-2,6-bisphosphate 2-phosphatase activity|metal ion binding				0		Acute lymphoblastic leukemia(62;0.136)																---	---	---	---
Unknown	0	broad.mit.edu	37	9	97408237	97408238	+	IGR	INS	-	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:97408237_97408238insC								FBP1 (5706 upstream) : C9orf3 (80756 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	97480450	97480450	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:97480450delA								FBP1 (77919 upstream) : C9orf3 (8544 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	98432997	98432998	+	IGR	INS	-	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:98432997_98432998insT								PTCH1 (153750 upstream) : C9orf130 (135374 downstream)																																			---	---	---	---
C9orf102	375748	broad.mit.edu	37	9	98733034	98733034	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:98733034delA	uc010mry.1	+						C9orf102_uc004avu.2_Intron|uc010msa.1_5'Flank|uc011lun.1_5'Flank					RecName: Full=Putative DNA repair and recombination protein RAD26-like;          EC=3.6.1.-;						DNA repair	nucleus	ATP binding|ATP-dependent helicase activity|DNA binding				0		Acute lymphoblastic leukemia(62;0.0559)																---	---	---	---
HSD17B3	3293	broad.mit.edu	37	9	99042059	99042060	+	Intron	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:99042059_99042060delTT	uc004awa.1	-						HSD17B3_uc010msc.1_Intron	NM_000197	NP_000188			estradiol 17 beta-dehydrogenase 3						androgen biosynthetic process|male genitalia development	endoplasmic reticulum membrane|microsome	binding|testosterone 17-beta-dehydrogenase (NAD+) activity|testosterone 17-beta-dehydrogenase (NADP+) activity				0		Acute lymphoblastic leukemia(62;0.0171)|all_hematologic(171;0.214)			NADH(DB00157)													---	---	---	---
Unknown	0	broad.mit.edu	37	9	99400691	99400691	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:99400691delT								CDC14B (18579 upstream) : C9orf21 (2843 downstream)																																			---	---	---	---
C9orf21	195827	broad.mit.edu	37	9	99405254	99405254	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:99405254delT	uc004awm.2	-							NM_153698	NP_714542			hypothetical protein LOC195827								antioxidant activity|oxidoreductase activity			large_intestine(1)	1		Acute lymphoblastic leukemia(62;0.0559)																---	---	---	---
Unknown	0	broad.mit.edu	37	9	99423445	99423445	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:99423445delT								C9orf21 (5846 upstream) : LOC441455 (64658 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	99428631	99428631	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:99428631delT								C9orf21 (11032 upstream) : LOC441455 (59472 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	99675796	99675797	+	IGR	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:99675796_99675797delTT								LOC441454 (3060 upstream) : FAM22G (14795 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	100654273	100654274	+	IGR	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:100654273_100654274delTT								FOXE1 (35287 upstream) : C9orf156 (12498 downstream)																																			---	---	---	---
ANP32B	10541	broad.mit.edu	37	9	100777785	100777785	+	3'UTR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:100777785delA	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	100794459	100794460	+	IGR	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:100794459_100794460delAA								ANP32B (16237 upstream) : NANS (13429 downstream)																																			---	---	---	---
COL15A1	1306	broad.mit.edu	37	9	101712764	101712765	+	Intron	INS	-	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:101712764_101712765insC	uc004azb.1	+						COL15A1_uc004aza.2_Intron	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)																---	---	---	---
TGFBR1	7046	broad.mit.edu	37	9	101911437	101911437	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:101911437delT	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)																---	---	---	---
Unknown	0	broad.mit.edu	37	9	102022541	102022541	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:102022541delA								SEC61B (29641 upstream) : NR4A3 (561596 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	102073365	102073365	+	IGR	DEL	A	-	-	rs10988759	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:102073365delA								SEC61B (80465 upstream) : NR4A3 (510772 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	102140348	102140348	+	5'Flank	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:102140348delG	uc004azm.1	-						uc004azn.1_5'Flank|uc004baa.1_5'Flank					DQ673922																														---	---	---	---
Unknown	0	broad.mit.edu	37	9	102207509	102207509	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:102207509delT								SEC61B (214609 upstream) : NR4A3 (376628 downstream)																																			---	---	---	---
TEX10	54881	broad.mit.edu	37	9	103102057	103102057	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:103102057delT	uc004bas.2	-						TEX10_uc011lvf.1_Intron|TEX10_uc011lvg.1_Intron|TEX10_uc011lvh.1_Intron	NM_017746	NP_060216			testis expressed 10 isoform 1							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)														---	---	---	---
Unknown	0	broad.mit.edu	37	9	103682593	103682593	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:103682593delT								MURC (332422 upstream) : LPPR1 (108438 downstream)																																			---	---	---	---
RNF20	56254	broad.mit.edu	37	9	104304249	104304249	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:104304249delA	uc004bbn.2	+							NM_019592	NP_062538			ring finger protein 20						histone H2B ubiquitination|histone monoubiquitination|negative regulation of cell migration|positive regulation of transcription, DNA-dependent|protein polyubiquitination|ubiquitin-dependent protein catabolic process	nucleolus|ubiquitin ligase complex	histone binding|p53 binding|transcription coactivator activity|ubiquitin protein ligase binding|ubiquitin-protein ligase activity|zinc ion binding			ovary(4)|lung(1)|breast(1)|kidney(1)|skin(1)	8		all_hematologic(171;8.99e-06)|Acute lymphoblastic leukemia(62;0.000365)|Myeloproliferative disorder(762;0.0255)		OV - Ovarian serous cystadenocarcinoma(323;2.88e-19)|STAD - Stomach adenocarcinoma(157;0.00311)														---	---	---	---
Unknown	0	broad.mit.edu	37	9	104917421	104917421	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:104917421delT								GRIN3A (416559 upstream) : CYLC2 (840172 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	105025469	105025470	+	IGR	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:105025469_105025470delTT								GRIN3A (524607 upstream) : CYLC2 (732123 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	105450500	105450503	+	IGR	DEL	CACT	-	-	rs71358330		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:105450500_105450503delCACT								GRIN3A (949638 upstream) : CYLC2 (307090 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	106059136	106059136	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:106059136delT	uc004bbt.2	-											Homo sapiens cDNA clone IMAGE:5266449.																														---	---	---	---
Unknown	0	broad.mit.edu	37	9	106195878	106195878	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:106195878delT								CYLC2 (415108 upstream) : SMC2 (660663 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	106713236	106713236	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:106713236delA								CYLC2 (932466 upstream) : SMC2 (143305 downstream)																																			---	---	---	---
ABCA1	19	broad.mit.edu	37	9	107555303	107555303	+	Intron	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:107555303delG	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	107558122	107558122	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:107558122delA	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	107593503	107593503	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:107593503delT	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)													---	---	---	---
Unknown	0	broad.mit.edu	37	9	107708056	107708056	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:107708056delA								ABCA1 (17620 upstream) : SLC44A1 (298873 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	107723323	107723326	+	IGR	DEL	GGAG	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-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	107824144	107824147	+	IGR	DEL	TTTT	-	-	rs111671025		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:107824144_107824147delTTTT								ABCA1 (133708 upstream) : SLC44A1 (182782 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	107886948	107886948	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:107886948delA								ABCA1 (196512 upstream) : SLC44A1 (119981 downstream)																																			---	---	---	---
SLC44A1	23446	broad.mit.edu	37	9	108127668	108127669	+	Intron	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:108127668_108127669delTT	uc004bcn.2	+						SLC44A1_uc010mtk.1_Intron|SLC44A1_uc004bco.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)													---	---	---	---
FKTN	2218	broad.mit.edu	37	9	108367073	108367073	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:108367073delA	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																		---	---	---	---
FKTN	2218	broad.mit.edu	37	9	108382270	108382270	+	Frame_Shift_Del	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-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																		---	---	---	---
Unknown	0	broad.mit.edu	37	9	108596155	108596155	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:108596155delA								TMEM38B (58711 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	108608254	108608254	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:108608254delA								TMEM38B (70810 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	108988395	108988396	+	Intron	DEL	CT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:108988395_108988396delCT	uc004bcw.2	+											Homo sapiens, clone IMAGE:5538960, mRNA.																														---	---	---	---
Unknown	0	broad.mit.edu	37	9	109225963	109225964	+	Intron	DEL	AG	-	-	rs146094942		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:109225963_109225964delAG	uc004bcx.2	+											Homo sapiens, clone IMAGE:4246712, mRNA.																														---	---	---	---
Unknown	0	broad.mit.edu	37	9	109472814	109472814	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:109472814delT								TMEM38B (935370 upstream) : ZNF462 (152564 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	109927797	109927797	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:109927797delA								ZNF462 (154008 upstream) : RAD23B (117747 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	110288169	110288171	+	IGR	DEL	AAC	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:110288169_110288171delAAC								KLF4 (36122 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	110447885	110447885	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:110447885delA								KLF4 (195838 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	110484547	110484547	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:110484547delT								KLF4 (232500 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	110746965	110746966	+	IGR	DEL	GT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:110746965_110746966delGT								KLF4 (494918 upstream) : ACTL7B (869905 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	110779049	110779049	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:110779049delT								KLF4 (527002 upstream) : ACTL7B (837822 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	110851629	110851629	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:110851629delT								KLF4 (599582 upstream) : ACTL7B (765242 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	111025280	111025281	+	IGR	DEL	GT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:111025280_111025281delGT								KLF4 (773233 upstream) : ACTL7B (591590 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	111253424	111253424	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:111253424delA								None (None upstream) : ACTL7B (363447 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	111468560	111468560	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:111468560delA								None (None upstream) : ACTL7B (148311 downstream)																																			---	---	---	---
IKBKAP	8518	broad.mit.edu	37	9	111672440	111672440	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:111672440delT	uc004bdm.3	-						IKBKAP_uc004bdl.2_Intron|IKBKAP_uc011lwc.1_Intron|IKBKAP_uc010mtq.2_Intron	NM_003640	NP_003631			inhibitor of kappa light polypeptide gene						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																		---	---	---	---
IKBKAP	8518	broad.mit.edu	37	9	111689457	111689458	+	Intron	INS	-	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:111689457_111689458insA	uc004bdm.3	-						IKBKAP_uc011lwc.1_Intron|IKBKAP_uc010mtq.2_Intron	NM_003640	NP_003631			inhibitor of kappa light polypeptide gene						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																		---	---	---	---
EPB41L4B	54566	broad.mit.edu	37	9	112066091	112066091	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:112066091delT	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	112347619	112347619	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:112347619delA								PTPN3 (87026 upstream) : PALM2 (55453 downstream)																																			---	---	---	---
PALM2-AKAP2	445815	broad.mit.edu	37	9	112563988	112563989	+	Intron	INS	-	TG	TG	rs142422555	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:112563988_112563989insTG	uc004bei.2	+						PALM2_uc004bef.2_Intron|PALM2_uc004beg.2_Intron|PALM2_uc004beh.3_Intron|PALM2-AKAP2_uc004bek.3_Intron|PALM2-AKAP2_uc004bej.3_Intron	NM_001136562	NP_001130034			A kinase (PRKA) anchor protein 2 isoform 2								enzyme binding			ovary(3)|central_nervous_system(2)|skin(1)	6																		---	---	---	---
PALM2-AKAP2	445815	broad.mit.edu	37	9	112704882	112704882	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:112704882delT	uc004bei.2	+						PALM2_uc004bef.2_Intron|PALM2_uc004beg.2_Intron|PALM2_uc004beh.3_Intron|PALM2-AKAP2_uc004bek.3_Intron|PALM2-AKAP2_uc004bej.3_Intron|PALM2-AKAP2_uc004bel.1_Intron	NM_001136562	NP_001130034			A kinase (PRKA) anchor protein 2 isoform 2								enzyme binding			ovary(3)|central_nervous_system(2)|skin(1)	6																		---	---	---	---
Unknown	0	broad.mit.edu	37	9	113048917	113048919	+	IGR	DEL	AAA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:113048917_113048919delAAA								TXN (30084 upstream) : TXNDC8 (16949 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	113064915	113064918	+	IGR	DEL	TTTT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:113064915_113064918delTTTT								TXN (46082 upstream) : TXNDC8 (950 downstream)																																			---	---	---	---
TXNDC8	255220	broad.mit.edu	37	9	113072481	113072486	+	Intron	DEL	GTGTGT	-	-	rs12378546		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:113072481_113072486delGTGTGT	uc004bes.2	-						TXNDC8_uc011lwl.1_Intron	NM_001003936	NP_001003936			thioredoxin domain containing 8						cell differentiation|cell redox homeostasis|glycerol ether metabolic process|multicellular organismal development|spermatogenesis	Golgi apparatus	electron carrier activity|protein disulfide oxidoreductase activity				0																		---	---	---	---
SVEP1	79987	broad.mit.edu	37	9	113225006	113225007	+	Intron	DEL	AG	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:113225006_113225007delAG	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	113449623	113449623	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:113449623delT	uc004bey.2	+						MUSK_uc004bex.2_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																		---	---	---	---
Unknown	0	broad.mit.edu	37	9	113982821	113982822	+	IGR	INS	-	AGGG	AGGG	rs146446287	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:113982821_113982822insAGGG								LPAR1 (181295 upstream) : OR2K2 (106942 downstream)																																			---	---	---	---
C9orf84	158401	broad.mit.edu	37	9	114520479	114520479	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:114520479delA	uc004bfr.2	-						C9orf84_uc011lwt.1_Intron|C9orf84_uc004bfs.1_Intron|C9orf84_uc004bfq.2_Intron|C9orf84_uc010mug.2_Intron	NM_173521	NP_775792			hypothetical protein LOC158401 isoform 1											ovary(2)	2																		---	---	---	---
HSDL2	84263	broad.mit.edu	37	9	115232835	115232835	+	3'UTR	DEL	A	-	-	rs3832711		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:115232835delA	uc004bga.1	+	11					HSDL2_uc011lwv.1_3'UTR|HSDL2_uc004bgb.1_3'UTR|HSDL2_uc004bgc.1_3'UTR|HSDL2_uc011lww.1_3'UTR|uc004bge.1_Intron	NM_032303	NP_115679			hydroxysteroid dehydrogenase like 2							peroxisome	oxidoreductase activity|sterol binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	9	115237481	115237482	+	Intron	INS	-	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:115237481_115237482insT	uc004bge.1	-											Homo sapiens cDNA FLJ27510 fis, clone TST08253.																														---	---	---	---
KIAA1958	158405	broad.mit.edu	37	9	115412884	115412885	+	Intron	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:115412884_115412885delAA	uc004bgf.1	+						KIAA1958_uc011lwx.1_Intron	NM_133465	NP_597722			hypothetical protein LOC158405											skin(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	9	115504338	115504338	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:115504338delT								C9orf80 (23951 upstream) : SNX30 (8796 downstream)																																			---	---	---	---
SNX30	401548	broad.mit.edu	37	9	115572149	115572149	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:115572149delT	uc004bgj.3	+							NM_001012994	NP_001013012			sorting nexin family member 30						cell communication|protein transport	cytoplasm	phosphatidylinositol binding				0																		---	---	---	---
SLC46A2	57864	broad.mit.edu	37	9	115655802	115655802	+	5'Flank	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:115655802delC	uc004bgk.2	-							NM_033051	NP_149040			solute carrier family 46, member 2							integral to membrane|plasma membrane	symporter activity			central_nervous_system(1)	1																		---	---	---	---
FKBP15	23307	broad.mit.edu	37	9	115945526	115945526	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:115945526delT	uc004bgs.2	-						FKBP15_uc010muu.1_Intron|FKBP15_uc004bgr.2_Intron|FKBP15_uc011lxc.1_Intron|FKBP15_uc011lxd.1_Intron|FKBP15_uc010mut.1_Intron	NM_015258	NP_056073			FK506 binding protein 15, 133kDa						endocytosis|protein folding	axon|early endosome	actin binding			ovary(3)	3																		---	---	---	---
FKBP15	23307	broad.mit.edu	37	9	116001871	116001871	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:116001871delT	uc010muu.1	-						SLC31A1_uc004bgu.2_Intron|SLC31A1_uc004bgv.3_Intron	NM_015258	NP_056073			FK506 binding protein 15, 133kDa						endocytosis|protein folding	axon|early endosome	actin binding			ovary(3)	3																		---	---	---	---
PRPF4	9128	broad.mit.edu	37	9	116039102	116039104	+	Intron	DEL	TTT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:116039102_116039104delTTT	uc004bgx.2	+						FKBP15_uc010muu.1_5'Flank|CDC26_uc004bgw.2_5'Flank|PRPF4_uc004bgy.2_Intron	NM_004697	NP_004688			PRP4 pre-mRNA processing factor 4 homolog							Cajal body|nuclear speck|spliceosomal complex|U4/U6 snRNP	protein binding			ovary(2)|pancreas(1)	3																		---	---	---	---
PRPF4	9128	broad.mit.edu	37	9	116049339	116049339	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:116049339delA	uc004bgx.2	+						PRPF4_uc004bgy.2_Intron	NM_004697	NP_004688			PRP4 pre-mRNA processing factor 4 homolog							Cajal body|nuclear speck|spliceosomal complex|U4/U6 snRNP	protein binding			ovary(2)|pancreas(1)	3																		---	---	---	---
AKNA	80709	broad.mit.edu	37	9	117125868	117125869	+	Intron	INS	-	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:117125868_117125869insT	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																		---	---	---	---
C9orf91	203197	broad.mit.edu	37	9	117392560	117392563	+	Intron	DEL	ATCC	-	-	rs72109873		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:117392560_117392563delATCC	uc004bjd.3	+						C9orf91_uc004bje.3_Intron|C9orf91_uc004bjf.3_Intron	NM_153045	NP_694590			hypothetical protein LOC203197							integral to membrane				pancreas(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	9	117778205	117778206	+	IGR	INS	-	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:117778205_117778206insA								TNFSF8 (85435 upstream) : TNC (4600 downstream)																																			---	---	---	---
TNC	3371	broad.mit.edu	37	9	117784852	117784852	+	Intron	DEL	T	-	-	rs113120666		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:117784852delT	uc004bjj.3	-						TNC_uc010mvf.2_Intron	NM_002160	NP_002151			tenascin C precursor						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	117803101	117803101	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:117803101delT	uc004bjj.3	-						TNC_uc010mvf.2_Intron	NM_002160	NP_002151			tenascin C precursor						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																		---	---	---	---
DEC1	50514	broad.mit.edu	37	9	117984732	117984732	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:117984732delA	uc004bjk.1	+							NM_017418	NP_059114			deleted in esophageal cancer 1						negative regulation of cell proliferation					ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	9	118616204	118616205	+	IGR	DEL	TA	-	-	rs150719347		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:118616204_118616205delTA								DEC1 (451281 upstream) : C9orf27 (34341 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	119177679	119177679	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:119177679delT								PAPPA (13080 upstream) : ASTN2 (9828 downstream)																																			---	---	---	---
ASTN2	23245	broad.mit.edu	37	9	119256229	119256229	+	Intron	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:119256229delG	uc004bjs.1	-						ASTN2_uc004bjr.1_Intron|ASTN2_uc004bjt.1_Intron|ASTN2_uc004bjp.1_Intron|ASTN2_uc004bjq.1_Intron|ASTN2_uc011lxr.1_Intron|ASTN2_uc011lxs.1_Intron|ASTN2_uc011lxt.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	119311538	119311539	+	Intron	DEL	AA	-	-	rs78762881		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:119311538_119311539delAA	uc004bjs.1	-						ASTN2_uc004bjr.1_Intron|ASTN2_uc004bjt.1_Intron|ASTN2_uc004bjp.1_Intron|ASTN2_uc004bjq.1_Intron|ASTN2_uc011lxr.1_Intron|ASTN2_uc011lxs.1_Intron|ASTN2_uc011lxt.1_Intron|uc004bju.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	119659996	119659996	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:119659996delA	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	119738054	119738057	+	Intron	DEL	TATC	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:119738054_119738057delTATC	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	119827079	119827080	+	Intron	DEL	AA	-	-	rs11321268		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:119827079_119827080delAA	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	120053892	120053893	+	Intron	INS	-	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:120053892_120053893insT	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	120241882	120241882	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:120241882delT								ASTN2 (64565 upstream) : TLR4 (224578 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	120250593	120250595	+	IGR	DEL	TTT	-	-	rs111551162		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:120250593_120250595delTTT								ASTN2 (73276 upstream) : TLR4 (215865 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	120287775	120287775	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:120287775delT								ASTN2 (110458 upstream) : TLR4 (178685 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	120809549	120809549	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:120809549delT								TLR4 (329785 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	121238520	121238520	+	IGR	DEL	T	-	-	rs73657962	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:121238520delT								TLR4 (758756 upstream) : DBC1 (690388 downstream)																																			---	---	---	---
DBC1	1620	broad.mit.edu	37	9	121990762	121990762	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:121990762delA	uc004bkc.2	-						DBC1_uc004bkd.2_Intron	NM_014618	NP_055433			deleted in bladder cancer 1 precursor						cell cycle arrest|cell death	cytoplasm	protein binding			skin(3)|ovary(2)|central_nervous_system(2)|large_intestine(1)	8																		---	---	---	---
Unknown	0	broad.mit.edu	37	9	122248188	122248189	+	IGR	DEL	TC	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:122248188_122248189delTC								DBC1 (116449 upstream) : MIR147 (759068 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	122969529	122969529	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:122969529delT								DBC1 (837790 upstream) : MIR147 (37728 downstream)																																			---	---	---	---
CDK5RAP2	55755	broad.mit.edu	37	9	123287898	123287898	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:123287898delT	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|CDK5RAP2_uc004bki.2_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																		---	---	---	---
CDK5RAP2	55755	broad.mit.edu	37	9	123295458	123295458	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:123295458delT	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|CDK5RAP2_uc004bki.2_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																		---	---	---	---
Unknown	0	broad.mit.edu	37	9	123568270	123568270	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:123568270delT								LOC402377 (7261 upstream) : PSMD5 (10064 downstream)																																			---	---	---	---
C5	727	broad.mit.edu	37	9	123730002	123730002	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:123730002delT	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)													---	---	---	---
Unknown	0	broad.mit.edu	37	9	123827606	123827607	+	IGR	DEL	AG	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:123827606_123827607delAG								C5 (15052 upstream) : CEP110 (9635 downstream)																																			---	---	---	---
GSN	2934	broad.mit.edu	37	9	124074857	124074857	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-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																		---	---	---	---
STOM	2040	broad.mit.edu	37	9	124110279	124110279	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:124110279delA	uc004blh.2	-						STOM_uc011lyk.1_Intron|STOM_uc004bli.2_Intron	NM_004099	NP_004090			stomatin isoform a						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)														---	---	---	---
GGTA1	2681	broad.mit.edu	37	9	124245229	124245229	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:124245229delA	uc004bll.1	-						GGTA1_uc004blj.1_Intron|GGTA1_uc004blk.1_Intron|GGTA1_uc004blm.1_Intron	NR_003191				RecName: Full=Inactive N-acetyllactosaminide alpha-1,3-galactosyltransferase;												0																		---	---	---	---
DAB2IP	153090	broad.mit.edu	37	9	124448465	124448465	+	Intron	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:124448465delC	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	124606589	124606590	+	Intron	INS	-	A	A	rs147019652	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:124606589_124606590insA	uc011lyl.1	-						TTLL11_uc004blr.2_Intron	NM_001139442	NP_001132914			tubulin tyrosine ligase-like family, member 11						protein modification process	cilium|microtubule basal body	tubulin-tyrosine ligase activity				0																		---	---	---	---
TTLL11	158135	broad.mit.edu	37	9	124752086	124752086	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:124752086delT	uc004blt.1	-						TTLL11_uc011lyl.1_Intron|TTLL11_uc004blr.2_Intron|TTLL11_uc011lym.1_Intron|TTLL11_uc004blu.1_Intron	NM_194252	NP_919228			tubulin tyrosine ligase-like family, member 11						protein modification process	cilium|microtubule basal body	tubulin-tyrosine ligase activity				0																		---	---	---	---
MORN5	254956	broad.mit.edu	37	9	124922149	124922150	+	5'Flank	INS	-	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:124922149_124922150insT	uc004blw.2	+						NDUFA8_uc004blv.2_5'Flank|MORN5_uc011lyn.1_5'Flank|MORN5_uc011lyo.1_5'Flank	NM_198469	NP_940871			MORN repeat containing 5												0																		---	---	---	---
RC3H2	54542	broad.mit.edu	37	9	125617396	125617403	+	Intron	DEL	AAAAAAAA	-	-	rs5900548		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:125617396_125617403delAAAAAAAA	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	125723280	125723280	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:125723280delA	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																		---	---	---	---
RABGAP1	23637	broad.mit.edu	37	9	125791597	125791598	+	Intron	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:125791597_125791598delTT	uc011lzh.1	+						RABGAP1_uc004bnl.3_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																		---	---	---	---
Unknown	0	broad.mit.edu	37	9	126795451	126795451	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:126795451delA								LHX2 (9 upstream) : NEK6 (224435 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	126904170	126904170	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:126904170delT								LHX2 (108728 upstream) : NEK6 (115716 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	127204917	127204917	+	IGR	DEL	T	-	-	rs79934263		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:127204917delT								PSMB7 (27196 upstream) : GPR144 (8506 downstream)																																			---	---	---	---
NR5A1	2516	broad.mit.edu	37	9	127258260	127258260	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:127258260delT	uc004boo.1	-							NM_004959	NP_004950			nuclear receptor subfamily 5, group A, member 1						cell-cell signaling|male gonad development|positive regulation of transcription from RNA polymerase II promoter|primary sex determination|regulation of steroid biosynthetic process|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor	nucleoplasm	enzyme binding|phospholipid binding|steroid hormone receptor activity|transcription coactivator activity|zinc ion binding				0																		---	---	---	---
OLFML2A	169611	broad.mit.edu	37	9	127541095	127541096	+	Intron	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:127541095_127541096delAA	uc004bov.2	+						OLFML2A_uc010mwr.1_Intron	NM_182487	NP_872293			olfactomedin-like 2A precursor												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	9	127593849	127593849	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:127593849delA								OLFML2A (16692 upstream) : WDR38 (21906 downstream)																																			---	---	---	---
SCAI	286205	broad.mit.edu	37	9	127822542	127822546	+	Intron	DEL	AAAAA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:127822542_127822546delAAAAA	uc004bpe.2	-						SCAI_uc004bpd.2_Intron|SCAI_uc010mwu.2_Intron	NM_001144877	NP_001138349			suppressor of cancer cell invasion isoform 2						negative regulation of cell migration|negative regulation of Rho protein signal transduction|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|integral to membrane|nucleus	protein binding|transcription corepressor activity			ovary(2)|breast(2)|central_nervous_system(1)	5																		---	---	---	---
SCAI	286205	broad.mit.edu	37	9	127888188	127888197	+	Intron	DEL	TACACACACA	-	-	rs149303657	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:127888188_127888197delTACACACACA	uc004bpe.2	-						SCAI_uc004bpd.2_Intron|SCAI_uc010mwu.2_Intron	NM_001144877	NP_001138349			suppressor of cancer cell invasion isoform 2						negative regulation of cell migration|negative regulation of Rho protein signal transduction|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|integral to membrane|nucleus	protein binding|transcription corepressor activity			ovary(2)|breast(2)|central_nervous_system(1)	5																		---	---	---	---
PPP6C	5537	broad.mit.edu	37	9	127935881	127935881	+	Intron	DEL	C	-	-	rs559409	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:127935881delC	uc004bpg.3	-						PPP6C_uc010mwv.2_Intron|PPP6C_uc010mww.2_Intron|PPP6C_uc011lzr.1_Intron	NM_002721	NP_002712			protein phosphatase 6, catalytic subunit isoform						G1/S transition of mitotic cell cycle|protein dephosphorylation	cytosol	metal ion binding|protein binding|protein serine/threonine phosphatase activity			ovary(1)|skin(1)	2																		---	---	---	---
PPP6C	5537	broad.mit.edu	37	9	127946375	127946376	+	Intron	INS	-	T	T	rs80282176		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:127946375_127946376insT	uc004bpg.3	-						PPP6C_uc010mwv.2_Intron|PPP6C_uc010mww.2_Intron|PPP6C_uc011lzr.1_Intron	NM_002721	NP_002712			protein phosphatase 6, catalytic subunit isoform						G1/S transition of mitotic cell cycle|protein dephosphorylation	cytosol	metal ion binding|protein binding|protein serine/threonine phosphatase activity			ovary(1)|skin(1)	2																		---	---	---	---
PPP6C	5537	broad.mit.edu	37	9	127949567	127949567	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:127949567delT	uc004bpg.3	-						PPP6C_uc010mwv.2_Intron|PPP6C_uc010mww.2_Intron|PPP6C_uc011lzr.1_Intron	NM_002721	NP_002712			protein phosphatase 6, catalytic subunit isoform						G1/S transition of mitotic cell cycle|protein dephosphorylation	cytosol	metal ion binding|protein binding|protein serine/threonine phosphatase activity			ovary(1)|skin(1)	2																		---	---	---	---
GAPVD1	26130	broad.mit.edu	37	9	128089106	128089106	+	Intron	DEL	A	-	-	rs75364733		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:128089106delA	uc010mwx.2	+						GAPVD1_uc011lzs.1_Intron|GAPVD1_uc004bpp.2_Intron|GAPVD1_uc004bpq.2_Intron|GAPVD1_uc004bpr.2_Intron|GAPVD1_uc004bps.2_Intron|GAPVD1_uc010mwy.1_Intron	NM_015635	NP_056450			GTPase activating protein and VPS9 domains 1						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																		---	---	---	---
Unknown	0	broad.mit.edu	37	9	128145848	128145848	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:128145848delT								GAPVD1 (18559 upstream) : MAPKAP1 (53826 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	128480399	128480399	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:128480399delA								MAPKAP1 (10886 upstream) : PBX3 (29218 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	128845261	128845266	+	IGR	DEL	TGTGTG	-	-	rs67982657		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:128845261_128845266delTGTGTG								PBX3 (115608 upstream) : FAM125B (243862 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	128894865	128894865	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:128894865delA								PBX3 (165212 upstream) : FAM125B (194263 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	128931548	128931548	+	IGR	DEL	A	-	-	rs113014093		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:128931548delA								PBX3 (201895 upstream) : FAM125B (157580 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	129008429	129008429	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:129008429delA								PBX3 (278776 upstream) : FAM125B (80699 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	129483669	129483669	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:129483669delA								LMX1B (20358 upstream) : ZBTB43 (83616 downstream)																																			---	---	---	---
RALGPS1	9649	broad.mit.edu	37	9	129784797	129784799	+	Intron	DEL	AAA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:129784797_129784799delAAA	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																		---	---	---	---
RALGPS1	9649	broad.mit.edu	37	9	129853725	129853725	+	Intron	DEL	T	-	-	rs79664084		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:129853725delT	uc004bqo.1	+						RALGPS1_uc011mab.1_Intron|RALGPS1_uc011mac.1_Intron|RALGPS1_uc004bqq.3_Intron|ANGPTL2_uc004bqr.1_Intron|ANGPTL2_uc010mxg.1_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																		---	---	---	---
FAM129B	64855	broad.mit.edu	37	9	130335592	130335592	+	Intron	DEL	T	-	-	rs61272563		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:130335592delT	uc004bri.2	-							NM_001035534	NP_001030611			hypothetical protein LOC64855 isoform 2								protein binding				0																		---	---	---	---
FAM129B	64855	broad.mit.edu	37	9	130340947	130340948	+	Intron	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:130340947_130340948delAA	uc004bri.2	-							NM_001035534	NP_001030611			hypothetical protein LOC64855 isoform 2								protein binding				0																		---	---	---	---
SH2D3C	10044	broad.mit.edu	37	9	130501789	130501789	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:130501789delA	uc004bsc.2	-						SH2D3C_uc010mxo.2_Intron|SH2D3C_uc004bry.2_Intron|SH2D3C_uc004brz.3_Intron|SH2D3C_uc011mak.1_Intron|SH2D3C_uc004bsa.2_Intron|SH2D3C_uc004bsb.2_Intron	NM_170600	NP_733745			SH2 domain containing 3C isoform a						JNK cascade|small GTPase mediated signal transduction	cytoplasm|membrane	guanyl-nucleotide exchange factor activity|SH3/SH2 adaptor activity			ovary(1)	1																		---	---	---	---
SH2D3C	10044	broad.mit.edu	37	9	130543826	130543826	+	5'Flank	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:130543826delT	uc004bsc.2	-						SH2D3C_uc004bsd.1_5'Flank	NM_170600	NP_733745			SH2 domain containing 3C isoform a						JNK cascade|small GTPase mediated signal transduction	cytoplasm|membrane	guanyl-nucleotide exchange factor activity|SH3/SH2 adaptor activity			ovary(1)	1																		---	---	---	---
ST6GALNAC4	27090	broad.mit.edu	37	9	130678351	130678352	+	Intron	DEL	CT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:130678351_130678352delCT	uc004bss.2	-						ST6GALNAC4_uc004bst.2_Intron	NM_175039	NP_778204			sialyltransferase 7D isoform a						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																		---	---	---	---
Unknown	0	broad.mit.edu	37	9	130874725	130874725	+	RNA	DEL	A	-	-	rs114005827	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:130874725delA	uc004btg.1	-	5		c.2567delT								Homo sapiens cDNA FLJ42733 fis, clone BRAWH2013871.																														---	---	---	---
CIZ1	25792	broad.mit.edu	37	9	130943401	130943403	+	Intron	DEL	TTT	-	-	rs78289689		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:130943401_130943403delTTT	uc004btt.2	-						CIZ1_uc004btr.2_Intron|CIZ1_uc004bts.2_Intron|CIZ1_uc011maq.1_Intron|CIZ1_uc004btu.2_Intron|CIZ1_uc011mar.1_Intron|CIZ1_uc011mas.1_Intron|CIZ1_uc004btw.2_Intron|CIZ1_uc004btv.2_Intron|CIZ1_uc004btx.2_Intron	NM_001131016	NP_001124488			CDKN1A interacting zinc finger protein 1 isoform							nucleus	nucleic acid binding|protein binding|zinc ion binding			ovary(2)|central_nervous_system(2)	4																		---	---	---	---
GLE1	2733	broad.mit.edu	37	9	131286201	131286201	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:131286201delA	uc004bvj.2	+						GLE1_uc004bvi.2_Intron|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																		---	---	---	---
GLE1	2733	broad.mit.edu	37	9	131302336	131302336	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-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																		---	---	---	---
PHYHD1	254295	broad.mit.edu	37	9	131689650	131689651	+	Intron	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:131689650_131689651delTT	uc004bwo.2	+						PHYHD1_uc004bwn.2_Intron|PHYHD1_uc004bwm.2_Intron|PHYHD1_uc004bwp.2_Intron	NM_001100876	NP_001094346			phytanoyl-CoA dioxygenase domain containing 1								metal ion binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen				0																OREG0019526	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
FAM73B	84895	broad.mit.edu	37	9	131825435	131825435	+	Intron	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:131825435delC	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	131932930	131932930	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:131932930delA								PPP2R4 (21707 upstream) : IER5L (4901 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	132120464	132120464	+	IGR	DEL	T	-	-	rs66949552		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:132120464delT								C9orf106 (35582 upstream) : C9orf50 (254042 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	132155353	132155357	+	IGR	DEL	ACTCA	-	-	rs79027122		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:132155353_132155357delACTCA								C9orf106 (70471 upstream) : C9orf50 (219149 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	132195280	132195280	+	IGR	DEL	G	-	-	rs66485033		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:132195280delG								C9orf106 (110398 upstream) : C9orf50 (179226 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	132205162	132205163	+	IGR	INS	-	G	G	rs140519160	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:132205162_132205163insG								C9orf106 (120280 upstream) : C9orf50 (169343 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	132553404	132553404	+	IGR	DEL	A	-	-	rs148466916		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:132553404delA								PTGES (38060 upstream) : TOR1B (12028 downstream)																																			---	---	---	---
USP20	10868	broad.mit.edu	37	9	132608032	132608032	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:132608032delA	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	132678318	132678318	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:132678318delA	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	132691689	132691703	+	Intron	DEL	AAAAAAAAAAAAAAA	-	-	rs11290487		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:132691689_132691703delAAAAAAAAAAAAAAA	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	132757052	132757052	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:132757052delA	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								---	---	---	---
Unknown	0	broad.mit.edu	37	9	133382797	133382798	+	IGR	DEL	AA	-	-	rs117844710	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:133382797_133382798delAA								ASS1 (6137 upstream) : LOC100272217 (69941 downstream)																																			---	---	---	---
LAMC3	10319	broad.mit.edu	37	9	133937081	133937081	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:133937081delT	uc004caa.1	+							NM_006059	NP_006050			laminin, gamma 3 precursor						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)														---	---	---	---
LAMC3	10319	broad.mit.edu	37	9	133959607	133959607	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:133959607delT	uc004caa.1	+						LAMC3_uc010mze.1_Intron	NM_006059	NP_006050			laminin, gamma 3 precursor						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	134052326	134052326	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:134052326delA	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	134088170	134088170	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:134088170delT	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	134178407	134178407	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:134178407delT	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)														---	---	---	---
Unknown	0	broad.mit.edu	37	9	134231576	134231576	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:134231576delA								PPAPDC3 (46927 upstream) : BAT2L1 (38024 downstream)																																			---	---	---	---
BAT2L1	84726	broad.mit.edu	37	9	134349675	134349675	+	Intron	DEL	T	-	-	rs75614597		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:134349675delT	uc004can.3	+						BAT2L1_uc010mzj.1_Intron|BAT2L1_uc004cao.3_Intron	NM_013318	NP_037450			HLA-B associated transcript 2-like								protein binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	9	134449682	134449683	+	IGR	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:134449682_134449683delTT								UCK1 (43020 upstream) : RAPGEF1 (2475 downstream)																																			---	---	---	---
RAPGEF1	2889	broad.mit.edu	37	9	134581656	134581656	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:134581656delT	uc004cbc.2	-						RAPGEF1_uc004cbb.2_Intron|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)														---	---	---	---
MED27	9442	broad.mit.edu	37	9	134888706	134888706	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:134888706delA	uc004cbe.1	-						MED27_uc004cbf.1_Intron|MED27_uc011mco.1_Intron|MED27_uc004cbg.3_Intron	NM_004269	NP_004260			mediator complex subunit 27						regulation of transcription from RNA polymerase II promoter|transcription initiation from RNA polymerase II promoter	cytoplasm|nucleolus|transcription factor complex	protein binding|transcription coactivator activity			skin(1)	1		Myeloproliferative disorder(178;0.206)		OV - Ovarian serous cystadenocarcinoma(145;6.82e-06)|Epithelial(140;0.000193)														---	---	---	---
MED27	9442	broad.mit.edu	37	9	134953129	134953130	+	Intron	DEL	AA	-	-	rs76460072		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:134953129_134953130delAA	uc004cbe.1	-						MED27_uc004cbf.1_Intron|MED27_uc011mco.1_Intron|MED27_uc004cbg.3_Intron	NM_004269	NP_004260			mediator complex subunit 27						regulation of transcription from RNA polymerase II promoter|transcription initiation from RNA polymerase II promoter	cytoplasm|nucleolus|transcription factor complex	protein binding|transcription coactivator activity			skin(1)	1		Myeloproliferative disorder(178;0.206)		OV - Ovarian serous cystadenocarcinoma(145;6.82e-06)|Epithelial(140;0.000193)														---	---	---	---
Unknown	0	broad.mit.edu	37	9	135134595	135134595	+	IGR	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:135134595delG								NTNG2 (16375 upstream) : SETX (2233 downstream)																																	OREG0019569	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
SETX	23064	broad.mit.edu	37	9	135147276	135147277	+	Intron	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:135147276_135147277delTT	uc004cbk.2	-						SETX_uc004cbj.2_Intron|SETX_uc010mzt.2_Intron	NM_015046	NP_055861			senataxin						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	135157106	135157107	+	Intron	INS	-	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:135157106_135157107insA	uc004cbk.2	-						SETX_uc004cbj.2_Intron|SETX_uc010mzt.2_Intron	NM_015046	NP_055861			senataxin						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	135253801	135253802	+	Intron	INS	-	GT	GT			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:135253801_135253802insGT	uc004cbl.2	-						TTF1_uc011mcp.1_Intron|TTF1_uc004cbm.2_Intron	NM_007344	NP_031370			transcription termination factor, RNA polymerase						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)														---	---	---	---
Unknown	0	broad.mit.edu	37	9	135968951	135968952	+	IGR	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:135968951_135968952delAA								CELP (6473 upstream) : RALGDS (4156 downstream)																																			---	---	---	---
C9orf96	169436	broad.mit.edu	37	9	136251707	136251708	+	Intron	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:136251707_136251708delTT	uc004cdk.2	+						C9orf96_uc004cdl.2_Intron	NM_153710	NP_714921			hypothetical protein LOC169436								ATP binding|protein kinase activity			stomach(2)|central_nervous_system(2)	4				OV - Ovarian serous cystadenocarcinoma(145;1.06e-07)|Epithelial(140;1.28e-06)|all cancers(34;1.46e-05)														---	---	---	---
ADAMTS13	11093	broad.mit.edu	37	9	136317113	136317113	+	Intron	DEL	T	-	-	rs111537834		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:136317113delT	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	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)														---	---	---	---
Unknown	0	broad.mit.edu	37	9	136609144	136609144	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:136609144delT								SARDH (4067 upstream) : VAV2 (17873 downstream)																																			---	---	---	---
WDR5	11091	broad.mit.edu	37	9	137022118	137022118	+	Intron	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:137022118delC	uc004cey.2	+						WDR5_uc004cez.2_Intron	NM_017588	NP_060058			WD repeat domain 5						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	137267244	137267244	+	Intron	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:137267244delG	uc004cfb.2	+						RXRA_uc004cfa.1_Intron	NM_002957	NP_002948			retinoid X receptor, alpha						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)													---	---	---	---
Unknown	0	broad.mit.edu	37	9	137397093	137397093	+	IGR	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:137397093delG								RXRA (64662 upstream) : COL5A1 (136559 downstream)																																			---	---	---	---
COL5A1	1289	broad.mit.edu	37	9	137615169	137615170	+	Intron	INS	-	A	A	rs147633835	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:137615169_137615170insA	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)														---	---	---	---
COL5A1	1289	broad.mit.edu	37	9	137720965	137720966	+	Intron	INS	-	TCAT	TCAT	rs139866702	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:137720965_137720966insTCAT	uc004cfe.2	+						uc004cff.2_Intron	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)														---	---	---	---
CAMSAP1	157922	broad.mit.edu	37	9	138764281	138764281	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:138764281delA	uc004cgr.3	-						CAMSAP1_uc004cgq.3_Intron|CAMSAP1_uc010nbg.2_Intron	NM_015447	NP_056262			calmodulin regulated spectrin-associated protein							cytoplasm|microtubule				ovary(1)|central_nervous_system(1)|pancreas(1)	3				OV - Ovarian serous cystadenocarcinoma(145;1.4e-06)|Epithelial(140;1.11e-05)														---	---	---	---
NACC2	138151	broad.mit.edu	37	9	138964091	138964091	+	Intron	DEL	A	-	-	rs112519476		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:138964091delA	uc004cgw.2	-						NACC2_uc010nbh.2_Intron	NM_144653	NP_653254			BTB (POZ) domain containing 14A						negative regulation of transcription, DNA-dependent|positive regulation of cell proliferation|protein homooligomerization	nuclear body					0																		---	---	---	---
QSOX2	169714	broad.mit.edu	37	9	139112565	139112566	+	Intron	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:139112565_139112566delTT	uc010nbi.2	-							NM_181701	NP_859052			quiescin Q6 sulfhydryl oxidase 2 precursor						cell redox homeostasis	extracellular region|integral to membrane|nuclear membrane|plasma membrane	thiol oxidase activity			ovary(1)	1		Myeloproliferative disorder(178;0.0511)		Epithelial(140;7.78e-08)|OV - Ovarian serous cystadenocarcinoma(145;1.55e-07)														---	---	---	---
QSOX2	169714	broad.mit.edu	37	9	139138294	139138294	+	5'Flank	DEL	T	-	-	rs113949011		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:139138294delT	uc010nbi.2	-							NM_181701	NP_859052			quiescin Q6 sulfhydryl oxidase 2 precursor						cell redox homeostasis	extracellular region|integral to membrane|nuclear membrane|plasma membrane	thiol oxidase activity			ovary(1)	1		Myeloproliferative disorder(178;0.0511)		Epithelial(140;7.78e-08)|OV - Ovarian serous cystadenocarcinoma(145;1.55e-07)														---	---	---	---
GPSM1	26086	broad.mit.edu	37	9	139230360	139230360	+	Intron	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:139230360delC	uc004chd.2	+						GPSM1_uc004chc.2_Intron	NM_001145638	NP_001139110			G-protein signaling modulator 1 (AGS3-like, C.						cell differentiation|nervous system development|signal transduction	cytosol|endoplasmic reticulum membrane|Golgi membrane|plasma membrane	binding|GTPase activator activity				0		Myeloproliferative disorder(178;0.0821)		OV - Ovarian serous cystadenocarcinoma(145;2.39e-06)|Epithelial(140;3.24e-06)														---	---	---	---
MAMDC4	158056	broad.mit.edu	37	9	139747655	139747656	+	Frame_Shift_Del	DEL	CA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:139747655_139747656delCA	uc004cjs.2	+	2	198_199	c.148_149delCA	c.(148-150)CAGfs	p.Q50fs	MAMDC4_uc011mej.1_5'UTR	NM_206920	NP_996803	Q6UXC1	AEGP_HUMAN	apical early endosomal glycoprotein precursor	50	LDL-receptor class A 1; truncated.|Extracellular (Potential).				protein transport	integral to membrane				breast(4)|upper_aerodigestive_tract(2)|central_nervous_system(1)	7	all_cancers(76;0.0763)|all_epithelial(76;0.198)	Myeloproliferative disorder(178;0.0511)		OV - Ovarian serous cystadenocarcinoma(145;1.52e-05)|Epithelial(140;0.000171)														---	---	---	---
CLIC3	9022	broad.mit.edu	37	9	139892736	139892736	+	5'Flank	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:139892736delT	uc004ckj.1	-							NM_004669	NP_004660			chloride intracellular channel 3						signal transduction	chloride channel complex|cytoplasm|nucleus	protein binding|voltage-gated chloride channel activity				0	all_cancers(76;0.11)	Myeloproliferative disorder(178;0.0511)	STAD - Stomach adenocarcinoma(284;0.123)	OV - Ovarian serous cystadenocarcinoma(145;2.94e-05)|Epithelial(140;0.00048)														---	---	---	---
EHMT1	79813	broad.mit.edu	37	9	140552304	140552304	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:140552304delT	uc011mfc.1	+						EHMT1_uc004coa.2_Intron|EHMT1_uc004cob.1_Intron	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)														---	---	---	---
Unknown	0	broad.mit.edu	37	10	111730	111732	+	IGR	DEL	GTA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:111730_111732delGTA								TUBB8 (16226 upstream) : ZMYND11 (68692 downstream)																																			---	---	---	---
ZMYND11	10771	broad.mit.edu	37	10	225900	225900	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:225900delT	uc010pzt.1	+						ZMYND11_uc001ifk.2_Intron|ZMYND11_uc010pzu.1_Intron|ZMYND11_uc010pzv.1_Intron|ZMYND11_uc010pzw.1_Intron|ZMYND11_uc001ifm.2_Intron|ZMYND11_uc010pzx.1_5'Flank|ZMYND11_uc001ifn.2_5'Flank|ZMYND11_uc009xhg.2_5'Flank	NM_006624	NP_006615			zinc finger, MYND domain containing 11 isoform						cell cycle|cell proliferation|interspecies interaction between organisms|negative regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0		all_cancers(4;1.32e-05)|all_lung(4;3.67e-05)|Lung NSC(4;0.000301)|all_epithelial(10;0.000416)|Colorectal(49;0.14)	OV - Ovarian serous cystadenocarcinoma(33;0.132)	Epithelial(11;0.00289)|all cancers(11;0.0108)|Lung(33;0.0689)|OV - Ovarian serous cystadenocarcinoma(14;0.106)														---	---	---	---
LARP4B	23185	broad.mit.edu	37	10	869264	869265	+	Intron	DEL	GA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:869264_869265delGA	uc001ifs.1	-							NM_015155	NP_055970			La ribonucleoprotein domain family, member 4B								nucleotide binding|RNA binding			ovary(2)|central_nervous_system(1)	3																		---	---	---	---
LARP4B	23185	broad.mit.edu	37	10	870045	870045	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:870045delA	uc001ifs.1	-							NM_015155	NP_055970			La ribonucleoprotein domain family, member 4B								nucleotide binding|RNA binding			ovary(2)|central_nervous_system(1)	3																		---	---	---	---
Unknown	0	broad.mit.edu	37	10	969013	969014	+	IGR	INS	-	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:969013_969014insA								LARP4B (37311 upstream) : GTPBP4 (65335 downstream)																																			---	---	---	---
ADARB2	105	broad.mit.edu	37	10	1283322	1283322	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:1283322delA	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	1699287	1699287	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:1699287delT	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	3042290	3042290	+	IGR	DEL	G	-	-	rs112145826		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:3042290delG								None (None upstream) : PFKP (67462 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	3075369	3075369	+	IGR	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:3075369delG								None (None upstream) : PFKP (34383 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	3098143	3098143	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:3098143delA								None (None upstream) : PFKP (11609 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	3265954	3265954	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:3265954delT								PITRM1 (50951 upstream) : KLF6 (552235 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	3363695	3363695	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:3363695delA	uc001igy.1	+											Homo sapiens cDNA clone IMAGE:5278070.																														---	---	---	---
Unknown	0	broad.mit.edu	37	10	3453552	3453553	+	Intron	DEL	CG	-	-	rs73584855	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:3453552_3453553delCG	uc001igy.1	+											Homo sapiens cDNA clone IMAGE:5278070.																														---	---	---	---
Unknown	0	broad.mit.edu	37	10	4121875	4121877	+	Intron	DEL	TTT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:4121875_4121877delTTT	uc001ihc.1	+											Homo sapiens cDNA FLJ31241 fis, clone KIDNE2004985.																														---	---	---	---
Unknown	0	broad.mit.edu	37	10	4240001	4240001	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:4240001delA								KLF6 (412528 upstream) : LOC100216001 (381443 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	4283550	4283551	+	IGR	DEL	AC	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:4283550_4283551delAC								KLF6 (456077 upstream) : LOC100216001 (337893 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	4399039	4399039	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:4399039delT								KLF6 (571566 upstream) : LOC100216001 (222405 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	4762676	4762676	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:4762676delT								LOC100216001 (42414 upstream) : AKR1E2 (105726 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	4854780	4854780	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:4854780delA								LOC100216001 (134518 upstream) : AKR1E2 (13622 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	5360869	5360869	+	IGR	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:5360869delG								AKR1C4 (99959 upstream) : UCN3 (46107 downstream)																																			---	---	---	---
TUBAL3	79861	broad.mit.edu	37	10	5440715	5440716	+	Intron	INS	-	T	T	rs145712533	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:5440715_5440716insT	uc001ihy.2	-						TUBAL3_uc001ihz.2_Intron	NM_024803	NP_079079			tubulin, alpha-like 3						microtubule-based movement|protein polymerization	cytoplasm|microtubule	GTP binding|GTPase activity|structural molecule activity			skin(1)	1																		---	---	---	---
NET1	10276	broad.mit.edu	37	10	5495005	5495005	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:5495005delT	uc001iia.2	+						NET1_uc010qar.1_Intron|NET1_uc001iib.2_Intron|NET1_uc010qas.1_Intron	NM_001047160	NP_001040625			neuroepithelial cell transforming gene 1 isoform						apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of cell growth|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol|nucleus	Rho guanyl-nucleotide exchange factor activity			breast(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	10	5544942	5544942	+	IGR	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:5544942delG								CALML5 (3409 upstream) : CALML3 (21982 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	5628089	5628092	+	IGR	DEL	CAAA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:5628089_5628092delCAAA								CALML3 (59864 upstream) : ASB13 (52728 downstream)																																			---	---	---	---
C10orf18	54906	broad.mit.edu	37	10	5771784	5771784	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:5771784delT	uc001iij.2	+						C10orf18_uc001iik.2_5'Flank	NM_017782	NP_060252			hypothetical protein LOC54906											ovary(1)|central_nervous_system(1)	2																		---	---	---	---
GDI2	2665	broad.mit.edu	37	10	5829471	5829471	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:5829471delA	uc001iil.3	-						GDI2_uc001iim.3_Intron|GDI2_uc009xid.2_Intron	NM_001494	NP_001485			GDP dissociation inhibitor 2 isoform 1						protein transport|small GTPase mediated signal transduction	cell surface|cytosol|membrane	protein binding|Rab GDP-dissociation inhibitor activity				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	10	6023982	6023984	+	IGR	DEL	TTT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:6023982_6023984delTTT								IL15RA (3840 upstream) : IL2RA (29522 downstream)																																			---	---	---	---
IL2RA	3559	broad.mit.edu	37	10	6053512	6053512	+	3'UTR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:6053512delT	uc001iiz.1	-	8					IL2RA_uc009xih.1_3'UTR	NM_000417	NP_000408			interleukin 2 receptor, alpha chain precursor						cell proliferation	integral to membrane	interleukin-2 receptor activity			ovary(1)|skin(1)	2					Aldesleukin(DB00041)|Basiliximab(DB00074)|Daclizumab(DB00111)|Denileukin diftitox(DB00004)													---	---	---	---
PRKCQ	5588	broad.mit.edu	37	10	6482618	6482622	+	Intron	DEL	AGAGG	-	-	rs117613395	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:6482618_6482622delAGAGG	uc001ijj.1	-						PRKCQ_uc009xim.1_Intron|PRKCQ_uc001iji.1_Intron|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																		---	---	---	---
SFMBT2	57713	broad.mit.edu	37	10	7385184	7385184	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:7385184delT	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																		---	---	---	---
SFMBT2	57713	broad.mit.edu	37	10	7421639	7421639	+	Intron	DEL	A	-	-	rs140101292		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:7421639delA	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																		---	---	---	---
ITIH5	80760	broad.mit.edu	37	10	7615467	7615467	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:7615467delA	uc001ijq.2	-						ITIH5_uc001ijp.2_Intron|ITIH5_uc001ijr.1_Intron	NM_030569	NP_085046			inter-alpha trypsin inhibitor heavy chain						hyaluronan metabolic process	extracellular region	serine-type endopeptidase inhibitor activity			ovary(2)|central_nervous_system(2)	4																		---	---	---	---
ITIH5	80760	broad.mit.edu	37	10	7662155	7662155	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:7662155delA	uc001ijq.2	-						ITIH5_uc001ijp.2_5'Flank|ITIH5_uc001ijr.1_Intron	NM_030569	NP_085046			inter-alpha trypsin inhibitor heavy chain						hyaluronan metabolic process	extracellular region	serine-type endopeptidase inhibitor activity			ovary(2)|central_nervous_system(2)	4																		---	---	---	---
Unknown	0	broad.mit.edu	37	10	7718583	7718583	+	IGR	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:7718583delG								ITIH5 (9649 upstream) : ITIH2 (26653 downstream)																																			---	---	---	---
TAF3	83860	broad.mit.edu	37	10	7978835	7978835	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:7978835delT	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																		---	---	---	---
TAF3	83860	broad.mit.edu	37	10	8052875	8052875	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:8052875delA	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	8121082	8121083	+	IGR	DEL	AA	-	-	rs75045270		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:8121082_8121083delAA								GATA3 (3920 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	8589751	8589752	+	IGR	DEL	TC	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:8589751_8589752delTC								GATA3 (472589 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	8801718	8801718	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:8801718delA								GATA3 (684556 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	9290691	9290691	+	IGR	DEL	A	-	-	rs76469636		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:9290691delA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	9946989	9946989	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:9946989delA								None (None upstream) : SFTA1P (879413 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	10576178	10576180	+	IGR	DEL	AAA	-	-	rs148241138		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:10576178_10576180delAAA								None (None upstream) : SFTA1P (250222 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	10724606	10724606	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:10724606delT								None (None upstream) : SFTA1P (101796 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	10725973	10725974	+	IGR	INS	-	A	A	rs138450170	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:10725973_10725974insA								None (None upstream) : SFTA1P (100428 downstream)																																			---	---	---	---
CDC123	8872	broad.mit.edu	37	10	12239380	12239381	+	Intron	DEL	AT	-	-	rs10906096	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:12239380_12239381delAT	uc001ill.2	+						NUDT5_uc001ilj.2_5'Flank|NUDT5_uc001ilk.2_5'Flank|CDC123_uc009xja.2_Intron|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	12408658	12408658	+	Intron	DEL	A	-	-	rs113268184		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:12408658delA	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	12436330	12436330	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:12436330delT	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	12583887	12583887	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:12583887delT	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	12741998	12741998	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:12741998delA	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)														---	---	---	---
OPTN	10133	broad.mit.edu	37	10	13151191	13151192	+	Frame_Shift_Ins	INS	-	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:13151191_13151192insC	uc001ilu.1	+	4	507_508	c.69_70insC	c.(67-72)GGACCCfs	p.G23fs	OPTN_uc001ilv.1_Frame_Shift_Ins_p.G23fs|OPTN_uc001ilw.1_Frame_Shift_Ins_p.G23fs|OPTN_uc001ilx.1_Frame_Shift_Ins_p.G23fs|OPTN_uc001ily.1_Frame_Shift_Ins_p.G23fs|OPTN_uc010qbr.1_5'UTR|OPTN_uc001ilz.1_Frame_Shift_Ins_p.G23fs	NM_001008213	NP_001008214	Q96CV9	OPTN_HUMAN	optineurin	23_24					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																		---	---	---	---
Unknown	0	broad.mit.edu	37	10	13465134	13465134	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:13465134delA								SEPHS1 (74854 upstream) : BEND7 (15350 downstream)																																			---	---	---	---
BEND7	222389	broad.mit.edu	37	10	13518099	13518099	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:13518099delT	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	13767538	13767538	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:13767538delT	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																		---	---	---	---
FRMD4A	55691	broad.mit.edu	37	10	14000601	14000601	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:14000601delT	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																		---	---	---	---
NMT2	9397	broad.mit.edu	37	10	15171968	15171968	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:15171968delT	uc001inz.1	-						NMT2_uc001ioa.1_Intron|NMT2_uc009xjo.1_Intron|NMT2_uc010qbz.1_Intron	NM_004808	NP_004799			N-myristoyltransferase 2						N-terminal protein myristoylation|protein lipoylation	Golgi apparatus|plasma membrane	glycylpeptide N-tetradecanoyltransferase activity			ovary(1)	1																		---	---	---	---
NMT2	9397	broad.mit.edu	37	10	15193059	15193061	+	Intron	DEL	TTT	-	-	rs112852108	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:15193059_15193061delTTT	uc001inz.1	-						NMT2_uc001ioa.1_Intron|NMT2_uc009xjo.1_Intron|NMT2_uc010qbz.1_Intron	NM_004808	NP_004799			N-myristoyltransferase 2						N-terminal protein myristoylation|protein lipoylation	Golgi apparatus|plasma membrane	glycylpeptide N-tetradecanoyltransferase activity			ovary(1)	1																		---	---	---	---
FAM171A1	221061	broad.mit.edu	37	10	15256758	15256759	+	Intron	DEL	TT	-	-	rs79674551		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:15256758_15256759delTT	uc001iob.2	-							NM_001010924	NP_001010924			hypothetical protein LOC221061 precursor							integral to membrane				ovary(2)|breast(1)|skin(1)	4																		---	---	---	---
FAM171A1	221061	broad.mit.edu	37	10	15257899	15257899	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:15257899delA	uc001iob.2	-							NM_001010924	NP_001010924			hypothetical protein LOC221061 precursor							integral to membrane				ovary(2)|breast(1)|skin(1)	4																		---	---	---	---
ITGA8	8516	broad.mit.edu	37	10	15644736	15644736	+	Intron	DEL	C	-	-	rs10795310	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:15644736delC	uc001ioc.1	-						ITGA8_uc010qcb.1_Intron	NM_003638	NP_003629			integrin, alpha 8 precursor						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	15748228	15748228	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:15748228delT	uc001ioc.1	-						ITGA8_uc010qcb.1_Intron	NM_003638	NP_003629			integrin, alpha 8 precursor						cell differentiation|cell-cell adhesion|cell-matrix adhesion|integrin-mediated signaling pathway|nervous system development	integrin complex	receptor activity			ovary(3)|lung(3)	6																		---	---	---	---
Unknown	0	broad.mit.edu	37	10	16119450	16119450	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:16119450delT								FAM188A (216931 upstream) : PTER (359517 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	16441872	16441872	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:16441872delA								FAM188A (539353 upstream) : PTER (37095 downstream)																																			---	---	---	---
RSU1	6251	broad.mit.edu	37	10	16647514	16647514	+	Intron	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:16647514delC	uc001iok.2	-						RSU1_uc001iol.2_Intron|RSU1_uc001iom.2_Intron	NM_152724	NP_689937			ras suppressor protein 1 isoform 2						cell junction assembly|signal transduction	cytosol	protein binding			central_nervous_system(1)	1				GBM - Glioblastoma multiforme(1;7.54e-08)														---	---	---	---
RSU1	6251	broad.mit.edu	37	10	16668049	16668050	+	Intron	DEL	TT	-	-	rs112699947		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:16668049_16668050delTT	uc001iok.2	-						RSU1_uc001iol.2_Intron|RSU1_uc001iom.2_Intron	NM_152724	NP_689937			ras suppressor protein 1 isoform 2						cell junction assembly|signal transduction	cytosol	protein binding			central_nervous_system(1)	1				GBM - Glioblastoma multiforme(1;7.54e-08)														---	---	---	---
RSU1	6251	broad.mit.edu	37	10	16740386	16740387	+	Intron	INS	-	CTA	CTA			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:16740386_16740387insCTA	uc001iok.2	-						RSU1_uc001iol.2_Intron|RSU1_uc001iom.2_Intron	NM_152724	NP_689937			ras suppressor protein 1 isoform 2						cell junction assembly|signal transduction	cytosol	protein binding			central_nervous_system(1)	1				GBM - Glioblastoma multiforme(1;7.54e-08)														---	---	---	---
RSU1	6251	broad.mit.edu	37	10	16824883	16824884	+	Intron	DEL	GT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:16824883_16824884delGT	uc001iok.2	-						RSU1_uc001iol.2_Intron|RSU1_uc001iom.2_Intron|RSU1_uc001ion.2_Intron	NM_152724	NP_689937			ras suppressor protein 1 isoform 2						cell junction assembly|signal transduction	cytosol	protein binding			central_nervous_system(1)	1				GBM - Glioblastoma multiforme(1;7.54e-08)														---	---	---	---
ST8SIA6	338596	broad.mit.edu	37	10	17428175	17428176	+	Intron	DEL	CA	-	-	rs78807428		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:17428175_17428176delCA	uc001ipd.2	-						ST8SIA6_uc010qce.1_Intron|uc001ipe.2_5'Flank|uc001ipf.1_5'Flank	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																		---	---	---	---
ST8SIA6	338596	broad.mit.edu	37	10	17472574	17472574	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:17472574delT	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																		---	---	---	---
CACNB2	783	broad.mit.edu	37	10	18676690	18676691	+	Intron	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:18676690_18676691delTT	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|CACNB2_uc009xkb.1_Intron|CACNB2_uc010qcm.1_Intron|CACNB2_uc001ipz.2_Intron|CACNB2_uc001ipy.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)													---	---	---	---
NSUN6	221078	broad.mit.edu	37	10	18852520	18852521	+	Intron	INS	-	CAT	CAT			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:18852520_18852521insCAT	uc010qcp.1	-							NM_182543	NP_872349			NOL1/NOP2/Sun domain family, member 6								methyltransferase activity|RNA binding			ovary(2)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	10	19240256	19240256	+	IGR	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:19240256delG								ARL5B (273316 upstream) : PLXDC2 (865116 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	19858405	19858405	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:19858405delA	uc010qcq.1	+											SubName: Full=cDNA FLJ60310;																														---	---	---	---
Unknown	0	broad.mit.edu	37	10	19923747	19923749	+	Intron	DEL	AAC	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:19923747_19923749delAAC	uc010qcr.1	+											Homo sapiens cDNA FLJ60310 complete cds.																														---	---	---	---
Unknown	0	broad.mit.edu	37	10	20019763	20019764	+	Intron	DEL	AC	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:20019763_20019764delAC	uc010qcr.1	+						uc001iqf.2_5'Flank					Homo sapiens cDNA FLJ60310 complete cds.																														---	---	---	---
PLXDC2	84898	broad.mit.edu	37	10	20416118	20416118	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:20416118delT	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																		---	---	---	---
PLXDC2	84898	broad.mit.edu	37	10	20556770	20556770	+	Intron	DEL	T	-	-	rs72082285		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:20556770delT	uc001iqg.1	+						PLXDC2_uc001iqh.1_Intron|PLXDC2_uc009xkc.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	20621172	20621172	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:20621172delT								PLXDC2 (52057 upstream) : NEBL (447733 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	20757148	20757148	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:20757148delT								PLXDC2 (188033 upstream) : NEBL (311757 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	20829482	20829482	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:20829482delT								PLXDC2 (260367 upstream) : NEBL (239423 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	21019472	21019472	+	IGR	DEL	A	-	-	rs143010725	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:21019472delA								PLXDC2 (450357 upstream) : NEBL (49433 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	21051732	21051732	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:21051732delA								PLXDC2 (482617 upstream) : NEBL (17173 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	21052831	21052831	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:21052831delA								PLXDC2 (483716 upstream) : NEBL (16074 downstream)																																			---	---	---	---
NEBL	10529	broad.mit.edu	37	10	21363004	21363004	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:21363004delA	uc001iqk.2	-							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	21571446	21571446	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:21571446delA								NEBL (108330 upstream) : C10orf114 (211976 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	21741095	21741095	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:21741095delA								NEBL (277979 upstream) : C10orf114 (42327 downstream)																																			---	---	---	---
MLLT10	8028	broad.mit.edu	37	10	21872802	21872802	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:21872802delT	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	21877756	21877757	+	Intron	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:21877756_21877757delTT	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	21943702	21943702	+	Intron	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:21943702delG	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	21977574	21977574	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:21977574delA	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	22039229	22039229	+	IGR	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:22039229delC								MLLT10 (6674 upstream) : DNAJC1 (6249 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	22335214	22335216	+	IGR	DEL	TTT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:22335214_22335216delTTT								DNAJC1 (42564 upstream) : COMMD3 (270083 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	22405692	22405693	+	IGR	INS	-	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:22405692_22405693insA								DNAJC1 (113042 upstream) : COMMD3 (199606 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	22519349	22519349	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:22519349delT								DNAJC1 (226699 upstream) : COMMD3 (85950 downstream)																																			---	---	---	---
SPAG6	9576	broad.mit.edu	37	10	22634637	22634638	+	Intron	DEL	CT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:22634637_22634638delCT	uc001iri.2	+						SPAG6_uc001irj.2_Intron|SPAG6_uc010qct.1_Intron|SPAG6_uc009xkh.2_5'UTR	NM_012443	NP_036575			sperm associated antigen 6 isoform 1						cell projection organization|spermatid development	axoneme|cilium|cytoplasm|flagellum|microtubule	binding			breast(1)	1																		---	---	---	---
SPAG6	9576	broad.mit.edu	37	10	22690261	22690261	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:22690261delT	uc001iri.2	+						SPAG6_uc001irj.2_Intron|SPAG6_uc010qct.1_Intron|SPAG6_uc009xkh.2_Intron	NM_012443	NP_036575			sperm associated antigen 6 isoform 1						cell projection organization|spermatid development	axoneme|cilium|cytoplasm|flagellum|microtubule	binding			breast(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	10	22764619	22764619	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:22764619delA								SPAG6 (58081 upstream) : PIP4K2A (59148 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	22787531	22787531	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:22787531delT								SPAG6 (80993 upstream) : PIP4K2A (36236 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	23011798	23011798	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:23011798delT								PIP4K2A (8295 upstream) : ARMC3 (205156 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	23604750	23604750	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:23604750delT								PTF1A (121571 upstream) : C10orf67 (771 downstream)																																			---	---	---	---
KIAA1217	56243	broad.mit.edu	37	10	24038350	24038350	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:24038350delT	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	24110905	24110905	+	Intron	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:24110905delC	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	24494702	24494702	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:24494702delA	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	24529785	24529785	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:24529785delT	uc001iru.3	+						KIAA1217_uc001irs.2_Intron|KIAA1217_uc001irt.3_Intron|KIAA1217_uc010qcy.1_Intron|KIAA1217_uc010qcz.1_Intron|KIAA1217_uc001irv.1_Intron	NM_019590	NP_062536			sickle tail isoform 1						embryonic skeletal system development	cytoplasm				ovary(5)|skin(2)	7																		---	---	---	---
KIAA1217	56243	broad.mit.edu	37	10	24780861	24780862	+	Intron	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:24780861_24780862delTT	uc001iru.3	+						KIAA1217_uc001irs.2_Intron|KIAA1217_uc001irt.3_Intron|KIAA1217_uc010qcy.1_Intron|KIAA1217_uc010qcz.1_Intron|KIAA1217_uc001irv.1_Intron|KIAA1217_uc010qda.1_Intron|KIAA1217_uc001irw.2_Intron|KIAA1217_uc001irz.2_Intron|KIAA1217_uc001irx.2_Intron|KIAA1217_uc001iry.2_Intron	NM_019590	NP_062536			sickle tail isoform 1						embryonic skeletal system development	cytoplasm				ovary(5)|skin(2)	7																		---	---	---	---
KIAA1217	56243	broad.mit.edu	37	10	24818561	24818561	+	Intron	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:24818561delC	uc001iru.3	+						KIAA1217_uc001irs.2_Intron|KIAA1217_uc001irt.3_Intron|KIAA1217_uc010qcy.1_Intron|KIAA1217_uc010qcz.1_Intron|KIAA1217_uc010qda.1_Intron|KIAA1217_uc001irw.2_Intron|KIAA1217_uc001irz.2_Intron|KIAA1217_uc001irx.2_Intron|KIAA1217_uc001iry.2_Intron	NM_019590	NP_062536			sickle tail isoform 1						embryonic skeletal system development	cytoplasm				ovary(5)|skin(2)	7																		---	---	---	---
Unknown	0	broad.mit.edu	37	10	25099371	25099372	+	IGR	INS	-	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:25099371_25099372insT								ARHGAP21 (86774 upstream) : PRTFDC1 (38182 downstream)																																			---	---	---	---
PRTFDC1	56952	broad.mit.edu	37	10	25216011	25216011	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:25216011delA	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																		---	---	---	---
Unknown	0	broad.mit.edu	37	10	25429913	25429914	+	IGR	INS	-	AC	AC	rs147746187	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:25429913_25429914insAC								ENKUR (78705 upstream) : LOC100128811 (17087 downstream)																																			---	---	---	---
GPR158	57512	broad.mit.edu	37	10	25847162	25847163	+	Intron	DEL	GT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:25847162_25847163delGT	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																		---	---	---	---
Unknown	0	broad.mit.edu	37	10	25990404	25990404	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:25990404delT	uc001isl.1	+											Homo sapiens cDNA FLJ41446 fis, clone BRSTN2003590.																														---	---	---	---
Unknown	0	broad.mit.edu	37	10	26616639	26616639	+	IGR	DEL	G	-	-	rs76713492		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:26616639delG								GAD2 (23148 upstream) : APBB1IP (110627 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	27172148	27172148	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:27172148delA								ABI1 (22189 upstream) : NCRNA00202 (47987 downstream)																																			---	---	---	---
ANKRD26	22852	broad.mit.edu	37	10	27356351	27356352	+	Intron	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:27356351_27356352delTT	uc001ith.2	-						ANKRD26_uc001itg.2_Intron|ANKRD26_uc009xku.1_Intron	NM_014915	NP_055730			ankyrin repeat domain 26							centrosome				large_intestine(1)|haematopoietic_and_lymphoid_tissue(1)|ovary(1)|skin(1)	4																		---	---	---	---
YME1L1	10730	broad.mit.edu	37	10	27409239	27409239	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:27409239delA	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																		---	---	---	---
ACBD5	91452	broad.mit.edu	37	10	27518474	27518474	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:27518474delA	uc010qdp.1	-						ACBD5_uc010qdm.1_Intron|ACBD5_uc010qdn.1_Intron|ACBD5_uc010qdo.1_Intron|ACBD5_uc001ito.2_Intron|ACBD5_uc001itp.2_Intron|ACBD5_uc001itq.2_Intron|ACBD5_uc001itr.1_Intron	NM_145698	NP_663736			acyl-Coenzyme A binding domain containing 5						transport	integral to membrane|peroxisomal membrane	fatty-acyl-CoA binding				0																		---	---	---	---
ACBD5	91452	broad.mit.edu	37	10	27520499	27520499	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:27520499delA	uc010qdp.1	-						ACBD5_uc010qdm.1_Intron|ACBD5_uc010qdn.1_Intron|ACBD5_uc010qdo.1_Intron|ACBD5_uc001ito.2_Intron|ACBD5_uc001itp.2_Intron|ACBD5_uc001itq.2_Intron|ACBD5_uc001itr.1_Intron	NM_145698	NP_663736			acyl-Coenzyme A binding domain containing 5						transport	integral to membrane|peroxisomal membrane	fatty-acyl-CoA binding				0																		---	---	---	---
MKX	283078	broad.mit.edu	37	10	28023575	28023575	+	Frame_Shift_Del	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:28023575delG	uc001ity.3	-	5	873	c.648delC	c.(646-648)CCCfs	p.P216fs	MKX_uc001itx.3_Frame_Shift_Del_p.P216fs	NM_173576	NP_775847	Q8IYA7	MKX_HUMAN	mohawk homeobox	216					muscle organ development	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			ovary(1)	1																		---	---	---	---
ARMC4	55130	broad.mit.edu	37	10	28140516	28140516	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:28140516delA	uc009xky.2	-						ARMC4_uc010qds.1_Intron|ARMC4_uc010qdt.1_Intron|ARMC4_uc001itz.2_Intron	NM_018076	NP_060546			armadillo repeat containing 4								binding			ovary(4)|skin(2)	6																		---	---	---	---
MPP7	143098	broad.mit.edu	37	10	28408845	28408845	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:28408845delT	uc001iua.1	-						MPP7_uc009xkz.1_Intron|MPP7_uc001iub.1_Intron|MPP7_uc009xla.2_Intron|MPP7_uc010qdv.1_Intron	NM_173496	NP_775767			palmitoylated membrane protein 7						establishment of cell polarity|positive regulation of protein complex assembly|protein localization to adherens junction|tight junction assembly	MPP7-DLG1-LIN7 complex|tight junction	protein complex scaffold|protein domain specific binding|protein heterodimerization activity|signaling adaptor activity			ovary(1)	1																		---	---	---	---
MPP7	143098	broad.mit.edu	37	10	28464219	28464221	+	Intron	DEL	AAA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:28464219_28464221delAAA	uc001iua.1	-						MPP7_uc009xkz.1_Intron|MPP7_uc001iub.1_Intron|MPP7_uc009xla.2_Intron|MPP7_uc010qdv.1_Intron	NM_173496	NP_775767			palmitoylated membrane protein 7						establishment of cell polarity|positive regulation of protein complex assembly|protein localization to adherens junction|tight junction assembly	MPP7-DLG1-LIN7 complex|tight junction	protein complex scaffold|protein domain specific binding|protein heterodimerization activity|signaling adaptor activity			ovary(1)	1																		---	---	---	---
MPP7	143098	broad.mit.edu	37	10	28534263	28534263	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:28534263delT	uc001iua.1	-						MPP7_uc001iub.1_Intron|MPP7_uc009xla.2_Intron|MPP7_uc010qdv.1_Intron	NM_173496	NP_775767			palmitoylated membrane protein 7						establishment of cell polarity|positive regulation of protein complex assembly|protein localization to adherens junction|tight junction assembly	MPP7-DLG1-LIN7 complex|tight junction	protein complex scaffold|protein domain specific binding|protein heterodimerization activity|signaling adaptor activity			ovary(1)	1																		---	---	---	---
MPP7	143098	broad.mit.edu	37	10	28565959	28565960	+	Intron	DEL	AA	-	-	rs79011306		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:28565959_28565960delAA	uc001iua.1	-						MPP7_uc001iub.1_Intron|MPP7_uc009xla.2_Intron|MPP7_uc010qdv.1_Intron	NM_173496	NP_775767			palmitoylated membrane protein 7						establishment of cell polarity|positive regulation of protein complex assembly|protein localization to adherens junction|tight junction assembly	MPP7-DLG1-LIN7 complex|tight junction	protein complex scaffold|protein domain specific binding|protein heterodimerization activity|signaling adaptor activity			ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	10	28635913	28635914	+	IGR	INS	-	G	G	rs149821099	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:28635913_28635914insG								MPP7 (43918 upstream) : WAC (185513 downstream)																																			---	---	---	---
WAC	51322	broad.mit.edu	37	10	28824471	28824471	+	Intron	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:28824471delG	uc001iuf.2	+						WAC_uc001iud.2_Intron|WAC_uc001iue.2_Intron|WAC_uc009xlb.2_Intron|WAC_uc001iug.2_Intron|WAC_uc001iuh.2_Intron	NM_016628	NP_057712			WW domain-containing adapter with a coiled-coil						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																		---	---	---	---
WAC	51322	broad.mit.edu	37	10	28897478	28897478	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:28897478delT	uc001iuf.2	+						WAC_uc001iud.2_Intron|WAC_uc001iue.2_Intron|WAC_uc001iug.2_Intron|WAC_uc001iuh.2_Intron	NM_016628	NP_057712			WW domain-containing adapter with a coiled-coil						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																		---	---	---	---
Unknown	0	broad.mit.edu	37	10	29001953	29001953	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:29001953delT								BAMBI (30085 upstream) : LYZL1 (576037 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	29230843	29230844	+	IGR	INS	-	TG	TG	rs142773151	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:29230843_29230844insTG								BAMBI (258975 upstream) : LYZL1 (347146 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	29571121	29571121	+	IGR	DEL	A	-	-	rs138149856		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:29571121delA								BAMBI (599253 upstream) : LYZL1 (6869 downstream)																																			---	---	---	---
KIAA1462	57608	broad.mit.edu	37	10	30352743	30352743	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:30352743delT	uc001iuz.2	-											RecName: Full=Uncharacterized protein KIAA1462;											ovary(4)	4																		---	---	---	---
Unknown	0	broad.mit.edu	37	10	30696468	30696468	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:30696468delA								MTPAP (33091 upstream) : MAP3K8 (26398 downstream)																																			---	---	---	---
MAP3K8	1326	broad.mit.edu	37	10	30728362	30728362	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-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)																---	---	---	---
Unknown	0	broad.mit.edu	37	10	30801483	30801483	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:30801483delA								MAP3K8 (50722 upstream) : LYZL2 (99226 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	30900666	30900669	+	IGR	DEL	GAAA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:30900666_30900669delGAAA								MAP3K8 (149905 upstream) : LYZL2 (40 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	30930923	30930923	+	IGR	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:30930923delG								LYZL2 (12276 upstream) : ZNF438 (202644 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	31013394	31013394	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:31013394delT								LYZL2 (94747 upstream) : ZNF438 (120173 downstream)																																			---	---	---	---
ZNF438	220929	broad.mit.edu	37	10	31201312	31201312	+	Intron	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:31201312delC	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	32404710	32404710	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:32404710delT								KIF5B (59339 upstream) : EPC1 (153149 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	32529019	32529019	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:32529019delT								KIF5B (183648 upstream) : EPC1 (28840 downstream)																																			---	---	---	---
NRP1	8829	broad.mit.edu	37	10	33492448	33492448	+	Intron	DEL	A	-	-	rs28417729		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:33492448delA	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	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	33674387	33674388	+	IGR	INS	-	AG	AG			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:33674387_33674388insAG								NRP1 (50381 upstream) : PARD3 (725710 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	34115056	34115057	+	IGR	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:34115056_34115057delTT								NRP1 (491050 upstream) : PARD3 (285041 downstream)																																			---	---	---	---
PARD3	56288	broad.mit.edu	37	10	34653363	34653364	+	Intron	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:34653363_34653364delTT	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|PARD3_uc001ixs.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	34733989	34733989	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:34733989delT	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_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	34928784	34928785	+	Intron	DEL	AC	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:34928784_34928785delAC	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)																---	---	---	---
PARD3	56288	broad.mit.edu	37	10	35106639	35106639	+	5'Flank	DEL	T	-	-	rs76981437		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:35106639delT	uc010qej.1	-						PARD3_uc010qek.1_5'Flank|PARD3_uc010qel.1_5'Flank|PARD3_uc010qem.1_5'Flank|PARD3_uc010qen.1_5'Flank|PARD3_uc010qeo.1_5'Flank|PARD3_uc010qep.1_5'Flank|PARD3_uc010qeq.1_5'Flank|PARD3_uc001ixq.1_5'Flank|PARD3_uc001ixr.1_5'Flank|PARD3_uc001ixu.1_5'Flank	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)																---	---	---	---
CCNY	219771	broad.mit.edu	37	10	35563693	35563693	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:35563693delT	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	36189536	36189537	+	IGR	DEL	GT	-	-	rs72228039		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:36189536_36189537delGT								FZD8 (259174 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	36445039	36445039	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:36445039delT								FZD8 (514677 upstream) : ANKRD30A (969746 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	36478772	36478772	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:36478772delA								FZD8 (548410 upstream) : ANKRD30A (936013 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	36518049	36518049	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:36518049delA								FZD8 (587687 upstream) : ANKRD30A (896736 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	38541287	38541287	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:38541287delT								LOC100129055 (38015 upstream) : HSD17B7P2 (104021 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	38804086	38804090	+	IGR	DEL	ACCCT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:38804086_38804090delACCCT								LOC399744 (63006 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	38872243	38872247	+	IGR	DEL	TAGCT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:38872243_38872247delTAGCT								LOC399744 (131163 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	38872332	38872334	+	IGR	DEL	TTG	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:38872332_38872334delTTG								LOC399744 (131252 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	38902676	38902676	+	IGR	DEL	G	-	-	rs77057906		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:38902676delG								LOC399744 (161596 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	39101146	39101147	+	IGR	INS	-	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:39101146_39101147insC								LOC399744 (360066 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	42668328	42668328	+	IGR	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:42668328delG								None (None upstream) : LOC441666 (158987 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	42674824	42674824	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:42674824delA								None (None upstream) : LOC441666 (152491 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	42700107	42700108	+	IGR	INS	-	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-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	42721668	42721670	+	IGR	DEL	TCA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:42721668_42721670delTCA								None (None upstream) : LOC441666 (105645 downstream)																																			---	---	---	---
ZNF33B	7582	broad.mit.edu	37	10	43108490	43108491	+	Intron	INS	-	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:43108490_43108491insA	uc001jaf.1	-						ZNF33B_uc009xmg.1_Intron|ZNF33B_uc001jae.1_Intron|ZNF33B_uc001jag.1_Intron|ZNF33B_uc001jad.2_Intron	NM_006955	NP_008886			zinc finger protein 33B							nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	10	43201894	43201894	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:43201894delA								ZNF33B (67902 upstream) : BMS1 (76060 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	43459095	43459095	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:43459095delT								BMS1 (128712 upstream) : RET (113422 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	43878119	43878120	+	IGR	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:43878119_43878120delTT								FXYD4 (6336 upstream) : HNRNPF (2945 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	44929696	44929696	+	IGR	DEL	T	-	-	rs141063612	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:44929696delT								CXCL12 (49154 upstream) : TMEM72 (477068 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	45000450	45000451	+	IGR	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:45000450_45000451delAA								CXCL12 (119908 upstream) : TMEM72 (406313 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	45022737	45022737	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:45022737delT								CXCL12 (142195 upstream) : TMEM72 (384027 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	45038364	45038365	+	IGR	DEL	TT	-	-	rs145307787		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:45038364_45038365delTT								CXCL12 (157822 upstream) : TMEM72 (368399 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	45719241	45719242	+	IGR	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:45719241_45719242delAA								LOC100133308 (69197 upstream) : OR13A1 (78860 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	46974872	46974872	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:46974872delA								SYT15 (4271 upstream) : GPRIN2 (18674 downstream)																																			---	---	---	---
ANXA8	653145	broad.mit.edu	37	10	47015715	47015716	+	Intron	DEL	AC	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:47015715_47015716delAC	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	47046822	47046824	+	Intron	DEL	ACG	-	-	rs148953514	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:47046822_47046824delACG	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	47129045	47129045	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:47129045delA	uc001jed.3	-						uc001jef.2_Intron					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	47135037	47135038	+	Intron	INS	-	T	T	rs151144614		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:47135037_47135038insT	uc001jed.3	-						uc001jef.2_Intron|LOC728643_uc001jeg.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	47370000	47370000	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:47370000delT								LOC642826 (126498 upstream) : FAM35B2 (9720 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	47734364	47734366	+	IGR	DEL	TTG	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:47734364_47734366delTTG								ANTXRL (32918 upstream) : ANXA8L2 (12554 downstream)																																			---	---	---	---
GDF10	2662	broad.mit.edu	37	10	48428552	48428552	+	Intron	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:48428552delG	uc001jfb.2	-						GDF10_uc009xnp.2_Intron|GDF10_uc009xnq.1_3'UTR	NM_004962	NP_004953			growth differentiation factor 10 precursor						growth|skeletal system development|transforming growth factor beta receptor signaling pathway	extracellular space	cytokine activity|growth factor activity			lung(1)|central_nervous_system(1)	2																		---	---	---	---
MAPK8	5599	broad.mit.edu	37	10	49632499	49632499	+	Intron	DEL	T	-	-	rs78072348		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-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	49956730	49956730	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:49956730delT	uc001jha.3	+							NM_020945	NP_065996			WDFY family member 4							integral to membrane	binding				0																		---	---	---	---
C10orf71	118461	broad.mit.edu	37	10	50515755	50515755	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:50515755delT	uc010qgp.1	+							NM_199459	NP_955629			hypothetical protein LOC118461 isoform 2												0																		---	---	---	---
ERCC6	2074	broad.mit.edu	37	10	50715003	50715003	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:50715003delA	uc001jhs.3	-						ERCC6_uc001jhr.3_5'Flank	NM_000124	NP_000115			excision repair cross-complementing rodent						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					---	---	---	---
Unknown	0	broad.mit.edu	37	10	50760658	50760660	+	IGR	DEL	GAG	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:50760658_50760660delGAG								PGBD3 (13074 upstream) : CHAT (56481 downstream)																																			---	---	---	---
PARG	8505	broad.mit.edu	37	10	51048437	51048437	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:51048437delA	uc001jif.2	-						PARG_uc001jih.2_Intron|PARG_uc001jig.2_Intron|PARG_uc010qgv.1_Intron|PARG_uc009xoi.2_Intron|PARG_uc010qgw.1_Intron|PARG_uc009xoj.2_Intron|PARG_uc010qgx.1_Intron	NM_003631	NP_003622			poly (ADP-ribose) glycohydrolase						carbohydrate metabolic process	nucleus	poly(ADP-ribose) glycohydrolase activity			ovary(2)	2				Epithelial(53;0.213)														---	---	---	---
PARG	8505	broad.mit.edu	37	10	51532041	51532042	+	Intron	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:51532041_51532042delTT	uc001jih.2	-						uc010qha.1_Intron|uc001jin.2_Intron|uc010qhb.1_Intron|uc010qhc.1_Intron	NM_003631	NP_003622			poly (ADP-ribose) glycohydrolase						carbohydrate metabolic process	nucleus	poly(ADP-ribose) glycohydrolase activity			ovary(2)	2				Epithelial(53;0.213)														---	---	---	---
ASAH2	56624	broad.mit.edu	37	10	52004600	52004601	+	Intron	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:52004600_52004601delTT	uc001jjd.2	-						ASAH2_uc009xos.2_Intron	NM_019893	NP_063946			N-acylsphingosine amidohydrolase 2 isoform a						apoptosis|ceramide metabolic process|signal transduction	integral to membrane|mitochondrion|plasma membrane	ceramidase activity				0																		---	---	---	---
SGMS1	259230	broad.mit.edu	37	10	52187733	52187734	+	Intron	DEL	GA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:52187733_52187734delGA	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	52358671	52358671	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:52358671delA	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																		---	---	---	---
PRKG1	5592	broad.mit.edu	37	10	53299874	53299875	+	Intron	INS	-	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:53299874_53299875insA	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	53351524	53351524	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:53351524delA	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	54238732	54238732	+	IGR	DEL	A	-	-	rs79603317		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:54238732delA								DKK1 (161316 upstream) : MBL2 (286409 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	54766639	54766639	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:54766639delA								MBL2 (235179 upstream) : PCDH15 (795896 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	54805913	54805913	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:54805913delA								MBL2 (274453 upstream) : PCDH15 (756622 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	54894742	54894743	+	IGR	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:54894742_54894743delAA								MBL2 (363282 upstream) : PCDH15 (667792 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	55161159	55161161	+	IGR	DEL	AAA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:55161159_55161161delAAA								MBL2 (629699 upstream) : PCDH15 (401374 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	55390475	55390476	+	IGR	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:55390475_55390476delAA								MBL2 (859015 upstream) : PCDH15 (172059 downstream)																																			---	---	---	---
PCDH15	65217	broad.mit.edu	37	10	55728687	55728688	+	Intron	INS	-	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:55728687_55728688insA	uc001jju.1	-						PCDH15_uc010qhq.1_Intron|PCDH15_uc010qhr.1_Intron|PCDH15_uc010qhs.1_Intron|PCDH15_uc010qht.1_Intron|PCDH15_uc010qhu.1_Intron|PCDH15_uc001jjv.1_Intron|PCDH15_uc010qhv.1_Intron|PCDH15_uc010qhw.1_Intron|PCDH15_uc010qhx.1_Intron|PCDH15_uc010qhy.1_Intron|PCDH15_uc010qhz.1_Intron|PCDH15_uc010qia.1_Intron|PCDH15_uc010qib.1_Intron	NM_033056	NP_149045			protocadherin 15 isoform CD1-4 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	56564319	56564319	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:56564319delA	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	57191843	57191844	+	Intron	DEL	AC	-	-	rs72011193		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:57191843_57191844delAC	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	57501419	57501419	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:57501419delA								PCDH15 (113717 upstream) : ZWINT (615780 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	58290379	58290380	+	IGR	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:58290379_58290380delAA								ZWINT (169345 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	58931140	58931140	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:58931140delA								ZWINT (810106 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	59819417	59819417	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:59819417delA								None (None upstream) : IPMK (136201 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	59905136	59905136	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:59905136delA								None (None upstream) : IPMK (50482 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	59948921	59948922	+	IGR	INS	-	A	A	rs139449732	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:59948921_59948922insA								None (None upstream) : IPMK (6696 downstream)																																			---	---	---	---
CCDC6	8030	broad.mit.edu	37	10	61657015	61657016	+	Intron	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:61657015_61657016delTT	uc001jks.3	-							NM_005436	NP_005427			coiled-coil domain containing 6							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	61804842	61804842	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:61804842delA	uc001jky.2	-						ANK3_uc001jkw.2_Intron|ANK3_uc009xpa.2_Intron|ANK3_uc001jkx.2_Intron|ANK3_uc010qih.1_Intron|ANK3_uc001jkz.3_Intron|ANK3_uc001jkv.2_Intron	NM_020987	NP_066267			ankyrin 3 isoform 1						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	61958418	61958418	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:61958418delA	uc001jky.2	-						ANK3_uc010qih.1_Intron|ANK3_uc001jkz.3_Intron|ANK3_uc001jlb.1_Intron|ANK3_uc001jlc.1_Intron	NM_020987	NP_066267			ankyrin 3 isoform 1						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	61960082	61960082	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:61960082delA	uc001jky.2	-						ANK3_uc010qih.1_Intron|ANK3_uc001jkz.3_Intron|ANK3_uc001jlb.1_Intron|ANK3_uc001jlc.1_Intron	NM_020987	NP_066267			ankyrin 3 isoform 1						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	62445155	62445155	+	Intron	DEL	A	-	-	rs78361999		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:62445155delA	uc001jkz.3	-							NM_001149	NP_001140			ankyrin 3 isoform 2						establishment of protein localization|signal transduction	basolateral plasma membrane|cytoplasm|cytoskeleton	protein binding			skin(9)|ovary(6)|pancreas(2)|central_nervous_system(2)	19																		---	---	---	---
Unknown	0	broad.mit.edu	37	10	62505240	62505240	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:62505240delA								ANK3 (12085 upstream) : CDK1 (32883 downstream)																																			---	---	---	---
CDK1	983	broad.mit.edu	37	10	62537225	62537225	+	5'Flank	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:62537225delA	uc001jld.2	+						CDK1_uc010qii.1_5'Flank|CDK1_uc001jle.2_5'Flank|CDK1_uc001jlf.2_5'Flank|CDK1_uc001jlg.2_5'Flank	NM_001786	NP_001777			cell division cycle 2 isoform 1						activation of MAPK activity|activation of MAPKK activity|anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|anti-apoptosis|axon guidance|cell division|epidermal growth factor receptor signaling pathway|innate immune response|insulin receptor signaling pathway|mitosis|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|nerve growth factor receptor signaling pathway|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|protein localization to kinetochore|Ras protein signal transduction|regulation of transcription involved in G1/S phase of mitotic cell cycle|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|midbody|nucleoplasm|spindle microtubule	ATP binding|cyclin-dependent protein kinase activity|RNA polymerase II carboxy-terminal domain kinase activity			ovary(1)	1																		---	---	---	---
CDK1	983	broad.mit.edu	37	10	62539146	62539146	+	Intron	DEL	T	-	-	rs113107747		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:62539146delT	uc001jld.2	+						CDK1_uc010qii.1_Intron|CDK1_uc001jle.2_Intron|CDK1_uc001jlf.2_Intron|CDK1_uc001jlg.2_5'Flank	NM_001786	NP_001777			cell division cycle 2 isoform 1						activation of MAPK activity|activation of MAPKK activity|anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|anti-apoptosis|axon guidance|cell division|epidermal growth factor receptor signaling pathway|innate immune response|insulin receptor signaling pathway|mitosis|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|nerve growth factor receptor signaling pathway|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|protein localization to kinetochore|Ras protein signal transduction|regulation of transcription involved in G1/S phase of mitotic cell cycle|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|midbody|nucleoplasm|spindle microtubule	ATP binding|cyclin-dependent protein kinase activity|RNA polymerase II carboxy-terminal domain kinase activity			ovary(1)	1																		---	---	---	---
RHOBTB1	9886	broad.mit.edu	37	10	62726063	62726063	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:62726063delA	uc001jlj.2	-						RHOBTB1_uc001jlk.2_Intron|RHOBTB1_uc001jlm.2_Intron	NM_014836	NP_055651			Rho-related BTB domain containing 1						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)																	---	---	---	---
Unknown	0	broad.mit.edu	37	10	63232695	63232695	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:63232695delA	uc001jlr.2	+											Homo sapiens, clone IMAGE:5222445, mRNA.																														---	---	---	---
ARID5B	84159	broad.mit.edu	37	10	63658541	63658542	+	5'Flank	INS	-	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:63658541_63658542insG	uc001jlt.1	+						ARID5B_uc010qil.1_5'Flank	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)																	---	---	---	---
ARID5B	84159	broad.mit.edu	37	10	63849081	63849082	+	Intron	DEL	TT	-	-	rs147430423	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:63849081_63849082delTT	uc001jlt.1	+							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)																	---	---	---	---
RTKN2	219790	broad.mit.edu	37	10	64022583	64022583	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:64022583delA	uc001jlw.2	-						ZNF365_uc001jly.3_Intron|RTKN2_uc001jlx.2_Intron	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	64425757	64425757	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:64425757delA	uc001jmd.1	+						ZNF365_uc001jmc.2_Intron|ZNF365_uc001jme.1_Intron|ZNF365_uc001jmf.1_Intron|ZNF365_uc009xpg.1_Intron	NM_199452	NP_955524			zinc finger protein 365 isoform D											ovary(1)|skin(1)	2	Prostate(12;0.0297)|all_hematologic(501;0.228)																	---	---	---	---
Unknown	0	broad.mit.edu	37	10	64811128	64811128	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:64811128delA								EGR2 (232201 upstream) : NRBF2 (81879 downstream)																																			---	---	---	---
NRBF2	29982	broad.mit.edu	37	10	64898244	64898247	+	Intron	DEL	AAAA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:64898244_64898247delAAAA	uc001jmj.3	+						NRBF2_uc010qip.1_Intron	NM_030759	NP_110386			nuclear receptor binding factor 2						regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor|transcription, DNA-dependent	cytoplasm|nucleoplasm	protein binding				0	Prostate(12;0.0119)|all_hematologic(501;0.191)																	---	---	---	---
JMJD1C	221037	broad.mit.edu	37	10	64952210	64952210	+	Intron	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:64952210delC	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_5'Flank	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)																	---	---	---	---
Unknown	0	broad.mit.edu	37	10	65630679	65630680	+	IGR	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:65630679_65630680delTT								REEP3 (248708 upstream) : ANXA2P3 (954605 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	65637612	65637612	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:65637612delT	uc001jmu.1	-											full-length cDNA clone CS0DI034YJ20 of Placenta Cot 25-normalized of Homo sapiens (human).																														---	---	---	---
Unknown	0	broad.mit.edu	37	10	66115472	66115475	+	IGR	DEL	TATT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:66115472_66115475delTATT								REEP3 (733501 upstream) : ANXA2P3 (469810 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	67222011	67222011	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:67222011delT								ANXA2P3 (635377 upstream) : CTNNA3 (457714 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	67518241	67518243	+	IGR	DEL	AAA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:67518241_67518243delAAA								ANXA2P3 (931607 upstream) : CTNNA3 (161482 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	67608599	67608599	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:67608599delA								None (None upstream) : CTNNA3 (71126 downstream)																																			---	---	---	---
CTNNA3	29119	broad.mit.edu	37	10	67816873	67816873	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:67816873delT	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	68148971	68148971	+	Intron	DEL	T	-	-	rs2441723	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:68148971delT	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	68462053	68462053	+	Intron	DEL	T	-	-	rs77063480		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:68462053delT	uc009xpn.1	-						CTNNA3_uc001jmw.2_Intron|CTNNA3_uc001jmx.3_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	68715640	68715640	+	Intron	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:68715640delG	uc009xpn.1	-						CTNNA3_uc001jmw.2_Intron|CTNNA3_uc001jmx.3_Intron|CTNNA3_uc009xpo.1_Intron|LRRTM3_uc001jmz.1_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	68729855	68729855	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:68729855delA	uc009xpn.1	-						CTNNA3_uc001jmw.2_Intron|CTNNA3_uc001jmx.3_Intron|CTNNA3_uc009xpo.1_Intron|LRRTM3_uc001jmz.1_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	68825697	68825698	+	Intron	DEL	AA	-	-	rs67792149		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:68825697_68825698delAA	uc009xpn.1	-						CTNNA3_uc001jmw.2_Intron|CTNNA3_uc001jmx.3_Intron|CTNNA3_uc009xpo.1_Intron|LRRTM3_uc001jmz.1_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	68872382	68872382	+	Intron	DEL	T	-	-	rs71938524		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:68872382delT	uc009xpn.1	-						CTNNA3_uc001jmw.2_Intron|CTNNA3_uc001jmx.3_Intron|CTNNA3_uc009xpo.1_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	69101054	69101054	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:69101054delT	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																		---	---	---	---
CTNNA3	29119	broad.mit.edu	37	10	69166870	69166871	+	Intron	INS	-	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:69166870_69166871insA	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																		---	---	---	---
MYPN	84665	broad.mit.edu	37	10	69928583	69928583	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:69928583delA	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	70110477	70110477	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:70110477delT	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																		---	---	---	---
RUFY2	55680	broad.mit.edu	37	10	70147115	70147115	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:70147115delA	uc001job.2	-						RUFY2_uc001jnz.1_Intron|RUFY2_uc001joc.2_Intron|RUFY2_uc010qiw.1_Intron|RUFY2_uc001jod.1_Intron|RUFY2_uc009xpv.1_Intron	NM_017987	NP_060457			RUN and FYVE domain-containing 2 isoform a							nucleus	metal ion binding			ovary(1)	1																		---	---	---	---
DNA2	1763	broad.mit.edu	37	10	70187111	70187111	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:70187111delA	uc001jof.2	-						DNA2_uc001jog.1_Intron|DNA2_uc001joh.1_Intron	NM_001080449	NP_001073918			DNA replication helicase 2 homolog						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																		---	---	---	---
Unknown	0	broad.mit.edu	37	10	70304123	70304124	+	IGR	DEL	TT	-	-	rs71716010		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:70304123_70304124delTT								SLC25A16 (16539 upstream) : TET1 (15993 downstream)																																			---	---	---	---
TET1	80312	broad.mit.edu	37	10	70434912	70434912	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:70434912delA	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																		---	---	---	---
CCAR1	55749	broad.mit.edu	37	10	70478992	70478992	+	5'Flank	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:70478992delA	uc001joo.2	+						CCAR1_uc001jol.1_5'Flank|CCAR1_uc001jom.1_5'Flank|CCAR1_uc009xpx.1_5'Flank|CCAR1_uc001jon.1_5'Flank|CCAR1_uc010qiz.1_5'Flank|CCAR1_uc010qja.1_5'Flank|CCAR1_uc010qjb.1_5'Flank	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																		---	---	---	---
CCAR1	55749	broad.mit.edu	37	10	70482404	70482404	+	Intron	DEL	G	-	-	rs58074554	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:70482404delG	uc001joo.2	+						CCAR1_uc001jol.1_Intron|CCAR1_uc001jom.1_Intron|CCAR1_uc009xpx.1_Intron|CCAR1_uc001jon.1_Intron|CCAR1_uc010qiz.1_Intron|CCAR1_uc010qja.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																		---	---	---	---
STOX1	219736	broad.mit.edu	37	10	70604866	70604866	+	Intron	DEL	C	-	-	rs10998458	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:70604866delC	uc001jos.2	+						STOX1_uc001jor.2_Intron|STOX1_uc009xpy.2_Intron|STOX1_uc001joq.2_Intron	NM_001130161	NP_001123633			storkhead box 1 isoform a							cytoplasm|nucleolus	DNA binding			kidney(1)|skin(1)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	10	70806094	70806094	+	IGR	DEL	T	-	-	rs80276509		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:70806094delT								KIAA1279 (29360 upstream) : SRGN (41734 downstream)																																			---	---	---	---
VPS26A	9559	broad.mit.edu	37	10	70908838	70908838	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:70908838delT	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																		---	---	---	---
HK1	3098	broad.mit.edu	37	10	71028204	71028204	+	5'Flank	DEL	A	-	-	rs34941976		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:71028204delA	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																		---	---	---	---
Unknown	0	broad.mit.edu	37	10	71416454	71416455	+	IGR	DEL	GA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:71416454_71416455delGA								C10orf35 (23107 upstream) : COL13A1 (145189 downstream)																																			---	---	---	---
COL13A1	1305	broad.mit.edu	37	10	71708097	71708098	+	Intron	INS	-	T	T	rs145869018	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:71708097_71708098insT	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	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)													---	---	---	---
KIAA1274	27143	broad.mit.edu	37	10	72245966	72245969	+	Intron	DEL	TTTT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:72245966_72245969delTTTT	uc001jrd.3	+							NM_014431	NP_055246			KIAA1274											ovary(2)|central_nervous_system(1)	3																		---	---	---	---
ADAMTS14	140766	broad.mit.edu	37	10	72471218	72471218	+	Intron	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:72471218delC	uc001jrh.2	+						ADAMTS14_uc001jrg.2_Intron	NM_080722	NP_542453			ADAM metallopeptidase with thrombospondin type 1						collagen catabolic process|proteolysis	proteinaceous extracellular matrix	metalloendopeptidase activity|zinc ion binding			ovary(5)|upper_aerodigestive_tract(1)	6																		---	---	---	---
ADAMTS14	140766	broad.mit.edu	37	10	72520048	72520048	+	Intron	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:72520048delG	uc001jrh.2	+						ADAMTS14_uc001jrg.2_Intron	NM_080722	NP_542453			ADAM metallopeptidase with thrombospondin type 1						collagen catabolic process|proteolysis	proteinaceous extracellular matrix	metalloendopeptidase activity|zinc ion binding			ovary(5)|upper_aerodigestive_tract(1)	6																		---	---	---	---
SGPL1	8879	broad.mit.edu	37	10	72599676	72599676	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:72599676delA	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	72759349	72759350	+	IGR	DEL	TG	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:72759349_72759350delTG								PCBD1 (110808 upstream) : UNC5B (212948 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	72787550	72787550	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:72787550delA								PCBD1 (139009 upstream) : UNC5B (184748 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	72813372	72813372	+	IGR	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:72813372delC								PCBD1 (164831 upstream) : UNC5B (158926 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	72856018	72856019	+	IGR	DEL	GT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:72856018_72856019delGT								PCBD1 (207477 upstream) : UNC5B (116279 downstream)																																			---	---	---	---
C10orf54	64115	broad.mit.edu	37	10	73510204	73510204	+	3'UTR	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:73510204delG	uc001jsd.2	-	7					CDH23_uc001jrx.3_Intron|C10orf54_uc001jse.2_3'UTR|C10orf54_uc009xqm.2_3'UTR	NM_022153	NP_071436			platelet receptor Gi24 precursor							integral to membrane	receptor activity			ovary(1)|breast(1)|central_nervous_system(1)	3																		---	---	---	---
CDH23	64072	broad.mit.edu	37	10	73566233	73566233	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:73566233delA	uc001jrx.3	+						CDH23_uc001jsg.3_Intron|CDH23_uc001jsh.3_Intron|CDH23_uc001jsi.3_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																		---	---	---	---
ASCC1	51008	broad.mit.edu	37	10	73887716	73887716	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:73887716delA	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																		---	---	---	---
ASCC1	51008	broad.mit.edu	37	10	73940733	73940733	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:73940733delT	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																		---	---	---	---
CCDC109A	90550	broad.mit.edu	37	10	74528777	74528778	+	Intron	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:74528777_74528778delTT	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)																	---	---	---	---
OIT3	170392	broad.mit.edu	37	10	74653469	74653469	+	5'UTR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:74653469delA	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)																	---	---	---	---
P4HA1	5033	broad.mit.edu	37	10	74813675	74813677	+	Intron	DEL	TTT	-	-	rs112306423		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:74813675_74813677delTTT	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)													---	---	---	---
TTC18	118491	broad.mit.edu	37	10	75063350	75063350	+	Intron	DEL	A	-	-	rs113319202		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:75063350delA	uc009xrc.2	-						TTC18_uc001jty.2_Intron|TTC18_uc009xrd.1_Intron	NM_145170	NP_660153			tetratricopeptide repeat domain 18								binding			ovary(2)|central_nervous_system(1)	3	Prostate(51;0.0119)																	---	---	---	---
USP54	159195	broad.mit.edu	37	10	75281774	75281774	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:75281774delA	uc001juo.2	-						USP54_uc010qkk.1_Intron|USP54_uc001juk.2_Intron|USP54_uc001jul.2_Intron|USP54_uc001jum.2_Intron|USP54_uc001jun.2_Intron|USP54_uc001jup.2_Intron	NM_152586	NP_689799			ubiquitin specific peptidase 54						ubiquitin-dependent protein catabolic process		protein binding|ubiquitin thiolesterase activity			breast(3)|lung(2)|kidney(1)	6	Prostate(51;0.0112)																	---	---	---	---
KIAA0913	23053	broad.mit.edu	37	10	75550607	75550607	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:75550607delA	uc009xrl.2	+						KIAA0913_uc001jve.2_Intron|KIAA0913_uc001jvf.2_Intron|KIAA0913_uc001jvh.2_5'Flank|KIAA0913_uc001jvi.2_5'Flank|KIAA0913_uc010qkr.1_5'Flank|KIAA0913_uc001jvj.2_5'Flank	NM_015037	NP_055852			hypothetical protein LOC23053								zinc ion binding			breast(1)	1	Prostate(51;0.0112)																	---	---	---	---
CAMK2G	818	broad.mit.edu	37	10	75626224	75626224	+	Intron	DEL	A	-	-	rs34839580		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:75626224delA	uc001jvv.1	-						CAMK2G_uc001jvm.1_Intron|CAMK2G_uc001jvo.1_Intron|CAMK2G_uc001jvq.1_Intron|CAMK2G_uc001jvr.1_Intron|CAMK2G_uc001jvp.1_Intron|CAMK2G_uc001jvs.1_Intron|CAMK2G_uc001jvt.1_Intron|CAMK2G_uc001jvu.1_Intron|CAMK2G_uc010qkv.1_Intron	NM_172171	NP_751911			calcium/calmodulin-dependent protein kinase II						insulin secretion|interferon-gamma-mediated signaling pathway|synaptic transmission	calcium- and calmodulin-dependent protein kinase complex|cytosol|endocytic vesicle membrane|nucleoplasm|plasma membrane	ATP binding|calcium-dependent protein serine/threonine phosphatase activity|calmodulin binding|calmodulin-dependent protein kinase activity			lung(1)|stomach(1)	2	Prostate(51;0.0112)																	---	---	---	---
CAMK2G	818	broad.mit.edu	37	10	75630925	75630927	+	Intron	DEL	AAA	-	-	rs113182710		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:75630925_75630927delAAA	uc001jvv.1	-						CAMK2G_uc001jvm.1_Intron|CAMK2G_uc001jvo.1_Intron|CAMK2G_uc001jvq.1_Intron|CAMK2G_uc001jvr.1_Intron|CAMK2G_uc001jvp.1_Intron|CAMK2G_uc001jvs.1_Intron|CAMK2G_uc001jvt.1_Intron|CAMK2G_uc001jvu.1_Intron|CAMK2G_uc010qkv.1_Intron	NM_172171	NP_751911			calcium/calmodulin-dependent protein kinase II						insulin secretion|interferon-gamma-mediated signaling pathway|synaptic transmission	calcium- and calmodulin-dependent protein kinase complex|cytosol|endocytic vesicle membrane|nucleoplasm|plasma membrane	ATP binding|calcium-dependent protein serine/threonine phosphatase activity|calmodulin binding|calmodulin-dependent protein kinase activity			lung(1)|stomach(1)	2	Prostate(51;0.0112)																	---	---	---	---
Unknown	0	broad.mit.edu	37	10	75711838	75711838	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:75711838delT								C10orf55 (29303 upstream) : VCL (43113 downstream)																																			---	---	---	---
AP3M1	26985	broad.mit.edu	37	10	75905982	75905983	+	Intron	INS	-	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:75905982_75905983insG	uc001jwf.2	-						AP3M1_uc001jwg.2_Intron|AP3M1_uc001jwh.2_Intron|AP3M1_uc010qla.1_Intron	NM_207012	NP_996895			adaptor-related protein complex 3, mu 1 subunit						protein targeting to lysosome|vesicle-mediated transport	clathrin adaptor complex|Golgi apparatus|lysosome	protein binding				0	Prostate(51;0.0112)																	---	---	---	---
Unknown	0	broad.mit.edu	37	10	76543565	76543565	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:76543565delA								ADK (74506 upstream) : MYST4 (42814 downstream)																																			---	---	---	---
MYST4	23522	broad.mit.edu	37	10	76700037	76700040	+	Intron	DEL	TTTT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:76700037_76700040delTTTT	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	76787933	+	Intron	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:76787932_76787933delTT	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								---	---	---	---
SAMD8	142891	broad.mit.edu	37	10	76894397	76894397	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:76894397delA	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)																	---	---	---	---
Unknown	0	broad.mit.edu	37	10	76960329	76960329	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:76960329delT								SAMD8 (23722 upstream) : VDAC2 (10234 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	77231932	77231932	+	IGR	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:77231932delC								C10orf41 (63193 upstream) : MIR606 (80284 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	77293539	77293540	+	IGR	DEL	GA	-	-	rs146089151	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:77293539_77293540delGA								C10orf41 (124800 upstream) : MIR606 (18676 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	77307859	77307861	+	IGR	DEL	AAA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:77307859_77307861delAAA								C10orf41 (139120 upstream) : MIR606 (4355 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	77523132	77523133	+	IGR	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:77523132_77523133delAA								MIR606 (210821 upstream) : C10orf11 (19386 downstream)																																			---	---	---	---
C10orf11	83938	broad.mit.edu	37	10	77559592	77559592	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:77559592delT	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	77632059	77632059	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:77632059delT	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	77732307	77732307	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:77732307delT	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	78387624	78387624	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:78387624delT								C10orf11 (70500 upstream) : KCNMA1 (241735 downstream)																																			---	---	---	---
KCNMA1	3778	broad.mit.edu	37	10	78828579	78828579	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:78828579delA	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	78853394	78853395	+	Intron	INS	-	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:78853394_78853395insA	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)													---	---	---	---
DLG5	9231	broad.mit.edu	37	10	79624230	79624230	+	Intron	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:79624230delC	uc001jzk.2	-						DLG5_uc009xru.1_Intron|uc001jzm.1_5'Flank	NM_004747	NP_004738			discs large homolog 5						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)															---	---	---	---
Unknown	0	broad.mit.edu	37	10	79908105	79908105	+	IGR	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:79908105delC								RPS24 (91535 upstream) : LOC283050 (794979 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	80000136	80000136	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:80000136delT								RPS24 (183566 upstream) : LOC283050 (702948 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	80093630	80093630	+	Intron	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:80093630delG	uc010qlp.1	+						uc001jzw.1_Intron					SubName: Full=cDNA FLJ57363;																														---	---	---	---
LOC283050	283050	broad.mit.edu	37	10	80736243	80736243	+	Intron	DEL	T	-	-	rs67154338		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:80736243delT	uc001jzz.2	-						LOC283050_uc001jzx.2_Intron|LOC283050_uc001jzy.2_Intron	NR_024431				Homo sapiens cDNA FLJ40604 fis, clone THYMU2011806.												0																		---	---	---	---
LOC283050	283050	broad.mit.edu	37	10	80756281	80756282	+	Intron	INS	-	C	C	rs142929405	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:80756281_80756282insC	uc001jzz.2	-						LOC283050_uc001jzx.2_Intron|LOC283050_uc001jzy.2_Intron	NR_024431				Homo sapiens cDNA FLJ40604 fis, clone THYMU2011806.												0																		---	---	---	---
PPIF	10105	broad.mit.edu	37	10	81113328	81113329	+	Intron	INS	-	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:81113328_81113329insG	uc001kai.2	+						PPIF_uc001kaj.2_Intron	NM_005729	NP_005720			peptidylprolyl isomerase F precursor						protein folding	membrane fraction|mitochondrial matrix	peptidyl-prolyl cis-trans isomerase activity			skin(1)	1	all_cancers(46;0.0893)|Breast(12;8.52e-05)|all_epithelial(25;0.00449)|Prostate(51;0.00985)		Epithelial(14;0.00242)|all cancers(16;0.0069)|Colorectal(32;0.229)		Dimethyl sulfoxide(DB01093)|L-Proline(DB00172)													---	---	---	---
Unknown	0	broad.mit.edu	37	10	81231642	81231642	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:81231642delA								ZCCHC24 (26259 upstream) : EIF5AL1 (40715 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	81323401	81323402	+	IGR	DEL	AC	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:81323401_81323402delAC								SFTPA2 (3238 upstream) : SFTPA1 (47310 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	81379238	81379240	+	IGR	DEL	TTG	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:81379238_81379240delTTG								SFTPA1 (4037 upstream) : LOC650623 (63491 downstream)																																			---	---	---	---
LOC219347	219347	broad.mit.edu	37	10	81830734	81830734	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:81830734delA	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																		---	---	---	---
C10orf57	80195	broad.mit.edu	37	10	81841422	81841422	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:81841422delA	uc001kbl.2	+						LOC219347_uc001kbk.2_5'Flank|LOC219347_uc001kbi.3_5'Flank|LOC219347_uc009xsk.2_5'Flank|LOC219347_uc009xsl.2_5'Flank|LOC219347_uc009xsm.2_5'Flank|LOC219347_uc001kbj.3_5'Flank|C10orf57_uc009xsn.2_Frame_Shift_Del_p.S38fs|C10orf57_uc010qlv.1_Intron|C10orf57_uc010qlw.1_Intron|C10orf57_uc001kbn.3_RNA|C10orf57_uc009xsp.2_RNA|C10orf57_uc001kbo.3_Intron	NM_025125	NP_079401			hypothetical protein LOC80195							integral to membrane					0	Prostate(51;0.0095)|all_epithelial(25;0.175)		Epithelial(14;0.0793)|Colorectal(32;0.109)|all cancers(16;0.154)															---	---	---	---
PLAC9	219348	broad.mit.edu	37	10	81899976	81899977	+	Intron	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:81899976_81899977delAA	uc001kbp.1	+							NM_001012973	NP_001012991			placenta-specific 9 precursor							extracellular region					0	Prostate(51;0.0095)|all_epithelial(25;0.175)		Colorectal(32;0.109)															---	---	---	---
Unknown	0	broad.mit.edu	37	10	82095804	82095804	+	IGR	DEL	A	-	-	rs72815321	byFrequency;by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:82095804delA								MAT1A (46370 upstream) : DYDC1 (60 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	82597968	82597968	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:82597968delT								SH2D4B (191652 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	82693378	82693378	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:82693378delA								SH2D4B (287062 upstream) : NRG3 (941692 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	82856196	82856196	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:82856196delT								SH2D4B (449880 upstream) : NRG3 (778874 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	82927620	82927620	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:82927620delT								SH2D4B (521304 upstream) : NRG3 (707450 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	83149603	83149604	+	IGR	INS	-	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:83149603_83149604insT								SH2D4B (743287 upstream) : NRG3 (485466 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	83296293	83296293	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:83296293delT								SH2D4B (889977 upstream) : NRG3 (338777 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	83357597	83357597	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:83357597delA								SH2D4B (951281 upstream) : NRG3 (277473 downstream)																																			---	---	---	---
NRG3	10718	broad.mit.edu	37	10	83841129	83841130	+	Intron	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:83841129_83841130delTT	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	84348260	84348260	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:84348260delT	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	84673873	84673874	+	Intron	INS	-	T	T	rs142606522	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:84673873_84673874insT	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	85044415	85044415	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:85044415delA								NRG3 (297480 upstream) : GHITM (854770 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	85104145	85104145	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:85104145delT								NRG3 (357210 upstream) : GHITM (795040 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	85924085	85924085	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:85924085delA								GHITM (10774 upstream) : C10orf99 (9469 downstream)																																			---	---	---	---
CDHR1	92211	broad.mit.edu	37	10	85970001	85970001	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:85970001delT	uc001kcv.2	+						CDHR1_uc001kcw.2_Intron|CDHR1_uc009xst.2_Intron|CDHR1_uc001kcx.2_5'Flank	NM_033100	NP_149091			protocadherin 21 precursor						homophilic cell adhesion		calcium ion binding|receptor activity			ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	10	86024448	86024448	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:86024448delA								RGR (5504 upstream) : FAM190B (63962 downstream)																																	OREG0020336	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
FAM190B	54462	broad.mit.edu	37	10	86144760	86144761	+	Intron	INS	-	AC	AC			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:86144760_86144761insAC	uc001kdh.1	+						FAM190B_uc010qmd.1_Intron	NM_018999	NP_061872			granule cell antiserum positive 14											ovary(3)|skin(1)	4																		---	---	---	---
Unknown	0	broad.mit.edu	37	10	86307997	86307997	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:86307997delT								FAM190B (29721 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	86525159	86525160	+	IGR	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:86525159_86525160delTT								FAM190B (246883 upstream) : GRID1 (834152 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	86532817	86532817	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:86532817delT								FAM190B (254541 upstream) : GRID1 (826495 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	87049850	87049851	+	IGR	INS	-	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:87049850_87049851insA								FAM190B (771574 upstream) : GRID1 (309461 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	87216556	87216557	+	IGR	INS	-	TG	TG	rs138320897	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:87216556_87216557insTG								FAM190B (938280 upstream) : GRID1 (142755 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	87317547	87317547	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:87317547delA								None (None upstream) : GRID1 (41765 downstream)																																			---	---	---	---
GRID1	2894	broad.mit.edu	37	10	87876870	87876871	+	Intron	INS	-	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:87876870_87876871insA	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)			---	---	---	---
GRID1	2894	broad.mit.edu	37	10	88086224	88086224	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:88086224delA	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	88241608	88241608	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:88241608delA	uc001kdo.2	-						WAPAL_uc001kdn.2_Intron|WAPAL_uc009xsw.2_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																		---	---	---	---
Unknown	0	broad.mit.edu	37	10	88356715	88356715	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:88356715delT								WAPAL (75174 upstream) : OPN4 (57599 downstream)																																			---	---	---	---
BMPR1A	657	broad.mit.edu	37	10	88513557	88513557	+	5'Flank	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:88513557delG	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				---	---	---	---
Unknown	0	broad.mit.edu	37	10	88959804	88959806	+	IGR	DEL	AAA	-	-	rs72014147		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:88959804_88959806delAAA								FAM35A (8584 upstream) : LOC728190 (5739 downstream)																																			---	---	---	---
LOC728190	728190	broad.mit.edu	37	10	88998040	88998040	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:88998040delT	uc009xtc.2	-						LOC728190_uc009xtd.2_Intron					Homo sapiens cDNA FLJ34397 fis, clone HCHON2001110.												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	10	89149251	89149252	+	IGR	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:89149251_89149252delTT								FAM22D (18799 upstream) : MINPP1 (114971 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	89175515	89175516	+	IGR	INS	-	ATAC	ATAC	rs148340360	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:89175515_89175516insATAC								FAM22D (45063 upstream) : MINPP1 (88707 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	89330604	89330605	+	IGR	INS	-	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:89330604_89330605insA								MINPP1 (17436 upstream) : PAPSS2 (88871 downstream)																																			---	---	---	---
PAPSS2	9060	broad.mit.edu	37	10	89422638	89422638	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:89422638delT	uc001kex.2	+						PAPSS2_uc001kew.2_Intron|PAPSS2_uc009xtg.1_Intron	NM_004670	NP_004661			3'-phosphoadenosine 5'-phosphosulfate synthase 2						3'-phosphoadenosine 5'-phosphosulfate biosynthetic process|skeletal system development|sulfate assimilation|xenobiotic metabolic process	cytosol	adenylylsulfate kinase activity|ATP binding|protein binding|sulfate adenylyltransferase (ATP) activity			central_nervous_system(1)|skin(1)	2		Melanoma(5;0.019)|Colorectal(252;0.123)		UCEC - Uterine corpus endometrioid carcinoma (6;0.00164)|Colorectal(12;0.000323)|COAD - Colon adenocarcinoma(12;0.00124)														---	---	---	---
CFLP1	142913	broad.mit.edu	37	10	89583981	89583981	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:89583981delA	uc001kfa.2	+											Homo sapiens cofilin pseudogene 1, mRNA (cDNA clone IMAGE:5168640).												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	10	89797434	89797434	+	IGR	DEL	T	-	-	rs72300036		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:89797434delT								PTEN (68903 upstream) : RNLS (94623 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	89798680	89798683	+	IGR	DEL	TTTT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:89798680_89798683delTTTT								PTEN (70149 upstream) : RNLS (93374 downstream)																																			---	---	---	---
ANKRD22	118932	broad.mit.edu	37	10	90585659	90585659	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:90585659delA	uc001kfj.3	-							NM_144590	NP_653191			ankyrin repeat domain 22												0		Colorectal(252;0.0163)		Colorectal(12;6.29e-05)|COAD - Colon adenocarcinoma(12;7.69e-05)														---	---	---	---
STAMBPL1	57559	broad.mit.edu	37	10	90681950	90681950	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:90681950delA	uc001kfk.2	+						STAMBPL1_uc010qmx.1_Intron|STAMBPL1_uc009xto.2_Intron|STAMBPL1_uc001kfl.2_Intron|STAMBPL1_uc001kfn.2_Intron	NM_020799	NP_065850			STAM binding protein-like 1								metal ion binding|metallopeptidase activity|protein binding			ovary(1)	1		Colorectal(252;0.0381)		Colorectal(12;6.38e-05)|COAD - Colon adenocarcinoma(12;7.75e-05)														---	---	---	---
Unknown	0	broad.mit.edu	37	10	90918803	90918804	+	IGR	DEL	AG	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:90918803_90918804delAG								FAS (143262 upstream) : CH25H (46892 downstream)																																			---	---	---	---
LIPA	3988	broad.mit.edu	37	10	91059510	91059510	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:91059510delA	uc001kgc.3	-						LIPA_uc001kgb.3_Intron|uc001kgd.2_Intron|IFIT2_uc009xts.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	91279542	91279542	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:91279542delT	uc001kgm.2	-							NM_213606	NP_998771			solute carrier family 16 (monocarboxylic acid							integral to membrane|plasma membrane	symporter activity			skin(1)	1																		---	---	---	---
KIF20B	9585	broad.mit.edu	37	10	91483917	91483917	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:91483917delT	uc001kgs.1	+						KIF20B_uc001kgr.1_Intron|KIF20B_uc001kgt.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	92092563	92092563	+	IGR	DEL	T	-	-	rs11299000		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:92092563delT								KIF20B (557863 upstream) : HTR7 (408015 downstream)																																			---	---	---	---
PCGF5	84333	broad.mit.edu	37	10	93014281	93014281	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:93014281delT	uc001khh.2	+						PCGF5_uc010qnk.1_Intron|PCGF5_uc001khi.2_Intron	NM_032373	NP_115749			polycomb group ring finger 5						regulation of transcription, DNA-dependent|transcription, DNA-dependent	centrosome|PcG protein complex	zinc ion binding			lung(1)	1																		---	---	---	---
PCGF5	84333	broad.mit.edu	37	10	93017251	93017251	+	Intron	DEL	G	-	-	rs150944560		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:93017251delG	uc001khh.2	+						PCGF5_uc010qnk.1_Intron|PCGF5_uc001khi.2_Intron	NM_032373	NP_115749			polycomb group ring finger 5						regulation of transcription, DNA-dependent|transcription, DNA-dependent	centrosome|PcG protein complex	zinc ion binding			lung(1)	1																		---	---	---	---
TNKS2	80351	broad.mit.edu	37	10	93572113	93572113	+	Intron	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:93572113delC	uc001khp.2	+							NM_025235	NP_079511			tankyrase, TRF1-interacting ankyrin-related						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	93600113	93600113	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:93600113delA	uc001khp.2	+							NM_025235	NP_079511			tankyrase, TRF1-interacting ankyrin-related						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	93609253	93609253	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:93609253delT	uc001khp.2	+							NM_025235	NP_079511			tankyrase, TRF1-interacting ankyrin-related						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)																---	---	---	---
BTAF1	9044	broad.mit.edu	37	10	93741816	93741816	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:93741816delT	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	94039693	94039693	+	Intron	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:94039693delG	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	94190455	94190455	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:94190455delA								MARCH5 (76734 upstream) : IDE (23145 downstream)																																			---	---	---	---
IDE	3416	broad.mit.edu	37	10	94296845	94296845	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:94296845delA	uc001kia.2	-							NM_004969	NP_004960			insulin-degrading enzyme isoform 1 precursor						beta-amyloid metabolic process|bradykinin catabolic process|interspecies interaction between organisms|sex differentiation	cell surface|extracellular space|soluble fraction	ATP binding|metalloendopeptidase activity|protein homodimerization activity|signal transducer activity|zinc ion binding			ovary(2)|central_nervous_system(1)	3					Bacitracin(DB00626)|Insulin Glargine recombinant(DB00047)|Insulin Lyspro recombinant(DB00046)|Insulin recombinant(DB00030)|Insulin, porcine(DB00071)													---	---	---	---
IDE	3416	broad.mit.edu	37	10	94302503	94302503	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:94302503delA	uc001kia.2	-							NM_004969	NP_004960			insulin-degrading enzyme isoform 1 precursor						beta-amyloid metabolic process|bradykinin catabolic process|interspecies interaction between organisms|sex differentiation	cell surface|extracellular space|soluble fraction	ATP binding|metalloendopeptidase activity|protein homodimerization activity|signal transducer activity|zinc ion binding			ovary(2)|central_nervous_system(1)	3					Bacitracin(DB00626)|Insulin Glargine recombinant(DB00047)|Insulin Lyspro recombinant(DB00046)|Insulin recombinant(DB00030)|Insulin, porcine(DB00071)													---	---	---	---
Unknown	0	broad.mit.edu	37	10	94516096	94516096	+	IGR	DEL	T	-	-	rs72073496		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:94516096delT								HHEX (60690 upstream) : EXOC6 (74839 downstream)																																			---	---	---	---
EXOC6	54536	broad.mit.edu	37	10	94670968	94670968	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:94670968delT	uc001kig.2	+						EXOC6_uc010qnr.1_Intron|EXOC6_uc001kie.2_Intron|EXOC6_uc009xub.2_Intron|EXOC6_uc009xuc.2_Intron	NM_019053	NP_061926			SEC15-like 1 isoform a						protein transport|vesicle docking involved in exocytosis	exocyst				skin(1)	1		Colorectal(252;0.123)																---	---	---	---
EXOC6	54536	broad.mit.edu	37	10	94818799	94818799	+	3'UTR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:94818799delT	uc001kig.2	+	22					EXOC6_uc010qnr.1_3'UTR|EXOC6_uc001kie.2_3'UTR|EXOC6_uc009xub.2_3'UTR|EXOC6_uc009xuc.2_3'UTR|EXOC6_uc001kih.2_RNA|EXOC6_uc001kii.2_3'UTR|CYP26C1_uc010qns.1_5'Flank|CYP26C1_uc009xud.2_5'Flank	NM_019053	NP_061926			SEC15-like 1 isoform a						protein transport|vesicle docking involved in exocytosis	exocyst				skin(1)	1		Colorectal(252;0.123)																---	---	---	---
Unknown	0	broad.mit.edu	37	10	94861587	94861587	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:94861587delT								CYP26A1 (23946 upstream) : MYOF (204600 downstream)																																			---	---	---	---
MYOF	26509	broad.mit.edu	37	10	95115765	95115765	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:95115765delA	uc001kin.2	-						MYOF_uc001kio.2_Intron|MYOF_uc009xue.2_Intron	NM_013451	NP_038479			myoferlin isoform a						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	95201148	95201150	+	Intron	DEL	TTT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:95201148_95201150delTTT	uc001kin.2	-						MYOF_uc001kio.2_Intron|MYOF_uc001kip.3_Intron|MYOF_uc009xuf.2_Intron	NM_013451	NP_038479			myoferlin isoform a						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	95215432	95215432	+	Intron	DEL	A	-	-	rs114363550	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:95215432delA	uc001kin.2	-						MYOF_uc001kio.2_Intron|MYOF_uc001kip.3_Intron|MYOF_uc009xuf.2_Intron	NM_013451	NP_038479			myoferlin isoform a						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																		---	---	---	---
C10orf4	118924	broad.mit.edu	37	10	95436266	95436266	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:95436266delT	uc001kiz.1	-						C10orf4_uc001kiv.1_Intron|C10orf4_uc001kja.1_Intron	NM_145246	NP_660289			FRA10AC1 protein							nucleus	protein binding				0		Colorectal(252;0.122)																---	---	---	---
LGI1	9211	broad.mit.edu	37	10	95549725	95549725	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:95549725delA	uc001kjc.3	+						LGI1_uc010qnv.1_Intron|LGI1_uc001kjd.3_Intron|LGI1_uc009xui.2_Intron|LGI1_uc001kje.2_Intron	NM_005097	NP_005088			leucine-rich, glioma inactivated 1 precursor						axon guidance|cell proliferation|positive regulation of cell growth|positive regulation of synaptic transmission	cell junction|extracellular space|synapse	receptor binding			ovary(2)|central_nervous_system(1)|skin(1)	4		Colorectal(252;0.124)																---	---	---	---
PLCE1	51196	broad.mit.edu	37	10	95790332	95790332	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:95790332delA	uc001kjk.2	+						PLCE1_uc010qnx.1_5'Flank	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)																---	---	---	---
NOC3L	64318	broad.mit.edu	37	10	96094287	96094287	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:96094287delA	uc001kjq.1	-							NM_022451	NP_071896			nucleolar complex associated 3 homolog							nuclear speck|nucleolus	binding			ovary(1)	1		Colorectal(252;0.0897)																---	---	---	---
TBC1D12	23232	broad.mit.edu	37	10	96234262	96234263	+	Intron	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:96234262_96234263delAA	uc001kjr.2	+							NM_015188	NP_056003			TBC1 domain family, member 12							intracellular	Rab GTPase activator activity				0		Colorectal(252;0.0429)																---	---	---	---
Unknown	0	broad.mit.edu	37	10	96749439	96749439	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:96749439delT								CYP2C9 (292 upstream) : CYP2C8 (47091 downstream)																																			---	---	---	---
SORBS1	10580	broad.mit.edu	37	10	97076210	97076211	+	Intron	DEL	AA	-	-	rs71726321		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:97076210_97076211delAA	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	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	97090255	97090255	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:97090255delT	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	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)														---	---	---	---
TCTN3	26123	broad.mit.edu	37	10	97442251	97442251	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:97442251delA	uc001klb.3	-						TCTN3_uc001kla.3_Intron|TCTN3_uc010qoi.1_Intron	NM_015631	NP_056446			tectonic 3 isoform a precursor						apoptosis	integral to membrane					0		Colorectal(252;0.0815)		Epithelial(162;1.69e-07)|all cancers(201;5.63e-06)														---	---	---	---
ENTPD1	953	broad.mit.edu	37	10	97587542	97587542	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:97587542delA	uc001klh.3	+						ENTPD1_uc001kle.1_Intron|ENTPD1_uc001kli.3_Intron|uc001klg.1_Intron|ENTPD1_uc010qoj.1_Intron|ENTPD1_uc010qok.1_Intron|ENTPD1_uc010qol.1_Intron|ENTPD1_uc010qom.1_Intron|ENTPD1_uc010qon.1_Intron|ENTPD1_uc009xva.2_Intron|ENTPD1_uc009xuz.2_Intron	NM_001776	NP_001767			ectonucleoside triphosphate diphosphohydrolase 1						cell adhesion	integral to plasma membrane	ATP binding			ovary(3)	3		Colorectal(252;0.0821)		Epithelial(162;1.31e-07)|all cancers(201;5.33e-06)														---	---	---	---
Unknown	0	broad.mit.edu	37	10	97834837	97834837	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:97834837delT	uc001klg.1	-						uc001klj.1_Intron|uc009xvb.1_Intron					Homo sapiens cDNA FLJ34077 fis, clone FCBBF3003481, weakly similar to ZINC FINGER PROTEIN 195.																														---	---	---	---
BLNK	29760	broad.mit.edu	37	10	97974311	97974311	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:97974311delA	uc001kls.3	-						BLNK_uc001kme.3_Intron|BLNK_uc001klt.3_Intron|BLNK_uc009xvc.2_Intron|BLNK_uc001klu.3_Intron|BLNK_uc001klv.3_Intron|BLNK_uc001klw.3_Intron|BLNK_uc001klx.3_Intron|BLNK_uc001kly.3_Intron|BLNK_uc001klz.3_Intron|BLNK_uc001kma.3_Intron|BLNK_uc001kmb.3_Intron|BLNK_uc001kmc.3_Intron|BLNK_uc001kmd.3_Intron|BLNK_uc009xvd.2_Intron	NM_013314	NP_037446			B-cell linker isoform 1						B cell differentiation|humoral immune response|inflammatory response|intracellular signal transduction	cytoplasm|plasma membrane	SH3/SH2 adaptor activity|transmembrane receptor protein tyrosine kinase adaptor activity			skin(2)	2		Colorectal(252;0.083)		Epithelial(162;7.89e-08)|all cancers(201;2.27e-06)														---	---	---	---
TLL2	7093	broad.mit.edu	37	10	98188564	98188564	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:98188564delT	uc001kml.1	-						TLL2_uc009xvf.1_Intron	NM_012465	NP_036597			tolloid-like 2 precursor						cell differentiation|multicellular organismal development|proteolysis	extracellular region	calcium ion binding|metalloendopeptidase activity|zinc ion binding			ovary(1)|pancreas(1)|skin(1)	3		Colorectal(252;0.0846)		Epithelial(162;1.51e-07)|all cancers(201;7.59e-06)														---	---	---	---
TM9SF3	56889	broad.mit.edu	37	10	98287149	98287150	+	Intron	INS	-	A	A	rs3789958	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:98287149_98287150insA	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)														---	---	---	---
TM9SF3	56889	broad.mit.edu	37	10	98312908	98312908	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:98312908delA	uc001kmm.3	-						TM9SF3_uc010qot.1_Intron|TM9SF3_uc001kmn.1_5'Flank	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)														---	---	---	---
PIK3AP1	118788	broad.mit.edu	37	10	98358183	98358183	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:98358183delT	uc001kmq.2	-						PIK3AP1_uc001kmo.2_Intron|PIK3AP1_uc001kmp.2_Intron	NM_152309	NP_689522			phosphoinositide-3-kinase adaptor protein 1							cytoplasm|plasma membrane				upper_aerodigestive_tract(3)|ovary(1)|skin(1)	5		Colorectal(252;0.0442)		Epithelial(162;6.29e-08)|all cancers(201;3.18e-06)														---	---	---	---
Unknown	0	broad.mit.edu	37	10	98540684	98540684	+	IGR	DEL	T	-	-	rs71966346		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:98540684delT								PIK3AP1 (60405 upstream) : MIR607 (47742 downstream)																																			---	---	---	---
C10orf12	26148	broad.mit.edu	37	10	98667738	98667739	+	Intron	INS	-	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:98667738_98667739insT	uc009xvg.1	+						LCOR_uc001kmr.2_Intron|LCOR_uc001kms.1_Intron|LCOR_uc001kmt.1_Intron|LCOR_uc001kmu.1_Intron	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)														---	---	---	---
MMS19	64210	broad.mit.edu	37	10	99221731	99221731	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-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					---	---	---	---
AVPI1	60370	broad.mit.edu	37	10	99442361	99442361	+	Intron	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:99442361delC	uc001koh.1	-						AVPI1_uc001koi.2_Intron	NM_021732	NP_068378			vasopressin-induced protein, 32kDa						cell cycle					breast(1)	1		Colorectal(252;0.162)		Epithelial(162;8.37e-11)|all cancers(201;7.94e-09)														---	---	---	---
CRTAC1	55118	broad.mit.edu	37	10	99656065	99656065	+	Intron	DEL	T	-	-	rs72364343		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:99656065delT	uc001kou.1	-						CRTAC1_uc001kov.2_Intron|CRTAC1_uc001kot.1_Intron	NM_018058	NP_060528			cartilage acidic protein 1 precursor							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)														---	---	---	---
CRTAC1	55118	broad.mit.edu	37	10	99761307	99761308	+	Intron	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:99761307_99761308delAA	uc001kou.1	-						CRTAC1_uc001kov.2_Intron	NM_018058	NP_060528			cartilage acidic protein 1 precursor							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)														---	---	---	---
Unknown	0	broad.mit.edu	37	10	99847157	99847158	+	IGR	INS	-	G	G	rs150834312	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:99847157_99847158insG								CRTAC1 (56572 upstream) : C10orf28 (47223 downstream)																																			---	---	---	---
C10orf28	27291	broad.mit.edu	37	10	99994585	99994585	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:99994585delT	uc001kow.3	+						C10orf28_uc001kox.3_Intron|C10orf28_uc001koy.3_Intron|C10orf28_uc009xvx.2_Intron|C10orf28_uc009xvy.2_Intron|C10orf28_uc001koz.3_Intron	NM_014472	NP_055287			growth inhibition and differentiation related								nucleotide binding			large_intestine(1)|skin(1)	2		Colorectal(252;0.234)		Epithelial(162;7.18e-11)|all cancers(201;8.75e-09)														---	---	---	---
PYROXD2	84795	broad.mit.edu	37	10	100167268	100167268	+	Intron	DEL	C	-	-	rs140910348	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:100167268delC	uc001kpc.2	-						PYROXD2_uc001kpb.2_Intron|PYROXD2_uc001kpd.2_Intron|PYROXD2_uc010qpe.1_Intron	NM_032709	NP_116098			pyridine nucleotide-disulphide oxidoreductase								oxidoreductase activity			central_nervous_system(1)	1																		---	---	---	---
HPSE2	60495	broad.mit.edu	37	10	100320321	100320321	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:100320321delT	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	100991456	100991456	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:100991456delA	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)														---	---	---	---
ABCC2	1244	broad.mit.edu	37	10	101554309	101554309	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:101554309delT	uc001kqf.2	+							NM_000392	NP_000383			ATP-binding cassette, sub-family C (CFTR/MRP),							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)													---	---	---	---
DNMBP	23268	broad.mit.edu	37	10	101771089	101771089	+	5'Flank	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:101771089delT	uc001kqj.2	-							NM_015221	NP_056036			dynamin binding protein						intracellular signal transduction|regulation of Rho protein signal transduction	cell junction|cytoskeleton|Golgi stack|synapse	protein binding|Rho guanyl-nucleotide exchange factor activity			ovary(5)|skin(1)	6		Colorectal(252;0.234)		Epithelial(162;2.94e-10)|all cancers(201;3.15e-08)														---	---	---	---
Unknown	0	broad.mit.edu	37	10	101905606	101905606	+	IGR	DEL	T	-	-	rs11190403	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:101905606delT								CPN1 (63964 upstream) : ERLIN1 (4242 downstream)																																			---	---	---	---
PKD2L1	9033	broad.mit.edu	37	10	102057331	102057331	+	Frame_Shift_Del	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:102057331delC	uc001kqx.1	-	5	1147	c.764delG	c.(763-765)GGCfs	p.G255fs	PKD2L1_uc009xwm.1_Frame_Shift_Del_p.G208fs	NM_016112	NP_057196	Q9P0L9	PK2L1_HUMAN	polycystic kidney disease 2-like 1	255	Extracellular (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)														---	---	---	---
Unknown	0	broad.mit.edu	37	10	102450197	102450197	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:102450197delT								HIF1AN (136517 upstream) : PAX2 (55271 downstream)																																			---	---	---	---
FAM178A	55719	broad.mit.edu	37	10	102712001	102712002	+	Intron	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:102712001_102712002delAA	uc001krt.3	+						FAM178A_uc001krs.2_Intron	NM_018121	NP_060591			hypothetical protein LOC55719 isoform 1												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	10	102922402	102922403	+	IGR	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:102922402_102922403delAA								TLX1 (24857 upstream) : LBX1 (64331 downstream)																																	OREG0020463	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
BTRC	8945	broad.mit.edu	37	10	103189448	103189448	+	Intron	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:103189448delC	uc001kta.2	+						BTRC_uc001ksz.1_Intron|BTRC_uc001ktb.2_Intron|BTRC_uc001ktc.2_Intron	NM_033637	NP_378663			beta-transducin repeat containing protein						anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|interspecies interaction between organisms|negative regulation of transcription, DNA-dependent|positive regulation of proteolysis|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|protein destabilization|viral reproduction|Wnt receptor signaling pathway	cytosol|nucleus|SCF ubiquitin ligase complex				ovary(1)	1		Colorectal(252;0.234)		Epithelial(162;1.05e-08)|all cancers(201;6.59e-07)														---	---	---	---
FGF8	2253	broad.mit.edu	37	10	103530412	103530412	+	Intron	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:103530412delC	uc001ktp.1	-						FGF8_uc001ktq.1_Intron|FGF8_uc001ktr.1_Intron|FGF8_uc001kts.1_Intron|FGF8_uc009xwr.1_Intron	NM_033164	NP_149354			fibroblast growth factor 8 isoform E precursor						bone development|dopaminergic neuron differentiation|fibroblast growth factor receptor signaling pathway|gastrulation|gonad development|insulin receptor signaling pathway|mesonephros development|metanephros development|negative regulation of cardiac muscle tissue development|neuroepithelial cell differentiation|odontogenesis|positive regulation of cell division|positive regulation of cell proliferation	extracellular region|extracellular space	growth factor activity|growth factor activity|type 1 fibroblast growth factor receptor binding|type 2 fibroblast growth factor receptor binding				0		Colorectal(252;0.122)		Epithelial(162;3.94e-09)|all cancers(201;2.13e-07)														---	---	---	---
KCNIP2	30819	broad.mit.edu	37	10	103593625	103593625	+	Intron	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:103593625delC	uc001kub.2	-						KCNIP2_uc001ktz.2_Intron|KCNIP2_uc009xwu.2_Intron|KCNIP2_uc009xwv.2_Intron|KCNIP2_uc001kuc.2_Intron|KCNIP2_uc001kue.2_Intron|KCNIP2_uc001kud.2_Intron|KCNIP2_uc001kuf.2_Intron|KCNIP2_uc001kua.2_Intron|KCNIP2_uc009xww.2_Intron|KCNIP2_uc010qqh.1_Intron|KCNIP2_uc010qqi.1_Intron	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)														---	---	---	---
HPS6	79803	broad.mit.edu	37	10	103822546	103822547	+	5'Flank	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:103822546_103822547delTT	uc001kuj.2	+							NM_024747	NP_079023			Hermansky-Pudlak syndrome-6							cytosol|early endosome membrane|endoplasmic reticulum|microsome					0		Colorectal(252;0.122)		Epithelial(162;5.93e-08)|all cancers(201;1.03e-06)										Hermansky-Pudlak_syndrome				---	---	---	---
HPS6	79803	broad.mit.edu	37	10	103824555	103824556	+	5'Flank	INS	-	TC	TC	rs142433475	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:103824555_103824556insTC	uc001kuj.2	+							NM_024747	NP_079023			Hermansky-Pudlak syndrome-6							cytosol|early endosome membrane|endoplasmic reticulum|microsome					0		Colorectal(252;0.122)		Epithelial(162;5.93e-08)|all cancers(201;1.03e-06)										Hermansky-Pudlak_syndrome				---	---	---	---
NOLC1	9221	broad.mit.edu	37	10	103919299	103919299	+	Frame_Shift_Del	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:103919299delA	uc001kuo.2	+	7	1068	c.833delA	c.(832-834)CAAfs	p.Q278fs	NOLC1_uc001kup.2_Frame_Shift_Del_p.Q288fs|NOLC1_uc001kuq.2_Frame_Shift_Del_p.Q279fs|NOLC1_uc009xxb.1_5'UTR|NOLC1_uc001kur.2_5'UTR	NM_004741	NP_004732	Q14978	NOLC1_HUMAN	nucleolar and coiled-body phosphoprotein 1	278	11 X 12 AA approximate repeats of an acidic serine cluster.|Interacts with RPA194.				mitosis|rRNA processing	cytoplasm|nucleolus	ATP binding|GTP binding|protein binding			ovary(1)	1		Colorectal(252;0.122)		Epithelial(162;5.19e-08)|all cancers(201;9.43e-07)														---	---	---	---
NOLC1	9221	broad.mit.edu	37	10	103923009	103923009	+	3'UTR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:103923009delA	uc001kuo.2	+	13					NOLC1_uc001kup.2_3'UTR|NOLC1_uc001kuq.2_3'UTR|NOLC1_uc009xxb.1_3'UTR|NOLC1_uc001kur.2_3'UTR	NM_004741	NP_004732			nucleolar and coiled-body phosphoprotein 1						mitosis|rRNA processing	cytoplasm|nucleolus	ATP binding|GTP binding|protein binding			ovary(1)	1		Colorectal(252;0.122)		Epithelial(162;5.19e-08)|all cancers(201;9.43e-07)														---	---	---	---
GBF1	8729	broad.mit.edu	37	10	104018532	104018536	+	Intron	DEL	AAAAA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:104018532_104018536delAAAAA	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)														---	---	---	---
SUFU	51684	broad.mit.edu	37	10	104367672	104367673	+	Intron	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:104367672_104367673delAA	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				---	---	---	---
AS3MT	57412	broad.mit.edu	37	10	104657872	104657875	+	Intron	DEL	TTTT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:104657872_104657875delTTTT	uc001kwk.2	+						AS3MT_uc001kwj.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)														---	---	---	---
INA	9118	broad.mit.edu	37	10	105046452	105046455	+	Intron	DEL	AAAA	-	-	rs141629461		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:105046452_105046455delAAAA	uc001kws.2	+							NM_032727	NP_116116			internexin neuronal intermediate filament						cell differentiation|nervous system development	neurofilament	structural constituent of cytoskeleton			ovary(1)|breast(1)	2				Epithelial(162;3.45e-09)|all cancers(201;9.17e-08)|BRCA - Breast invasive adenocarcinoma(275;0.198)														---	---	---	---
PCGF6	84108	broad.mit.edu	37	10	105063140	105063140	+	3'UTR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:105063140delA	uc001kwt.2	-	10					PCGF6_uc001kwu.2_3'UTR|PCGF6_uc009xxk.2_RNA|PCGF6_uc009xxl.2_RNA|PCGF6_uc009xxm.2_RNA	NM_001011663	NP_001011663			polycomb group ring finger 6 isoform a						negative regulation of transcription, DNA-dependent	PcG protein complex	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			kidney(1)	1		Colorectal(252;0.0747)|Breast(234;0.128)		Epithelial(162;2.57e-09)|all cancers(201;7.21e-08)|BRCA - Breast invasive adenocarcinoma(275;0.205)														---	---	---	---
PCGF6	84108	broad.mit.edu	37	10	105086146	105086150	+	Intron	DEL	AAAAA	-	-	rs74678577		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:105086146_105086150delAAAAA	uc001kwt.2	-						PCGF6_uc001kwu.2_Intron|PCGF6_uc009xxk.2_Intron|PCGF6_uc009xxl.2_Intron|PCGF6_uc009xxm.2_Intron	NM_001011663	NP_001011663			polycomb group ring finger 6 isoform a						negative regulation of transcription, DNA-dependent	PcG protein complex	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			kidney(1)	1		Colorectal(252;0.0747)|Breast(234;0.128)		Epithelial(162;2.57e-09)|all cancers(201;7.21e-08)|BRCA - Breast invasive adenocarcinoma(275;0.205)														---	---	---	---
SH3PXD2A	9644	broad.mit.edu	37	10	105478519	105478528	+	Intron	DEL	ACACACACAC	-	-	rs67793190		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:105478519_105478528delACACACACAC	uc001kxj.1	-						SH3PXD2A_uc010qqu.1_Intron	NM_014631	NP_055446			SH3 multiple domains 1						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	105765548	105765548	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:105765548delT	uc001kxo.1	+						SLK_uc001kxp.1_Intron	NM_014720	NP_055535			serine/threonine kinase 2						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)														---	---	---	---
C10orf79	80217	broad.mit.edu	37	10	105940052	105940052	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:105940052delT	uc001kxw.2	-						C10orf79_uc009xxq.2_Intron|C10orf79_uc001kxx.3_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)														---	---	---	---
C10orf79	80217	broad.mit.edu	37	10	105945708	105945708	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:105945708delT	uc001kxw.2	-						C10orf79_uc009xxq.2_Intron|C10orf79_uc001kxx.3_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)														---	---	---	---
CCDC147	159686	broad.mit.edu	37	10	106206778	106206778	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:106206778delT	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)														---	---	---	---
SORCS3	22986	broad.mit.edu	37	10	106845752	106845752	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-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)														---	---	---	---
SORCS3	22986	broad.mit.edu	37	10	107005471	107005473	+	Intron	DEL	CTC	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:107005471_107005473delCTC	uc001kyi.1	+						SORCS3_uc010qqz.1_Intron	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	107006174	107006174	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:107006174delT	uc001kyi.1	+						SORCS3_uc010qqz.1_Intron	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	107376746	107376746	+	IGR	DEL	A	-	-	rs75678656		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:107376746delA								SORCS3 (351753 upstream) : SORCS1 (956676 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	107624159	107624160	+	IGR	INS	-	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:107624159_107624160insA								SORCS3 (599166 upstream) : SORCS1 (709262 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	108278653	108278654	+	IGR	DEL	TG	-	-	rs72220286		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:108278653_108278654delTG								None (None upstream) : SORCS1 (54768 downstream)																																			---	---	---	---
SORCS1	114815	broad.mit.edu	37	10	108346170	108346170	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:108346170delT	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	108359126	108359126	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:108359126delA	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	109816658	109816659	+	IGR	DEL	CA	-	-	rs111558543		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:109816658_109816659delCA								SORCS1 (892366 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	110130218	110130218	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:110130218delA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	110227481	110227481	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:110227481delT								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	110558107	110558108	+	IGR	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:110558107_110558108delAA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	111057196	111057196	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:111057196delA								None (None upstream) : XPNPEP1 (567328 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	111327008	111327008	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:111327008delA								None (None upstream) : XPNPEP1 (297516 downstream)																																			---	---	---	---
XPNPEP1	7511	broad.mit.edu	37	10	111651337	111651337	+	Intron	DEL	T	-	-	rs112429910		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:111651337delT	uc001kyp.1	-						XPNPEP1_uc009xxt.1_Intron|XPNPEP1_uc001kyq.1_Intron|XPNPEP1_uc010qrb.1_Intron	NM_020383	NP_065116			X-prolyl aminopeptidase (aminopeptidase P) 1,						bradykinin catabolic process|proteolysis		manganese ion binding|metalloaminopeptidase activity|protein homodimerization activity			ovary(3)|pancreas(1)	4		Breast(234;0.174)		Epithelial(162;1.64e-05)|all cancers(201;0.000564)|BRCA - Breast invasive adenocarcinoma(275;0.0721)														---	---	---	---
Unknown	0	broad.mit.edu	37	10	112177916	112177919	+	IGR	DEL	TTTT	-	-	rs138640372		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:112177916_112177919delTTTT								SMNDC1 (113209 upstream) : DUSP5 (79706 downstream)																																			---	---	---	---
RBM20	282996	broad.mit.edu	37	10	112535365	112535365	+	Intron	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:112535365delC	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	112588564	112588564	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:112588564delT	uc001kzf.2	+							NM_001134363	NP_001127835			RNA binding motif protein 20							nucleus	nucleotide binding|RNA binding|zinc ion binding				0																		---	---	---	---
SHOC2	8036	broad.mit.edu	37	10	112748632	112748632	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:112748632delT	uc001kzl.3	+						SHOC2_uc009xxx.2_Intron|SHOC2_uc010qrg.1_Intron|SHOC2_uc001kzn.2_Intron|MIR548E_hsa-mir-548e|MI0006344_5'Flank	NM_007373	NP_031399			soc-2 suppressor of clear homolog						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)														---	---	---	---
Unknown	0	broad.mit.edu	37	10	112802818	112802818	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:112802818delA								SHOC2 (29394 upstream) : ADRA2A (33972 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	112925226	112925226	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:112925226delT								ADRA2A (84566 upstream) : GPAM (984396 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	113030433	113030433	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-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	113155855	113155856	+	IGR	DEL	AC	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:113155855_113155856delAC								ADRA2A (315195 upstream) : GPAM (753766 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	113258422	113258422	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:113258422delT								ADRA2A (417762 upstream) : GPAM (651200 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	113954970	113954971	+	IGR	INS	-	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:113954970_113954971insA								GPAM (11445 upstream) : TECTB (88522 downstream)																																			---	---	---	---
ACSL5	51703	broad.mit.edu	37	10	114136409	114136409	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:114136409delA	uc001kzs.2	+						ACSL5_uc001kzt.2_Intron|ACSL5_uc001kzu.2_Intron	NM_203379	NP_976313			acyl-CoA synthetase long-chain family member 5						fatty acid metabolic process|long-chain fatty-acyl-CoA biosynthetic process|triglyceride biosynthetic process	endoplasmic reticulum membrane|integral to membrane|mitochondrial outer membrane	ATP binding|long-chain fatty acid-CoA ligase activity			large_intestine(2)|skin(1)	3		Colorectal(252;0.117)|Breast(234;0.222)		Epithelial(162;0.0343)|all cancers(201;0.137)														---	---	---	---
TCF7L2	6934	broad.mit.edu	37	10	114749121	114749121	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:114749121delA	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	114887003	114887006	+	Intron	DEL	TTTT	-	-	rs113225449		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:114887003_114887006delTTTT	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_5'Flank|TCF7L2_uc010qrx.1_5'Flank	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)														---	---	---	---
NRAP	4892	broad.mit.edu	37	10	115351797	115351797	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-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)														---	---	---	---
NRAP	4892	broad.mit.edu	37	10	115390099	115390101	+	Intron	DEL	GTG	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:115390099_115390101delGTG	uc001laj.2	-						NRAP_uc009xyb.2_5'Flank|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)														---	---	---	---
NHLRC2	374354	broad.mit.edu	37	10	115618199	115618199	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:115618199delA	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)														---	---	---	---
C10orf118	55088	broad.mit.edu	37	10	115899340	115899340	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:115899340delA	uc001lbb.1	-						C10orf118_uc009xyd.1_Intron|C10orf118_uc001lbc.1_Intron|C10orf118_uc009xye.1_Intron	NM_018017	NP_060487			CTCL tumor antigen L14-2											ovary(2)	2		Colorectal(252;0.172)|Breast(234;0.188)		Epithelial(162;0.0161)|all cancers(201;0.0397)														---	---	---	---
C10orf118	55088	broad.mit.edu	37	10	115899378	115899378	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:115899378delA	uc001lbb.1	-						C10orf118_uc009xyd.1_Intron|C10orf118_uc001lbc.1_Intron|C10orf118_uc009xye.1_Intron	NM_018017	NP_060487			CTCL tumor antigen L14-2											ovary(2)	2		Colorectal(252;0.172)|Breast(234;0.188)		Epithelial(162;0.0161)|all cancers(201;0.0397)														---	---	---	---
TDRD1	56165	broad.mit.edu	37	10	115957316	115957316	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:115957316delT	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)														---	---	---	---
ABLIM1	3983	broad.mit.edu	37	10	116325403	116325403	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:116325403delT	uc010qsg.1	-						ABLIM1_uc010qsh.1_Intron|ABLIM1_uc010qsi.1_Intron|ABLIM1_uc010qsk.1_Intron|ABLIM1_uc009xyp.2_Intron|ABLIM1_uc009xyo.2_Intron	NM_002313	NP_002304			actin-binding LIM protein 1 isoform a						axon guidance|cytoskeleton organization|organ morphogenesis|visual perception	actin cytoskeleton|cytoplasm	actin binding|zinc ion binding			breast(1)	1		Colorectal(252;0.0373)|Breast(234;0.231)		Epithelial(162;0.0132)|all cancers(201;0.0383)														---	---	---	---
ABLIM1	3983	broad.mit.edu	37	10	116375575	116375578	+	Intron	DEL	AAAA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:116375575_116375578delAAAA	uc010qsg.1	-						ABLIM1_uc010qsh.1_Intron|ABLIM1_uc010qsi.1_Intron|ABLIM1_uc010qsk.1_Intron|ABLIM1_uc009xyp.2_Intron|ABLIM1_uc001lbz.1_Intron	NM_002313	NP_002304			actin-binding LIM protein 1 isoform a						axon guidance|cytoskeleton organization|organ morphogenesis|visual perception	actin cytoskeleton|cytoplasm	actin binding|zinc ion binding			breast(1)	1		Colorectal(252;0.0373)|Breast(234;0.231)		Epithelial(162;0.0132)|all cancers(201;0.0383)														---	---	---	---
ABLIM1	3983	broad.mit.edu	37	10	116450448	116450448	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:116450448delT	uc001lbz.1	-											Homo sapiens cDNA FLJ25105 fis, clone CBR01442.						axon guidance|cytoskeleton organization|organ morphogenesis|visual perception	actin cytoskeleton|cytoplasm	actin binding|zinc ion binding			breast(1)	1		Colorectal(252;0.0373)|Breast(234;0.231)		Epithelial(162;0.0132)|all cancers(201;0.0383)														---	---	---	---
ABLIM1	3983	broad.mit.edu	37	10	116481250	116481250	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:116481250delT	uc001lbz.1	-											Homo sapiens cDNA FLJ25105 fis, clone CBR01442.						axon guidance|cytoskeleton organization|organ morphogenesis|visual perception	actin cytoskeleton|cytoplasm	actin binding|zinc ion binding			breast(1)	1		Colorectal(252;0.0373)|Breast(234;0.231)		Epithelial(162;0.0132)|all cancers(201;0.0383)														---	---	---	---
Unknown	0	broad.mit.edu	37	10	116659775	116659776	+	IGR	INS	-	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:116659775_116659776insT								FAM160B1 (190 upstream) : TRUB1 (38139 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	116777121	116777121	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:116777121delA								TRUB1 (39683 upstream) : ATRNL1 (76003 downstream)																																			---	---	---	---
ATRNL1	26033	broad.mit.edu	37	10	116970800	116970803	+	Intron	DEL	TTTT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:116970800_116970803delTTTT	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)														---	---	---	---
ATRNL1	26033	broad.mit.edu	37	10	117071374	117071374	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:117071374delT	uc001lcg.2	+						ATRNL1_uc010qsm.1_Intron|ATRNL1_uc010qsn.1_Intron	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)														---	---	---	---
ATRNL1	26033	broad.mit.edu	37	10	117587829	117587830	+	Intron	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:117587829_117587830delAA	uc001lcg.2	+						ATRNL1_uc010qsm.1_Intron|ATRNL1_uc010qsn.1_Intron	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	117883747	117883747	+	Intron	DEL	T	-	-	rs75139097		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:117883747delT	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)														---	---	---	---
PNLIPRP1	5407	broad.mit.edu	37	10	118353962	118353962	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:118353962delT	uc001lco.1	+						PNLIPRP1_uc001lcp.2_Intron|PNLIPRP1_uc009xys.1_RNA	NM_006229	NP_006220			pancreatic lipase-related protein 1 precursor						lipid metabolic process		calcium ion binding|triglyceride lipase activity			ovary(1)|breast(1)	2				all cancers(201;0.0161)														---	---	---	---
HSPA12A	259217	broad.mit.edu	37	10	118538445	118538446	+	Intron	INS	-	AAC	AAC			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:118538445_118538446insAAC	uc001lcu.2	-							NM_025015	NP_079291			heat shock 70kDa protein 12A								ATP binding			ovary(1)	1				all cancers(201;0.0158)														---	---	---	---
Unknown	0	broad.mit.edu	37	10	118618628	118618628	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:118618628delA	uc001lcw.2	+											SubName: Full=Putative uncharacterized protein C10orf134;																														---	---	---	---
KIAA1598	57698	broad.mit.edu	37	10	118708404	118708404	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:118708404delA	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	119159392	119159392	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:119159392delA								PDZD8 (24455 upstream) : EMX2OS (84413 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	119341809	119341810	+	IGR	DEL	CT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:119341809_119341810delCT								EMX2 (32753 upstream) : RAB11FIP2 (422619 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	119402240	119402240	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:119402240delT								EMX2 (93184 upstream) : RAB11FIP2 (362189 downstream)																																			---	---	---	---
C10orf84	63877	broad.mit.edu	37	10	120096057	120096057	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:120096057delT	uc001ldo.2	-						C10orf84_uc010qss.1_Intron	NM_022063	NP_071346			hypothetical protein LOC63877												0		Colorectal(252;0.101)		all cancers(201;0.0244)														---	---	---	---
Unknown	0	broad.mit.edu	37	10	120327561	120327562	+	IGR	DEL	CT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:120327561_120327562delCT								C10orf84 (225722 upstream) : PRLHR (25354 downstream)																																			---	---	---	---
PRLHR	2834	broad.mit.edu	37	10	120358154	120358154	+	5'Flank	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:120358154delT	uc001ldp.1	-							NM_004248	NP_004239			G protein-coupled receptor 10						female pregnancy	integral to plasma membrane	neuropeptide Y receptor activity				0		Colorectal(252;0.0429)|Lung NSC(174;0.142)|all_lung(145;0.175)		all cancers(201;0.0166)														---	---	---	---
EIF3A	8661	broad.mit.edu	37	10	120836450	120836451	+	Intron	DEL	AA	-	-	rs111738995		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:120836450_120836451delAA	uc001ldu.2	-						EIF3A_uc010qsu.1_Intron	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)														---	---	---	---
GRK5	2869	broad.mit.edu	37	10	121142436	121142438	+	Intron	DEL	TTT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:121142436_121142438delTTT	uc001led.2	+						GRK5_uc009xzh.2_Intron|GRK5_uc010qta.1_Intron	NM_005308	NP_005299			G protein-coupled receptor kinase 5						G-protein signaling, coupled to cAMP nucleotide second messenger|regulation of G-protein coupled receptor protein signaling pathway|tachykinin receptor signaling pathway	cytoplasm|plasma membrane|soluble fraction	ATP binding|G-protein coupled receptor kinase activity|phospholipid binding|protein kinase C binding|signal transducer activity			lung(2)|stomach(1)	3		Lung NSC(174;0.0971)|all_lung(145;0.127)|Ovarian(717;0.249)		all cancers(201;0.0227)														---	---	---	---
RGS10	6001	broad.mit.edu	37	10	121302235	121302237	+	5'Flank	DEL	GAG	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:121302235_121302237delGAG	uc001leg.2	-							NM_001005339	NP_001005339			regulator of G-protein signaling 10 isoform a						negative regulation of signal transduction	cytoplasm|plasma membrane	GTPase activator activity|protein binding|signal transducer activity				0		Lung NSC(174;0.094)|all_lung(145;0.123)		all cancers(201;0.00105)|GBM - Glioblastoma multiforme(135;0.195)														---	---	---	---
TIAL1	7073	broad.mit.edu	37	10	121347864	121347864	+	Intron	DEL	T	-	-	rs58919083		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-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)														---	---	---	---
SEC23IP	11196	broad.mit.edu	37	10	121683939	121683940	+	Intron	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:121683939_121683940delTT	uc001leu.1	+						SEC23IP_uc010qtc.1_Intron|SEC23IP_uc009xzk.1_Intron	NM_007190	NP_009121			Sec23-interacting protein p125						Golgi organization|intracellular protein transport	endoplasmic reticulum|ER to Golgi transport vesicle membrane|ER-Golgi intermediate compartment	metal ion binding			ovary(3)	3		Lung NSC(174;0.109)|all_lung(145;0.142)|all_neural(114;0.234)		all cancers(201;0.00515)														---	---	---	---
Unknown	0	broad.mit.edu	37	10	121931711	121931711	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:121931711delT								SEC23IP (230466 upstream) : PPAPDC1A (284755 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	121966539	121966539	+	IGR	DEL	A	-	-	rs7082794	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:121966539delA								SEC23IP (265294 upstream) : PPAPDC1A (249927 downstream)																																			---	---	---	---
PPAPDC1A	196051	broad.mit.edu	37	10	122255148	122255148	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:122255148delT	uc001lev.1	+						PPAPDC1A_uc010qtd.1_Intron|PPAPDC1A_uc009xzl.1_Intron|PPAPDC1A_uc001lew.1_Intron|PPAPDC1A_uc001lex.1_Intron	NM_001030059	NP_001025230			phosphatidic acid phosphatase type 2 domain						phospholipid dephosphorylation	integral to membrane	phosphatidate phosphatase activity			breast(1)	1		Lung NSC(174;0.1)|all_lung(145;0.132)		all cancers(201;0.0117)														---	---	---	---
WDR11	55717	broad.mit.edu	37	10	122659295	122659295	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:122659295delA	uc010qtf.1	+						WDR11_uc010qte.1_Intron|WDR11_uc001lfd.1_Intron|WDR11_uc009xzn.2_Intron	NM_018117	NP_060587			bromodomain and WD repeat domain containing 2							integral to membrane					0																		---	---	---	---
Unknown	0	broad.mit.edu	37	10	122969211	122969212	+	IGR	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:122969211_122969212delTT								WDR11 (300176 upstream) : FGFR2 (268633 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	123047385	123047385	+	IGR	DEL	T	-	-	rs68155647		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:123047385delT								WDR11 (378350 upstream) : FGFR2 (190460 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	123133653	123133654	+	IGR	DEL	GT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:123133653_123133654delGT								WDR11 (464618 upstream) : FGFR2 (104191 downstream)																																			---	---	---	---
FGFR2	2263	broad.mit.edu	37	10	123310734	123310734	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:123310734delA	uc010qtk.1	-						FGFR2_uc010qtg.1_Intron|FGFR2_uc010qth.1_Intron|FGFR2_uc010qti.1_Intron|FGFR2_uc010qtj.1_Intron|FGFR2_uc010qtl.1_Intron|FGFR2_uc010qtm.1_Intron|FGFR2_uc001lfl.3_Intron|FGFR2_uc001lfm.2_Intron|FGFR2_uc001lfn.3_Intron|FGFR2_uc010qtn.1_Intron|FGFR2_uc010qto.1_Intron|FGFR2_uc001lfo.1_Intron|FGFR2_uc010qtp.1_Intron|FGFR2_uc010qtq.1_Intron	NM_000141	NP_000132			fibroblast growth factor receptor 2 isoform 1						angiogenesis|axonogenesis|bone mineralization|bone morphogenesis|branch elongation involved in salivary gland morphogenesis|branching involved in embryonic placenta morphogenesis|branching morphogenesis of a nerve|bud elongation involved in lung branching|cell fate commitment|cell growth|cell-cell signaling|cellular response to protein stimulus|embryonic digestive tract morphogenesis|embryonic pattern specification|epithelial cell proliferation involved in salivary gland morphogenesis|fibroblast growth factor receptor signaling pathway involved in hemopoiesis|fibroblast growth factor receptor signaling pathway involved in mammary gland specification|fibroblast growth factor receptor signaling pathway involved in negative regulation of apoptosis in bone marrow|fibroblast growth factor receptor signaling pathway involved in orbitofrontal cortex development|fibroblast growth factor receptor signaling pathway involved in positive regulation of cell proliferation in bone marrow|hair follicle morphogenesis|insulin receptor signaling pathway|lacrimal gland development|lateral sprouting from an epithelium|limb bud formation|lung alveolus development|lung lobe morphogenesis|lung-associated mesenchyme development|mammary gland bud formation|membranous septum morphogenesis|mesenchymal cell differentiation involved in lung development|mesenchymal cell proliferation involved in lung development|midbrain development|multicellular organism growth|negative regulation of transcription from RNA polymerase II promoter|odontogenesis|organ growth|otic vesicle formation|outflow tract septum morphogenesis|positive regulation of canonical Wnt receptor signaling pathway|positive regulation of cardiac muscle cell proliferation|positive regulation of cell cycle|positive regulation of cell division|positive regulation of epithelial cell proliferation involved in lung morphogenesis|positive regulation of ERK1 and ERK2 cascade|positive regulation of mesenchymal cell proliferation|positive regulation of transcription from RNA polymerase II promoter|post-embryonic development|prostate epithelial cord arborization involved in prostate glandular acinus morphogenesis|prostate epithelial cord elongation|pyramidal neuron development|regulation of branching involved in prostate gland morphogenesis|regulation of cell fate commitment|regulation of fibroblast growth factor receptor signaling pathway|regulation of multicellular organism growth|regulation of smooth muscle cell differentiation|regulation of smoothened signaling pathway|squamous basal epithelial stem cell differentiation involved in prostate gland acinus development|ureteric bud development|ventricular cardiac muscle tissue morphogenesis|ventricular zone neuroblast division	cell cortex|cell surface|excitatory synapse|extracellular region|integral to membrane|nucleus|plasma membrane	ATP binding|fibroblast growth factor binding|fibroblast growth factor binding|fibroblast growth factor receptor activity|heparin binding|protein binding			endometrium(44)|skin(28)|lung(11)|ovary(4)|cervix(2)|stomach(2)|breast(2)|upper_aerodigestive_tract(1)|soft_tissue(1)|central_nervous_system(1)	96		Lung NSC(174;0.0841)|all_lung(145;0.106)|all_neural(114;0.107)	STAD - Stomach adenocarcinoma(1;7.52e-05)|all cancers(1;0.0722)	all cancers(201;9.73e-05)|GBM - Glioblastoma multiforme(135;0.0845)	Palifermin(DB00039)		5	Mis		gastric. NSCLC|endometrial		Crouzon|Pfeiffer|and Apert syndromes		Apert_syndrome|Saethre-Chotzen_syndrome				---	---	---	---
FGFR2	2263	broad.mit.edu	37	10	123313322	123313322	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:123313322delA	uc010qtk.1	-						FGFR2_uc010qtg.1_Intron|FGFR2_uc010qth.1_Intron|FGFR2_uc010qti.1_Intron|FGFR2_uc010qtj.1_Intron|FGFR2_uc010qtl.1_Intron|FGFR2_uc010qtm.1_Intron|FGFR2_uc001lfl.3_Intron|FGFR2_uc001lfm.2_Intron|FGFR2_uc001lfn.3_Intron|FGFR2_uc010qtn.1_Intron|FGFR2_uc010qto.1_Intron|FGFR2_uc001lfo.1_Intron|FGFR2_uc010qtp.1_Intron|FGFR2_uc010qtq.1_Intron	NM_000141	NP_000132			fibroblast growth factor receptor 2 isoform 1						angiogenesis|axonogenesis|bone mineralization|bone morphogenesis|branch elongation involved in salivary gland morphogenesis|branching involved in embryonic placenta morphogenesis|branching morphogenesis of a nerve|bud elongation involved in lung branching|cell fate commitment|cell growth|cell-cell signaling|cellular response to protein stimulus|embryonic digestive tract morphogenesis|embryonic pattern specification|epithelial cell proliferation involved in salivary gland morphogenesis|fibroblast growth factor receptor signaling pathway involved in hemopoiesis|fibroblast growth factor receptor signaling pathway involved in mammary gland specification|fibroblast growth factor receptor signaling pathway involved in negative regulation of apoptosis in bone marrow|fibroblast growth factor receptor signaling pathway involved in orbitofrontal cortex development|fibroblast growth factor receptor signaling pathway involved in positive regulation of cell proliferation in bone marrow|hair follicle morphogenesis|insulin receptor signaling pathway|lacrimal gland development|lateral sprouting from an epithelium|limb bud formation|lung alveolus development|lung lobe morphogenesis|lung-associated mesenchyme development|mammary gland bud formation|membranous septum morphogenesis|mesenchymal cell differentiation involved in lung development|mesenchymal cell proliferation involved in lung development|midbrain development|multicellular organism growth|negative regulation of transcription from RNA polymerase II promoter|odontogenesis|organ growth|otic vesicle formation|outflow tract septum morphogenesis|positive regulation of canonical Wnt receptor signaling pathway|positive regulation of cardiac muscle cell proliferation|positive regulation of cell cycle|positive regulation of cell division|positive regulation of epithelial cell proliferation involved in lung morphogenesis|positive regulation of ERK1 and ERK2 cascade|positive regulation of mesenchymal cell proliferation|positive regulation of transcription from RNA polymerase II promoter|post-embryonic development|prostate epithelial cord arborization involved in prostate glandular acinus morphogenesis|prostate epithelial cord elongation|pyramidal neuron development|regulation of branching involved in prostate gland morphogenesis|regulation of cell fate commitment|regulation of fibroblast growth factor receptor signaling pathway|regulation of multicellular organism growth|regulation of smooth muscle cell differentiation|regulation of smoothened signaling pathway|squamous basal epithelial stem cell differentiation involved in prostate gland acinus development|ureteric bud development|ventricular cardiac muscle tissue morphogenesis|ventricular zone neuroblast division	cell cortex|cell surface|excitatory synapse|extracellular region|integral to membrane|nucleus|plasma membrane	ATP binding|fibroblast growth factor binding|fibroblast growth factor binding|fibroblast growth factor receptor activity|heparin binding|protein binding			endometrium(44)|skin(28)|lung(11)|ovary(4)|cervix(2)|stomach(2)|breast(2)|upper_aerodigestive_tract(1)|soft_tissue(1)|central_nervous_system(1)	96		Lung NSC(174;0.0841)|all_lung(145;0.106)|all_neural(114;0.107)	STAD - Stomach adenocarcinoma(1;7.52e-05)|all cancers(1;0.0722)	all cancers(201;9.73e-05)|GBM - Glioblastoma multiforme(135;0.0845)	Palifermin(DB00039)		5	Mis		gastric. NSCLC|endometrial		Crouzon|Pfeiffer|and Apert syndromes		Apert_syndrome|Saethre-Chotzen_syndrome				---	---	---	---
ATE1	11101	broad.mit.edu	37	10	123624258	123624259	+	Intron	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:123624258_123624259delTT	uc001lfp.2	-						ATE1_uc001lfq.2_Intron|ATE1_uc010qtr.1_Intron|ATE1_uc010qts.1_Intron|ATE1_uc010qtt.1_Intron|ATE1_uc001lfr.2_Intron|ATE1_uc009xzu.2_Intron	NM_007041	NP_008972			arginyltransferase 1 isoform 2						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)																---	---	---	---
ATE1	11101	broad.mit.edu	37	10	123679074	123679074	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:123679074delA	uc001lfp.2	-						ATE1_uc001lfq.2_Intron|ATE1_uc010qtr.1_Intron|ATE1_uc010qts.1_Intron|ATE1_uc010qtt.1_Intron|ATE1_uc001lfr.2_Intron|ATE1_uc009xzu.2_Intron	NM_007041	NP_008972			arginyltransferase 1 isoform 2						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)																---	---	---	---
DMBT1	1755	broad.mit.edu	37	10	124379705	124379705	+	Intron	DEL	T	-	-	rs72298879		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:124379705delT	uc001lgk.1	+						DMBT1_uc001lgl.1_Intron|DMBT1_uc001lgm.1_Intron|DMBT1_uc009xzz.1_Intron|DMBT1_uc010qtx.1_Intron|DMBT1_uc009yab.1_Intron|DMBT1_uc009yac.1_5'Flank	NM_007329	NP_015568			deleted in malignant brain tumors 1 isoform b						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)																---	---	---	---
Unknown	0	broad.mit.edu	37	10	124439899	124439899	+	IGR	DEL	A	-	-	rs113923089		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:124439899delA								DMBT1 (36647 upstream) : C10orf120 (17328 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	124474347	124474350	+	IGR	DEL	AAAA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:124474347_124474350delAAAA								C10orf120 (15009 upstream) : FLJ46361 (41860 downstream)																																			---	---	---	---
C10orf88	80007	broad.mit.edu	37	10	124711563	124711564	+	Intron	INS	-	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:124711563_124711564insT	uc001lgw.2	-						C10orf88_uc001lgx.2_Intron	NM_024942	NP_079218			hypothetical protein LOC80007												0		all_neural(114;0.0765)|Lung NSC(174;0.163)|all_lung(145;0.205)		Colorectal(40;0.0686)|COAD - Colon adenocarcinoma(40;0.0735)														---	---	---	---
Unknown	0	broad.mit.edu	37	10	124853908	124853908	+	IGR	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:124853908delC								ACADSB (36103 upstream) : HMX3 (41659 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	124870942	124870942	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:124870942delA								ACADSB (53137 upstream) : HMX3 (24625 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	124994810	124994810	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:124994810delT								BUB3 (69924 upstream) : GPR26 (431061 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	125276359	125276360	+	Intron	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:125276359_125276360delAA	uc001lhg.1	+											full-length cDNA clone CS0DD008YJ14 of Neuroblastoma Cot 50-normalized of Homo sapiens (human).																														---	---	---	---
CPXM2	119587	broad.mit.edu	37	10	125486227	125486227	+	Intron	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:125486227delG	uc001lhj.2	-											Homo sapiens cDNA FLJ56000 complete cds, highly similar to Carboxypeptidase-like protein X2 precursor.						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)														---	---	---	---
Unknown	0	broad.mit.edu	37	10	125859452	125859452	+	IGR	DEL	T	-	-	rs75041712		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:125859452delT								CHST15 (6246 upstream) : OAT (226420 downstream)																																			---	---	---	---
FAM53B	9679	broad.mit.edu	37	10	126360342	126360342	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:126360342delT	uc001lhv.1	-						FAM53B_uc001lhu.1_Intron|FAM53B_uc001lhw.2_Intron	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	126484988	126484988	+	IGR	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:126484988delC								METTL10 (4549 upstream) : FAM175B (5366 downstream)																																			---	---	---	---
FAM175B	23172	broad.mit.edu	37	10	126512500	126512501	+	Intron	INS	-	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:126512500_126512501insT	uc001lib.3	+							NM_032182	NP_115558			hypothetical protein LOC23172							BRISC complex	polyubiquitin binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	10	126595890	126595891	+	IGR	DEL	TG	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:126595890_126595891delTG								FAM175B (70652 upstream) : ZRANB1 (33081 downstream)																																			---	---	---	---
ZRANB1	54764	broad.mit.edu	37	10	126660077	126660077	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:126660077delT	uc001lic.2	+						ZRANB1_uc010qug.1_Intron	NM_017580	NP_060050			zinc finger, RAN-binding domain containing 1						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)														---	---	---	---
Unknown	0	broad.mit.edu	37	10	126956371	126956371	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:126956371delT								CTBP2 (106747 upstream) : LOC100169752 (306569 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	127128542	127128543	+	IGR	INS	-	TG	TG	rs147319577	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:127128542_127128543insTG								CTBP2 (278918 upstream) : LOC100169752 (134397 downstream)																																			---	---	---	---
UROS	7390	broad.mit.edu	37	10	127494796	127494796	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:127494796delT	uc001liw.3	-						UROS_uc001liv.3_Intron|UROS_uc010quh.1_Intron|UROS_uc001lix.3_Intron|UROS_uc001liy.3_Intron|UROS_uc001liz.2_Intron	NM_000375	NP_000366			uroporphyrinogen III synthase						heme biosynthetic process|uroporphyrinogen III biosynthetic process	cytosol|mitochondrion	uroporphyrinogen-III synthase activity				0		all_lung(145;0.00756)|Lung NSC(174;0.0116)|Colorectal(57;0.0855)|all_neural(114;0.0937)|Breast(234;0.203)																---	---	---	---
DHX32	55760	broad.mit.edu	37	10	127583984	127583984	+	Intron	DEL	C	-	-	rs35683577		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:127583984delC	uc001ljg.1	-						FANK1_uc010quk.1_5'Flank|FANK1_uc001ljh.3_5'Flank|FANK1_uc009yan.2_5'Flank	NM_018180	NP_060650			DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 32							mitochondrion|nucleus	ATP binding|helicase activity			breast(2)|ovary(1)|lung(1)	4		all_lung(145;0.00751)|Lung NSC(174;0.0115)|Colorectal(57;0.0846)|all_neural(114;0.0936)																---	---	---	---
FANK1	92565	broad.mit.edu	37	10	127696199	127696200	+	Intron	INS	-	TG	TG	rs148785811	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:127696199_127696200insTG	uc001ljh.3	+						FANK1_uc009yan.2_Intron|FANK1_uc001lji.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)																---	---	---	---
C10orf90	118611	broad.mit.edu	37	10	128134744	128134744	+	Intron	DEL	A	-	-	rs10751552	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:128134744delA	uc001ljq.2	-						C10orf90_uc001ljp.2_Intron|C10orf90_uc010qum.1_Intron|C10orf90_uc001ljo.2_Intron	NM_001004298	NP_001004298			hypothetical protein LOC118611											ovary(1)|skin(1)	2		all_epithelial(44;4.51e-05)|all_lung(145;0.0068)|Lung NSC(174;0.0105)|Colorectal(57;0.0848)|all_neural(114;0.0936)|Breast(234;0.203)		COAD - Colon adenocarcinoma(40;0.0442)|Colorectal(40;0.0479)														---	---	---	---
C10orf90	118611	broad.mit.edu	37	10	128207119	128207119	+	Intron	DEL	A	-	-	rs11288069		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:128207119delA	uc001ljq.2	-						C10orf90_uc010qum.1_Intron|C10orf90_uc009yao.2_Intron|C10orf90_uc001ljs.1_Intron	NM_001004298	NP_001004298			hypothetical protein LOC118611											ovary(1)|skin(1)	2		all_epithelial(44;4.51e-05)|all_lung(145;0.0068)|Lung NSC(174;0.0105)|Colorectal(57;0.0848)|all_neural(114;0.0936)|Breast(234;0.203)		COAD - Colon adenocarcinoma(40;0.0442)|Colorectal(40;0.0479)														---	---	---	---
Unknown	0	broad.mit.edu	37	10	128411952	128411952	+	IGR	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:128411952delC								C10orf90 (52873 upstream) : DOCK1 (182071 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	128439171	128439172	+	IGR	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:128439171_128439172delTT								C10orf90 (80092 upstream) : DOCK1 (154851 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	128514029	128514029	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:128514029delA								C10orf90 (154950 upstream) : DOCK1 (79994 downstream)																																			---	---	---	---
DOCK1	1793	broad.mit.edu	37	10	128615113	128615113	+	Intron	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:128615113delG	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	128829898	128829899	+	Intron	INS	-	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:128829898_128829899insT	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	129051984	129051984	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:129051984delA	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	129170209	129170209	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:129170209delA	uc001ljt.2	+						DOCK1_uc010qun.1_Intron|DOCK1_uc009yaq.2_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	129282930	129282930	+	IGR	DEL	T	-	-	rs111998761		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:129282930delT								DOCK1 (32149 upstream) : NPS (64683 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	129413895	129413895	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:129413895delT								NPS (62960 upstream) : FOXI2 (121643 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	129573920	129573923	+	IGR	DEL	ACAC	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:129573920_129573923delACAC								FOXI2 (34470 upstream) : CLRN3 (102191 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	130206378	130206379	+	IGR	INS	-	T	T	rs146271706	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:130206378_130206379insT								MKI67 (281910 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	130373762	130373764	+	IGR	DEL	TTT	-	-	rs36090700		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:130373762_130373764delTTT								MKI67 (449294 upstream) : MGMT (891690 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	130373950	130373950	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:130373950delA								MKI67 (449482 upstream) : MGMT (891504 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	130991272	130991272	+	IGR	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:130991272delC								None (None upstream) : MGMT (274182 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	131092607	131092607	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:131092607delA								None (None upstream) : MGMT (172847 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	131254726	131254726	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:131254726delT								None (None upstream) : MGMT (10728 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	132201766	132201766	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:132201766delA								GLRX3 (218982 upstream) : TCERG1L (688890 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	132669624	132669624	+	IGR	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:132669624delG								GLRX3 (686840 upstream) : TCERG1L (221032 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	132756901	132756902	+	IGR	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:132756901_132756902delAA								GLRX3 (774117 upstream) : TCERG1L (133754 downstream)																																			---	---	---	---
TCERG1L	256536	broad.mit.edu	37	10	133099921	133099921	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:133099921delA	uc001lkp.2	-							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	133141966	133141966	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:133141966delT								TCERG1L (31982 upstream) : PPP2R2D (605994 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	133285107	133285108	+	IGR	INS	-	TG	TG	rs148941741	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:133285107_133285108insTG								TCERG1L (175123 upstream) : PPP2R2D (462852 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	133528748	133528748	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:133528748delA								TCERG1L (418764 upstream) : PPP2R2D (219212 downstream)																																			---	---	---	---
BNIP3	664	broad.mit.edu	37	10	133798154	133798154	+	5'Flank	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:133798154delG	uc001lkv.1	-						BNIP3_uc010qut.1_5'Flank	NM_004052	NP_004043			BCL2/adenovirus E1B 19kD-interacting protein 3						cellular response to cobalt ion|cellular response to hypoxia|cellular response to mechanical stimulus|chromatin remodeling|defense response to virus|DNA fragmentation involved in apoptotic nuclear change|induction of apoptosis|interspecies interaction between organisms|mitochondrial fragmentation involved in apoptosis|negative regulation of membrane potential|negative regulation of mitochondrial fusion|negative regulation of survival gene product expression|neuron apoptosis|positive regulation of mitochondrial fission|positive regulation of protein complex disassembly|positive regulation of release of cytochrome c from mitochondria|reactive oxygen species metabolic process|regulation of mitochondrial membrane permeability	dendrite|integral to mitochondrial outer membrane|nuclear envelope|nucleoplasm	GTPase binding|protein heterodimerization activity|protein homodimerization activity			lung(1)|skin(1)	2		all_cancers(35;4e-11)|all_epithelial(44;5.07e-08)|Ovarian(717;2.61e-05)|Lung NSC(174;0.00237)|all_lung(145;0.00354)|Breast(234;0.023)|all_neural(114;0.0299)|Colorectal(31;0.109)|Melanoma(40;0.123)|Glioma(114;0.203)		Epithelial(32;1.59e-12)|all cancers(32;3.75e-11)|OV - Ovarian serous cystadenocarcinoma(35;2.57e-08)|BRCA - Breast invasive adenocarcinoma(275;0.208)														---	---	---	---
PWWP2B	170394	broad.mit.edu	37	10	134218255	134218255	+	Frame_Shift_Del	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:134218255delC	uc001lll.3	+	2	280	c.251delC	c.(250-252)TCCfs	p.S84fs	PWWP2B_uc009ybe.2_Frame_Shift_Del_p.S84fs	NM_138499	NP_612508	Q6NUJ5	PWP2B_HUMAN	PWWP domain containing 2 isoform 1	84											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)														---	---	---	---
INPP5A	3632	broad.mit.edu	37	10	134384172	134384175	+	Intron	DEL	TTTT	-	-	rs72138962		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:134384172_134384175delTTTT	uc001llp.2	+						INPP5A_uc001llo.1_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)														---	---	---	---
Unknown	0	broad.mit.edu	37	10	134655149	134655150	+	Intron	INS	-	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:134655149_134655150insC	uc010qux.1	-							NM_017609	NP_060079			Homo sapiens cDNA, FLJ17989.																														---	---	---	---
Unknown	0	broad.mit.edu	37	10	134865224	134865224	+	IGR	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:134865224delC								C10orf93 (109160 upstream) : GPR123 (19209 downstream)																																			---	---	---	---
GPR123	84435	broad.mit.edu	37	10	134944149	134944150	+	3'UTR	DEL	CC	-	-	rs10543497		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:134944149_134944150delCC	uc001llx.3	+	7					GPR123_uc001llw.2_3'UTR	NM_001083909	NP_001077378			G protein-coupled receptor 123							integral to membrane|plasma membrane	G-protein coupled receptor activity				0		all_cancers(35;1.8e-10)|all_epithelial(44;8.95e-09)|Lung NSC(174;0.000845)|all_lung(145;0.00144)|all_neural(114;0.0299)|Colorectal(31;0.0585)|Melanoma(40;0.123)|Glioma(114;0.203)		OV - Ovarian serous cystadenocarcinoma(35;9.16e-06)|Epithelial(32;1.21e-05)|all cancers(32;1.63e-05)														---	---	---	---
KNDC1	85442	broad.mit.edu	37	10	134997778	134997779	+	Intron	DEL	CA	-	-	rs149543308		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:134997778_134997779delCA	uc001llz.1	+						KNDC1_uc001lma.1_Intron	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)														---	---	---	---
Unknown	0	broad.mit.edu	37	10	135047772	135047772	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:135047772delT								UTF1 (2711 upstream) : VENTX (3636 downstream)																																			---	---	---	---
PAOX	196743	broad.mit.edu	37	10	135198800	135198800	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:135198800delA	uc001lmv.2	+						PAOX_uc001lmw.2_Intron|PAOX_uc001lmx.2_Intron|PAOX_uc001lmy.2_Intron|PAOX_uc001lmz.2_Intron|PAOX_uc001lna.2_Intron|PAOX_uc001lnb.2_Intron|PAOX_uc001lnc.2_Intron	NM_152911	NP_690875			polyamine oxidase isoform 1						polyamine biosynthetic process|xenobiotic metabolic process	peroxisomal matrix	polyamine oxidase activity				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)		all cancers(32;4.39e-07)|OV - Ovarian serous cystadenocarcinoma(35;1.21e-06)|Epithelial(32;1.94e-06)														---	---	---	---
Unknown	0	broad.mit.edu	37	10	135406847	135406847	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:135406847delT								SYCE1 (23385 upstream) : FRG2B (31757 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	340682	340682	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:340682delT								IFITM3 (19768 upstream) : B4GALNT4 (29113 downstream)																																			---	---	---	---
PTDSS2	81490	broad.mit.edu	37	11	478736	478736	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:478736delA	uc001lpj.2	+						PTDSS2_uc009ybv.1_Intron	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)													---	---	---	---
PTDSS2	81490	broad.mit.edu	37	11	484687	484691	+	Intron	DEL	TGTGC	-	-	rs146753775	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:484687_484691delTGTGC	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)													---	---	---	---
DEAF1	10522	broad.mit.edu	37	11	664275	664275	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:664275delA	uc001lqq.1	-						DEAF1_uc009ycf.1_Intron	NM_021008	NP_066288			deformed epidermal autoregulatory factor 1						embryonic skeletal system development|germ cell development|neural tube closure|regulation of mammary gland epithelial cell proliferation|regulation of transcription, DNA-dependent|transcription from RNA polymerase II promoter	cytoplasm|cytoplasm|extracellular region|nucleus	protein binding|zinc ion binding				0		all_cancers(49;1.24e-08)|all_epithelial(84;1.87e-05)|Breast(177;0.000286)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.106)|all_lung(207;0.136)		all cancers(45;1.76e-27)|Epithelial(43;8.42e-27)|OV - Ovarian serous cystadenocarcinoma(40;6.55e-21)|BRCA - Breast invasive adenocarcinoma(625;4.83e-05)|Lung(200;0.0259)|LUSC - Lung squamous cell carcinoma(625;0.075)														---	---	---	---
PNPLA2	57104	broad.mit.edu	37	11	822324	822324	+	Intron	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:822324delG	uc001lrt.2	+						PNPLA2_uc009ycl.2_5'Flank	NM_020376	NP_065109			patatin-like phospholipase domain containing 2						negative regulation of sequestering of triglyceride|positive regulation of triglyceride catabolic process	integral to membrane|lipid particle|plasma membrane	triglyceride lipase activity				0		all_cancers(49;4.75e-06)|all_epithelial(84;0.00204)|Breast(177;0.00234)|Ovarian(85;0.0228)|Medulloblastoma(188;0.0321)|all_neural(188;0.0762)		all cancers(45;1.63e-25)|Epithelial(43;1.28e-24)|OV - Ovarian serous cystadenocarcinoma(40;7.09e-19)|BRCA - Breast invasive adenocarcinoma(625;4.23e-05)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)														---	---	---	---
MUC5B	727897	broad.mit.edu	37	11	1150988	1150989	+	Intron	INS	-	CT	CT			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:1150988_1150989insCT	uc009ycr.1	+							NM_017511	NP_059981			SubName: Full=Mucin 5AC, oligomeric mucus/gel-forming;						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)														---	---	---	---
LOC338651	338651	broad.mit.edu	37	11	1597091	1597092	+	Intron	DEL	TT	-	-	rs111828646		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:1597091_1597092delTT	uc009ycx.1	+						LOC338651_uc001ltt.1_Intron	NR_021489				SubName: Full=cDNA FLJ30579 fis, clone BRAWH2006989, weakly similar to DNA-DIRECTED RNA POLYMERASE II LARGEST SUBUNIT;          EC=2.7.7.6;												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	11	1695967	1695968	+	IGR	DEL	AC	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:1695967_1695968delAC								FAM99A (6882 upstream) : FAM99B (8532 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	1932248	1932248	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:1932248delT								LSP1 (18756 upstream) : TNNT3 (8551 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	2147420	2147421	+	IGR	DEL	GT	-	-	rs148407216		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:2147420_2147421delGT								H19 (128355 upstream) : IGF2 (2927 downstream)																																			---	---	---	---
KCNQ1	3784	broad.mit.edu	37	11	2648899	2648900	+	Intron	DEL	TA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:2648899_2648900delTA	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)													---	---	---	---
KCNQ1	3784	broad.mit.edu	37	11	2848853	2848853	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:2848853delA	uc001lwn.2	+						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)													---	---	---	---
CARS	833	broad.mit.edu	37	11	3045128	3045128	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-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	3362340	3362340	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:3362340delT								MRGPRE (108724 upstream) : ZNF195 (17671 downstream)																																	OREG0020697	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
STIM1	6786	broad.mit.edu	37	11	3882466	3882469	+	Intron	DEL	TTTT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:3882466_3882469delTTTT	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	4135384	4135384	+	Intron	DEL	A	-	-	rs78379041		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:4135384delA	uc001lyw.3	+						RRM1_uc009yej.2_5'Flank|RRM1_uc009yeh.1_Intron|RRM1_uc009yei.2_Intron|RRM1_uc010qyc.1_Intron|RRM1_uc010qyd.1_5'Flank	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	4572932	4572932	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:4572932delT								OR52M1 (5559 upstream) : C11orf40 (19722 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	4765214	4765214	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:4765214delT								OR51E2 (46138 upstream) : OR51F1 (24996 downstream)																																			---	---	---	---
OR51B5	282763	broad.mit.edu	37	11	5455070	5455070	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:5455070delA	uc001maq.1	-						HBG2_uc001mak.1_Intron|HBE1_uc001mam.1_Intron	NM_001005567	NP_001005567			olfactory receptor, family 51, subfamily B,						sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			skin(1)	1		Medulloblastoma(188;0.0075)|all_neural(188;0.0572)|Breast(177;0.0675)		Epithelial(150;3.05e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)														---	---	---	---
TRIM5	85363	broad.mit.edu	37	11	5695371	5695371	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:5695371delA	uc001mbm.1	-						TRIM5_uc001mbl.1_Intron|TRIM5_uc001mbn.2_Intron|TRIM5_uc001mbo.2_Intron|TRIM5_uc001mbp.2_Intron	NM_033034	NP_149023			tripartite motif protein TRIM5 isoform alpha						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	5729574	5729574	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:5729574delT	uc001mbr.2	+						TRIM5_uc001mbq.1_Intron|TRIM22_uc009yet.1_Intron|TRIM22_uc009yes.2_Intron|TRIM22_uc010qzm.1_Intron|TRIM22_uc009yeu.2_Intron|OR56B1_uc001mbs.1_Intron|OR56B1_uc009yev.1_Intron	NM_006074	NP_006065			tripartite motif-containing 22						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)														---	---	---	---
TRIM22	10346	broad.mit.edu	37	11	5759768	5759769	+	Intron	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:5759768_5759769delTT	uc009yet.1	+						TRIM5_uc001mbq.1_Intron	NM_006074	NP_006065			tripartite motif-containing 22						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)														---	---	---	---
OR56A1	120796	broad.mit.edu	37	11	6049169	6049171	+	5'Flank	DEL	AAA	-	-	rs111685831		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:6049169_6049171delAAA	uc010qzw.1	-							NM_001001917	NP_001001917			olfactory receptor, family 56, subfamily A,						sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(2)|breast(1)	3		Medulloblastoma(188;0.00776)|all_neural(188;0.0652)|Breast(177;0.114)		Epithelial(150;7.01e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)														---	---	---	---
TRIM3	10612	broad.mit.edu	37	11	6472757	6472757	+	Intron	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:6472757delC	uc001mdh.2	-						TRIM3_uc001mdi.2_Intron|TRIM3_uc010raj.1_Intron|TRIM3_uc009yfd.2_Intron|TRIM3_uc010rak.1_Intron	NM_006458	NP_006449			tripartite motif-containing 3						nervous system development|protein transport	early endosome	protein C-terminus binding|zinc ion binding			central_nervous_system(2)|large_intestine(1)|ovary(1)|skin(1)	5		all_lung(207;9.97e-06)|Lung NSC(207;1.74e-05)|Medulloblastoma(188;0.00225)|Breast(177;0.0204)|all_neural(188;0.0212)		Epithelial(150;9.34e-10)|Lung(200;0.0234)|LUSC - Lung squamous cell carcinoma(625;0.133)|BRCA - Breast invasive adenocarcinoma(625;0.135)														---	---	---	---
ARFIP2	23647	broad.mit.edu	37	11	6500261	6500261	+	Intron	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:6500261delC	uc001mdk.2	-						ARFIP2_uc001mdl.2_Intron|ARFIP2_uc010ral.1_Intron|ARFIP2_uc010ram.1_Intron|ARFIP2_uc010ran.1_Intron|ARFIP2_uc001mdm.2_Intron|FXC1_uc001mdn.3_5'Flank|FXC1_uc001mdo.3_5'Flank	NM_012402	NP_036534			ADP-ribosylation factor interacting protein 2						actin cytoskeleton organization|cellular component movement|lamellipodium assembly|ruffle organization|small GTPase mediated signal transduction	cell cortex|plasma membrane|ruffle	GTP binding|GTP-dependent protein binding|Rac GTPase binding				0		Medulloblastoma(188;0.00263)|all_neural(188;0.026)|Breast(177;0.029)		Epithelial(150;3.41e-08)|BRCA - Breast invasive adenocarcinoma(625;0.189)														---	---	---	---
DNHD1	144132	broad.mit.edu	37	11	6522829	6522831	+	Intron	DEL	AGA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:6522829_6522831delAGA	uc001mdw.3	+						DNHD1_uc001mdp.2_Intron	NM_144666	NP_653267			dynein heavy chain domain 1 isoform 1						microtubule-based movement	dynein complex	microtubule motor activity			ovary(2)	2		Medulloblastoma(188;0.00776)|all_neural(188;0.0652)|Breast(177;0.171)		Epithelial(150;3.93e-08)|BRCA - Breast invasive adenocarcinoma(625;0.13)														---	---	---	---
Unknown	0	broad.mit.edu	37	11	6594952	6594952	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:6594952delA								DNHD1 (1700 upstream) : RRP8 (26202 downstream)																																			---	---	---	---
SYT9	143425	broad.mit.edu	37	11	7438396	7438399	+	Intron	DEL	TTTG	-	-	rs150070704	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:7438396_7438399delTTTG	uc001mfe.2	+						SYT9_uc001mfd.2_Intron|SYT9_uc009yfi.2_Intron	NM_175733	NP_783860			synaptotagmin IX							cell junction|integral to membrane|synaptic vesicle membrane	metal ion binding|transporter activity			ovary(2)|large_intestine(1)	3				Epithelial(150;1.34e-07)|LUSC - Lung squamous cell carcinoma(625;0.0949)														---	---	---	---
PPFIBP2	8495	broad.mit.edu	37	11	7670311	7670311	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:7670311delT	uc001mfj.3	+						PPFIBP2_uc010rbb.1_Intron|PPFIBP2_uc001mfk.1_Intron|PPFIBP2_uc010rbc.1_Intron|PPFIBP2_uc010rbe.1_Intron|PPFIBP2_uc001mfl.3_Intron|PPFIBP2_uc009yfj.1_Intron	NM_003621	NP_003612			PTPRF interacting protein, binding protein 2						cell communication|DNA integration	intracellular	DNA binding|integrase activity|protein binding			ovary(2)|breast(2)	4				Epithelial(150;2.01e-07)|BRCA - Breast invasive adenocarcinoma(625;0.236)														---	---	---	---
Unknown	0	broad.mit.edu	37	11	7699700	7699701	+	IGR	INS	-	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:7699700_7699701insA								CYB5R2 (4706 upstream) : OVCH2 (12744 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	7699729	7699730	+	IGR	INS	-	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:7699729_7699730insA								CYB5R2 (4735 upstream) : OVCH2 (12715 downstream)																																			---	---	---	---
RIC3	79608	broad.mit.edu	37	11	8160039	8160039	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:8160039delA	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)														---	---	---	---
Unknown	0	broad.mit.edu	37	11	9122814	9122815	+	IGR	INS	-	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:9122814_9122815insT								FLJ46111 (5077 upstream) : DENND5A (37562 downstream)																																			---	---	---	---
DENND5A	23258	broad.mit.edu	37	11	9274193	9274193	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:9274193delA	uc001mhl.2	-						DENND5A_uc010rbw.1_Intron|DENND5A_uc010rbx.1_Intron	NM_015213	NP_056028			RAB6 interacting protein 1											liver(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	11	9376006	9376006	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:9376006delA								TMEM41B (39710 upstream) : IPO7 (30163 downstream)																																			---	---	---	---
ZNF143	7702	broad.mit.edu	37	11	9494462	9494463	+	Intron	DEL	TT	-	-	rs141312409		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:9494462_9494463delTT	uc001mhr.2	+						ZNF143_uc009yfu.2_Intron|ZNF143_uc010rby.1_Intron	NM_003442	NP_003433			zinc finger protein 143						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)														---	---	---	---
ZNF143	7702	broad.mit.edu	37	11	9537365	9537365	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:9537365delA	uc001mhr.2	+						ZNF143_uc009yfu.2_Intron|ZNF143_uc010rby.1_Intron	NM_003442	NP_003433			zinc finger protein 143						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)														---	---	---	---
SWAP70	23075	broad.mit.edu	37	11	9742749	9742750	+	Intron	INS	-	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:9742749_9742750insT	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	10064542	10064542	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:10064542delA	uc001mib.2	-						SBF2_uc001mif.3_Intron|SBF2_uc001mij.2_5'Flank	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)														---	---	---	---
SBF2	81846	broad.mit.edu	37	11	10204097	10204098	+	Intron	DEL	TT	-	-	rs71805628		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:10204097_10204098delTT	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)														---	---	---	---
SBF2	81846	broad.mit.edu	37	11	10228848	10228849	+	Intron	INS	-	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:10228848_10228849insA	uc001mib.2	-							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)														---	---	---	---
MRVI1	10335	broad.mit.edu	37	11	10600390	10600391	+	Intron	INS	-	CTCT	CTCT	rs144870266	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:10600390_10600391insCTCT	uc010rcc.1	-						uc001miu.2_Intron|MRVI1_uc001miw.2_Intron|MRVI1_uc010rcb.1_Intron|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)														---	---	---	---
USP47	55031	broad.mit.edu	37	11	11898457	11898457	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:11898457delA	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-4200-01A-01D-1126-08	TCGA-BR-4200-11A-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)														---	---	---	---
Unknown	0	broad.mit.edu	37	11	12067680	12067681	+	IGR	DEL	CA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:12067680_12067681delCA								DKK3 (36364 upstream) : MICAL2 (47862 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	12686657	12686657	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-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	12736532	12736532	+	Intron	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:12736532delG	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	13196787	13196787	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:13196787delA								RASSF10 (164140 upstream) : ARNTL (102538 downstream)																																			---	---	---	---
BTBD10	84280	broad.mit.edu	37	11	13410208	13410208	+	3'UTR	DEL	A	-	-	rs138959637		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:13410208delA	uc001mkz.2	-	9					BTBD10_uc010rcl.1_3'UTR|BTBD10_uc001mla.2_3'UTR|BTBD10_uc009ygn.2_RNA|BTBD10_uc010rcm.1_3'UTR	NM_032320	NP_115696			K+ channel tetramerization protein							nucleus					0				Epithelial(150;0.0214)														---	---	---	---
FAR1	84188	broad.mit.edu	37	11	13729920	13729920	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:13729920delA	uc001mld.2	+						FAR1_uc009ygp.2_Intron	NM_032228	NP_115604			fatty acyl CoA reductase 1						ether lipid biosynthetic process	integral to membrane|peroxisomal matrix|peroxisomal membrane	protein binding			ovary(1)|skin(1)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	11	13884230	13884230	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:13884230delT								FAR1 (130339 upstream) : SPON1 (99684 downstream)																																			---	---	---	---
SPON1	10418	broad.mit.edu	37	11	14285581	14285584	+	Intron	DEL	AAAA	-	-	rs113927403		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:14285581_14285584delAAAA	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)														---	---	---	---
PSMA1	5682	broad.mit.edu	37	11	14642989	14642990	+	Intron	INS	-	TT	TT			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:14642989_14642990insTT	uc001mll.2	-							NM_148976	NP_683877			proteasome alpha 1 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|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	cytoplasm|nucleus|polysome|proteasome core complex, alpha-subunit complex	protein binding|RNA binding|threonine-type endopeptidase activity			upper_aerodigestive_tract(1)|skin(1)	2																		---	---	---	---
PDE3B	5140	broad.mit.edu	37	11	14786424	14786424	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:14786424delT	uc001mln.2	+						PDE3B_uc001mlm.2_Intron|PDE3B_uc010rcr.1_Intron	NM_000922	NP_000913			phosphodiesterase 3B						cAMP catabolic process|insulin receptor signaling pathway|negative regulation of lipid catabolic process|platelet activation	cytosol|endoplasmic reticulum|Golgi apparatus|guanyl-nucleotide exchange factor complex|integral to membrane|microsome	3',5'-cyclic-AMP phosphodiesterase activity|3',5'-cyclic-GMP phosphodiesterase activity|cGMP-inhibited cyclic-nucleotide phosphodiesterase activity|metal ion binding|protein kinase B binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	11	15413869	15413872	+	IGR	DEL	AGTG	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:15413869_15413872delAGTG								INSC (145117 upstream) : SOX6 (574124 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	15460015	15460015	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:15460015delA								INSC (191263 upstream) : SOX6 (527981 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	15469132	15469132	+	IGR	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:15469132delG								INSC (200380 upstream) : SOX6 (518864 downstream)																																			---	---	---	---
SOX6	55553	broad.mit.edu	37	11	16043937	16043938	+	Intron	DEL	CT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:16043937_16043938delCT	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	16497344	16497344	+	Intron	DEL	A	-	-	rs4590834		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:16497344delA	uc001mmg.2	-						SOX6_uc001mmh.1_Intron|SOX6_uc001mmi.3_Intron|SOX6_uc001mmj.2_Intron	NM_033326	NP_201583			SRY (sex determining region Y)-box 6 isoform 2						muscle organ development	nucleus	sequence-specific DNA binding transcription factor activity			ovary(3)	3																		---	---	---	---
SOX6	55553	broad.mit.edu	37	11	16714275	16714276	+	Intron	DEL	AC	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:16714275_16714276delAC	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																		---	---	---	---
Unknown	0	broad.mit.edu	37	11	17039191	17039191	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:17039191delT								PLEKHA7 (3228 upstream) : RPS13 (56749 downstream)																																			---	---	---	---
PIK3C2A	5286	broad.mit.edu	37	11	17104277	17104277	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:17104277delT	uc009ygu.1	-											Synthetic construct DNA, clone: pF1KB6002, Homo sapiens PIK3C2A gene for phosphoinositide-3-kinase, class 2, alpha polypeptide, complete cds, without stop codon, in Flexi system.						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)													---	---	---	---
PIK3C2A	5286	broad.mit.edu	37	11	17168274	17168274	+	Intron	DEL	A	-	-	rs75779456		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:17168274delA	uc001mmq.3	-						PIK3C2A_uc009ygu.1_Intron|PIK3C2A_uc010rcw.1_Intron|PIK3C2A_uc001mmr.3_Intron|PIK3C2A_uc010rcx.1_Intron|PIK3C2A_uc009ygv.1_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)													---	---	---	---
PIK3C2A	5286	broad.mit.edu	37	11	17189575	17189575	+	Intron	DEL	C	-	-	rs139723868		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:17189575delC	uc001mmq.3	-						PIK3C2A_uc009ygu.1_Intron|PIK3C2A_uc010rcw.1_Intron|PIK3C2A_uc001mmr.3_Intron|PIK3C2A_uc010rcx.1_Intron|PIK3C2A_uc009ygv.1_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)													---	---	---	---
ABCC8	6833	broad.mit.edu	37	11	17500183	17500183	+	5'Flank	DEL	T	-	-	rs5789988		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:17500183delT	uc001mnc.2	-						ABCC8_uc010rcy.1_5'Flank	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)													---	---	---	---
SERGEF	26297	broad.mit.edu	37	11	17941151	17941151	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:17941151delT	uc001mnm.2	-						SERGEF_uc009yhd.2_Intron|SERGEF_uc001mnn.2_Intron|SERGEF_uc010rcz.1_Intron	NM_012139	NP_036271			deafness locus associated putative guanine						negative regulation of protein secretion|signal transduction	cytoplasm|nucleus	protein binding|Ran guanyl-nucleotide exchange factor activity			central_nervous_system(1)	1																		---	---	---	---
TPH1	7166	broad.mit.edu	37	11	18054800	18054800	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:18054800delA	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	18101291	18101291	+	IGR	DEL	A	-	-	rs67725526		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:18101291delA								TPH1 (38956 upstream) : SAAL1 (600 downstream)																																			---	---	---	---
HPS5	11234	broad.mit.edu	37	11	18327933	18327933	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:18327933delA	uc001mod.1	-						HPS5_uc001moe.1_Intron|HPS5_uc001mof.1_Intron	NM_181507	NP_852608			Hermansky-Pudlak syndrome 5 isoform a							cytosol				ovary(1)|pancreas(1)|skin(1)	3														Hermansky-Pudlak_syndrome				---	---	---	---
Unknown	0	broad.mit.edu	37	11	18409213	18409213	+	5'Flank	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:18409213delA	hsa-mir-3159|MI0014188	+																																									---	---	---	---
TSG101	7251	broad.mit.edu	37	11	18532491	18532492	+	Intron	INS	-	AAT	AAT	rs138256552	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:18532491_18532492insAAT	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																		---	---	---	---
PTPN5	84867	broad.mit.edu	37	11	18802871	18802873	+	Intron	DEL	TTT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:18802871_18802873delTTT	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																		---	---	---	---
Unknown	0	broad.mit.edu	37	11	18837666	18837667	+	IGR	INS	-	T	T	rs146168201	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:18837666_18837667insT								PTPN5 (24277 upstream) : MRGPRX1 (117694 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	18894389	18894389	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:18894389delT								PTPN5 (81000 upstream) : MRGPRX1 (60972 downstream)																																			---	---	---	---
NAV2	89797	broad.mit.edu	37	11	19680992	19680992	+	Intron	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:19680992delG	uc001mpp.2	+							NM_001111018	NP_001104488			neuron navigator 2 isoform 3							nucleus	ATP binding|helicase activity			skin(4)|ovary(1)|pancreas(1)	6																		---	---	---	---
Unknown	0	broad.mit.edu	37	11	20367882	20367883	+	IGR	DEL	AG	-	-	rs150864132		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:20367882_20367883delAG								DBX1 (186012 upstream) : HTATIP2 (17348 downstream)																																			---	---	---	---
NELL1	4745	broad.mit.edu	37	11	21056964	21056964	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:21056964delA	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	21216631	21216631	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:21216631delA	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																		---	---	---	---
Unknown	0	broad.mit.edu	37	11	21680464	21680465	+	IGR	INS	-	A	A	rs1675040		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:21680464_21680465insA								NELL1 (83237 upstream) : ANO5 (534257 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	21792048	21792048	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:21792048delT								NELL1 (194821 upstream) : ANO5 (422674 downstream)																																			---	---	---	---
ANO5	203859	broad.mit.edu	37	11	22213410	22213410	+	5'Flank	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:22213410delT	uc001mqi.2	+						ANO5_uc001mqj.2_5'Flank	NM_213599	NP_998764			anoctamin 5 isoform a							chloride channel complex|endoplasmic reticulum membrane	chloride channel activity			central_nervous_system(3)|ovary(1)	4																		---	---	---	---
Unknown	0	broad.mit.edu	37	11	22402462	22402462	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:22402462delT								SLC17A6 (1418 upstream) : FANCF (241617 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	22566339	22566339	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:22566339delA								SLC17A6 (165295 upstream) : FANCF (77740 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	22573347	22573347	+	IGR	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:22573347delC								SLC17A6 (172303 upstream) : FANCF (70732 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	22632547	22632547	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:22632547delT								SLC17A6 (231503 upstream) : FANCF (11532 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	22857448	22857448	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:22857448delT	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	23328110	23328110	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:23328110delT								SVIP (476728 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	23471094	23471094	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:23471094delA								SVIP (619712 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	23549477	23549477	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:23549477delA								SVIP (698095 upstream) : LUZP2 (969079 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	23838449	23838449	+	IGR	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:23838449delC								SVIP (987067 upstream) : LUZP2 (680107 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	24175278	24175279	+	IGR	INS	-	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:24175278_24175279insT								None (None upstream) : LUZP2 (343277 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	24199723	24199723	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:24199723delT								None (None upstream) : LUZP2 (318833 downstream)																																			---	---	---	---
LUZP2	338645	broad.mit.edu	37	11	24619228	24619229	+	Intron	INS	-	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:24619228_24619229insT	uc001mqs.2	+						LUZP2_uc009yif.2_Intron|LUZP2_uc009yig.2_Intron	NM_001009909	NP_001009909			leucine zipper protein 2 precursor							extracellular region				ovary(1)|skin(1)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	11	25177517	25177518	+	IGR	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:25177517_25177518delTT								LUZP2 (73335 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	25199282	25199282	+	IGR	DEL	A	-	-	rs66929363		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:25199282delA								LUZP2 (95100 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	25789630	25789630	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:25789630delA								LUZP2 (685448 upstream) : ANO3 (421199 downstream)																																			---	---	---	---
ANO3	63982	broad.mit.edu	37	11	26265012	26265012	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:26265012delA	uc010rdr.1	+							NM_031418	NP_113606			transmembrane protein 16C							chloride channel complex	chloride channel activity			ovary(2)|central_nervous_system(1)|pancreas(1)	4																		---	---	---	---
ANO3	63982	broad.mit.edu	37	11	26531035	26531035	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:26531035delT	uc001mqt.3	+						ANO3_uc010rdr.1_Intron|ANO3_uc010rds.1_Intron|ANO3_uc010rdt.1_Intron	NM_031418	NP_113606			transmembrane protein 16C							chloride channel complex	chloride channel activity			ovary(2)|central_nervous_system(1)|pancreas(1)	4																		---	---	---	---
Unknown	0	broad.mit.edu	37	11	26802994	26802994	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:26802994delA								SLC5A12 (58020 upstream) : FIBIN (212634 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	26823218	26823218	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:26823218delA								SLC5A12 (78244 upstream) : FIBIN (192410 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	26929382	26929382	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:26929382delT								SLC5A12 (184408 upstream) : FIBIN (86246 downstream)																																			---	---	---	---
FIBIN	387758	broad.mit.edu	37	11	27018160	27018161	+	3'UTR	DEL	AC	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:27018160_27018161delAC	uc001mrd.2	+	1						NM_203371	NP_976249			fin bud initiation factor homolog precursor							extracellular region|Golgi apparatus					0																		---	---	---	---
LGR4	55366	broad.mit.edu	37	11	27390693	27390693	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-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	27484417	27484417	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:27484417delA	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																		---	---	---	---
Unknown	0	broad.mit.edu	37	11	27950168	27950169	+	IGR	INS	-	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:27950168_27950169insA								BDNF (206563 upstream) : KIF18A (91994 downstream)																																			---	---	---	---
METT5D1	196074	broad.mit.edu	37	11	28177725	28177725	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:28177725delA	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	28873556	28873557	+	IGR	DEL	TT	-	-	rs112794626		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:28873556_28873557delTT								METT5D1 (518502 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	28949889	28949889	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:28949889delT								METT5D1 (594835 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	29024871	29024871	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:29024871delA								METT5D1 (669817 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	29276300	29276300	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:29276300delT								METT5D1 (921246 upstream) : KCNA4 (755466 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	29349036	29349036	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:29349036delA								METT5D1 (993982 upstream) : KCNA4 (682730 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	29582319	29582319	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:29582319delA								None (None upstream) : KCNA4 (449447 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	29959411	29959411	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:29959411delA								None (None upstream) : KCNA4 (72355 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	29978773	29978773	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:29978773delT								None (None upstream) : KCNA4 (52993 downstream)																																			---	---	---	---
MPPED2	744	broad.mit.edu	37	11	30580324	30580324	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:30580324delT	uc001msr.2	-						MPPED2_uc001msq.3_Intron|MPPED2_uc009yji.2_Intron	NM_001584	NP_001575			metallophosphoesterase domain containing 2						nervous system development		hydrolase activity|metal ion binding			skin(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	11	30777014	30777015	+	IGR	INS	-	A	A	rs145855040	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:30777014_30777015insA								MPPED2 (169084 upstream) : DCDC1 (187734 downstream)																																			---	---	---	---
DCDC1	341019	broad.mit.edu	37	11	31202365	31202365	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:31202365delT	uc001msu.1	-											SubName: Full=Putative uncharacterized protein ENSP00000343496;						intracellular signal transduction					skin(1)	1	Lung SC(675;0.225)																	---	---	---	---
IMMP1L	196294	broad.mit.edu	37	11	31467275	31467276	+	Intron	DEL	TT	-	-	rs71676051		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:31467275_31467276delTT	uc001msy.1	-						IMMP1L_uc001msz.1_Intron	NM_144981	NP_659418			IMP1 inner mitochondrial membrane						proteolysis	mitochondrial inner membrane	serine-type peptidase activity				0	Lung SC(675;0.225)																	---	---	---	---
IMMP1L	196294	broad.mit.edu	37	11	31493601	31493602	+	Intron	DEL	TC	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:31493601_31493602delTC	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)																	---	---	---	---
PAX6	5080	broad.mit.edu	37	11	31812317	31812317	+	Frame_Shift_Del	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:31812317delG	uc001mtd.3	-	11	2014	c.1124delC	c.(1123-1125)CCAfs	p.P375fs	PAX6_uc001mte.3_Frame_Shift_Del_p.P375fs|PAX6_uc001mtg.3_Frame_Shift_Del_p.P389fs|PAX6_uc001mtf.3_Frame_Shift_Del_p.P375fs|PAX6_uc001mth.3_Frame_Shift_Del_p.P375fs|PAX6_uc009yjr.2_Frame_Shift_Del_p.P375fs	NM_001127612	NP_001121084	P26367	PAX6_HUMAN	paired box gene 6 isoform a	375	Pro/Ser/Thr-rich.		P -> Q (in AN; reduced DNA binding ability).		blood vessel development|central nervous system development|cornea development in camera-type eye|glucose homeostasis|iris morphogenesis|negative regulation of neurogenesis|neuron fate commitment|pancreatic A cell development|positive regulation of transcription, DNA-dependent|response to wounding|visual perception	cytoplasm|nuclear chromatin	R-SMAD binding|RNA polymerase II core promoter sequence-specific DNA binding|sequence-specific DNA binding RNA polymerase II transcription factor activity|ubiquitin-protein ligase activity			lung(4)|ovary(2)|pancreas(1)|central_nervous_system(1)|skin(1)	9	Lung SC(675;0.225)													Wilms_tumor-Aniridia-ambiguous_Genitals-mental_Retardation				---	---	---	---
RCN1	5954	broad.mit.edu	37	11	31856399	31856400	+	Intron	DEL	TC	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:31856399_31856400delTC	uc010rea.1	+							NM_002901	NP_002892			reticulocalbin 1 precursor							endoplasmic reticulum lumen	calcium ion binding			large_intestine(1)	1	Lung SC(675;0.225)																	---	---	---	---
RCN1	5954	broad.mit.edu	37	11	31887374	31887374	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:31887374delA	uc010rea.1	+							NM_002901	NP_002892			reticulocalbin 1 precursor							endoplasmic reticulum lumen	calcium ion binding			large_intestine(1)	1	Lung SC(675;0.225)																	---	---	---	---
RCN1	5954	broad.mit.edu	37	11	32072376	32072376	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:32072376delT	uc010rea.1	+							NM_002901	NP_002892			reticulocalbin 1 precursor							endoplasmic reticulum lumen	calcium ion binding			large_intestine(1)	1	Lung SC(675;0.225)																	---	---	---	---
Unknown	0	broad.mit.edu	37	11	32847308	32847308	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:32847308delA								CCDC73 (31121 upstream) : PRRG4 (4181 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	33204877	33204877	+	Intron	DEL	T	-	-	rs75698803		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:33204877delT	uc001muk.2	+											Homo sapiens hypothetical protein LOC338739, mRNA (cDNA clone IMAGE:5172825), partial cds.																														---	---	---	---
HIPK3	10114	broad.mit.edu	37	11	33352931	33352931	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:33352931delT	uc001mul.1	+						HIPK3_uc001mum.1_Intron|HIPK3_uc009yjv.1_Intron|HIPK3_uc009yjw.1_Intron	NM_005734	NP_005725			homeodomain interacting protein kinase 3 isoform						anti-apoptosis|apoptosis|negative regulation of JUN kinase activity|peptidyl-serine phosphorylation|peptidyl-threonine phosphorylation|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm	ATP binding|protein serine/threonine kinase activity			large_intestine(1)|skin(1)|stomach(1)|ovary(1)|pancreas(1)	5																		---	---	---	---
HIPK3	10114	broad.mit.edu	37	11	33361114	33361114	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:33361114delA	uc001mul.1	+						HIPK3_uc001mum.1_Intron|HIPK3_uc009yjv.1_Intron	NM_005734	NP_005725			homeodomain interacting protein kinase 3 isoform						anti-apoptosis|apoptosis|negative regulation of JUN kinase activity|peptidyl-serine phosphorylation|peptidyl-threonine phosphorylation|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm	ATP binding|protein serine/threonine kinase activity			large_intestine(1)|skin(1)|stomach(1)|ovary(1)|pancreas(1)	5																		---	---	---	---
C11orf41	25758	broad.mit.edu	37	11	33628918	33628918	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:33628918delA	uc001mup.3	+							NM_012194	NP_036326			hypothetical protein LOC25758							integral to membrane				ovary(2)	2																		---	---	---	---
FBXO3	26273	broad.mit.edu	37	11	33794356	33794356	+	Intron	DEL	A	-	-	rs6484666	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:33794356delA	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)														---	---	---	---
Unknown	0	broad.mit.edu	37	11	34427410	34427411	+	IGR	DEL	TC	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:34427410_34427411delTC								ABTB2 (48608 upstream) : CAT (33067 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	34495210	34495210	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:34495210delT								CAT (1607 upstream) : ELF5 (5132 downstream)																																			---	---	---	---
ELF5	2001	broad.mit.edu	37	11	34525014	34525014	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:34525014delT	uc001mvo.1	-						ELF5_uc001mvp.1_Intron|ELF5_uc009ykd.1_Intron|ELF5_uc001mvq.1_Intron	NM_198381	NP_938195			E74-like factor 5 ESE-2a						cell proliferation|transcription from RNA polymerase II promoter	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			skin(1)	1		Acute lymphoblastic leukemia(5;0.0087)|all_hematologic(20;0.0384)																---	---	---	---
Unknown	0	broad.mit.edu	37	11	34765467	34765468	+	IGR	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:34765467_34765468delTT								EHF (82386 upstream) : APIP (131246 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	35132504	35132504	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:35132504delT								PDHX (114830 upstream) : CD44 (27913 downstream)																																			---	---	---	---
TRIM44	54765	broad.mit.edu	37	11	35817802	35817805	+	Intron	DEL	CTCG	-	-	rs142372380		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:35817802_35817805delCTCG	uc001mwi.2	+							NM_017583	NP_060053			DIPB protein							intracellular	protein binding|zinc ion binding			skin(1)	1	all_lung(20;0.0317)|Lung NSC(22;0.0661)|all_epithelial(35;0.115)	all_hematologic(20;0.107)																---	---	---	---
LDLRAD3	143458	broad.mit.edu	37	11	36141058	36141058	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:36141058delT	uc001mwk.1	+						LDLRAD3_uc010rey.1_Intron|LDLRAD3_uc010rez.1_Intron|LDLRAD3_uc010rfa.1_Intron	NM_174902	NP_777562			low density lipoprotein receptor class A domain							integral to membrane	receptor activity			central_nervous_system(1)	1	all_lung(20;0.089)|Lung NSC(22;0.175)|all_epithelial(35;0.177)	all_hematologic(20;0.124)																---	---	---	---
Unknown	0	broad.mit.edu	37	11	36949301	36949302	+	IGR	DEL	AC	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:36949301_36949302delAC								C11orf74 (252911 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	37347192	37347192	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:37347192delA								C11orf74 (650802 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	37443481	37443482	+	IGR	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:37443481_37443482delTT								C11orf74 (747091 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	38328096	38328096	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:38328096delA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	38695281	38695282	+	IGR	DEL	TC	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:38695281_38695282delTC								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	39275997	39275998	+	IGR	DEL	GA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:39275997_39275998delGA								None (None upstream) : LRRC4C (859755 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	39373803	39373803	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:39373803delT								None (None upstream) : LRRC4C (761950 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	39726790	39726790	+	IGR	DEL	T	-	-	rs72242375		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:39726790delT								None (None upstream) : LRRC4C (408963 downstream)																																			---	---	---	---
LRRC4C	57689	broad.mit.edu	37	11	40598860	40598861	+	Intron	INS	-	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:40598860_40598861insT	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	41883236	41883236	+	IGR	DEL	T	-	-	rs11352242		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:41883236delT								LRRC4C (401913 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	42306700	42306700	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:42306700delA								LRRC4C (825377 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	42993213	42993214	+	IGR	DEL	GA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:42993213_42993214delGA								None (None upstream) : API5 (340291 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	43593258	43593258	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:43593258delA								MIR670 (11955 upstream) : MIR129-2 (9686 downstream)																																			---	---	---	---
CD82	3732	broad.mit.edu	37	11	44611394	44611394	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:44611394delT	uc001myc.2	+						CD82_uc001myd.2_Intron	NM_002231	NP_002222			CD82 antigen isoform 1							integral to plasma membrane	protein binding			ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	11	44795043	44795043	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:44795043delT								CD82 (153730 upstream) : TSPAN18 (86836 downstream)																																			---	---	---	---
SYT13	57586	broad.mit.edu	37	11	45279389	45279389	+	Intron	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:45279389delG	uc001myq.2	-						SYT13_uc009yku.1_Intron	NM_020826	NP_065877			synaptotagmin XIII							transport vesicle				ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	11	45386545	45386545	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:45386545delA								SYT13 (78661 upstream) : CHST1 (283882 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	45596999	45596999	+	IGR	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:45596999delC								SYT13 (289115 upstream) : CHST1 (73428 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	45726350	45726351	+	5'Flank	DEL	AA	-	-	rs35491923		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:45726350_45726351delAA	uc001nai.2	-						uc010rgc.1_5'Flank|uc001naj.2_5'Flank|uc001nak.2_5'Flank|uc001nal.2_5'Flank					DQ572786																														---	---	---	---
DKFZp779M0652	374387	broad.mit.edu	37	11	45791808	45791808	+	5'Flank	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:45791808delA	uc001nbn.2	+							NR_027134				SubName: Full=Putative uncharacterized protein DKFZp779M0652;												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	11	46734806	46734807	+	IGR	DEL	AA	-	-	rs71948832		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:46734806_46734807delAA								ZNF408 (7345 upstream) : F2 (5936 downstream)																																			---	---	---	---
F2	2147	broad.mit.edu	37	11	46742602	46742602	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:46742602delT	uc001ndf.3	+						F2_uc001ndg.3_Intron	NM_000506	NP_000497			coagulation factor II preproprotein						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)													---	---	---	---
LRP4	4038	broad.mit.edu	37	11	46913979	46913979	+	Intron	DEL	T	-	-	rs145068033	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:46913979delT	uc001ndn.3	-							NM_002334	NP_002325			low density lipoprotein receptor-related protein						endocytosis|negative regulation of canonical Wnt receptor signaling pathway|Wnt receptor signaling pathway	integral to membrane	calcium ion binding|receptor activity			skin(2)|upper_aerodigestive_tract(1)|ovary(1)	4				Lung(87;0.159)														---	---	---	---
C11orf49	79096	broad.mit.edu	37	11	47109269	47109270	+	Intron	DEL	TG	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:47109269_47109270delTG	uc001ndp.2	+						C11orf49_uc001nds.2_Intron|C11orf49_uc001ndq.2_Intron|C11orf49_uc001ndr.2_Intron|C11orf49_uc010rgx.1_Intron|C11orf49_uc010rgy.1_Intron|C11orf49_uc010rgz.1_Intron	NM_024113	NP_077018			hypothetical protein LOC79096 isoform 3												0																		---	---	---	---
DDB2	1643	broad.mit.edu	37	11	47251370	47251373	+	Intron	DEL	TTTT	-	-	rs35972351		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:47251370_47251373delTTTT	uc001neb.2	+						DDB2_uc001nec.2_Intron|DDB2_uc009yli.1_Intron|DDB2_uc001ned.2_Intron|DDB2_uc001nee.2_Intron|DDB2_uc001nef.2_Intron|DDB2_uc001neg.2_Intron|DDB2_uc001neh.2_Intron	NM_000107	NP_000098			damage-specific DNA binding protein 2						nucleotide-excision repair, DNA damage removal|protein autoubiquitination|protein polyubiquitination|response to UV	nucleoplasm|protein complex	damaged DNA binding|protein binding			kidney(2)|ovary(1)	3								Mis|N			skin basal cell|skin squamous cell|melanoma		Direct_reversal_of_damage|NER	Xeroderma_Pigmentosum				---	---	---	---
CELF1	10658	broad.mit.edu	37	11	47495124	47495124	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:47495124delA	uc001nfl.2	-						CELF1_uc001nfm.2_Intron|CELF1_uc001nfn.2_Intron|CELF1_uc001nfo.1_Intron|CELF1_uc010rhm.1_Intron|CELF1_uc001nfp.2_Intron|CELF1_uc001nfq.1_Intron|CELF1_uc001nfr.1_Intron	NM_001025596	NP_001020767			CUG triplet repeat, RNA-binding protein 1						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																		---	---	---	---
FNBP4	23360	broad.mit.edu	37	11	47777188	47777191	+	Intron	DEL	AAAA	-	-	rs148840598		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:47777188_47777191delAAAA	uc009ylv.2	-						FNBP4_uc001ngj.2_Intron|FNBP4_uc001ngl.2_Intron	NM_015308	NP_056123			formin binding protein 4											ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	11	47892386	47892386	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:47892386delT								NUP160 (22329 upstream) : PTPRJ (109724 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	47895231	47895234	+	IGR	DEL	TTTT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:47895231_47895234delTTTT								NUP160 (25174 upstream) : PTPRJ (106876 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	47966472	47966472	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:47966472delA								NUP160 (96415 upstream) : PTPRJ (35638 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	47982602	47982603	+	IGR	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:47982602_47982603delTT								NUP160 (112545 upstream) : PTPRJ (19507 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	48322676	48322676	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:48322676delT								OR4X1 (36347 upstream) : OR4S1 (5099 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	48670109	48670109	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:48670109delT								OR4A47 (158837 upstream) : FOLH1 (498079 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	48738332	48738332	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:48738332delT								OR4A47 (227060 upstream) : FOLH1 (429856 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	49056787	49056787	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:49056787delT								OR4A47 (545515 upstream) : FOLH1 (111401 downstream)																																			---	---	---	---
FOLH1	2346	broad.mit.edu	37	11	49223959	49223960	+	Intron	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:49223959_49223960delTT	uc001ngy.2	-						FOLH1_uc001ngz.2_Intron|FOLH1_uc009yly.2_Intron|FOLH1_uc009ylz.2_Intron|FOLH1_uc009yma.2_Intron|FOLH1_uc001nha.2_Intron	NM_004476	NP_004467			folate hydrolase 1 isoform 1						proteolysis	cytoplasm|integral to plasma membrane|membrane fraction|nucleus	carboxypeptidase activity|dipeptidase activity|metal ion binding|metallopeptidase activity			large_intestine(1)|ovary(1)|skin(1)	3					Capromab(DB00089)|L-Glutamic Acid(DB00142)													---	---	---	---
Unknown	0	broad.mit.edu	37	11	49454957	49454968	+	IGR	DEL	TTTTTTTTTTTT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:49454957_49454968delTTTTTTTTTTTT								FOLH1 (224735 upstream) : LOC440040 (125112 downstream)																																			---	---	---	---
LOC440040	440040	broad.mit.edu	37	11	49670278	49670278	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:49670278delT	uc010rhy.1	+						LOC440040_uc009ymb.2_Intron	NR_027044				SubName: Full=cDNA FLJ60249, highly similar to Metabotropic glutamate receptor 5;												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	11	49946662	49946663	+	IGR	INS	-	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:49946662_49946663insA								LOC440040 (114695 upstream) : OR4C13 (27312 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	49976928	49976928	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:49976928delA								OR4C13 (2026 upstream) : OR4C12 (26182 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	50234700	50234701	+	IGR	DEL	GA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:50234700_50234701delGA								OR4C12 (230663 upstream) : LOC441601 (4299 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	51438303	51438303	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:51438303delA								OR4A5 (25908 upstream) : OR4C46 (76979 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	54818022	54818023	+	IGR	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:54818022_54818023delAA								None (None upstream) : TRIM48 (211635 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	54958759	54958759	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:54958759delT								None (None upstream) : TRIM48 (70899 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	55607259	55607259	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:55607259delA								OR5D16 (47 upstream) : SPRYD5 (43514 downstream)																																			---	---	---	---
OR5W2	390148	broad.mit.edu	37	11	55682137	55682137	+	5'Flank	DEL	A	-	-	rs79964529		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:55682137delA	uc010rir.1	-							NM_001001960	NP_001001960			olfactory receptor, family 5, subfamily W,						sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)|skin(1)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	11	56045603	56045603	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:56045603delT								OR5T1 (1508 upstream) : OR8H1 (12002 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	56672103	56672104	+	IGR	DEL	AA	-	-	rs139349671		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:56672103_56672104delAA								OR9G4 (160816 upstream) : OR5AK2 (84285 downstream)																																			---	---	---	---
SSRP1	6749	broad.mit.edu	37	11	57094651	57094651	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:57094651delT	uc001njt.2	-						TNKS1BP1_uc001njs.2_5'Flank|TNKS1BP1_uc009ymd.1_5'Flank	NM_003146	NP_003137			structure specific recognition protein 1						DNA repair|DNA replication|positive regulation of viral transcription|regulation of transcription, DNA-dependent|transcription elongation from RNA polymerase II promoter|viral reproduction	chromosome|cytoplasm|nucleoplasm	DNA binding|protein binding			ovary(2)	2																		---	---	---	---
P2RX3	5024	broad.mit.edu	37	11	57116940	57116942	+	Intron	DEL	AAA	-	-	rs147483912		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:57116940_57116942delAAA	uc001nju.2	+							NM_002559	NP_002550			purinergic receptor P2X3						positive regulation of calcium ion transport into cytosol|positive regulation of calcium-mediated signaling	integral to plasma membrane	ATP binding|extracellular ATP-gated cation channel activity|purinergic nucleotide receptor activity				0																		---	---	---	---
RTN4RL2	349667	broad.mit.edu	37	11	57235787	57235788	+	Intron	DEL	CT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:57235787_57235788delCT	uc010rjt.1	+							NM_178570	NP_848665			reticulon 4 receptor-like 2 precursor						axon regeneration	anchored to plasma membrane	receptor activity				0																		---	---	---	---
RTN4RL2	349667	broad.mit.edu	37	11	57239338	57239339	+	Intron	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:57239338_57239339delTT	uc010rjt.1	+							NM_178570	NP_848665			reticulon 4 receptor-like 2 precursor						axon regeneration	anchored to plasma membrane	receptor activity				0																		---	---	---	---
UBE2L6	9246	broad.mit.edu	37	11	57332277	57332277	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:57332277delA	uc001nkn.1	-						UBE2L6_uc001nko.1_Intron	NM_004223	NP_004214			ubiquitin-conjugating enzyme E2L 6 isoform 1						negative regulation of type I interferon production	cytosol	protein binding|ubiquitin-protein ligase activity			ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	11	57389202	57389203	+	IGR	DEL	TT	-	-	rs71773092		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:57389202_57389203delTT								SERPING1 (6876 upstream) : MIR130A (19468 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	57702294	57702294	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:57702294delT								CTNND1 (115643 upstream) : OR9Q1 (89059 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	57708017	57708018	+	IGR	DEL	AT	-	-	rs143467640		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:57708017_57708018delAT								CTNND1 (121366 upstream) : OR9Q1 (83335 downstream)																																			---	---	---	---
OR9Q1	219956	broad.mit.edu	37	11	57937324	57937324	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:57937324delT	uc001nmj.2	+							NM_001005212	NP_001005212			olfactory receptor, family 9, subfamily Q,						sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)	1		Breast(21;0.222)																---	---	---	---
Unknown	0	broad.mit.edu	37	11	59184103	59184103	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:59184103delA								OR5AN1 (51237 upstream) : OR5A2 (5351 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	59230126	59230126	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:59230126delA								OR4D6 (4749 upstream) : OR4D10 (14777 downstream)																																			---	---	---	---
OR4D9	390199	broad.mit.edu	37	11	59280555	59280555	+	5'Flank	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:59280555delT	uc010rkv.1	+							NM_001004711	NP_001004711			olfactory receptor, family 4, subfamily D,						sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	11	59329196	59329196	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:59329196delA								OR4D9 (45868 upstream) : OSBP (12675 downstream)																																			---	---	---	---
OSBP	5007	broad.mit.edu	37	11	59348896	59348897	+	Intron	DEL	CA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:59348896_59348897delCA	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	59368589	59368595	+	Intron	DEL	AAAAAAA	-	-	rs34934607		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:59368589_59368595delAAAAAAA	uc001noc.1	-						OSBP_uc009ymr.1_5'Flank	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)														---	---	---	---
PATL1	219988	broad.mit.edu	37	11	59427010	59427011	+	Intron	INS	-	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:59427010_59427011insT	uc001noe.3	-						PATL1_uc009yms.1_Intron|PATL1_uc010rkw.1_5'Flank	NM_152716	NP_689929			protein associated with topoisomerase II homolog						cytoplasmic mRNA processing body assembly|deadenylation-dependent decapping of nuclear-transcribed mRNA	cytoplasmic mRNA processing body	protein binding|RNA binding			ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	11	59487445	59487445	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:59487445delT								OR10V1 (6127 upstream) : STX3 (35444 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	59494827	59494827	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:59494827delA								OR10V1 (13509 upstream) : STX3 (28062 downstream)																																			---	---	---	---
GIF	2694	broad.mit.edu	37	11	59611620	59611620	+	Intron	DEL	T	-	-	rs72085643		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-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	59872251	59872253	+	IGR	DEL	TTC	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:59872251_59872253delTTC								MS4A2 (6237 upstream) : MS4A6A (66828 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	59997717	59997718	+	5'Flank	DEL	GA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:59997717_59997718delGA	uc001nov.2	-						uc001now.2_5'Flank|uc001nox.2_5'Flank|uc001noy.2_5'Flank|uc009ymw.2_5'Flank					Homo sapiens mRNA for hypothetical protein, partial cds, clone:Hsa11-digit17-05-01-R.																														---	---	---	---
Unknown	0	broad.mit.edu	37	11	60022792	60022793	+	IGR	INS	-	A	A	rs139883084	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:60022792_60022793insA								MS4A6A (70653 upstream) : MS4A4A (25346 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	60486770	60486770	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:60486770delA								MS4A8B (3488 upstream) : MS4A15 (37570 downstream)																																			---	---	---	---
PRPF19	27339	broad.mit.edu	37	11	60666410	60666411	+	Intron	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:60666410_60666411delAA	uc001nqf.2	-							NM_014502	NP_055317			PRP19/PSO4 pre-mRNA processing factor 19						DNA repair|protein polyubiquitination|spliceosome assembly	catalytic step 2 spliceosome|nuclear speck|spindle|ubiquitin ligase complex	DNA binding|identical protein binding|ubiquitin-ubiquitin ligase activity			ovary(1)	1																OREG0020994	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
TMEM132A	54972	broad.mit.edu	37	11	60702925	60702925	+	Intron	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:60702925delG	uc001nqj.2	+						TMEM132A_uc001nqi.2_Intron|TMEM132A_uc001nqm.2_5'UTR	NM_178031	NP_821174			transmembrane protein 132A isoform b							endoplasmic reticulum membrane|Golgi membrane|integral to membrane				skin(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	11	60726671	60726672	+	IGR	DEL	AG	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:60726671_60726672delAG								SLC15A3 (7414 upstream) : CD6 (12443 downstream)																																			---	---	---	---
SYT7	9066	broad.mit.edu	37	11	61298930	61298930	+	Intron	DEL	G	-	-	rs113828292		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:61298930delG	uc001nrv.2	-						SYT7_uc009ynr.2_Intron	NM_004200	NP_004191			synaptotagmin VII							cell junction|integral to membrane|synaptic vesicle membrane	transporter activity			ovary(3)|pancreas(1)	4																		---	---	---	---
SYT7	9066	broad.mit.edu	37	11	61336647	61336647	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:61336647delT	uc001nrv.2	-						SYT7_uc009ynr.2_Intron	NM_004200	NP_004191			synaptotagmin VII							cell junction|integral to membrane|synaptic vesicle membrane	transporter activity			ovary(3)|pancreas(1)	4																		---	---	---	---
AHNAK	79026	broad.mit.edu	37	11	62242237	62242237	+	Intron	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:62242237delG	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)																---	---	---	---
HNRNPUL2	221092	broad.mit.edu	37	11	62485317	62485317	+	Intron	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:62485317delG	uc001nuw.2	-						HNRNPUL2_uc001nuu.1_Intron	NM_001079559	NP_001073027			heterogeneous nuclear ribonucleoprotein U-like						cell killing	nucleus	ATP binding|nucleic acid binding				0																		---	---	---	---
ZBTB3	79842	broad.mit.edu	37	11	62521744	62521744	+	5'Flank	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:62521744delC	uc001nuz.2	-							NM_024784	NP_079060			zinc finger and BTB domain containing 3						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			breast(2)|ovary(1)	3																		---	---	---	---
SLC3A2	6520	broad.mit.edu	37	11	62647814	62647815	+	Intron	INS	-	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:62647814_62647815insA	uc001nwd.2	+						SLC3A2_uc001nwb.2_Intron|SLC3A2_uc001nwc.2_Intron|SLC3A2_uc001nwe.2_Intron|SLC3A2_uc001nwf.2_Intron|SLC3A2_uc001nwg.2_5'Flank|SLC3A2_uc010rml.1_5'Flank	NM_002394	NP_002385			solute carrier family 3, member 2 isoform c						blood coagulation|carbohydrate metabolic process|cell growth|cellular nitrogen compound metabolic process|leucine import|leukocyte migration|tryptophan transport	apical plasma membrane|cell surface|integral to membrane|melanosome	calcium:sodium antiporter activity|catalytic activity|cation binding|neutral amino acid transmembrane transporter activity|protein binding				0																		---	---	---	---
SLC3A2	6520	broad.mit.edu	37	11	62649529	62649529	+	Frame_Shift_Del	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:62649529delA	uc001nwd.2	+	5	1116	c.892delA	c.(892-894)AAAfs	p.K298fs	SLC3A2_uc001nwb.2_Frame_Shift_Del_p.K329fs|SLC3A2_uc001nwc.2_Frame_Shift_Del_p.K299fs|SLC3A2_uc001nwe.2_Frame_Shift_Del_p.K267fs|SLC3A2_uc001nwf.2_Frame_Shift_Del_p.K236fs|SLC3A2_uc001nwg.2_Frame_Shift_Del_p.K197fs|SLC3A2_uc010rml.1_5'Flank	NM_002394	NP_002385	P08195	4F2_HUMAN	solute carrier family 3, member 2 isoform c	298	Extracellular (Potential).				blood coagulation|carbohydrate metabolic process|cell growth|cellular nitrogen compound metabolic process|leucine import|leukocyte migration|tryptophan transport	apical plasma membrane|cell surface|integral to membrane|melanosome	calcium:sodium antiporter activity|catalytic activity|cation binding|neutral amino acid transmembrane transporter activity|protein binding				0																		---	---	---	---
SLC22A25	387601	broad.mit.edu	37	11	62967016	62967016	+	Intron	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:62967016delC	uc001nwr.1	-						SLC22A10_uc010rmo.1_Intron|SLC22A25_uc009yoq.1_Intron|SLC22A25_uc001nws.1_Intron|SLC22A25_uc001nwt.1_Intron	NM_199352	NP_955384			putative UST1-like organic anion transporter						transmembrane transport	integral to membrane				ovary(3)|skin(1)	4																		---	---	---	---
SLC22A10	387775	broad.mit.edu	37	11	63046871	63046871	+	Intron	DEL	T	-	-	rs1789327	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:63046871delT	uc010rmo.1	+											Homo sapiens mRNA for putative protein product of HMFN2567, complete cds.							integral to membrane	transmembrane transporter activity			ovary(2)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	11	63265032	63265032	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:63265032delT								HRASLS5 (6352 upstream) : LGALS12 (8492 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	63389685	63389687	+	IGR	DEL	AAC	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:63389685_63389687delAAC								PLA2G16 (7744 upstream) : ATL3 (6750 downstream)																																			---	---	---	---
NUDT22	84304	broad.mit.edu	37	11	63995181	63995181	+	Intron	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:63995181delG	uc001nyp.3	+						TRPT1_uc010rnc.1_5'Flank|TRPT1_uc010rnd.1_5'Flank|TRPT1_uc001nyn.2_5'Flank|TRPT1_uc001nyo.2_5'Flank|TRPT1_uc010rne.1_5'Flank|TRPT1_uc010rnf.1_5'Flank|NUDT22_uc009ype.2_Intron|NUDT22_uc001nyq.3_Intron|NUDT22_uc010rng.1_Intron|DNAJC4_uc001nys.2_5'Flank|DNAJC4_uc001nyt.2_5'Flank|DNAJC4_uc001nyu.2_5'Flank	NM_032344	NP_115720			nudix (nucleoside diphosphate linked moiety								hydrolase activity				0																		---	---	---	---
RASGRP2	10235	broad.mit.edu	37	11	64509190	64509191	+	Intron	DEL	GA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:64509190_64509191delGA	uc009ypu.2	-						RASGRP2_uc001oat.2_5'Flank|RASGRP2_uc001oau.2_5'Flank|RASGRP2_uc009ypv.2_Intron|RASGRP2_uc009ypw.2_Intron	NM_001098671	NP_001092141			RAS guanyl releasing protein 2						platelet activation|Ras protein signal transduction|regulation of cell growth|regulation of small GTPase mediated signal transduction	cell junction|cytosol|ruffle membrane|synapse|synaptosome	calcium ion binding|diacylglycerol binding|guanyl-nucleotide exchange factor activity				0																		---	---	---	---
PYGM	5837	broad.mit.edu	37	11	64529666	64529666	+	5'Flank	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:64529666delA	uc001oax.3	-						PYGM_uc001oay.3_5'Flank	NM_005609	NP_005600			muscle glycogen phosphorylase isoform 1						glucose metabolic process|glycogen catabolic process	cytosol	glycogen phosphorylase activity|protein binding			ovary(2)	2					Pyridoxal Phosphate(DB00114)													---	---	---	---
ATG2A	23130	broad.mit.edu	37	11	64662599	64662599	+	Frame_Shift_Del	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:64662599delC	uc001obx.2	-	41	5778	c.5663delG	c.(5662-5664)GGCfs	p.G1888fs	uc009ypx.2_5'Flank|ATG2A_uc001obw.2_Frame_Shift_Del_p.G653fs	NM_015104	NP_055919	Q2TAZ0	ATG2A_HUMAN	autophagy related 2A	1888							protein binding			ovary(1)|central_nervous_system(1)	2																		---	---	---	---
PPP2R5B	5526	broad.mit.edu	37	11	64701872	64701873	+	3'UTR	INS	-	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:64701872_64701873insG	uc001oby.2	+	14					PPP2R5B_uc001obz.2_3'UTR	NM_006244	NP_006235			beta isoform of regulatory subunit B56, protein						signal transduction	cytoplasm|protein phosphatase type 2A complex	protein binding|protein phosphatase type 2A regulator activity			ovary(2)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	11	64752335	64752335	+	IGR	DEL	T	-	-	rs111294051		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:64752335delT								C11orf85 (12778 upstream) : BATF2 (3082 downstream)																																			---	---	---	---
ARL2	402	broad.mit.edu	37	11	64787014	64787014	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:64787014delA	uc001och.3	+						ARL2_uc010rnu.1_3'UTR|SNX15_uc001oci.3_Intron	NM_001667	NP_001658			ADP-ribosylation factor-like 2						cell cycle|centrosome organization|maintenance of protein location in nucleus|negative regulation of GTPase activity|positive regulation of cell-substrate adhesion|positive regulation of microtubule polymerization|small GTPase mediated signal transduction|tight junction assembly|tubulin complex assembly	centrosome|lateral plasma membrane|mitochondrial intermembrane space|nucleus	GTP binding|GTPase activity|GTPase inhibitor activity|protein binding				0																		---	---	---	---
SYVN1	84447	broad.mit.edu	37	11	64899850	64899850	+	Intron	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:64899850delG	uc001odb.2	-						SYVN1_uc001odc.2_Intron|SYVN1_uc009yqc.2_Intron	NM_172230	NP_757385			synoviolin 1 isoform b						ER-associated protein catabolic process|response to stress	endoplasmic reticulum membrane|integral to membrane|nucleus	acid-amino acid ligase activity|protein binding|zinc ion binding			ovary(1)	1																		---	---	---	---
SLC22A20	440044	broad.mit.edu	37	11	64997100	64997100	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:64997100delT	uc010roc.1	+							NM_001004326	NP_001004326			solute carrier family 22, member 20						ion transport	integral to membrane	transmembrane transporter activity			central_nervous_system(1)	1																		---	---	---	---
POLA2	23649	broad.mit.edu	37	11	65041317	65041317	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:65041317delA	uc001odj.2	+						POLA2_uc009yqf.1_Intron|POLA2_uc010rod.1_Intron	NM_002689	NP_002680			DNA-directed DNA polymerase alpha 2						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	nucleoplasm	DNA binding				0					Dacarbazine(DB00851)													---	---	---	---
CDC42EP2	10435	broad.mit.edu	37	11	65079801	65079801	+	5'Flank	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:65079801delT	uc001odl.2	+							NM_006779	NP_006770			Cdc42 effector protein 2						actin filament organization|positive regulation of actin filament polymerization|positive regulation of pseudopodium assembly|regulation of cell shape	cytoplasm|cytoskeleton|endomembrane system|plasma membrane	GTP-Rho binding|Rho GTPase activator activity				0																		---	---	---	---
NEAT1	283131	broad.mit.edu	37	11	65190755	65190755	+	RNA	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:65190755delT	uc001odv.2	+	1		c.511delT			NEAT1_uc010rog.1_RNA					Human MEN1 region clone epsilon/beta mRNA, 5' fragment.												0																		---	---	---	---
KCNK7	10089	broad.mit.edu	37	11	65364466	65364466	+	5'Flank	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:65364466delT	uc001oes.2	-						KCNK7_uc001oeq.2_5'Flank|KCNK7_uc001oer.2_5'Flank|KCNK7_uc001oeu.2_5'Flank	NM_033347	NP_203133			potassium channel, subfamily K, member 7 isoform							integral to membrane	potassium channel activity|voltage-gated ion channel activity				0																		---	---	---	---
KAT5	10524	broad.mit.edu	37	11	65481128	65481128	+	Frame_Shift_Del	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:65481128delT	uc001ofi.2	+	6	756	c.506delT	c.(505-507)GTTfs	p.V169fs	KAT5_uc001ofj.2_Frame_Shift_Del_p.V117fs|KAT5_uc001ofk.2_Frame_Shift_Del_p.V202fs|KAT5_uc010roo.1_Frame_Shift_Del_p.V150fs|KAT5_uc001ofl.2_5'UTR	NM_006388	NP_006379	Q92993	KAT5_HUMAN	K(lysine) acetyltransferase 5 isoform 2	169					androgen receptor signaling pathway|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator|double-strand break repair|interspecies interaction between organisms|negative regulation of interleukin-2 production|negative regulation of transcription from RNA polymerase II promoter|positive regulation of transcription, DNA-dependent|regulation of growth|transcription, DNA-dependent	NuA4 histone acetyltransferase complex|nucleolus|perinuclear region of cytoplasm|Piccolo NuA4 histone acetyltransferase complex	androgen receptor binding|histone acetyltransferase activity|metal ion binding|repressing transcription factor binding|transcription coactivator activity				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	11	65583962	65583965	+	IGR	DEL	AAAC	-	-	rs72398545		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:65583962_65583965delAAAC								OVOL1 (19279 upstream) : SNX32 (17445 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	66016394	66016394	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:66016394delT								PACS1 (4181 upstream) : KLC2 (8371 downstream)																																			---	---	---	---
RAB1B	81876	broad.mit.edu	37	11	66039143	66039143	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-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																		---	---	---	---
ACTN3	89	broad.mit.edu	37	11	66321928	66321929	+	Intron	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:66321928_66321929delAA	uc001oio.1	+						ACTN3_uc010rpi.1_Intron	NM_001104	NP_001095			actinin, alpha 3						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																		---	---	---	---
RBM4B	83759	broad.mit.edu	37	11	66436924	66436924	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-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																		---	---	---	---
SYT12	91683	broad.mit.edu	37	11	66788795	66788795	+	5'Flank	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:66788795delT	uc009yrl.2	+						SYT12_uc001oju.2_5'Flank	NM_177963	NP_808878			synaptotagmin XII							cell junction|integral to membrane|synaptic vesicle membrane				ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	11	66851917	66851917	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:66851917delA								RHOD (12430 upstream) : KDM2A (34823 downstream)																																			---	---	---	---
LOC100130987	100130987	broad.mit.edu	37	11	67106844	67106844	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:67106844delA	uc010rpo.1	+							NR_024469				Homo sapiens cDNA FLJ38836 fis, clone MESAN2002519, weakly similar to Mus musculus cell cycle checkpoint control protein Mrad9 gene.												0																		---	---	---	---
RAD9A	5883	broad.mit.edu	37	11	67162701	67162701	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:67162701delT	uc001okr.2	+						RAD9A_uc001oks.2_5'Flank	NM_004584	NP_004575			RAD9 homolog						DNA damage checkpoint|DNA repair|DNA replication|DNA replication checkpoint	nucleoplasm	3'-5' exonuclease activity|exodeoxyribonuclease III activity|histone deacetylase binding|protein kinase binding|SH3 domain binding				0			BRCA - Breast invasive adenocarcinoma(15;8.53e-07)										Direct_reversal_of_damage|Other_conserved_DNA_damage_response_genes					---	---	---	---
AIP	9049	broad.mit.edu	37	11	67254767	67254767	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:67254767delT	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_				---	---	---	---
NDUFV1	4723	broad.mit.edu	37	11	67377309	67377309	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:67377309delT	uc001omj.2	+						NDUFV1_uc010rpv.1_Intron|NDUFV1_uc001oml.2_Intron|NDUFV1_uc001omk.3_Intron|NDUFV1_uc009yrz.1_Intron|NDUFV1_uc010rpw.1_5'Flank	NM_007103	NP_009034			NADH dehydrogenase ubiquinone flavoprotein 1						mitochondrial electron transport, NADH to ubiquinone|transport	mitochondrial respiratory chain complex I	4 iron, 4 sulfur cluster binding|FMN binding|metal ion binding|NAD binding|NADH dehydrogenase (ubiquinone) activity			skin(1)	1					NADH(DB00157)													---	---	---	---
Unknown	0	broad.mit.edu	37	11	67452297	67452297	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:67452297delT								ALDH3B2 (3612 upstream) : LOC645332 (106943 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	67458560	67458560	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:67458560delT								ALDH3B2 (9875 upstream) : LOC645332 (100680 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	67508978	67508978	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:67508978delT								ALDH3B2 (60293 upstream) : LOC645332 (50262 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	67534304	67534305	+	IGR	INS	-	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:67534304_67534305insA								ALDH3B2 (85619 upstream) : LOC645332 (24935 downstream)																																			---	---	---	---
SUV420H1	51111	broad.mit.edu	37	11	67974681	67974684	+	Intron	DEL	AAAA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:67974681_67974684delAAAA	uc001onm.1	-						SUV420H1_uc001onn.1_Intron|SUV420H1_uc009ysf.2_Intron|SUV420H1_uc001ono.1_Intron|SUV420H1_uc001onp.2_Intron|SUV420H1_uc010rqa.1_Intron|SUV420H1_uc001onq.2_Intron	NM_017635	NP_060105			suppressor of variegation 4-20 homolog 1 isoform						regulation of transcription, DNA-dependent|transcription, DNA-dependent		protein binding			ovary(2)|kidney(1)	3																		---	---	---	---
C11orf24	53838	broad.mit.edu	37	11	68036580	68036582	+	Intron	DEL	TTT	-	-	rs147773525		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:68036580_68036582delTTT	uc001onr.3	-						C11orf24_uc001ons.2_5'Flank	NM_022338	NP_071733			hypothetical protein LOC53838 precursor							integral to membrane					0																		---	---	---	---
LRP5	4041	broad.mit.edu	37	11	68173144	68173144	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:68173144delT	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																		---	---	---	---
SAPS3	55291	broad.mit.edu	37	11	68333840	68333841	+	Intron	INS	-	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:68333840_68333841insT	uc001onw.2	+						SAPS3_uc001onv.2_Intron|SAPS3_uc001ony.3_Intron|SAPS3_uc001onx.2_Intron|SAPS3_uc009ysh.2_Intron|SAPS3_uc001onu.2_Intron|SAPS3_uc010rqc.1_Intron|SAPS3_uc010rqd.1_Intron	NM_001164161	NP_001157633			SAPS domain family, member 3 isoform 6						regulation of phosphoprotein phosphatase activity	cytoplasm|nucleus	protein phosphatase binding				0			LUAD - Lung adenocarcinoma(13;0.102)															---	---	---	---
Unknown	0	broad.mit.edu	37	11	68617319	68617319	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:68617319delT								CPT1A (7920 upstream) : MRPL21 (41428 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	68968715	68968716	+	IGR	DEL	GT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:68968715_68968716delGT								TPCN2 (38808 upstream) : MYEOV (92906 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	69342434	69342434	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:69342434delA								MYEOV (185985 upstream) : CCND1 (113439 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	69383779	69383780	+	IGR	DEL	TG	-	-	rs5792477		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:69383779_69383780delTG								MYEOV (227330 upstream) : CCND1 (72093 downstream)																																			---	---	---	---
FGF19	9965	broad.mit.edu	37	11	69521837	69521838	+	5'Flank	DEL	AT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:69521837_69521838delAT	uc001opf.2	-							NM_005117	NP_005108			fibroblast growth factor 19 precursor						fibroblast growth factor receptor signaling pathway|insulin receptor signaling pathway|negative regulation of bile acid biosynthetic process|nervous system development|positive regulation of cell proliferation|positive regulation of ERK1 and ERK2 cascade|positive regulation of glucose import|positive regulation of JNK cascade	extracellular region	fibroblast growth factor receptor binding|growth factor activity			skin(1)	1	all_cancers(3;5.53e-114)|all_epithelial(3;1.34e-121)|Breast(3;9.28e-34)|all_lung(4;1.99e-21)|Lung NSC(4;4.65e-21)|Hepatocellular(3;6.15e-15)|Melanoma(5;1.89e-05)|Ovarian(3;0.0348)		Epithelial(3;3.05e-56)|all cancers(3;2.69e-50)|Lung(3;1.13e-16)|LUSC - Lung squamous cell carcinoma(11;3.74e-15)|STAD - Stomach adenocarcinoma(18;0.0278)|LUAD - Lung adenocarcinoma(13;0.0537)															---	---	---	---
FGF4	2249	broad.mit.edu	37	11	69592735	69592735	+	5'Flank	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:69592735delT	uc001opg.1	-						FGF4_uc010rqj.1_5'Flank	NM_002007	NP_001998			fibroblast growth factor 4 precursor						cell-cell signaling|chondroblast differentiation|fibroblast growth factor receptor signaling pathway|insulin receptor signaling pathway|mesenchymal cell proliferation|positive regulation of cell division|positive regulation of cell proliferation|positive regulation of ERK1 and ERK2 cascade	extracellular region	growth factor activity|heparin binding				0	Melanoma(5;1.89e-05)		LUSC - Lung squamous cell carcinoma(11;3.74e-15)|STAD - Stomach adenocarcinoma(18;0.0278)		Pentosan Polysulfate(DB00686)													---	---	---	---
Unknown	0	broad.mit.edu	37	11	70037287	70037288	+	IGR	DEL	GT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:70037287_70037288delGT								ANO1 (1638 upstream) : FADD (11981 downstream)																																			---	---	---	---
PPFIA1	8500	broad.mit.edu	37	11	70220486	70220487	+	Intron	INS	-	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:70220486_70220487insA	uc001opo.2	+						PPFIA1_uc001opn.1_Intron|PPFIA1_uc001opp.2_Intron|PPFIA1_uc001opr.2_Intron|PPFIA1_uc001ops.2_Intron|uc001opt.1_RNA	NM_003626	NP_003617			PTPRF interacting protein alpha 1 isoform b						cell-matrix adhesion	cytoplasm	protein binding|signal transducer activity			lung(2)|ovary(1)	3			BRCA - Breast invasive adenocarcinoma(2;1.04e-44)|LUSC - Lung squamous cell carcinoma(11;1.46e-14)|STAD - Stomach adenocarcinoma(18;0.0513)															---	---	---	---
SHANK2	22941	broad.mit.edu	37	11	70803641	70803641	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:70803641delA	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)															---	---	---	---
NUMA1	4926	broad.mit.edu	37	11	71746453	71746453	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:71746453delT	uc001orl.1	-						NUMA1_uc001ork.1_Intron|NUMA1_uc001orm.1_Intron|NUMA1_uc009ysx.1_Intron|NUMA1_uc001oro.1_Intron|NUMA1_uc009ysy.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								---	---	---	---
NUMA1	4926	broad.mit.edu	37	11	71787831	71787832	+	Intron	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:71787831_71787832delAA	uc001orl.1	-						NUMA1_uc001ork.1_Intron|NUMA1_uc001orm.1_Intron|NUMA1_uc001oro.1_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								---	---	---	---
Unknown	0	broad.mit.edu	37	11	71894244	71894247	+	IGR	DEL	AAAA	-	-	rs113847016		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:71894244_71894247delAAAA								FOLR3 (43310 upstream) : FOLR1 (6355 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	71918436	71918437	+	IGR	DEL	AA	-	-	rs35124063		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:71918436_71918437delAA								FOLR1 (11070 upstream) : FOLR2 (9382 downstream)																																			---	---	---	---
CLPB	81570	broad.mit.edu	37	11	72062923	72062923	+	Intron	DEL	T	-	-	rs78067564		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:72062923delT	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																		---	---	---	---
CLPB	81570	broad.mit.edu	37	11	72100806	72100806	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:72100806delA	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	72378914	72378917	+	Intron	DEL	AAAA	-	-	rs34893653		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:72378914_72378917delAAAA	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-4200-01A-01D-1126-08	TCGA-BR-4200-11A-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																		---	---	---	---
ARAP1	116985	broad.mit.edu	37	11	72462757	72462757	+	Intron	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:72462757delC	uc001osu.2	-						ARAP1_uc001osv.2_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	72602129	72602129	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:72602129delT	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)															---	---	---	---
FCHSD2	9873	broad.mit.edu	37	11	72613431	72613431	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:72613431delA	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)															---	---	---	---
FCHSD2	9873	broad.mit.edu	37	11	72661474	72661474	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:72661474delT	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)															---	---	---	---
P2RY2	5029	broad.mit.edu	37	11	72938392	72938393	+	Intron	DEL	TG	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:72938392_72938393delTG	uc001otj.2	+						P2RY2_uc001otk.2_Intron|P2RY2_uc001otl.2_Intron	NM_002564	NP_002555			purinergic receptor P2Y2						activation of phospholipase C activity by G-protein coupled receptor protein signaling pathway coupled to IP3 second messenger	integral to plasma membrane	purinergic nucleotide receptor activity, G-protein coupled			ovary(2)|lung(1)|skin(1)	4					Suramin(DB04786)													---	---	---	---
ARHGEF17	9828	broad.mit.edu	37	11	73046611	73046611	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:73046611delA	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																OREG0021213	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
FAM168A	23201	broad.mit.edu	37	11	73302189	73302189	+	Intron	DEL	A	-	-	rs80292545		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:73302189delA	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	73418757	73418757	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:73418757delT	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																		---	---	---	---
C2CD3	26005	broad.mit.edu	37	11	73730729	73730729	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:73730729delT	uc001out.2	-											Homo sapiens mRNA for hypothetical protein, complete cds, clone:Hsa11-digit29-22-02-04-C.							centrosome				ovary(4)|pancreas(2)|skin(1)	7	Breast(11;4.16e-06)																	---	---	---	---
Unknown	0	broad.mit.edu	37	11	74140696	74140697	+	IGR	INS	-	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:74140696_74140697insC								PGM2L1 (31194 upstream) : KCNE3 (25191 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	74294155	74294156	+	IGR	INS	-	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:74294155_74294156insA								LIPT2 (89400 upstream) : POLD3 (9473 downstream)																																			---	---	---	---
SLCO2B1	11309	broad.mit.edu	37	11	74826486	74826486	+	Intron	DEL	A	-	-	rs112067482		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:74826486delA	uc010rrp.1	+											Homo sapiens mRNA for KIAA0880 protein, partial cds.						sodium-independent organic anion transport	integral to membrane	sodium-independent organic anion transmembrane transporter activity			ovary(1)|breast(1)	2					Ergoloid mesylate(DB01049)													---	---	---	---
Unknown	0	broad.mit.edu	37	11	75458769	75458769	+	IGR	DEL	A	-	-	rs112191139		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:75458769delA								MOGAT2 (16439 upstream) : DGAT2 (21009 downstream)																																			---	---	---	---
UVRAG	7405	broad.mit.edu	37	11	75605395	75605395	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:75605395delA	uc001oxc.2	+						UVRAG_uc010rrw.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																		---	---	---	---
UVRAG	7405	broad.mit.edu	37	11	75704953	75704953	+	Intron	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:75704953delG	uc001oxc.2	+						UVRAG_uc010rrw.1_Intron|UVRAG_uc001oxd.2_Intron|UVRAG_uc010rrx.1_Intron|UVRAG_uc009yuh.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	75860785	75860786	+	IGR	INS	-	G	G	rs144739230	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:75860785_75860786insG								UVRAG (5504 upstream) : WNT11 (36585 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	75893677	75893677	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:75893677delA								UVRAG (38396 upstream) : WNT11 (3694 downstream)																																			---	---	---	---
C11orf30	56946	broad.mit.edu	37	11	76187041	76187042	+	Intron	DEL	TC	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:76187041_76187042delTC	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	76246877	+	Intron	DEL	TTT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:76246875_76246877delTTT	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																		---	---	---	---
ACER3	55331	broad.mit.edu	37	11	76730622	76730622	+	Intron	DEL	A	-	-	rs621257		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:76730622delA	uc009yum.1	+						ACER3_uc001oxu.2_Intron|ACER3_uc009yun.1_Intron|ACER3_uc009yuo.1_Intron|ACER3_uc010rsh.1_Intron|ACER3_uc010rsi.1_Intron|ACER3_uc010rsj.1_Intron	NM_018367	NP_060837			phytoceramidase, alkaline						ceramide metabolic process|phytosphingosine biosynthetic process|positive regulation of cell proliferation|sphingosine biosynthetic process	integral to endoplasmic reticulum membrane|integral to Golgi membrane	phytoceramidase activity				0																		---	---	---	---
CAPN5	726	broad.mit.edu	37	11	76810891	76810891	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:76810891delT	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																		---	---	---	---
PAK1	5058	broad.mit.edu	37	11	77116720	77116729	+	Intron	DEL	ACACACACAC	-	-	rs72497267		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:77116720_77116729delACACACACAC	uc001oyh.3	-						PAK1_uc010rso.1_Intron|PAK1_uc001oyg.3_Intron|PAK1_uc001oyi.1_Intron	NM_002576	NP_002567			p21-activated kinase 1 isoform 2						apoptosis|axon guidance|cytoskeleton organization|ER-nucleus signaling pathway|positive regulation of JUN kinase activity|positive regulation of peptidyl-serine phosphorylation|protein autophosphorylation|T cell costimulation|T cell receptor signaling pathway	cytosol|focal adhesion|Golgi apparatus	ATP binding|collagen binding|protein binding|protein serine/threonine kinase activity			skin(2)|stomach(1)|lung(1)	4	all_cancers(14;1.75e-18)																	---	---	---	---
Unknown	0	broad.mit.edu	37	11	77189256	77189257	+	IGR	DEL	TT	-	-	rs80224372		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:77189256_77189257delTT								PAK1 (4148 upstream) : AQP11 (111179 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	77193043	77193043	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:77193043delT								PAK1 (7935 upstream) : AQP11 (107393 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	77292288	77292288	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:77292288delT								PAK1 (107180 upstream) : AQP11 (8148 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	77294170	77294170	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:77294170delT								PAK1 (109062 upstream) : AQP11 (6266 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	77364316	77364316	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:77364316delA								CLNS1A (15465 upstream) : RSF1 (12959 downstream)																																			---	---	---	---
RSF1	51773	broad.mit.edu	37	11	77485820	77485820	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:77485820delT	uc001oyn.2	-						RSF1_uc001oyo.1_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	77496637	77496637	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:77496637delA	uc001oyn.2	-						RSF1_uc001oyo.1_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	77524322	77524322	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:77524322delT	uc001oyn.2	-						RSF1_uc001oyo.1_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)															---	---	---	---
INTS4	92105	broad.mit.edu	37	11	77639340	77639340	+	Intron	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:77639340delG	uc001oys.2	-						INTS4_uc001oyt.2_Intron|INTS4_uc001oyu.1_Intron	NM_033547	NP_291025			integrator complex subunit 4						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)															---	---	---	---
NARS2	79731	broad.mit.edu	37	11	78201091	78201092	+	Intron	INS	-	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:78201091_78201092insA	uc001ozi.2	-						NARS2_uc010rsq.1_Intron	NM_024678	NP_078954			asparaginyl-tRNA synthetase 2, mitochondrial						asparaginyl-tRNA aminoacylation	mitochondrial matrix	asparagine-tRNA ligase activity|ATP binding|nucleic acid binding			ovary(2)	2	all_cancers(14;2.63e-17)|all_epithelial(13;1.85e-19)				L-Asparagine(DB00174)													---	---	---	---
ODZ4	26011	broad.mit.edu	37	11	79019406	79019406	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:79019406delT	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	79050768	79050768	+	Intron	DEL	A	-	-	rs67817337		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:79050768delA	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	79841996	79841999	+	IGR	DEL	ATCC	-	-	rs71936660		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:79841996_79841999delATCC								ODZ4 (690301 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	79899723	79899723	+	IGR	DEL	A	-	-	rs72350657		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:79899723delA								ODZ4 (748028 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	80709142	80709143	+	IGR	INS	-	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:80709142_80709143insA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	81097338	81097339	+	IGR	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:81097338_81097339delAA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	81426005	81426005	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:81426005delT								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	81444963	81444965	+	IGR	DEL	TTT	-	-	rs35740493		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:81444963_81444965delTTT								None (None upstream) : FAM181B (998088 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	82015127	82015128	+	Intron	INS	-	AAG	AAG	rs77131889		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:82015127_82015128insAAG	uc001ozo.1	-											Homo sapiens cDNA clone IMAGE:5298883.																														---	---	---	---
Unknown	0	broad.mit.edu	37	11	82360127	82360135	+	IGR	DEL	CTTCTCCTC	-	-	rs146501461		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:82360127_82360135delCTTCTCCTC								None (None upstream) : FAM181B (82918 downstream)																																			---	---	---	---
ANKRD42	338699	broad.mit.edu	37	11	82966931	82966931	+	Frame_Shift_Del	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:82966931delA	uc001pab.1	+	12	1931	c.1509delA	c.(1507-1509)GTAfs	p.V503fs	ANKRD42_uc001paa.2_Frame_Shift_Del_p.*503fs			Q8N9B4	ANR42_HUMAN	SubName: Full=Several ankyrin repeat protein transcript variant 2; Flags: Fragment;	Error:Variant_position_missing_in_Q8N9B4_after_alignment										skin(1)	1																		---	---	---	---
DLG2	1740	broad.mit.edu	37	11	83483814	83483814	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:83483814delT	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	84056685	84056686	+	Intron	INS	-	TT	TT			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:84056685_84056686insTT	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)																---	---	---	---
DLG2	1740	broad.mit.edu	37	11	84117332	84117332	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:84117332delT	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)																---	---	---	---
DLG2	1740	broad.mit.edu	37	11	84270279	84270279	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:84270279delT	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)																---	---	---	---
DLG2	1740	broad.mit.edu	37	11	84328699	84328699	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:84328699delT	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)																---	---	---	---
DLG2	1740	broad.mit.edu	37	11	84617763	84617763	+	Intron	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:84617763delG	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)																---	---	---	---
DLG2	1740	broad.mit.edu	37	11	85069136	85069137	+	Intron	INS	-	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:85069136_85069137insA	uc001pak.2	-							NM_001142699	NP_001136171			chapsyn-110 isoform 1							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)																---	---	---	---
CCDC81	60494	broad.mit.edu	37	11	86096427	86096428	+	Intron	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:86096427_86096428delAA	uc001pbx.1	+						CCDC81_uc001pbw.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	86252287	86252287	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:86252287delT	uc001pbz.2	-						ME3_uc001pca.2_Intron|ME3_uc009yvk.2_Intron|ME3_uc010rtr.1_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)													---	---	---	---
ME3	10873	broad.mit.edu	37	11	86320622	86320623	+	Intron	DEL	CA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:86320622_86320623delCA	uc001pbz.2	-						ME3_uc001pca.2_Intron|ME3_uc009yvk.2_Intron|ME3_uc010rtr.1_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)													---	---	---	---
TMEM135	65084	broad.mit.edu	37	11	86766636	86766637	+	Intron	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:86766636_86766637delTT	uc001pch.2	+						TMEM135_uc010rtt.1_Intron|TMEM135_uc001pci.2_Intron|TMEM135_uc001pcg.1_Intron	NM_022918	NP_075069			transmembrane protein 135							integral to membrane					0		Acute lymphoblastic leukemia(157;2.26e-05)|all_hematologic(158;0.0123)																---	---	---	---
Unknown	0	broad.mit.edu	37	11	87217452	87217452	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:87217452delT								TMEM135 (182884 upstream) : RAB38 (628979 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	87296917	87296917	+	IGR	DEL	T	-	-	rs34830255		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:87296917delT								TMEM135 (262349 upstream) : RAB38 (549514 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	87443837	87443837	+	IGR	DEL	T	-	-	rs140838447		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:87443837delT								TMEM135 (409269 upstream) : RAB38 (402594 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	87610852	87610852	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:87610852delT								TMEM135 (576284 upstream) : RAB38 (235579 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	87738869	87738870	+	IGR	INS	-	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:87738869_87738870insT								TMEM135 (704301 upstream) : RAB38 (107561 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	87766894	87766903	+	IGR	DEL	TTTTTTTTTT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:87766894_87766903delTTTTTTTTTT								TMEM135 (732326 upstream) : RAB38 (79528 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	88024657	88024658	+	IGR	INS	-	AAG	AAG	rs147448644	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:88024657_88024658insAAG								RAB38 (116058 upstream) : CTSC (2103 downstream)																																			---	---	---	---
TYR	7299	broad.mit.edu	37	11	88934669	88934669	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:88934669delA	uc001pcs.2	+							NM_000372	NP_000363			tyrosinase precursor						eye pigment biosynthetic process|melanin biosynthetic process from tyrosine|visual perception	Golgi-associated vesicle|integral to membrane|lysosome|melanosome membrane|perinuclear region of cytoplasm	copper ion binding|monophenol monooxygenase activity|protein heterodimerization activity|protein homodimerization activity			ovary(2)|central_nervous_system(1)	3		Acute lymphoblastic leukemia(157;2.33e-05)|all_hematologic(158;0.0033)			Azelaic Acid(DB00548)|Mimosine(DB01055)|NADH(DB00157)									Oculocutaneous_Albinism				---	---	---	---
NOX4	50507	broad.mit.edu	37	11	89075388	89075388	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:89075388delA	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	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)																---	---	---	---
NOX4	50507	broad.mit.edu	37	11	89089598	89089598	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:89089598delA	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	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)																---	---	---	---
FOLH1B	219595	broad.mit.edu	37	11	89403521	89403522	+	Intron	INS	-	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:89403521_89403522insT	uc001pda.2	+							NM_153696	NP_710163			folate hydrolase 1B						proteolysis	cytoplasm	dipeptidase activity|metal ion binding|metallopeptidase activity			ovary(3)|skin(2)|central_nervous_system(1)	6																		---	---	---	---
TRIM49	57093	broad.mit.edu	37	11	89534160	89534162	+	Intron	DEL	AAA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:89534160_89534162delAAA	uc001pdb.2	-							NM_020358	NP_065091			ring finger protein 18							intracellular	zinc ion binding				0		Acute lymphoblastic leukemia(157;2.31e-05)|all_hematologic(158;0.00556)																---	---	---	---
Unknown	0	broad.mit.edu	37	11	89608307	89608307	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:89608307delA								TRIM53 (24165 upstream) : TRIM49L (36274 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	89632001	89632002	+	IGR	INS	-	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:89632001_89632002insT								TRIM53 (47859 upstream) : TRIM49L (12579 downstream)																																			---	---	---	---
NAALAD2	10003	broad.mit.edu	37	11	89868965	89868966	+	Intron	DEL	TT	-	-	rs34639551		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:89868965_89868966delTT	uc001pdf.3	+						NAALAD2_uc009yvx.2_Intron|NAALAD2_uc009yvy.2_Intron|NAALAD2_uc001pdd.2_Intron|NAALAD2_uc001pde.2_Intron	NM_005467	NP_005458			N-acetylated alpha-linked acidic dipeptidase 2						proteolysis	integral to membrane	carboxypeptidase activity|dipeptidase activity|dipeptidyl-peptidase activity|metal ion binding|metallopeptidase activity|serine-type peptidase activity			pancreas(1)|skin(1)	2		Acute lymphoblastic leukemia(157;2.31e-05)|all_hematologic(158;0.00556)																---	---	---	---
Unknown	0	broad.mit.edu	37	11	90024185	90024185	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:90024185delA								CHORDC1 (67653 upstream) : MIR1261 (578104 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	90464056	90464056	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:90464056delT								CHORDC1 (507524 upstream) : MIR1261 (138233 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	90671347	90671348	+	IGR	INS	-	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:90671347_90671348insG								MIR1261 (68977 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	91975625	91975625	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:91975625delT								None (None upstream) : FAT3 (109637 downstream)																																			---	---	---	---
FAT3	120114	broad.mit.edu	37	11	92175978	92175978	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:92175978delT	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	92498316	92498318	+	Intron	DEL	AAA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:92498316_92498318delAAA	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)			---	---	---	---
SLC36A4	120103	broad.mit.edu	37	11	92889583	92889584	+	Intron	INS	-	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:92889583_92889584insT	uc001pdn.2	-						SLC36A4_uc001pdm.2_Intron	NM_152313	NP_689526			solute carrier family 36 (proton/amino acid						L-alanine transport|proline transport|tryptophan transport	integral to membrane	symporter activity			ovary(2)|upper_aerodigestive_tract(1)	3		Acute lymphoblastic leukemia(157;2.26e-05)|all_hematologic(158;0.0123)																---	---	---	---
CCDC67	159989	broad.mit.edu	37	11	93088477	93088477	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:93088477delT	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)																---	---	---	---
MED17	9440	broad.mit.edu	37	11	93528207	93528208	+	Frame_Shift_Del	DEL	TA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:93528207_93528208delTA	uc001pem.3	+	6	1268_1269	c.993_994delTA	c.(991-996)ATTATCfs	p.I331fs		NM_004268	NP_004259	Q9NVC6	MED17_HUMAN	mediator complex subunit 17	331_332					androgen receptor signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription initiation from RNA polymerase II promoter	mediator complex|transcription factor 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		Acute lymphoblastic leukemia(157;2.31e-05)|all_hematologic(158;0.00824)																---	---	---	---
HEPHL1	341208	broad.mit.edu	37	11	93796647	93796647	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:93796647delT	uc001pep.2	+							NM_001098672	NP_001092142			hephaestin-like 1 precursor						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)																---	---	---	---
Unknown	0	broad.mit.edu	37	11	93936123	93936123	+	IGR	DEL	A	-	-	rs72176856		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:93936123delA								PANX1 (20988 upstream) : FOLR4 (102680 downstream)																																			---	---	---	---
GPR83	10888	broad.mit.edu	37	11	94133713	94133717	+	Intron	DEL	AAAAA	-	-	rs78906959		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:94133713_94133717delAAAAA	uc001pet.2	-							NM_016540	NP_057624			G protein-coupled receptor 83 precursor							integral to membrane|plasma membrane	neuropeptide Y receptor activity			central_nervous_system(2)|ovary(1)	3		Acute lymphoblastic leukemia(157;2.26e-05)|all_hematologic(158;0.0123)																---	---	---	---
FUT4	2526	broad.mit.edu	37	11	94276567	94276567	+	5'Flank	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:94276567delT	uc001pez.2	+						PIWIL4_uc010rue.1_5'Flank|PIWIL4_uc009ywk.1_5'Flank	NM_002033	NP_002024			fucosyltransferase 4						L-fucose catabolic process|protein glycosylation	Golgi cisterna membrane|integral to membrane|membrane fraction	alpha(1,3)-fucosyltransferase activity			skin(1)	1		Acute lymphoblastic leukemia(157;2.31e-05)|all_hematologic(158;0.00824)																---	---	---	---
CWC15	51503	broad.mit.edu	37	11	94704578	94704579	+	Frame_Shift_Del	DEL	CT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:94704578_94704579delCT	uc001pfd.3	-	3	327_328	c.204_205delAG	c.(202-207)AGAGCTfs	p.R68fs	CWC15_uc009ywl.1_Frame_Shift_Del_p.R68fs|KDM4D_uc001pfe.2_5'Flank	NM_016403	NP_057487	Q9P013	CWC15_HUMAN	CWC15 homolog	68_69	Potential.				nuclear mRNA splicing, via spliceosome	catalytic step 2 spliceosome	protein binding|RNA binding				0		Acute lymphoblastic leukemia(157;2.31e-05)|all_hematologic(158;0.00824)																---	---	---	---
Unknown	0	broad.mit.edu	37	11	94898581	94898581	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:94898581delA								ENDOD1 (32766 upstream) : SESN3 (7552 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	95663186	95663186	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:95663186delA								MTMR2 (5815 upstream) : MAML2 (48254 downstream)																																			---	---	---	---
MAML2	84441	broad.mit.edu	37	11	95859874	95859875	+	Intron	DEL	CA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:95859874_95859875delCA	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	96162978	96162978	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:96162978delA								JRKL (36251 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	96716587	96716589	+	IGR	DEL	TTT	-	-	rs146035523		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:96716587_96716589delTTT								JRKL (589860 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	96834100	96834100	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:96834100delT								JRKL (707373 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	97915095	97915096	+	IGR	INS	-	TTG	TTG	rs35370154		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:97915095_97915096insTTG								None (None upstream) : CNTN5 (976775 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	98537599	98537599	+	IGR	DEL	T	-	-	rs35925758		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:98537599delT								None (None upstream) : CNTN5 (354272 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	98596802	98596803	+	IGR	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:98596802_98596803delTT								None (None upstream) : CNTN5 (295068 downstream)																																			---	---	---	---
CNTN5	53942	broad.mit.edu	37	11	99354457	99354457	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:99354457delA	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	99538685	99538686	+	Intron	INS	-	A	A	rs146414177	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:99538685_99538686insA	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	99791642	99791642	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:99791642delT	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)														---	---	---	---
ARHGAP42	143872	broad.mit.edu	37	11	100849810	100849810	+	Intron	DEL	A	-	-	rs34577066		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:100849810delA	uc001pge.2	+						ARHGAP42_uc001pgd.2_Intron	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	101213015	101213015	+	IGR	DEL	T	-	-	rs74996886		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:101213015delT								PGR (212471 upstream) : TRPC6 (109281 downstream)																																			---	---	---	---
TRPC6	7225	broad.mit.edu	37	11	101405739	101405739	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:101405739delA	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)														---	---	---	---
KIAA1377	57562	broad.mit.edu	37	11	101832459	101832459	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:101832459delT	uc001pgm.2	+						KIAA1377_uc001pgn.2_Intron|KIAA1377_uc010run.1_Intron|KIAA1377_uc009yxa.1_Intron	NM_020802	NP_065853			hypothetical protein LOC57562								protein binding			breast(2)|ovary(1)|central_nervous_system(1)	4	all_epithelial(12;0.0104)	Acute lymphoblastic leukemia(157;0.000967)|all_hematologic(158;0.00931)		BRCA - Breast invasive adenocarcinoma(274;0.038)														---	---	---	---
KIAA1377	57562	broad.mit.edu	37	11	101859343	101859344	+	Intron	INS	-	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:101859343_101859344insA	uc001pgm.2	+						KIAA1377_uc001pgn.2_Intron|KIAA1377_uc010run.1_Intron	NM_020802	NP_065853			hypothetical protein LOC57562								protein binding			breast(2)|ovary(1)|central_nervous_system(1)	4	all_epithelial(12;0.0104)	Acute lymphoblastic leukemia(157;0.000967)|all_hematologic(158;0.00931)		BRCA - Breast invasive adenocarcinoma(274;0.038)														---	---	---	---
YAP1	10413	broad.mit.edu	37	11	102062910	102062910	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:102062910delT	uc001pgt.2	+						YAP1_uc001pgs.2_Intron|YAP1_uc001pgu.2_Intron|YAP1_uc001pgv.2_Intron|YAP1_uc010ruo.1_Intron|YAP1_uc001pgw.2_Intron|YAP1_uc010rup.1_Intron	NM_001130145	NP_001123617			Yes-associated protein 1, 65kDa isoform 1						cell proliferation|cellular response to gamma radiation|contact inhibition|hippo signaling cascade|regulation of transcription, DNA-dependent|response to DNA damage stimulus|transcription, DNA-dependent	cytoplasm|nucleus	protein binding|transcription coactivator activity|transcription corepressor activity|transcription regulatory region DNA binding			ovary(1)|lung(1)|central_nervous_system(1)	3	all_cancers(8;0.000575)|all_epithelial(12;0.00564)	Acute lymphoblastic leukemia(157;0.000994)|all_hematologic(158;0.00936)	Lung(13;0.245)	BRCA - Breast invasive adenocarcinoma(274;0.0189)														---	---	---	---
Unknown	0	broad.mit.edu	37	11	102123322	102123322	+	IGR	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:102123322delG								YAP1 (19168 upstream) : BIRC3 (64872 downstream)																																			---	---	---	---
TMEM123	114908	broad.mit.edu	37	11	102275787	102275787	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:102275787delT	uc001pha.2	-						TMEM123_uc009yxc.2_Intron	NM_052932	NP_443164			transmembrane protein 123 precursor						oncosis	external side of plasma membrane|integral to membrane	receptor activity			breast(2)	2	all_cancers(8;0.00027)|all_epithelial(12;0.0021)|Lung NSC(15;0.227)	Acute lymphoblastic leukemia(157;0.000967)|all_hematologic(158;0.0033)	Epithelial(9;0.0314)|Lung(13;0.109)|all cancers(10;0.12)|LUSC - Lung squamous cell carcinoma(19;0.151)	BRCA - Breast invasive adenocarcinoma(274;0.0149)														---	---	---	---
MMP7	4316	broad.mit.edu	37	11	102391546	102391546	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:102391546delA	uc001phb.2	-							NM_002423	NP_002414			matrix metalloproteinase 7 preproprotein						collagen catabolic process|proteolysis	extracellular space|proteinaceous extracellular matrix	metalloendopeptidase activity|zinc ion binding			ovary(1)	1	all_cancers(8;2.04e-05)|all_epithelial(12;0.00053)|Lung NSC(15;0.139)	Acute lymphoblastic leukemia(157;0.000967)|all_hematologic(158;0.0033)	Epithelial(9;0.0105)|all cancers(10;0.0496)|Lung(13;0.109)|LUSC - Lung squamous cell carcinoma(19;0.151)	BRCA - Breast invasive adenocarcinoma(274;0.0147)														---	---	---	---
MMP12	4321	broad.mit.edu	37	11	102741959	102741960	+	Intron	INS	-	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:102741959_102741960insA	uc001phk.2	-							NM_002426	NP_002417			matrix metalloproteinase 12 preproprotein						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)													---	---	---	---
Unknown	0	broad.mit.edu	37	11	102869567	102869567	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:102869567delA								MMP13 (43105 upstream) : DCUN1D5 (63255 downstream)																																			---	---	---	---
DYNC2H1	79659	broad.mit.edu	37	11	103141307	103141308	+	Intron	DEL	CT	-	-	rs72244184		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:103141307_103141308delCT	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	103304041	103304044	+	Intron	DEL	ATGG	-	-	rs34010108		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:103304041_103304044delATGG	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)														---	---	---	---
PDGFD	80310	broad.mit.edu	37	11	103872667	103872667	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:103872667delT	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	104610025	104610025	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:104610025delA								PDGFD (574998 upstream) : CASP12 (146417 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	104639094	104639094	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:104639094delT								PDGFD (604067 upstream) : CASP12 (117348 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	105287974	105287974	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:105287974delT								CARD18 (278168 upstream) : GRIA4 (192826 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	106176212	106176212	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:106176212delA								AASDHPPT (206793 upstream) : GUCY1A2 (381698 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	106339903	106339903	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:106339903delT								AASDHPPT (370484 upstream) : GUCY1A2 (218007 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	106414961	106414961	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:106414961delT								AASDHPPT (445542 upstream) : GUCY1A2 (142949 downstream)																																			---	---	---	---
GUCY1A2	2977	broad.mit.edu	37	11	106753216	106753216	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:106753216delA	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	107063038	107063039	+	IGR	DEL	CT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:107063038_107063039delCT								GUCY1A2 (173867 upstream) : CWF19L2 (134035 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	107568432	107568433	+	IGR	INS	-	A	A	rs11604030		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:107568432_107568433insA								ELMOD1 (30928 upstream) : SLN (9676 downstream)																																			---	---	---	---
SLC35F2	54733	broad.mit.edu	37	11	107686334	107686334	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:107686334delT	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)														---	---	---	---
CUL5	8065	broad.mit.edu	37	11	107940724	107940724	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-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)														---	---	---	---
CUL5	8065	broad.mit.edu	37	11	107942599	107942599	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:107942599delT	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)														---	---	---	---
NPAT	4863	broad.mit.edu	37	11	108047686	108047686	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:108047686delT	uc001pjz.3	-						NPAT_uc001pka.2_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	108110943	108110943	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:108110943delT	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)			---	---	---	---
C11orf65	160140	broad.mit.edu	37	11	108292668	108292668	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:108292668delT	uc001pkh.2	-						C11orf65_uc010rvx.1_Intron|C11orf65_uc009yxu.1_Intron	NM_152587	NP_689800			hypothetical protein LOC160140											ovary(1)	1		all_cancers(61;1.38e-11)|all_epithelial(67;3.16e-07)|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;8.21e-06)|BRCA - Breast invasive adenocarcinoma(274;1.01e-05)|all cancers(92;0.000189)|Colorectal(284;0.114)|OV - Ovarian serous cystadenocarcinoma(223;0.144)														---	---	---	---
Unknown	0	broad.mit.edu	37	11	109069814	109069814	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:109069814delA								DDX10 (258168 upstream) : C11orf87 (223061 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	109155233	109155234	+	IGR	DEL	AA	-	-	rs35511646		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:109155233_109155234delAA								DDX10 (343587 upstream) : C11orf87 (137641 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	109654684	109654685	+	IGR	INS	-	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:109654684_109654685insC								C11orf87 (354846 upstream) : ZC3H12C (309241 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	109687327	109687328	+	IGR	INS	-	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:109687327_109687328insT								C11orf87 (387489 upstream) : ZC3H12C (276598 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	109857635	109857636	+	IGR	INS	-	AG	AG	rs146631357	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:109857635_109857636insAG								C11orf87 (557797 upstream) : ZC3H12C (106290 downstream)																																			---	---	---	---
ZC3H12C	85463	broad.mit.edu	37	11	110035762	110035762	+	Frame_Shift_Del	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:110035762delC	uc009yxw.2	+	6	2003	c.1952delC	c.(1951-1953)TCCfs	p.S651fs	ZC3H12C_uc010rwc.1_Frame_Shift_Del_p.S652fs|ZC3H12C_uc010rwd.1_Frame_Shift_Del_p.S652fs|ZC3H12C_uc001pkr.3_Frame_Shift_Del_p.S620fs	NM_033390	NP_203748	Q9C0D7	ZC12C_HUMAN	zinc finger CCCH-type containing 12C	651							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)														---	---	---	---
RDX	5962	broad.mit.edu	37	11	110088581	110088582	+	Intron	DEL	TT	-	-	rs140204691		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:110088581_110088582delTT	uc009yxy.2	-						RDX_uc009yxx.1_Intron|RDX_uc009yxz.2_Intron|RDX_uc009yya.2_Intron	NM_002906	NP_002897			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)														---	---	---	---
RDX	5962	broad.mit.edu	37	11	110146971	110146971	+	Intron	DEL	T	-	-	rs11213338	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:110146971delT	uc001pku.2	-						RDX_uc009yxx.1_Intron|RDX_uc009yxy.2_Intron|RDX_uc009yxz.2_Intron|RDX_uc009yya.2_Intron|RDX_uc010rwe.1_Intron	NM_002906	NP_002897			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	110306545	110306545	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:110306545delT	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)													---	---	---	---
ARHGAP20	57569	broad.mit.edu	37	11	110555763	110555763	+	Intron	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:110555763delC	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	110722536	110722536	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:110722536delA								ARHGAP20 (138624 upstream) : C11orf53 (404171 downstream)																																			---	---	---	---
SIK2	23235	broad.mit.edu	37	11	111529465	111529465	+	Intron	DEL	A	-	-	rs112214279		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:111529465delA	uc001plt.2	+							NM_015191	NP_056006			SNF1-like kinase 2						intracellular protein kinase cascade|regulation of insulin receptor signaling pathway	Golgi apparatus	ATP binding|magnesium ion binding|protein binding|protein serine/threonine kinase activity			central_nervous_system(2)|skin(1)	3																		---	---	---	---
ALG9	79796	broad.mit.edu	37	11	111657261	111657261	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:111657261delA	uc001pmb.2	-						ALG9_uc001ply.2_Intron|ALG9_uc001plz.2_Intron|ALG9_uc010rwm.1_Intron|ALG9_uc010rwn.1_Intron|ALG9_uc010rwo.1_Intron	NM_001077690	NP_001071158			asparagine-linked glycosylation 9 protein						dolichol-linked oligosaccharide biosynthetic process|GPI anchor biosynthetic process|post-translational protein modification|protein N-linked glycosylation via asparagine	integral to membrane|intrinsic to endoplasmic reticulum membrane	alpha-1,2-mannosyltransferase activity			large_intestine(1)|ovary(1)	2		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)		Epithelial(105;6.81e-07)|BRCA - Breast invasive adenocarcinoma(274;1.15e-06)|all cancers(92;1.3e-05)|OV - Ovarian serous cystadenocarcinoma(223;0.0587)														---	---	---	---
Unknown	0	broad.mit.edu	37	11	111759853	111759853	+	IGR	DEL	T	-	-	rs150833390		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:111759853delT								C11orf1 (5058 upstream) : CRYAB (19497 downstream)																																			---	---	---	---
IL18	3606	broad.mit.edu	37	11	112014661	112014661	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:112014661delA	uc001pnb.1	-						IL18_uc001pna.1_Intron|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)														---	---	---	---
Unknown	0	broad.mit.edu	37	11	112332121	112332122	+	IGR	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:112332121_112332122delTT								PTS (191444 upstream) : NCAM1 (499873 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	112476114	112476115	+	IGR	DEL	GA	-	-	rs34198329		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:112476114_112476115delGA								PTS (335437 upstream) : NCAM1 (355880 downstream)																																			---	---	---	---
NCAM1	4684	broad.mit.edu	37	11	112980930	112980930	+	Intron	DEL	T	-	-	rs35220749		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:112980930delT	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	113106956	113106956	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:113106956delT								NCAM1 (-42201 upstream) : NCAM1 (-274961 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	113114787	113114787	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:113114787delT								NCAM1 (-34370 upstream) : NCAM1 (-282792 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	113175805	113175806	+	IGR	INS	-	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:113175805_113175806insA								NCAM1 (26648 upstream) : TTC12 (9445 downstream)																																			---	---	---	---
ANKK1	255239	broad.mit.edu	37	11	113266217	113266217	+	Intron	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:113266217delG	uc001pny.2	+							NM_178510	NP_848605			ankyrin repeat and kinase domain containing 1								ATP binding|protein serine/threonine kinase activity			lung(5)|stomach(1)|ovary(1)|breast(1)	8		all_cancers(61;1.53e-11)|all_epithelial(67;3e-06)|Melanoma(852;4.04e-05)|all_hematologic(158;0.000315)|Acute lymphoblastic leukemia(157;0.000966)|Breast(348;0.0461)|Medulloblastoma(222;0.0523)|all_neural(223;0.0663)|Prostate(24;0.194)		BRCA - Breast invasive adenocarcinoma(274;4.82e-06)|Epithelial(105;5.41e-05)|all cancers(92;0.000442)|OV - Ovarian serous cystadenocarcinoma(223;0.238)														---	---	---	---
Unknown	0	broad.mit.edu	37	11	114383759	114383759	+	IGR	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:114383759delC								REXO2 (62761 upstream) : FAM55A (8679 downstream)																																			---	---	---	---
FAM55B	120406	broad.mit.edu	37	11	114551184	114551184	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:114551184delA	uc009yyy.2	+							NM_182495	NP_872301			hypothetical protein LOC120406							integral to membrane				ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	11	114609549	114609549	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:114609549delT								FAM55B (31897 upstream) : CADM1 (430404 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	114968484	114968484	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:114968484delA								FAM55B (390832 upstream) : CADM1 (71469 downstream)																																			---	---	---	---
CADM1	23705	broad.mit.edu	37	11	115232611	115232614	+	Intron	DEL	TTTG	-	-	rs111921433		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:115232611_115232614delTTTG	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	115543666	115543667	+	IGR	INS	-	A	A	rs114461938	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:115543666_115543667insA								CADM1 (168425 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	116266790	116266790	+	IGR	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:116266790delC								CADM1 (891549 upstream) : BUD13 (352098 downstream)																																			---	---	---	---
ZNF259	8882	broad.mit.edu	37	11	116650308	116650309	+	Intron	DEL	AA	-	-	rs36064778		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:116650308_116650309delAA	uc001ppp.2	-						ZNF259_uc009yzd.2_Intron|ZNF259_uc001ppq.2_Intron	NM_003904	NP_003895			zinc finger protein 259						cell proliferation|signal transduction	cytoplasm|nucleolus					0	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;5.61e-06)|all cancers(92;0.000139)|OV - Ovarian serous cystadenocarcinoma(223;0.153)														---	---	---	---
SIK3	23387	broad.mit.edu	37	11	116766985	116766985	+	Frame_Shift_Del	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:116766985delT	uc001ppy.2	-	6	711	c.675delA	c.(673-675)CCAfs	p.P225fs	SIK3_uc001ppz.2_Frame_Shift_Del_p.P124fs|SIK3_uc001pqa.2_Frame_Shift_Del_p.P225fs	NM_025164	NP_079440	Q9Y2K2	SIK3_HUMAN	serine/threonine-protein kinase QSK	225	Protein kinase.					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																		---	---	---	---
Unknown	0	broad.mit.edu	37	11	116986180	116986182	+	IGR	DEL	AAA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:116986180_116986182delAAA								SIK3 (17187 upstream) : PAFAH1B2 (28858 downstream)																																			---	---	---	---
RNF214	257160	broad.mit.edu	37	11	117128802	117128803	+	Intron	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:117128802_117128803delTT	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)														---	---	---	---
BACE1	23621	broad.mit.edu	37	11	117159734	117159734	+	3'UTR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:117159734delT	uc001pqz.2	-	9					BACE1_uc001pqw.2_3'UTR|BACE1_uc001pqx.2_3'UTR|BACE1_uc001pqy.2_3'UTR|BACE1_uc010rxg.1_3'UTR|BACE1_uc010rxh.1_3'UTR|uc010rxi.1_5'Flank	NM_012104	NP_036236			beta-site APP-cleaving enzyme 1 isoform A						beta-amyloid metabolic process|membrane protein ectodomain proteolysis	cell surface|cytoplasmic vesicle membrane|endoplasmic reticulum|endosome|integral to plasma membrane|trans-Golgi network	aspartic-type endopeptidase activity|beta-aspartyl-peptidase activity|protein binding			ovary(1)	1	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;0.000563)|all cancers(92;0.0032)														---	---	---	---
BACE1	23621	broad.mit.edu	37	11	117164936	117164938	+	Intron	DEL	TTT	-	-	rs67342022		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:117164936_117164938delTTT	uc001pqz.2	-						BACE1_uc001pqw.2_Intron|BACE1_uc001pqx.2_Intron|BACE1_uc001pqy.2_Intron|BACE1_uc001pra.1_Intron|BACE1_uc010rxg.1_Intron|BACE1_uc010rxh.1_Intron|BACE1_uc009yzo.1_5'Flank	NM_012104	NP_036236			beta-site APP-cleaving enzyme 1 isoform A						beta-amyloid metabolic process|membrane protein ectodomain proteolysis	cell surface|cytoplasmic vesicle membrane|endoplasmic reticulum|endosome|integral to plasma membrane|trans-Golgi network	aspartic-type endopeptidase activity|beta-aspartyl-peptidase activity|protein binding			ovary(1)	1	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;0.000563)|all cancers(92;0.0032)														---	---	---	---
DSCAML1	57453	broad.mit.edu	37	11	117465775	117465776	+	Intron	DEL	AC	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:117465775_117465776delAC	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)														---	---	---	---
FXYD6	53826	broad.mit.edu	37	11	117740386	117740388	+	Intron	DEL	AAG	-	-	rs10534626		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:117740386_117740388delAAG	uc001pro.1	-						FXYD6_uc001prp.1_Intron|FXYD6_uc001prq.1_Intron|FXYD6_uc001prr.1_Intron|FXYD6_uc009yzq.1_Intron	NM_022003	NP_071286			FXYD domain-containing ion transport regulator 6							integral to membrane|plasma membrane	ion channel activity			central_nervous_system(1)|skin(1)	2	all_hematologic(175;0.0487)	Medulloblastoma(222;0.0425)|Breast(348;0.111)|all_hematologic(192;0.196)|all_neural(223;0.234)		BRCA - Breast invasive adenocarcinoma(274;1.89e-05)|Epithelial(105;0.00122)														---	---	---	---
Unknown	0	broad.mit.edu	37	11	117908134	117908135	+	Intron	INS	-	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:117908134_117908135insG	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.																														---	---	---	---
SCN2B	6327	broad.mit.edu	37	11	118034983	118034983	+	3'UTR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:118034983delA	uc001psf.2	-	4						NM_004588	NP_004579			sodium channel, voltage-gated, type II, beta						synaptic transmission	voltage-gated sodium channel complex	voltage-gated sodium channel 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;3.19e-05)|Epithelial(105;0.00117)														---	---	---	---
SCN2B	6327	broad.mit.edu	37	11	118047235	118047235	+	5'UTR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:118047235delA	uc001psf.2	-	1						NM_004588	NP_004579			sodium channel, voltage-gated, type II, beta						synaptic transmission	voltage-gated sodium channel complex	voltage-gated sodium channel 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;3.19e-05)|Epithelial(105;0.00117)														---	---	---	---
Unknown	0	broad.mit.edu	37	11	118206720	118206720	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:118206720delA								CD3E (19831 upstream) : CD3D (3069 downstream)																																			---	---	---	---
UBE4A	9354	broad.mit.edu	37	11	118243701	118243704	+	Intron	DEL	AAAA	-	-	rs34104337		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:118243701_118243704delAAAA	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	118324117	118324117	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:118324117delT	uc001pta.2	+						MLL_uc001ptb.2_Intron|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	118372188	118372190	+	Intron	DEL	AAA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:118372188_118372190delAAA	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								---	---	---	---
MLL	4297	broad.mit.edu	37	11	118392247	118392247	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:118392247delA	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-4200-01A-01D-1126-08	TCGA-BR-4200-11A-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																		---	---	---	---
ARCN1	372	broad.mit.edu	37	11	118445474	118445474	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:118445474delT	uc001ptq.2	+						ARCN1_uc009zah.2_Intron|ARCN1_uc010ryg.1_Intron|ARCN1_uc009zag.2_Intron	NM_001655	NP_001646			archain isoform 1						COPI coating of Golgi vesicle|intracellular protein transport|retrograde vesicle-mediated transport, Golgi to ER	clathrin adaptor complex|COPI vesicle coat|cytosol					0	all_hematologic(175;0.0349)	Medulloblastoma(222;0.0425)|all_hematologic(192;0.0564)|all_neural(223;0.234)		BRCA - Breast invasive adenocarcinoma(274;3.28e-05)														---	---	---	---
Unknown	0	broad.mit.edu	37	11	118563703	118563704	+	IGR	INS	-	A	A	rs142564183	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:118563703_118563704insA								TREH (13322 upstream) : DDX6 (54769 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	118703697	118703697	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:118703697delT								DDX6 (41725 upstream) : CXCR5 (50844 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	118716133	118716133	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:118716133delA								DDX6 (54161 upstream) : CXCR5 (38408 downstream)																																			---	---	---	---
CCDC84	338657	broad.mit.edu	37	11	118873663	118873663	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:118873663delT	uc001pul.2	+						CCDC84_uc010ryk.1_Intron|CCDC84_uc010ryl.1_Intron|CCDC84_uc010rym.1_Intron	NM_198489	NP_940891			coiled-coil domain containing 84											ovary(1)	1	all_hematologic(175;0.0839)	Medulloblastoma(222;0.0523)|all_neural(223;0.224)|all_hematologic(192;0.243)		BRCA - Breast invasive adenocarcinoma(274;7.72e-05)														---	---	---	---
HINFP	25988	broad.mit.edu	37	11	119000057	119000057	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:119000057delT	uc001pvp.2	+						HINFP_uc010rzb.1_Intron|HINFP_uc001pvq.2_Intron|HINFP_uc001pvr.2_5'Flank	NM_015517	NP_056332			MBD2 (methyl-CpG-binding protein)-interacting						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																		---	---	---	---
OAF	220323	broad.mit.edu	37	11	120088287	120088287	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:120088287delA	uc001pxb.2	+							NM_178507	NP_848602			OAF homolog precursor												0		Breast(109;0.00663)|Medulloblastoma(222;0.0523)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;5.1e-06)														---	---	---	---
POU2F3	25833	broad.mit.edu	37	11	120148331	120148331	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:120148331delA	uc001pxc.2	+						POU2F3_uc010rzk.1_Intron|POU2F3_uc010rzl.1_Intron	NM_014352	NP_055167			POU transcription factor						negative regulation by host of viral transcription	cytoplasm	sequence-specific DNA binding			ovary(1)|skin(1)	2		Breast(109;0.0011)|Medulloblastoma(222;0.0425)|Hepatocellular(160;0.0831)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;6.85e-06)														---	---	---	---
GRIK4	2900	broad.mit.edu	37	11	120439104	120439104	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:120439104delT	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	120815780	120815780	+	Intron	DEL	A	-	-	rs77482327		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:120815780delA	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)													---	---	---	---
Unknown	0	broad.mit.edu	37	11	121062988	121062988	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:121062988delT								TECTA (1475 upstream) : SC5DL (100400 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	121639764	121639765	+	IGR	INS	-	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:121639764_121639765insA								SORL1 (135293 upstream) : LOC399959 (320046 downstream)																																			---	---	---	---
LOC399959	399959	broad.mit.edu	37	11	122238332	122238332	+	RNA	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:122238332delA	uc009zbb.1	-	1		c.136delT								Homo sapiens cDNA FLJ34394 fis, clone HCHON2000676.												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	11	122459930	122459930	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:122459930delA								LOC399959 (221463 upstream) : UBASH3B (66468 downstream)																																			---	---	---	---
UBASH3B	84959	broad.mit.edu	37	11	122547250	122547250	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:122547250delA	uc001pyi.3	+							NM_032873	NP_116262			ubiquitin associated and SH3 domain containing,							cytoplasm|nucleus	protein tyrosine phosphatase activity			central_nervous_system(1)	1		Breast(109;0.00254)|Medulloblastoma(222;0.00877)|Lung NSC(97;0.0183)|all_lung(97;0.0186)|all_neural(223;0.0381)|all_hematologic(192;0.104)		BRCA - Breast invasive adenocarcinoma(274;1.37e-05)|OV - Ovarian serous cystadenocarcinoma(99;0.0463)														---	---	---	---
Unknown	0	broad.mit.edu	37	11	122747074	122747074	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:122747074delA								CRTAM (3729 upstream) : C11orf63 (6399 downstream)																																			---	---	---	---
ASAM	79827	broad.mit.edu	37	11	122949661	122949661	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:122949661delT	uc001pyt.2	-							NM_024769	NP_079045			adipocyte-specific adhesion molecule precursor							integral to membrane|tight junction					0		Breast(109;0.0025)|Lung NSC(97;0.0179)|all_lung(97;0.0182)|Medulloblastoma(222;0.0427)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;8.73e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0446)														---	---	---	---
ASAM	79827	broad.mit.edu	37	11	122954076	122954076	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:122954076delT	uc001pyt.2	-							NM_024769	NP_079045			adipocyte-specific adhesion molecule precursor							integral to membrane|tight junction					0		Breast(109;0.0025)|Lung NSC(97;0.0179)|all_lung(97;0.0182)|Medulloblastoma(222;0.0427)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;8.73e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0446)														---	---	---	---
Unknown	0	broad.mit.edu	37	11	123147129	123147129	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:123147129delA								ASAM (81122 upstream) : GRAMD1B (249399 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	123348493	123348495	+	IGR	DEL	TTG	-	-	rs145310922		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:123348493_123348495delTTG								ASAM (282486 upstream) : GRAMD1B (48033 downstream)																																			---	---	---	---
VWA5A	4013	broad.mit.edu	37	11	123994642	123994642	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-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	124145538	124145538	+	IGR	DEL	T	-	-	rs80354655		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:124145538delT								OR8G2 (49228 upstream) : OR8D1 (34199 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	124184767	124184767	+	IGR	DEL	A	-	-	rs35186047		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:124184767delA								OR8D1 (4105 upstream) : OR8D2 (4392 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	124236126	124236126	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:124236126delA								OR8D2 (46033 upstream) : OR8B2 (16173 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	124249981	124249981	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:124249981delT								OR8D2 (59888 upstream) : OR8B2 (2318 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	124465927	124465927	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:124465927delT								OR8A1 (24983 upstream) : PANX3 (15526 downstream)																																			---	---	---	---
SIAE	54414	broad.mit.edu	37	11	124505840	124505840	+	3'UTR	DEL	T	-	-	rs112916013		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:124505840delT	uc001qan.2	-	10						NM_170601	NP_733746			sialate O-acetylesterase precursor							extracellular region|lysosome	carboxylesterase activity|sialate O-acetylesterase activity				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;1.63e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0243)														---	---	---	---
SIAE	54414	broad.mit.edu	37	11	124519316	124519316	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:124519316delT	uc001qan.2	-							NM_170601	NP_733746			sialate O-acetylesterase precursor							extracellular region|lysosome	carboxylesterase activity|sialate O-acetylesterase activity				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;1.63e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0243)														---	---	---	---
CCDC15	80071	broad.mit.edu	37	11	124828880	124828880	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:124828880delT	uc001qbm.3	+							NM_025004	NP_079280			coiled-coil domain containing 15							centrosome				ovary(1)|central_nervous_system(1)	2	all_hematologic(175;0.215)	Breast(109;0.00222)|Lung NSC(97;0.0177)|all_lung(97;0.0179)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;1.68e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0413)														---	---	---	---
Unknown	0	broad.mit.edu	37	11	124917165	124917165	+	IGR	DEL	T	-	-	rs36005092		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:124917165delT								CCDC15 (5782 upstream) : SLC37A2 (15848 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	124926562	124926562	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:124926562delA								CCDC15 (15179 upstream) : SLC37A2 (6451 downstream)																																			---	---	---	---
TMEM218	219854	broad.mit.edu	37	11	124967519	124967520	+	Frame_Shift_Ins	INS	-	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:124967519_124967520insT	uc001qbs.2	-	4	982_983	c.330_331insA	c.(328-333)AAACCAfs	p.K110fs	TMEM218_uc001qbr.2_Frame_Shift_Ins_p.K136fs|TMEM218_uc010saw.1_Frame_Shift_Ins_p.K145fs|TMEM218_uc010sax.1_Frame_Shift_Ins_p.K110fs|TMEM218_uc001qbt.2_Frame_Shift_Ins_p.K145fs|TMEM218_uc010say.1_RNA	NM_001080546	NP_001074015	A2RU14	TM218_HUMAN	transmembrane protein 218	110_111						integral to membrane					0																		---	---	---	---
PKNOX2	63876	broad.mit.edu	37	11	125068738	125068740	+	Intron	DEL	TTT	-	-	rs2320850		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:125068738_125068740delTTT	uc001qbu.2	+						PKNOX2_uc010saz.1_Intron|PKNOX2_uc010sba.1_Intron|PKNOX2_uc010sbb.1_Intron	NM_022062	NP_071345			PBX/knotted 1 homeobox 2							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	125227104	125227105	+	Intron	INS	-	CT	CT			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:125227104_125227105insCT	uc001qbu.2	+						PKNOX2_uc010saz.1_Intron|PKNOX2_uc010sba.1_Intron|PKNOX2_uc010sbb.1_Intron	NM_022062	NP_071345			PBX/knotted 1 homeobox 2							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	125760199	125760199	+	Intron	DEL	A	-	-	rs35011154		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:125760199delA	uc009zbv.2	+						HYLS1_uc001qcx.3_Intron	NM_145014	NP_659451			hydrolethalus syndrome 1							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)														---	---	---	---
KIRREL3	84623	broad.mit.edu	37	11	126300339	126300339	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:126300339delA	uc001qea.2	-						KIRREL3_uc001qeb.2_Intron|ST3GAL4_uc001qdx.1_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)														---	---	---	---
KIRREL3	84623	broad.mit.edu	37	11	126687022	126687022	+	Intron	DEL	G	-	-	rs2040338	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:126687022delG	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	127183344	127183344	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:127183344delT	uc001qeh.2	+											Homo sapiens cDNA clone IMAGE:4794631.																														---	---	---	---
Unknown	0	broad.mit.edu	37	11	127392569	127392569	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:127392569delT								KIRREL3 (519214 upstream) : ETS1 (936087 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	127517050	127517051	+	IGR	DEL	TC	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:127517050_127517051delTC								KIRREL3 (643695 upstream) : ETS1 (811605 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	127975112	127975112	+	IGR	DEL	T	-	-	rs71992128		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:127975112delT								None (None upstream) : ETS1 (353544 downstream)																																			---	---	---	---
KCNJ1	3758	broad.mit.edu	37	11	128719604	128719604	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:128719604delT	uc001qep.1	-						KCNJ1_uc001qeq.1_Intron|KCNJ1_uc001qer.1_Intron|KCNJ1_uc001qes.1_Intron	NM_153767	NP_722451			potassium inwardly-rectifying channel J1 isoform						excretion	voltage-gated potassium channel complex	ATP binding|inward rectifier potassium channel activity			ovary(3)|breast(1)	4	all_hematologic(175;0.0641)	all_lung(97;4.89e-06)|Lung NSC(97;9.34e-06)|Breast(109;0.00123)|all_hematologic(192;0.00793)|Renal(330;0.0112)|all_neural(223;0.0189)|Medulloblastoma(222;0.0425)		OV - Ovarian serous cystadenocarcinoma(99;4.05e-06)|LUSC - Lung squamous cell carcinoma(976;0.008)|Lung(977;0.00942)	Acetohexamide(DB00414)|Chlorpropamide(DB00672)|Glibenclamide(DB01016)|Gliclazide(DB01120)|Glimepiride(DB00222)|Glipizide(DB01067)|Glycodiazine(DB01382)|Minoxidil(DB00350)|Nateglinide(DB00731)|Repaglinide(DB00912)|Tolazamide(DB00839)|Tolbutamide(DB01124)													---	---	---	---
KCNJ5	3762	broad.mit.edu	37	11	128765996	128765996	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:128765996delT	uc001qet.2	+						KCNJ5_uc009zck.2_Intron	NM_000890	NP_000881			potassium inwardly-rectifying channel J5						synaptic transmission	voltage-gated potassium channel complex	G-protein activated inward rectifier potassium channel activity|protein binding			skin(1)	1	all_hematologic(175;0.0641)	Lung NSC(97;0.00038)|all_lung(97;0.000817)|Breast(109;0.00123)|Medulloblastoma(222;0.0425)|all_neural(223;0.0837)		OV - Ovarian serous cystadenocarcinoma(99;0.0059)|LUSC - Lung squamous cell carcinoma(976;0.021)|Lung(977;0.0215)	Glibenclamide(DB01016)													---	---	---	---
TP53AIP1	63970	broad.mit.edu	37	11	128808317	128808318	+	Intron	DEL	CT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:128808317_128808318delCT	uc001qey.2	-						TP53AIP1_uc001qex.2_Intron|TP53AIP1_uc009zcm.1_Intron					RecName: Full=p53-regulated apoptosis-inducing protein 1;          Short=p53AIP1;						apoptosis	mitochondrion				lung(1)	1																		---	---	---	---
ARHGAP32	9743	broad.mit.edu	37	11	128948806	128948806	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:128948806delA	uc009zcp.2	-						ARHGAP32_uc009zcq.1_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																		---	---	---	---
ARHGAP32	9743	broad.mit.edu	37	11	128993225	128993225	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:128993225delA	uc009zcp.2	-						ARHGAP32_uc009zcq.1_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																		---	---	---	---
ARHGAP32	9743	broad.mit.edu	37	11	129006020	129006020	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:129006020delA	uc009zcp.2	-						ARHGAP32_uc009zcq.1_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																		---	---	---	---
PRDM10	56980	broad.mit.edu	37	11	129790312	129790313	+	Intron	INS	-	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:129790312_129790313insC	uc001qfm.2	-						PRDM10_uc001qfj.2_Intron|PRDM10_uc001qfk.2_Intron|PRDM10_uc001qfl.2_Intron|PRDM10_uc010sbx.1_Intron|PRDM10_uc001qfn.2_Intron	NM_020228	NP_064613			PR domain containing 10 isoform 1						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)														---	---	---	---
ST14	6768	broad.mit.edu	37	11	130044763	130044763	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:130044763delT	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)													---	---	---	---
SNX19	399979	broad.mit.edu	37	11	130775256	130775256	+	Intron	DEL	A	-	-	rs71475730		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:130775256delA	uc001qgk.3	-						SNX19_uc009zcw.2_Intron|SNX19_uc010sce.1_Intron|SNX19_uc010scf.1_Intron|SNX19_uc010scg.1_Intron	NM_014758	NP_055573			sorting nexin 19						cell communication|protein transport	cytoplasmic vesicle membrane	phosphatidylinositol binding|protein binding			ovary(2)|lung(2)	4	all_hematologic(175;0.0597)	Lung NSC(97;0.000272)|all_lung(97;0.000608)|Breast(109;0.000962)|all_neural(223;0.0298)|Medulloblastoma(222;0.0425)		OV - Ovarian serous cystadenocarcinoma(99;0.0195)|Lung(977;0.233)														---	---	---	---
Unknown	0	broad.mit.edu	37	11	131103463	131103463	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:131103463delA								SNX19 (317081 upstream) : NTM (136908 downstream)																																			---	---	---	---
NTM	50863	broad.mit.edu	37	11	132050793	132050793	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:132050793delA	uc001qgp.2	+						NTM_uc001qgm.2_Intron|NTM_uc010sch.1_Intron|NTM_uc010sci.1_Intron|NTM_uc010scj.1_Intron|NTM_uc001qgo.2_Intron|NTM_uc001qgq.2_Intron	NM_016522	NP_057606			neurotrimin isoform 1						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	132446282	132446282	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:132446282delT	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	133218325	133218325	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:133218325delT	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	133280487	133280487	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:133280487delT	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	133670344	133670344	+	IGR	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:133670344delG								OPCML (267941 upstream) : SPATA19 (40173 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	133930099	133930099	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:133930099delA								LOC100128239 (18863 upstream) : JAM3 (8721 downstream)																																			---	---	---	---
NCAPD3	23310	broad.mit.edu	37	11	134046128	134046128	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:134046128delA	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)														---	---	---	---
NCAPD3	23310	broad.mit.edu	37	11	134072805	134072805	+	Intron	DEL	A	-	-	rs34989286		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:134072805delA	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)														---	---	---	---
ACAD8	27034	broad.mit.edu	37	11	134128348	134128348	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:134128348delT	uc001qhk.2	+						ACAD8_uc009zdc.2_Intron|ACAD8_uc010sco.1_Intron|ACAD8_uc010scp.1_Intron|ACAD8_uc010scq.1_Intron|ACAD8_uc001qhl.2_Intron|ACAD8_uc010scr.1_Intron|ACAD8_uc009zde.1_5'Flank	NM_014384	NP_055199			acyl-Coenzyme A dehydrogenase family, member 8						branched chain family amino acid catabolic process|lipid metabolic process|regulation of transcription, DNA-dependent|transcription, DNA-dependent	mitochondrial matrix	acyl-CoA dehydrogenase activity|flavin adenine dinucleotide binding				0	all_hematologic(175;0.127)	all_cancers(12;8e-23)|all_epithelial(12;2.59e-16)|all_lung(97;1.19e-05)|Lung NSC(97;2.76e-05)|Breast(109;0.000182)|all_neural(223;0.0189)|Medulloblastoma(222;0.0245)|Esophageal squamous(93;0.0559)		Epithelial(10;1.92e-10)|all cancers(11;2.26e-09)|BRCA - Breast invasive adenocarcinoma(10;8.73e-09)|OV - Ovarian serous cystadenocarcinoma(99;0.00154)|Lung(977;0.21)														---	---	---	---
B3GAT1	27087	broad.mit.edu	37	11	134274990	134274990	+	Intron	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:134274990delG	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	134413157	134413157	+	IGR	DEL	C	-	-	rs35250983		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:134413157delC								B3GAT1 (131345 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	134643432	134643443	+	IGR	DEL	GAAGAGAAAGAA	-	-	rs144220076	by1000genomes;by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:134643432_134643443delGAAGAGAAAGAA								B3GAT1 (361620 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	169297	169297	+	IGR	DEL	T	-	-	rs75044168		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:169297delT								FAM138D (19885 upstream) : IQSEC3 (6906 downstream)																																			---	---	---	---
SLC6A13	6540	broad.mit.edu	37	12	366361	366362	+	Intron	INS	-	A	A	rs111856769		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:366361_366362insA	uc001qic.1	-						SLC6A13_uc009zdj.1_Intron|SLC6A13_uc010sdl.1_Intron	NM_016615	NP_057699			solute carrier family 6 (neurotransmitter						neurotransmitter secretion	integral to plasma membrane	gamma-aminobutyric acid:sodium symporter activity|neurotransmitter:sodium symporter activity				0	all_cancers(10;0.0416)|all_epithelial(11;0.0537)|all_lung(10;0.0989)|Lung NSC(10;0.139)|Ovarian(42;0.142)		OV - Ovarian serous cystadenocarcinoma(31;0.00153)|BRCA - Breast invasive adenocarcinoma(9;0.239)															---	---	---	---
Unknown	0	broad.mit.edu	37	12	672665	672666	+	IGR	DEL	AA	-	-	rs113272114		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:672665_672666delAA								B4GALNT3 (1607 upstream) : NINJ2 (797 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	854173	854174	+	IGR	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:854173_854174delAA								NINJ2 (81418 upstream) : WNK1 (8051 downstream)																																			---	---	---	---
ERC1	23085	broad.mit.edu	37	12	1299490	1299490	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:1299490delT	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)															---	---	---	---
FBXL14	144699	broad.mit.edu	37	12	1677334	1677334	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:1677334delA	uc001qjh.2	-							NM_152441	NP_689654			F-box and leucine-rich repeat protein 14							cytoplasm				ovary(1)	1	Ovarian(42;0.107)		OV - Ovarian serous cystadenocarcinoma(31;0.00115)															---	---	---	---
ADIPOR2	79602	broad.mit.edu	37	12	1855222	1855222	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:1855222delA	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)															---	---	---	---
ADIPOR2	79602	broad.mit.edu	37	12	1857791	1857791	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:1857791delT	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)															---	---	---	---
DCP1B	196513	broad.mit.edu	37	12	2061344	2061344	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:2061344delT	uc001qjx.1	-						DCP1B_uc010sdy.1_Intron	NM_152640	NP_689853			decapping enzyme Dcp1b						exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay	cytosol|nucleus	hydrolase activity|protein binding			skin(1)	1			OV - Ovarian serous cystadenocarcinoma(31;0.00193)															---	---	---	---
CACNA1C	775	broad.mit.edu	37	12	2173764	2173764	+	Intron	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:2173764delG	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	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	2435338	2435338	+	Intron	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:2435338delG	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	2656469	2656469	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:2656469delT	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_uc009zdy.1_Intron|CACNA1C_uc001qkv.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)													---	---	---	---
TSPAN9	10867	broad.mit.edu	37	12	3203705	3203707	+	Intron	DEL	TTT	-	-	rs111723388		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:3203705_3203707delTTT	uc001qlp.2	+							NM_006675	NP_006666			tetraspanin 9							integral to plasma membrane|membrane fraction				ovary(1)	1			OV - Ovarian serous cystadenocarcinoma(31;0.00153)|COAD - Colon adenocarcinoma(12;0.0831)															---	---	---	---
Unknown	0	broad.mit.edu	37	12	3422781	3422781	+	IGR	DEL	A	-	-	rs78659110	byFrequency;by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:3422781delA								TSPAN9 (27052 upstream) : PRMT8 (67734 downstream)																																	OREG0021590	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	3880433	3880433	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:3880433delA								EFCAB4B (18067 upstream) : PARP11 (37594 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	4162640	4162641	+	IGR	INS	-	GA	GA			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:4162640_4162641insGA								PARP11 (180032 upstream) : CCND2 (220261 downstream)																																			---	---	---	---
CCND2	894	broad.mit.edu	37	12	4382313	4382314	+	5'Flank	INS	-	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:4382313_4382314insG	uc001qmo.2	+							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								---	---	---	---
CCND2	894	broad.mit.edu	37	12	4409271	4409271	+	3'UTR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-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								---	---	---	---
FGF6	2251	broad.mit.edu	37	12	4545192	4545192	+	Intron	DEL	A	-	-	rs112225003	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:4545192delA	uc001qmr.1	-							NM_020996	NP_066276			fibroblast growth factor 6 precursor						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)															---	---	---	---
GALNT8	26290	broad.mit.edu	37	12	4836458	4836459	+	Intron	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:4836458_4836459delTT	uc001qne.1	+							NM_017417	NP_059113			polypeptide N-acetylgalactosaminyltransferase 8							Golgi membrane|integral to membrane	polypeptide N-acetylgalactosaminyltransferase activity|sugar binding			ovary(2)|pancreas(1)|skin(1)	4																		---	---	---	---
Unknown	0	broad.mit.edu	37	12	5149962	5149963	+	IGR	INS	-	TC	TC			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:5149962_5149963insTC								KCNA1 (122542 upstream) : KCNA5 (3122 downstream)																																			---	---	---	---
NTF3	4908	broad.mit.edu	37	12	5591974	5591974	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:5591974delT	uc001qnk.3	+							NM_001102654	NP_001096124			neurotrophin 3 isoform 1 preproprotein						signal transduction	extracellular region	growth factor activity|neurotrophin receptor binding			pancreas(1)	1																		---	---	---	---
NTF3	4908	broad.mit.edu	37	12	5603709	5603709	+	Frame_Shift_Del	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:5603709delC	uc001qnl.3	+	1	412	c.329delC	c.(328-330)ACCfs	p.T110fs	NTF3_uc001qnk.3_Frame_Shift_Del_p.T123fs	NM_002527	NP_002518	P20783	NTF3_HUMAN	neurotrophin 3 isoform 2 preproprotein	110					signal transduction	extracellular region	growth factor activity|neurotrophin receptor binding			pancreas(1)	1																		---	---	---	---
VWF	7450	broad.mit.edu	37	12	6170366	6170367	+	Intron	INS	-	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:6170366_6170367insA	uc001qnn.1	-						VWF_uc010set.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	6182037	6182039	+	Intron	DEL	TTT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:6182037_6182039delTTT	uc001qnn.1	-						VWF_uc010set.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	6382417	6382418	+	IGR	INS	-	TT	TT	rs61678188		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:6382417_6382418insTT								CD9 (34990 upstream) : PLEKHG6 (37184 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	6454602	6454603	+	IGR	DEL	CA	-	-	rs72657512		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:6454602_6454603delCA								TNFRSF1A (3341 upstream) : SCNN1A (1408 downstream)																																			---	---	---	---
LTBR	4055	broad.mit.edu	37	12	6489380	6489380	+	Intron	DEL	C	-	-	rs75736034		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:6489380delC	uc010sfc.1	+						SCNN1A_uc010sfb.1_5'Flank	NM_002342	NP_002333			lymphotoxin beta receptor precursor						apoptosis|cellular response to mechanical stimulus|interspecies interaction between organisms|positive regulation of I-kappaB kinase/NF-kappaB cascade	integral to membrane	protein binding|receptor activity			lung(2)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	12	6815014	6815014	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:6815014delT								C12orf53 (5202 upstream) : COPS7A (18136 downstream)																																			---	---	---	---
LEPREL2	10536	broad.mit.edu	37	12	6937452	6937453	+	5'Flank	DEL	TC	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:6937452_6937453delTC	uc001qra.1	+						LEPREL2_uc001qqz.1_Intron|LEPREL2_uc001qrb.1_5'Flank|GPR162_uc001qqy.1_Intron	NM_014262	NP_055077			leprecan-like 2 precursor						negative regulation of cell proliferation	endoplasmic reticulum	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				0					L-Proline(DB00172)|Succinic acid(DB00139)|Vitamin C(DB00126)													---	---	---	---
CD163	9332	broad.mit.edu	37	12	7648056	7648056	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:7648056delT	uc001qsz.3	-						CD163_uc001qta.3_Intron|CD163_uc009zfw.2_Intron	NM_004244	NP_004235			CD163 antigen isoform a						acute-phase response	extracellular region|integral to plasma membrane	protein binding|scavenger receptor activity			ovary(6)|pancreas(1)|skin(1)	8																		---	---	---	---
Unknown	0	broad.mit.edu	37	12	7690529	7690532	+	IGR	DEL	TGTC	-	-	rs150284118		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:7690529_7690532delTGTC								CD163 (34115 upstream) : APOBEC1 (111465 downstream)																																			---	---	---	---
APOBEC1	339	broad.mit.edu	37	12	7807953	7807953	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:7807953delA	uc001qtb.2	-						APOBEC1_uc001qtc.2_Intron|APOBEC1_uc010sgf.1_Intron	NM_001644	NP_001635			apolipoprotein B mRNA editing enzyme						cytidine to uridine editing|DNA demethylation|lipid metabolic process|mRNA modification|mRNA processing|negative regulation of methylation-dependent chromatin silencing	nucleoplasm	cytidine deaminase activity|RNA binding|zinc ion binding				0																		---	---	---	---
SLC2A14	144195	broad.mit.edu	37	12	7986785	7986785	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:7986785delT	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)														---	---	---	---
SLC2A14	144195	broad.mit.edu	37	12	8014266	8014267	+	Intron	INS	-	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:8014266_8014267insA	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)														---	---	---	---
Unknown	0	broad.mit.edu	37	12	8097182	8097182	+	IGR	DEL	T	-	-	rs75930840		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:8097182delT								SLC2A3 (8290 upstream) : FOXJ2 (88177 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	8770855	8770856	+	IGR	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:8770855_8770856delAA								AICDA (5413 upstream) : MFAP5 (27684 downstream)																																			---	---	---	---
MFAP5	8076	broad.mit.edu	37	12	8803278	8803278	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:8803278delA	uc001qut.1	-						MFAP5_uc001qus.2_Intron|MFAP5_uc009zge.1_Intron	NM_003480	NP_003471			microfibrillar associated protein 5 precursor							microfibril	extracellular matrix structural constituent			breast(1)	1	Lung SC(5;0.184)																	---	---	---	---
RIMKLB	57494	broad.mit.edu	37	12	8849560	8849560	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:8849560delT	uc001quu.2	+						RIMKLB_uc009zgf.1_Intron|RIMKLB_uc001qux.2_5'Flank|RIMKLB_uc010sgl.1_5'Flank|RIMKLB_uc001quw.2_5'Flank	NM_020734	NP_065785			ribosomal modification protein rimK-like family						protein modification process	cytoplasm	acid-amino acid ligase activity|ATP binding|metal ion binding				0																		---	---	---	---
PZP	5858	broad.mit.edu	37	12	9355861	9355862	+	Intron	INS	-	A	A	rs139813056	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:9355861_9355862insA	uc001qvl.2	-						PZP_uc009zgl.2_Intron	NM_002864	NP_002855			pregnancy-zone protein precursor											ovary(3)|upper_aerodigestive_tract(1)|large_intestine(1)	5																		---	---	---	---
CLEC2A	387836	broad.mit.edu	37	12	10080433	10080433	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:10080433delT	uc009zhc.2	-						CLEC2A_uc009zhb.2_Intron	NM_001130711	NP_001124183			C-type lectin domain family 2, member A						natural killer cell mediated cytotoxicity	integral to membrane|plasma membrane	protein homodimerization activity|receptor activity|sugar binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	12	10159064	10159064	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:10159064delT								CLEC1B (7165 upstream) : CLEC12B (4167 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	10660065	10660067	+	IGR	DEL	TTT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:10660065_10660067delTTT								KLRC1 (53081 upstream) : KLRA1 (81011 downstream)																																			---	---	---	---
STYK1	55359	broad.mit.edu	37	12	10783476	10783476	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:10783476delA	uc001qys.2	-							NM_018423	NP_060893			serine/threonine/tyrosine kinase 1							integral to membrane|plasma membrane	ATP binding|non-membrane spanning protein tyrosine kinase activity			central_nervous_system(3)|ovary(2)|lung(2)|breast(1)	8															HNSCC(73;0.22)			---	---	---	---
PRB4	5545	broad.mit.edu	37	12	11043438	11043438	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:11043438delT	uc001qzf.1	-						PRR4_uc009zhp.2_Intron|PRH1_uc001qzb.3_Intron|PRH1_uc001qzc.2_Intron	NM_002723	NP_002714			proline-rich protein BstNI subfamily 4							extracellular region				ovary(1)	1															HNSCC(22;0.051)			---	---	---	---
PRB4	5545	broad.mit.edu	37	12	11117585	11117585	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:11117585delT	uc001qzf.1	-						PRR4_uc009zhp.2_Intron|PRH1_uc001qzb.3_Intron|PRH1_uc001qzc.2_Intron|PRH1_uc001qzj.2_Intron	NM_002723	NP_002714			proline-rich protein BstNI subfamily 4							extracellular region				ovary(1)	1															HNSCC(22;0.051)			---	---	---	---
PRB4	5545	broad.mit.edu	37	12	11281526	11281526	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:11281526delT	uc001qzf.1	-						PRR4_uc009zhp.2_Intron|PRH1_uc001qzb.3_Intron|PRH1_uc001qzc.2_Intron|PRH1_uc001qzj.2_Intron	NM_002723	NP_002714			proline-rich protein BstNI subfamily 4							extracellular region				ovary(1)	1															HNSCC(22;0.051)			---	---	---	---
LOH12CR1	118426	broad.mit.edu	37	12	12510571	12510571	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-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)														---	---	---	---
DUSP16	80824	broad.mit.edu	37	12	12631271	12631271	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:12631271delT	uc001rao.1	-						DUSP16_uc001ram.1_5'Flank|DUSP16_uc001ran.1_Intron	NM_030640	NP_085143			dual specificity phosphatase 16						inactivation of MAPK activity|MAPK export from nucleus|MAPK phosphatase export from nucleus, leptomycin B sensitive	cytoplasmic membrane-bounded vesicle|nucleus	MAP kinase tyrosine/serine/threonine phosphatase activity|protein tyrosine phosphatase activity				0		Prostate(47;0.0687)		BRCA - Breast invasive adenocarcinoma(232;0.0203)														---	---	---	---
Unknown	0	broad.mit.edu	37	12	12738472	12738473	+	IGR	INS	-	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:12738472_12738473insA								DUSP16 (23155 upstream) : CREBL2 (26358 downstream)																																			---	---	---	---
APOLD1	81575	broad.mit.edu	37	12	12940757	12940758	+	3'UTR	DEL	TG	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:12940757_12940758delTG	uc001rau.3	+	2					DDX47_uc001rav.2_Intron|APOLD1_uc001raw.3_3'UTR	NM_001130415	NP_001123887			apolipoprotein L domain containing 1 isoform 1						angiogenesis|cell differentiation|lipid transport|lipoprotein metabolic process	extracellular region|integral to membrane|plasma membrane	lipid binding			ovary(1)	1		Prostate(47;0.0632)		BRCA - Breast invasive adenocarcinoma(232;0.0338)|GBM - Glioblastoma multiforme(207;0.149)														---	---	---	---
GRIN2B	2904	broad.mit.edu	37	12	13816217	13816217	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:13816217delT	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)													---	---	---	---
GRIN2B	2904	broad.mit.edu	37	12	13911289	13911289	+	Intron	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:13911289delC	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)													---	---	---	---
PLBD1	79887	broad.mit.edu	37	12	14656992	14656992	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:14656992delT	uc001rcc.1	-							NM_024829	NP_079105			phospholipase B domain containing 1						lipid catabolic process	extracellular region	hydrolase activity				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	12	14746364	14746364	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:14746364delT								PLBD1 (25573 upstream) : GUCY2C (19206 downstream)																																			---	---	---	---
ART4	420	broad.mit.edu	37	12	14983171	14983171	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:14983171delA	uc001rcl.1	-						ART4_uc009zid.1_Intron|ART4_uc009zie.1_Intron	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	15012270	15012270	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:15012270delT								ART4 (15857 upstream) : MGP (22557 downstream)																																			---	---	---	---
ERP27	121506	broad.mit.edu	37	12	15082073	15082073	+	Intron	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:15082073delC	uc001rco.2	-							NM_152321	NP_689534			endoplasmic reticulum protein 27 kDa precursor							endoplasmic reticulum lumen				breast(1)	1																		---	---	---	---
PDE6H	5149	broad.mit.edu	37	12	15126554	15126554	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:15126554delT	uc001rcr.2	+							NM_006205	NP_006196			phosphodiesterase 6H						visual perception		3',5'-cyclic-GMP phosphodiesterase activity|cGMP binding|enzyme inhibitor activity			ovary(1)|skin(1)	2																		---	---	---	---
PDE6H	5149	broad.mit.edu	37	12	15130881	15130881	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:15130881delT	uc001rcr.2	+							NM_006205	NP_006196			phosphodiesterase 6H						visual perception		3',5'-cyclic-GMP phosphodiesterase activity|cGMP binding|enzyme inhibitor activity			ovary(1)|skin(1)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	12	15241013	15241013	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:15241013delA								PDE6H (106216 upstream) : RERG (19705 downstream)																																			---	---	---	---
RERG	85004	broad.mit.edu	37	12	15283497	15283497	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:15283497delA	uc001rcs.2	-						RERG_uc001rct.2_Intron|RERG_uc010shu.1_Intron	NM_032918	NP_116307			RAS-like, estrogen-regulated, growth inhibitor						negative regulation of cell growth|negative regulation of cell proliferation|response to hormone stimulus|small GTPase mediated signal transduction	cytosol|membrane|nucleus	estrogen receptor binding|GDP binding|GTP binding|GTPase activity			lung(1)	1																		---	---	---	---
EPS8	2059	broad.mit.edu	37	12	15866044	15866044	+	5'Flank	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:15866044delT	uc009zif.2	-						EPS8_uc001rdb.2_Intron|EPS8_uc009zig.2_Intron	NM_004447	NP_004438			epidermal growth factor receptor pathway						cell proliferation|epidermal growth factor receptor signaling pathway		SH3/SH2 adaptor activity			ovary(2)|upper_aerodigestive_tract(1)|skin(1)	4		all_epithelial(100;1.87e-05)|Breast(259;0.000286)|Hepatocellular(102;0.244)		BRCA - Breast invasive adenocarcinoma(232;4.29e-05)|GBM - Glioblastoma multiforme(207;0.0264)														---	---	---	---
EPS8	2059	broad.mit.edu	37	12	15883336	15883336	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:15883336delT	uc001rdb.2	-						EPS8_uc009zig.2_Intron	NM_004447	NP_004438			epidermal growth factor receptor pathway						cell proliferation|epidermal growth factor receptor signaling pathway		SH3/SH2 adaptor activity			ovary(2)|upper_aerodigestive_tract(1)|skin(1)	4		all_epithelial(100;1.87e-05)|Breast(259;0.000286)|Hepatocellular(102;0.244)		BRCA - Breast invasive adenocarcinoma(232;4.29e-05)|GBM - Glioblastoma multiforme(207;0.0264)														---	---	---	---
Unknown	0	broad.mit.edu	37	12	17398442	17398442	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:17398442delT								LMO3 (635684 upstream) : RERGL (835362 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	17474803	17474803	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:17474803delT								LMO3 (712045 upstream) : RERGL (759001 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	18132270	18132270	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:18132270delT								None (None upstream) : RERGL (101534 downstream)																																			---	---	---	---
PIK3C2G	5288	broad.mit.edu	37	12	18640031	18640034	+	Intron	DEL	TGTG	-	-	rs71440368		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:18640031_18640034delTGTG	uc001rdt.2	+						PIK3C2G_uc010sia.1_Intron|PIK3C2G_uc010sib.1_Intron|PIK3C2G_uc010sic.1_Intron	NM_004570	NP_004561			phosphoinositide-3-kinase, class 2 gamma						cell communication|phosphatidylinositol-mediated signaling	membrane|phosphatidylinositol 3-kinase complex	1-phosphatidylinositol-3-kinase activity|ATP binding|phosphatidylinositol binding|phosphatidylinositol-4-phosphate 3-kinase activity			lung(8)|central_nervous_system(6)|breast(3)|stomach(2)|ovary(2)	21		Hepatocellular(102;0.194)																---	---	---	---
PLEKHA5	54477	broad.mit.edu	37	12	19406761	19406761	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:19406761delA	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	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)																	---	---	---	---
PLEKHA5	54477	broad.mit.edu	37	12	19420895	19420895	+	Intron	DEL	A	-	-	rs79773900		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:19420895delA	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	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)																	---	---	---	---
Unknown	0	broad.mit.edu	37	12	19790233	19790236	+	IGR	DEL	TTTT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:19790233_19790236delTTTT								AEBP2 (115060 upstream) : PDE3A (731961 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	20179446	20179450	+	IGR	DEL	CTTAA	-	-	rs138031363		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:20179446_20179450delCTTAA								AEBP2 (504273 upstream) : PDE3A (342747 downstream)																																			---	---	---	---
PDE3A	5139	broad.mit.edu	37	12	20679819	20679820	+	Intron	DEL	TG	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:20679819_20679820delTG	uc001reh.1	+							NM_000921	NP_000912			phosphodiesterase 3A						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)													---	---	---	---
SLCO1B3	28234	broad.mit.edu	37	12	20979489	20979489	+	Intron	DEL	T	-	-	rs34227535		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:20979489delT	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)																	---	---	---	---
PYROXD1	79912	broad.mit.edu	37	12	21614926	21614926	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:21614926delT	uc001rew.2	+						PYROXD1_uc009ziq.2_Intron|PYROXD1_uc009zir.2_Intron	NM_024854	NP_079130			pyridine nucleotide-disulphide oxidoreductase								oxidoreductase activity			ovary(1)	1																		---	---	---	---
KCNJ8	3764	broad.mit.edu	37	12	21918233	21918233	+	3'UTR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:21918233delT	uc001rff.2	-	3						NM_004982	NP_004973			potassium inwardly-rectifying channel J8							voltage-gated potassium channel complex					0					Levosimendan(DB00922)													---	---	---	---
ABCC9	10060	broad.mit.edu	37	12	22006858	22006858	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:22006858delA	uc001rfi.1	-						ABCC9_uc001rfh.2_Intron|ABCC9_uc001rfj.1_Intron	NM_005691	NP_005682			ATP-binding cassette, sub-family C, member 9						defense response to virus|potassium ion import	ATP-sensitive potassium channel complex	ATP binding|ATPase activity, coupled to transmembrane movement of substances|potassium channel regulator activity|sulfonylurea receptor activity			ovary(4)|skin(2)	6					Adenosine triphosphate(DB00171)|Glibenclamide(DB01016)													---	---	---	---
ABCC9	10060	broad.mit.edu	37	12	22025423	22025423	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:22025423delT	uc001rfi.1	-						ABCC9_uc001rfh.2_Intron|ABCC9_uc001rfj.1_Intron	NM_005691	NP_005682			ATP-binding cassette, sub-family C, member 9						defense response to virus|potassium ion import	ATP-sensitive potassium channel complex	ATP binding|ATPase activity, coupled to transmembrane movement of substances|potassium channel regulator activity|sulfonylurea receptor activity			ovary(4)|skin(2)	6					Adenosine triphosphate(DB00171)|Glibenclamide(DB01016)													---	---	---	---
ABCC9	10060	broad.mit.edu	37	12	22062206	22062206	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:22062206delT	uc001rfi.1	-						ABCC9_uc001rfh.2_Intron|ABCC9_uc001rfj.1_Intron	NM_005691	NP_005682			ATP-binding cassette, sub-family C, member 9						defense response to virus|potassium ion import	ATP-sensitive potassium channel complex	ATP binding|ATPase activity, coupled to transmembrane movement of substances|potassium channel regulator activity|sulfonylurea receptor activity			ovary(4)|skin(2)	6					Adenosine triphosphate(DB00171)|Glibenclamide(DB01016)													---	---	---	---
ST8SIA1	6489	broad.mit.edu	37	12	22460358	22460359	+	Intron	INS	-	TC	TC			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:22460358_22460359insTC	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																		---	---	---	---
KIAA0528	9847	broad.mit.edu	37	12	22625136	22625137	+	Intron	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:22625136_22625137delAA	uc001rfq.2	-						KIAA0528_uc010sir.1_Intron|KIAA0528_uc010sis.1_Intron|KIAA0528_uc010sit.1_Intron|KIAA0528_uc010siu.1_Intron|KIAA0528_uc001rfr.2_Intron	NM_014802	NP_055617			hypothetical protein LOC9847								protein binding			ovary(1)|large_intestine(1)|breast(1)|central_nervous_system(1)	4																		---	---	---	---
Unknown	0	broad.mit.edu	37	12	23530545	23530545	+	IGR	DEL	A	-	-	rs75571113		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:23530545delA								ETNK1 (686938 upstream) : SOX5 (154687 downstream)																																			---	---	---	---
SOX5	6660	broad.mit.edu	37	12	24385794	24385794	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:24385794delA	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	24600466	24600466	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:24600466delA	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																		---	---	---	---
KRAS	3845	broad.mit.edu	37	12	25374532	25374532	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:25374532delA	uc001rgp.1	-						KRAS_uc001rgq.1_Intron	NM_033360	NP_203524			c-K-ras2 protein isoform a precursor						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			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)				119	Mis		pancreatic|colorectal|lung|thyroid|AML|others				Cardiofaciocutaneous_syndrome|Noonan_syndrome	TSP Lung(1;<1E-08)|Multiple Myeloma(2;<1E-6)			---	---	---	---
Unknown	0	broad.mit.edu	37	12	25519704	25519705	+	IGR	DEL	AC	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:25519704_25519705delAC								KRAS (115841 upstream) : IFLTD1 (109311 downstream)																																			---	---	---	---
ITPR2	3709	broad.mit.edu	37	12	26877744	26877744	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:26877744delT	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)																	---	---	---	---
ITPR2	3709	broad.mit.edu	37	12	26971632	26971633	+	Intron	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:26971632_26971633delTT	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)																	---	---	---	---
C12orf11	55726	broad.mit.edu	37	12	27066793	27066794	+	Intron	DEL	AT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:27066793_27066794delAT	uc001rhk.3	-						C12orf11_uc001rhj.3_Intron|C12orf11_uc010sjk.1_Intron	NM_018164	NP_060634			hypothetical protein LOC55726						cell division|mitosis|regulation of mitotic cell cycle		protein binding			large_intestine(1)|ovary(1)|central_nervous_system(1)	3	Colorectal(261;0.0847)																	---	---	---	---
Unknown	0	broad.mit.edu	37	12	27214960	27214961	+	IGR	INS	-	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:27214960_27214961insA								MED21 (32278 upstream) : C12orf71 (19030 downstream)																																			---	---	---	---
STK38L	23012	broad.mit.edu	37	12	27416461	27416461	+	Intron	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:27416461delG	uc001rhr.2	+						STK38L_uc001rhs.2_Intron|STK38L_uc010sjm.1_Intron	NM_015000	NP_055815			serine/threonine kinase 38 like						intracellular protein kinase cascade|regulation of cellular component organization	actin cytoskeleton|cytoplasm	actin binding|ATP binding|magnesium ion binding|protein serine/threonine kinase activity			ovary(2)|haematopoietic_and_lymphoid_tissue(1)|lung(1)|kidney(1)	5	Colorectal(261;0.0847)																	---	---	---	---
STK38L	23012	broad.mit.edu	37	12	27455050	27455050	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:27455050delT	uc001rhr.2	+						STK38L_uc001rhs.2_Intron|STK38L_uc010sjm.1_Intron	NM_015000	NP_055815			serine/threonine kinase 38 like						intracellular protein kinase cascade|regulation of cellular component organization	actin cytoskeleton|cytoplasm	actin binding|ATP binding|magnesium ion binding|protein serine/threonine kinase activity			ovary(2)|haematopoietic_and_lymphoid_tissue(1)|lung(1)|kidney(1)	5	Colorectal(261;0.0847)																	---	---	---	---
C12orf70	341346	broad.mit.edu	37	12	27625299	27625299	+	Intron	DEL	C	-	-	rs441433	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:27625299delC	uc010sjq.1	+							NM_001145010	NP_001138482			hypothetical protein LOC341346							integral to membrane					0																		---	---	---	---
PPFIBP1	8496	broad.mit.edu	37	12	27769244	27769247	+	Intron	DEL	TTTT	-	-	rs66903966		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:27769244_27769247delTTTT	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)																	---	---	---	---
KLHDC5	57542	broad.mit.edu	37	12	27945088	27945089	+	Intron	INS	-	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:27945088_27945089insT	uc001rij.2	+						KLHDC5_uc009zjj.2_Intron	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	28022924	28022924	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:28022924delA								KLHDC5 (66952 upstream) : PTHLH (88094 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	28250447	28250447	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:28250447delT								PTHLH (125531 upstream) : CCDC91 (81763 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	28883333	28883333	+	IGR	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:28883333delG								CCDC91 (180235 upstream) : FAR2 (418899 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	28903598	28903598	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:28903598delT								CCDC91 (200500 upstream) : FAR2 (398634 downstream)																																			---	---	---	---
TMTC1	83857	broad.mit.edu	37	12	29748946	29748946	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:29748946delT	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)																	---	---	---	---
TMTC1	83857	broad.mit.edu	37	12	29931488	29931488	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:29931488delA	uc001rjb.2	-						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	30028611	30028611	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:30028611delA								TMTC1 (90919 upstream) : IPO8 (753312 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	30147691	30147691	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:30147691delT								TMTC1 (209999 upstream) : IPO8 (634232 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	30276553	30276553	+	IGR	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:30276553delG								TMTC1 (338861 upstream) : IPO8 (505370 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	30441060	30441060	+	IGR	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:30441060delG								TMTC1 (503368 upstream) : IPO8 (340863 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	30472616	30472616	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:30472616delT								TMTC1 (534924 upstream) : IPO8 (309307 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	30569078	30569079	+	IGR	DEL	TT	-	-	rs76627578		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:30569078_30569079delTT								TMTC1 (631386 upstream) : IPO8 (212844 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	30938520	30938520	+	IGR	DEL	A	-	-	rs34653818		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:30938520delA								CAPRIN2 (31072 upstream) : TSPAN11 (140842 downstream)																																			---	---	---	---
FAM60A	58516	broad.mit.edu	37	12	31467535	31467536	+	Intron	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:31467535_31467536delTT	uc010sjz.1	-						FAM60A_uc001rkd.2_Intron|FAM60A_uc010ska.1_Intron|FAM60A_uc001rke.2_Intron|FAM60A_uc010skb.1_Intron	NM_021238	NP_067061			family with sequence similarity 60, member A												0	all_cancers(9;5.22e-13)|all_epithelial(9;4e-13)|all_lung(12;1.2e-11)|Lung NSC(12;2.17e-09)|Acute lymphoblastic leukemia(23;0.0122)|all_hematologic(23;0.0207)|Lung SC(12;0.0592)|Esophageal squamous(101;0.162)																	---	---	---	---
DENND5B	160518	broad.mit.edu	37	12	31595513	31595513	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:31595513delT	uc001rki.1	-						DENND5B_uc001rkh.1_Intron|DENND5B_uc009zjq.1_Intron|DENND5B_uc001rkj.2_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	31723523	31723524	+	Intron	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:31723523_31723524delAA	uc001rki.1	-						DENND5B_uc001rkh.1_Intron|DENND5B_uc001rkj.2_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	31751127	31751127	+	IGR	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:31751127delG								DENND5B (7175 upstream) : C12orf72 (48967 downstream)																																			---	---	---	---
C12orf72	254013	broad.mit.edu	37	12	31817874	31817875	+	Intron	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:31817874_31817875delTT	uc009zjr.2	+						C12orf72_uc001rkl.2_Intron|C12orf72_uc001rkm.2_Intron	NM_001135864	NP_001129336			hypothetical protein LOC254013							cytoplasm	protein methyltransferase activity				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	12	31967844	31967844	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:31967844delA								H3F3C (22669 upstream) : C12orf35 (144509 downstream)																																			---	---	---	---
BICD1	636	broad.mit.edu	37	12	32503862	32503862	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:32503862delT	uc001rku.2	+						BICD1_uc001rkv.2_Intron|BICD1_uc010skd.1_Intron	NM_001714	NP_001705			bicaudal D homolog 1 isoform 1						anatomical structure morphogenesis|intracellular mRNA localization|microtubule anchoring at microtubule organizing center|minus-end-directed organelle transport along microtubule|positive regulation of receptor-mediated endocytosis|protein localization to organelle|RNA processing|stress granule assembly|viral reproduction	cytoplasmic vesicle|cytoskeleton|cytosol|host cell viral assembly compartment|membrane|perinuclear region of cytoplasm|trans-Golgi network	cytoskeletal adaptor activity|dynactin binding|dynein binding|proteinase activated receptor binding|Rab GTPase binding|structural constituent of cytoskeleton			large_intestine(1)|central_nervous_system(1)	2	all_cancers(9;5.13e-11)|all_epithelial(9;2.71e-11)|all_lung(12;6.66e-10)|Acute lymphoblastic leukemia(23;0.0122)|Lung SC(12;0.0213)|all_hematologic(23;0.0429)|Esophageal squamous(101;0.204)		OV - Ovarian serous cystadenocarcinoma(6;0.0201)															---	---	---	---
BICD1	636	broad.mit.edu	37	12	32525415	32525415	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:32525415delA	uc001rku.2	+						BICD1_uc001rkv.2_Intron|BICD1_uc010skd.1_Intron	NM_001714	NP_001705			bicaudal D homolog 1 isoform 1						anatomical structure morphogenesis|intracellular mRNA localization|microtubule anchoring at microtubule organizing center|minus-end-directed organelle transport along microtubule|positive regulation of receptor-mediated endocytosis|protein localization to organelle|RNA processing|stress granule assembly|viral reproduction	cytoplasmic vesicle|cytoskeleton|cytosol|host cell viral assembly compartment|membrane|perinuclear region of cytoplasm|trans-Golgi network	cytoskeletal adaptor activity|dynactin binding|dynein binding|proteinase activated receptor binding|Rab GTPase binding|structural constituent of cytoskeleton			large_intestine(1)|central_nervous_system(1)	2	all_cancers(9;5.13e-11)|all_epithelial(9;2.71e-11)|all_lung(12;6.66e-10)|Acute lymphoblastic leukemia(23;0.0122)|Lung SC(12;0.0213)|all_hematologic(23;0.0429)|Esophageal squamous(101;0.204)		OV - Ovarian serous cystadenocarcinoma(6;0.0201)															---	---	---	---
Unknown	0	broad.mit.edu	37	12	32622601	32622601	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:32622601delT								BICD1 (91461 upstream) : FGD4 (16305 downstream)																																			---	---	---	---
DNM1L	10059	broad.mit.edu	37	12	32875580	32875580	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:32875580delT	uc001rld.2	+						DNM1L_uc010skf.1_Intron|DNM1L_uc010skg.1_Intron|DNM1L_uc001rle.2_Intron|DNM1L_uc001rlf.2_Intron|DNM1L_uc010skh.1_Intron|DNM1L_uc001rlg.2_Intron|DNM1L_uc001rlh.2_Intron|DNM1L_uc010ski.1_Intron	NM_012062	NP_036192			dynamin 1-like isoform 1						cellular component disassembly involved in apoptosis|mitochondrial fragmentation involved in apoptosis|mitochondrial membrane organization|positive regulation of mitochondrial fission	cis-Golgi network|cytosol|endomembrane system|endoplasmic reticulum|mitochondrial outer membrane	GTP binding|GTPase activity|ubiquitin protein ligase binding			ovary(1)|pancreas(1)	2	Lung NSC(5;2.15e-06)|Acute lymphoblastic leukemia(23;0.0122)|all_hematologic(23;0.0429)|Esophageal squamous(101;0.239)																	---	---	---	---
DNM1L	10059	broad.mit.edu	37	12	32890767	32890767	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:32890767delT	uc001rld.2	+						DNM1L_uc001rle.2_Intron|DNM1L_uc001rlf.2_Intron|DNM1L_uc010skh.1_Intron|DNM1L_uc001rlg.2_Intron|DNM1L_uc001rlh.2_Intron|DNM1L_uc010ski.1_Intron	NM_012062	NP_036192			dynamin 1-like isoform 1						cellular component disassembly involved in apoptosis|mitochondrial fragmentation involved in apoptosis|mitochondrial membrane organization|positive regulation of mitochondrial fission	cis-Golgi network|cytosol|endomembrane system|endoplasmic reticulum|mitochondrial outer membrane	GTP binding|GTPase activity|ubiquitin protein ligase binding			ovary(1)|pancreas(1)	2	Lung NSC(5;2.15e-06)|Acute lymphoblastic leukemia(23;0.0122)|all_hematologic(23;0.0429)|Esophageal squamous(101;0.239)																	---	---	---	---
DNM1L	10059	broad.mit.edu	37	12	32895046	32895046	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:32895046delT	uc001rld.2	+						DNM1L_uc001rle.2_Intron|DNM1L_uc001rlf.2_Intron|DNM1L_uc010skh.1_Intron|DNM1L_uc001rlg.2_Intron|DNM1L_uc001rlh.2_Intron|DNM1L_uc010ski.1_Intron	NM_012062	NP_036192			dynamin 1-like isoform 1						cellular component disassembly involved in apoptosis|mitochondrial fragmentation involved in apoptosis|mitochondrial membrane organization|positive regulation of mitochondrial fission	cis-Golgi network|cytosol|endomembrane system|endoplasmic reticulum|mitochondrial outer membrane	GTP binding|GTPase activity|ubiquitin protein ligase binding			ovary(1)|pancreas(1)	2	Lung NSC(5;2.15e-06)|Acute lymphoblastic leukemia(23;0.0122)|all_hematologic(23;0.0429)|Esophageal squamous(101;0.239)																	---	---	---	---
Unknown	0	broad.mit.edu	37	12	33690794	33690794	+	IGR	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:33690794delG								SYT10 (98040 upstream) : ALG10 (484422 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	33853041	33853042	+	IGR	INS	-	A	A	rs145410397	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:33853041_33853042insA								SYT10 (260287 upstream) : ALG10 (322174 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	34540474	34540474	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:34540474delT								ALG10 (359240 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	34833236	34833237	+	IGR	INS	-	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:34833236_34833237insC								ALG10 (652002 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	37863202	37863204	+	IGR	DEL	CAC	-	-	rs140477359		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:37863202_37863204delCAC								None (None upstream) : ALG10B (847353 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	38470357	38470357	+	IGR	DEL	G	-	-	rs2204007	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:38470357delG								None (None upstream) : ALG10B (240200 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	38667550	38667550	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:38667550delA								None (None upstream) : ALG10B (43007 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	38764137	38764137	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:38764137delA								ALG10B (40610 upstream) : CPNE8 (281865 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	38926640	38926640	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:38926640delT								ALG10B (203113 upstream) : CPNE8 (119362 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	38938751	38938751	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:38938751delA	uc001rlq.2	-											Homo sapiens, clone IMAGE:5741868, mRNA.																														---	---	---	---
CPNE8	144402	broad.mit.edu	37	12	39139994	39139994	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:39139994delA	uc001rls.1	-							NM_153634	NP_705898			copine VIII											pancreas(1)	1	Esophageal squamous(101;0.187)	Lung NSC(34;0.137)|Melanoma(24;0.152)|all_lung(34;0.157)																---	---	---	---
Unknown	0	broad.mit.edu	37	12	39341644	39341644	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:39341644delA								CPNE8 (42224 upstream) : KIF21A (345387 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	39650928	39650929	+	IGR	INS	-	A	A	rs138696558	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:39650928_39650929insA								CPNE8 (351508 upstream) : KIF21A (36102 downstream)																																			---	---	---	---
ABCD2	225	broad.mit.edu	37	12	39973224	39973224	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:39973224delT	uc001rmb.2	-							NM_005164	NP_005155			ATP-binding cassette, sub-family D, member 2						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																		---	---	---	---
C12orf40	283461	broad.mit.edu	37	12	40081291	40081292	+	Intron	INS	-	G	G	rs139854754	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:40081291_40081292insG	uc001rmc.2	+						C12orf40_uc009zjv.1_Intron	NM_001031748	NP_001026918			hypothetical protein LOC283461											ovary(6)	6																		---	---	---	---
C12orf40	283461	broad.mit.edu	37	12	40112470	40112471	+	Intron	INS	-	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:40112470_40112471insT	uc001rmc.2	+						C12orf40_uc009zjv.1_Intron	NM_001031748	NP_001026918			hypothetical protein LOC283461											ovary(6)	6																		---	---	---	---
C12orf40	283461	broad.mit.edu	37	12	40113424	40113424	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:40113424delA	uc001rmc.2	+						C12orf40_uc009zjv.1_Intron	NM_001031748	NP_001026918			hypothetical protein LOC283461											ovary(6)	6																		---	---	---	---
Unknown	0	broad.mit.edu	37	12	40923610	40923610	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:40923610delT	uc001rmj.1	+											Homo sapiens mRNA; cDNA DKFZp686N11246 (from clone DKFZp686N11246).																														---	---	---	---
Unknown	0	broad.mit.edu	37	12	41015044	41015044	+	IGR	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:41015044delG								LRRK2 (251960 upstream) : CNTN1 (71314 downstream)																																			---	---	---	---
CNTN1	1272	broad.mit.edu	37	12	41274630	41274630	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:41274630delT	uc001rmm.1	+						CNTN1_uc009zjy.1_Intron|CNTN1_uc001rmn.1_Intron|CNTN1_uc001rmo.2_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)																---	---	---	---
Unknown	0	broad.mit.edu	37	12	42158889	42158889	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:42158889delA								PDZRN4 (190505 upstream) : GXYLT1 (316761 downstream)																																			---	---	---	---
GXYLT1	283464	broad.mit.edu	37	12	42481468	42481468	+	3'UTR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:42481468delA	uc001rms.3	-	8					GXYLT1_uc001rmt.3_3'UTR	NM_173601	NP_775872			glycosyltransferase 8 domain containing 3						O-glycan processing	integral to membrane	UDP-xylosyltransferase activity				0																		---	---	---	---
PRICKLE1	144165	broad.mit.edu	37	12	42923691	42923691	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:42923691delA	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	43064527	43064527	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:43064527delA								PRICKLE1 (80955 upstream) : ADAMTS20 (683486 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	43257947	43257947	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:43257947delT								PRICKLE1 (274375 upstream) : ADAMTS20 (490066 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	43527264	43527264	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:43527264delT								PRICKLE1 (543692 upstream) : ADAMTS20 (220749 downstream)																																			---	---	---	---
NELL2	4753	broad.mit.edu	37	12	44985267	44985268	+	Intron	INS	-	GATCCTG	GATCCTG	rs139598235	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:44985267_44985268insGATCCTG	uc001rog.2	-						NELL2_uc001rof.3_Intron|NELL2_uc001roh.2_Intron|NELL2_uc009zkd.2_Intron|NELL2_uc010skz.1_Intron|NELL2_uc010sla.1_Intron|NELL2_uc001roi.1_Intron|NELL2_uc010slb.1_Intron	NM_001145108	NP_001138580			NEL-like protein 2 isoform b precursor						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)														---	---	---	---
Unknown	0	broad.mit.edu	37	12	47279028	47279031	+	IGR	DEL	CTCT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:47279028_47279031delCTCT								SLC38A4 (59248 upstream) : AMIGO2 (190460 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	47648102	47648103	+	IGR	INS	-	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:47648102_47648103insG								FAM113B (17661 upstream) : RPAP3 (407613 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	47723533	47723533	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:47723533delT								FAM113B (93092 upstream) : RPAP3 (332183 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	48009299	48009299	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:48009299delA								FAM113B (378858 upstream) : RPAP3 (46417 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	48330018	48330018	+	IGR	DEL	T	-	-	rs67311844		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:48330018delT								VDR (31204 upstream) : TMEM106C (27312 downstream)																																			---	---	---	---
TMEM106C	79022	broad.mit.edu	37	12	48355297	48355299	+	5'Flank	DEL	AAA	-	-	rs111991221		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:48355297_48355299delAAA	uc001rqp.2	+						TMEM106C_uc001rqo.2_5'Flank|TMEM106C_uc001rqr.2_5'Flank|TMEM106C_uc001rqq.2_5'Flank	NM_024056	NP_076961			transmembrane protein 106C isoform a							endoplasmic reticulum membrane|integral to membrane					0		Acute lymphoblastic leukemia(13;0.11)		GBM - Glioblastoma multiforme(48;0.241)														---	---	---	---
SENP1	29843	broad.mit.edu	37	12	48458896	48458896	+	Frame_Shift_Del	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:48458896delT	uc001rqx.2	-	12	1673	c.1227delA	c.(1225-1227)AAAfs	p.K409fs	SENP1_uc001rqw.2_Frame_Shift_Del_p.K409fs|SENP1_uc001rqy.2_Frame_Shift_Del_p.K210fs|SENP1_uc001rqz.2_Frame_Shift_Del_p.K210fs|SENP1_uc009zkx.2_Frame_Shift_Del_p.K409fs	NM_014554	NP_055369	Q9P0U3	SENP1_HUMAN	sentrin/SUMO-specific protease 1	409					activation of caspase activity|induction of apoptosis by extracellular signals|protein desumoylation|proteolysis	cytoplasm|nucleus	endopeptidase activity|SUMO-specific protease activity	p.G410fs*3(1)		pancreas(2)|lung(1)	3		Acute lymphoblastic leukemia(13;0.108)|all_hematologic(14;0.214)																---	---	---	---
Unknown	0	broad.mit.edu	37	12	48701961	48701961	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:48701961delT								OR10AD1 (104886 upstream) : H1FNT (20802 downstream)																																			---	---	---	---
ADCY6	112	broad.mit.edu	37	12	49181194	49181194	+	Intron	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:49181194delC	uc001rsj.3	-						ADCY6_uc001rsi.3_Intron	NM_015270	NP_056085			adenylate cyclase 6 isoform a						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	ATP binding|metal ion binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	12	49269430	49269430	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:49269430delT								RND1 (9777 upstream) : CCDC65 (28463 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	49286116	49286116	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:49286116delT								RND1 (26463 upstream) : CCDC65 (11777 downstream)																																			---	---	---	---
MLL2	8085	broad.mit.edu	37	12	49433407	49433407	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:49433407delA	uc001rta.3	-							NM_003482	NP_003473			myeloid/lymphoid or mixed-lineage leukemia 2						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)			---	---	---	---
RHEBL1	121268	broad.mit.edu	37	12	49463357	49463374	+	Intron	DEL	CCAATCCTCCACTCTTCC	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:49463357_49463374delCCAATCCTCCACTCTTCC	uc001rtc.1	-						RHEBL1_uc001rtd.1_Intron|RHEBL1_uc009zlc.1_Intron	NM_144593	NP_653194			Ras homolog enriched in brain like 1 precursor						positive regulation of NF-kappaB transcription factor activity|small GTPase mediated signal transduction|TOR signaling cascade	cytoplasm|plasma membrane	GTP binding|GTPase activity|protein binding			lung(1)|breast(1)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	12	49675529	49675529	+	IGR	DEL	A	-	-	rs7485805	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:49675529delA								TUBA1C (8416 upstream) : PRPH (13380 downstream)																																			---	---	---	---
PRPH	5630	broad.mit.edu	37	12	49688878	49688878	+	5'Flank	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:49688878delC	uc001rtu.2	+							NM_006262	NP_006253			peripherin								structural molecule activity				0																		---	---	---	---
SPATS2	65244	broad.mit.edu	37	12	49766503	49766503	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-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																		---	---	---	---
SPATS2	65244	broad.mit.edu	37	12	49832790	49832791	+	Intron	INS	-	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:49832790_49832791insA	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																		---	---	---	---
SPATS2	65244	broad.mit.edu	37	12	49851222	49851223	+	Intron	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:49851222_49851223delTT	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	50057726	50057726	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:50057726delT	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																		---	---	---	---
FMNL3	91010	broad.mit.edu	37	12	50088696	50088696	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:50088696delA	uc001ruv.1	-						FMNL3_uc001ruw.1_Intron	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	50151817	50151820	+	Intron	DEL	AAAA	-	-	rs80171037		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:50151817_50151820delAAAA	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																		---	---	---	---
AQP5	362	broad.mit.edu	37	12	50354472	50354473	+	5'Flank	DEL	GA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:50354472_50354473delGA	uc001rvo.2	+							NM_001651	NP_001642			aquaporin 5						carbon dioxide transport|excretion|odontogenesis|pancreatic juice secretion	apical plasma membrane|integral to plasma membrane	protein binding|water channel activity				0																		---	---	---	---
LIMA1	51474	broad.mit.edu	37	12	50601249	50601249	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:50601249delA	uc001rwj.3	-						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																		---	---	---	---
LARP4	113251	broad.mit.edu	37	12	50824444	50824444	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:50824444delT	uc001rwp.1	+						LARP4_uc001rwo.1_Intron|LARP4_uc001rwq.1_Intron|LARP4_uc001rwr.1_Intron|LARP4_uc001rws.1_Intron|LARP4_uc001rwm.2_Intron|LARP4_uc001rwn.2_Intron	NM_052879	NP_443111			c-Mpl binding protein isoform a								nucleotide binding|RNA binding			ovary(1)	1																		---	---	---	---
LARP4	113251	broad.mit.edu	37	12	50861257	50861257	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:50861257delT	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	51125617	51125617	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:51125617delT	uc001rwv.2	+						DIP2B_uc009zlt.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																		---	---	---	---
TFCP2	7024	broad.mit.edu	37	12	51524477	51524478	+	Intron	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:51524477_51524478delAA	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																		---	---	---	---
TFCP2	7024	broad.mit.edu	37	12	51550127	51550127	+	Intron	DEL	G	-	-	rs66703823		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:51550127delG	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																		---	---	---	---
BIN2	51411	broad.mit.edu	37	12	51692860	51692863	+	Intron	DEL	AAAA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:51692860_51692863delAAAA	uc001ryg.2	-						BIN2_uc009zlz.2_Intron|BIN2_uc001ryh.2_Intron|BIN2_uc010sng.1_Intron	NM_016293	NP_057377			bridging integrator 2							cytoplasm	protein binding			ovary(1)	1																		---	---	---	---
BIN2	51411	broad.mit.edu	37	12	51701895	51701895	+	Intron	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:51701895delC	uc001ryg.2	-						BIN2_uc009zlz.2_Intron|BIN2_uc001ryh.2_Intron|BIN2_uc010sng.1_Intron	NM_016293	NP_057377			bridging integrator 2							cytoplasm	protein binding			ovary(1)	1																		---	---	---	---
SLC4A8	9498	broad.mit.edu	37	12	51811135	51811136	+	Intron	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:51811135_51811136delTT	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)														---	---	---	---
Unknown	0	broad.mit.edu	37	12	51929206	51929206	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:51929206delT								SLC4A8 (19659 upstream) : SCN8A (55814 downstream)																																			---	---	---	---
SCN8A	6334	broad.mit.edu	37	12	52014473	52014473	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:52014473delA	uc001ryw.2	+							NM_014191	NP_055006			sodium channel, voltage gated, type VIII, alpha						axon guidance|myelination|peripheral nervous system development	cytoplasmic membrane-bounded vesicle|node of Ranvier	ATP binding|voltage-gated sodium channel activity			ovary(7)	7				BRCA - Breast invasive adenocarcinoma(357;0.181)	Lamotrigine(DB00555)													---	---	---	---
SCN8A	6334	broad.mit.edu	37	12	52139670	52139670	+	Intron	DEL	T	-	-	rs77181043		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:52139670delT	uc001ryw.2	+						SCN8A_uc010snl.1_Intron|SCN8A_uc001ryx.1_Intron|SCN8A_uc001ryz.1_Intron|SCN8A_uc001ryy.2_Intron	NM_014191	NP_055006			sodium channel, voltage gated, type VIII, alpha						axon guidance|myelination|peripheral nervous system development	cytoplasmic membrane-bounded vesicle|node of Ranvier	ATP binding|voltage-gated sodium channel activity			ovary(7)	7				BRCA - Breast invasive adenocarcinoma(357;0.181)	Lamotrigine(DB00555)													---	---	---	---
Unknown	0	broad.mit.edu	37	12	52245501	52245501	+	IGR	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:52245501delG								FIGNL2 (29293 upstream) : ANKRD33 (36292 downstream)																																			---	---	---	---
KRT83	3889	broad.mit.edu	37	12	52711957	52711957	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:52711957delT	uc001saf.2	-							NM_002282	NP_002273			keratin 83						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)														---	---	---	---
KRT75	9119	broad.mit.edu	37	12	52829481	52829481	+	5'Flank	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:52829481delT	uc001saj.2	-							NM_004693	NP_004684			keratin 75							keratin filament	structural molecule activity				0				BRCA - Breast invasive adenocarcinoma(357;0.192)														---	---	---	---
Unknown	0	broad.mit.edu	37	12	52953476	52953476	+	IGR	DEL	T	-	-	rs71845539		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:52953476delT								KRT71 (6545 upstream) : KRT74 (6127 downstream)																																			---	---	---	---
KRT72	140807	broad.mit.edu	37	12	52982321	52982321	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-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)														---	---	---	---
Unknown	0	broad.mit.edu	37	12	53261035	53261036	+	IGR	DEL	GA	-	-	rs58646316		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:53261035_53261036delGA								KRT78 (18257 upstream) : KRT8 (29935 downstream)																																			---	---	---	---
KRT8	3856	broad.mit.edu	37	12	53308027	53308027	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:53308027delA	uc009zmk.1	-						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)													---	---	---	---
MFSD5	84975	broad.mit.edu	37	12	53644980	53644980	+	5'Flank	DEL	G	-	-	rs145734828	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:53644980delG	uc001sci.1	+						MFSD5_uc001sch.1_5'Flank	NM_032889	NP_116278			major facilitator superfamily domain containing						transport	integral to membrane				skin(2)|ovary(1)	3																		---	---	---	---
SP7	121340	broad.mit.edu	37	12	53723524	53723524	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:53723524delT	uc001sct.2	-						SP7_uc001scu.2_Intron|SP7_uc001scv.2_Intron	NM_152860	NP_690599			osterix						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0																		---	---	---	---
ATP5G2	517	broad.mit.edu	37	12	54064758	54064759	+	Intron	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:54064758_54064759delAA	uc009znc.2	-						ATP5G2_uc001sec.2_Intron|ATP5G2_uc001sed.2_Intron	NM_001002031	NP_001002031			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			ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	12	54206063	54206064	+	IGR	INS	-	TCTTTC	TCTTTC	rs140050304		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:54206063_54206064insTCTTTC								CALCOCO1 (84756 upstream) : HOXC13 (126512 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	54240732	54240733	+	IGR	DEL	TC	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:54240732_54240733delTC								CALCOCO1 (119425 upstream) : HOXC13 (91843 downstream)																																			---	---	---	---
HOXC9	3225	broad.mit.edu	37	12	54395876	54395877	+	Intron	DEL	AG	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:54395876_54395877delAG	uc001sep.2	+						HOXC9_uc001seq.2_Intron	NM_006897	NP_008828			homeobox C9						multicellular organismal development	nucleus	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			large_intestine(1)|pancreas(1)|skin(1)	3																		---	---	---	---
HOXC4	3221	broad.mit.edu	37	12	54426580	54426583	+	Intron	DEL	TTTT	-	-	rs113659413		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:54426580_54426583delTTTT	uc001seu.2	+						HOXC5_uc001set.2_Intron|HOXC5_uc001sew.2_5'Flank|MIR615_hsa-mir-615|MI0003628_5'Flank	NM_014620	NP_055435			homeobox C4							nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			ovary(1)	1																OREG0021884	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
CBX5	23468	broad.mit.edu	37	12	54646036	54646037	+	Intron	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:54646036_54646037delAA	uc001sfh.3	-						CBX5_uc001sfk.3_Intron|CBX5_uc001sfi.3_Intron|CBX5_uc001sfj.3_Intron	NM_001127322	NP_001120794			heterochromatin protein 1-alpha						blood coagulation|interspecies interaction between organisms|negative regulation of transcription, DNA-dependent	cytoplasm|histone deacetylase complex|histone methyltransferase complex|nuclear centromeric heterochromatin|nuclear envelope|nucleolus|transcriptional repressor complex	methylated histone residue binding|protein binding, bridging|repressing transcription factor binding				0																		---	---	---	---
COPZ1	22818	broad.mit.edu	37	12	54730796	54730797	+	Intron	INS	-	CT	CT	rs111512035		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:54730796_54730797insCT	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	54744007	54744008	+	Intron	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:54744007_54744008delTT	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																		---	---	---	---
Unknown	0	broad.mit.edu	37	12	54830231	54830231	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:54830231delA								ITGA5 (17181 upstream) : GTSF1 (19506 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	55056650	55056651	+	IGR	INS	-	TG	TG	rs147838817	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:55056650_55056651insTG								DCD (14501 upstream) : MUCL1 (191648 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	55446383	55446383	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:55446383delT								NEUROD4 (22583 upstream) : OR9K2 (77170 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	55562152	55562152	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:55562152delA								OR9K2 (37593 upstream) : OR10A7 (52657 downstream)																																			---	---	---	---
OR6C1	390321	broad.mit.edu	37	12	55713925	55713925	+	5'Flank	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:55713925delA	uc010spi.1	+							NM_001005182	NP_001005182			olfactory receptor, family 6, subfamily C,						sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			large_intestine(1)|ovary(1)	2																		---	---	---	---
CS	1431	broad.mit.edu	37	12	56668453	56668453	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:56668453delA	uc001sks.1	-						CS_uc010sql.1_Intron|CS_uc001skr.1_Intron|CS_uc001skt.1_Intron|CS_uc010sqm.1_Intron	NM_004077	NP_004068			citrate synthase precursor						cellular carbohydrate metabolic process|tricarboxylic acid cycle	mitochondrial matrix	citrate (Si)-synthase activity				0		Myeloproliferative disorder(1001;0.000374)		BRCA - Breast invasive adenocarcinoma(357;6.17e-07)														---	---	---	---
TIMELESS	8914	broad.mit.edu	37	12	56824949	56824949	+	Intron	DEL	C	-	-	rs79733408		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:56824949delC	uc001slf.2	-						TIMELESS_uc001slg.2_Intron	NM_003920	NP_003911			timeless homolog						cell division|circadian rhythm|detection of abiotic stimulus|mitosis|morphogenesis of an epithelium|negative regulation of transcription, DNA-dependent|regulation of S phase|response to DNA damage stimulus|transcription, DNA-dependent	nuclear chromatin				ovary(5)|breast(2)|pancreas(1)	8																		---	---	---	---
RBMS2	5939	broad.mit.edu	37	12	56949831	56949831	+	Intron	DEL	A	-	-	rs111255720		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:56949831delA	uc001sln.2	+						RBMS2_uc010sqp.1_Intron|RBMS2_uc010sqq.1_Intron|RBMS2_uc009zou.2_Intron	NM_002898	NP_002889			RNA binding motif, single stranded interacting						RNA processing	nucleus	nucleotide binding|RNA binding				0																		---	---	---	---
BAZ2A	11176	broad.mit.edu	37	12	56999550	56999552	+	Intron	DEL	TTT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:56999550_56999552delTTT	uc001slq.1	-						BAZ2A_uc001slp.1_Intron|BAZ2A_uc009zov.1_5'Flank|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																		---	---	---	---
Unknown	0	broad.mit.edu	37	12	57196635	57196636	+	IGR	INS	-	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:57196635_57196636insT								HSD17B6 (15061 upstream) : SDR9C7 (120983 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	57335432	57335433	+	IGR	INS	-	T	T	rs113707341		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:57335432_57335433insT								SDR9C7 (7387 upstream) : RDH16 (9785 downstream)																																			---	---	---	---
TAC3	6866	broad.mit.edu	37	12	57408490	57408491	+	Intron	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:57408490_57408491delTT	uc001smp.2	-						TAC3_uc001smr.2_Intron|TAC3_uc001smq.2_Intron|TAC3_uc001smt.2_Intron|TAC3_uc001sms.2_Intron|TAC3_uc010sqy.1_Intron|TAC3_uc001smu.2_Intron|TAC3_uc001smv.2_Intron|TAC3_uc001smo.2_Intron	NM_013251	NP_037383			tachykinin 3 precursor						female pregnancy|neuropeptide signaling pathway|tachykinin receptor signaling pathway	extracellular space|soluble fraction	receptor binding			ovary(1)|skin(1)	2																		---	---	---	---
LRP1	4035	broad.mit.edu	37	12	57572967	57572967	+	Intron	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:57572967delG	uc001snd.2	+							NM_002332	NP_002323			low density lipoprotein-related protein 1						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)													---	---	---	---
R3HDM2	22864	broad.mit.edu	37	12	57722519	57722519	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:57722519delT	uc001snt.2	-						R3HDM2_uc001sns.2_Intron|R3HDM2_uc009zpo.1_Intron	NM_014925	NP_055740			R3H domain containing 2							nucleus	nucleic acid binding			ovary(2)	2																		---	---	---	---
R3HDM2	22864	broad.mit.edu	37	12	57774552	57774552	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:57774552delA	uc001snt.2	-						R3HDM2_uc001sns.2_Intron|R3HDM2_uc009zpo.1_Intron	NM_014925	NP_055740			R3H domain containing 2							nucleus	nucleic acid binding			ovary(2)	2																		---	---	---	---
MARS	4141	broad.mit.edu	37	12	57884564	57884574	+	Intron	DEL	TTTTTTTTTTT	-	-	rs35674919		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:57884564_57884574delTTTTTTTTTTT	uc001sog.2	+						ARHGAP9_uc001sod.2_5'Flank|ARHGAP9_uc001soe.1_5'Flank|MARS_uc001sof.1_Intron|MARS_uc010srp.1_Intron|MARS_uc010srq.1_Intron	NM_004990	NP_004981			methionyl-tRNA synthetase						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)													---	---	---	---
DCTN2	10540	broad.mit.edu	37	12	57927806	57927806	+	Frame_Shift_Del	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:57927806delG	uc001som.1	-	7	731	c.599delC	c.(598-600)CCAfs	p.P200fs	DCTN2_uc009zpu.1_Frame_Shift_Del_p.P205fs|DCTN2_uc009zpv.1_Frame_Shift_Del_p.P113fs|DCTN2_uc009zpw.1_Frame_Shift_Del_p.P113fs|DCTN2_uc001soo.1_RNA|DCTN2_uc001son.1_Frame_Shift_Del_p.P113fs|DCTN2_uc001sop.1_Frame_Shift_Del_p.P113fs|DCTN2_uc001soq.1_RNA|DCTN2_uc009zpx.1_Frame_Shift_Del_p.P200fs	NM_006400	NP_006391	Q13561	DCTN2_HUMAN	dynactin 2	200					cell proliferation|G2/M transition of mitotic cell cycle|mitosis	centrosome|cytosol|dynactin complex|dynein complex|kinetochore|membrane|microtubule|vesicle	motor activity|protein binding			ovary(1)	1																		---	---	---	---
CDK4	1019	broad.mit.edu	37	12	58145599	58145599	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:58145599delA	uc001spv.2	-						CDK4_uc010ssb.1_Intron|CDK4_uc001spw.2_Intron	NM_000075	NP_000066			cyclin-dependent kinase 4						cell division|G1 phase of mitotic cell cycle|G1/S transition of mitotic cell cycle|positive regulation of fibroblast proliferation|regulation of gene expression|response to drug|S phase of mitotic cell cycle	cyclin-dependent protein kinase holoenzyme complex|cytosol|membrane	ATP binding|cyclin-dependent protein kinase activity|protein binding			lung(1)|breast(1)|central_nervous_system(1)	3	all_cancers(7;4.96e-69)|Lung NSC(6;5.5e-25)|all_lung(6;3.87e-23)|all_epithelial(6;1.66e-15)|Glioma(12;6.95e-05)|all_neural(12;0.00016)|Melanoma(17;0.122)		GBM - Glioblastoma multiforme(5;4.21e-120)|all cancers(5;3.75e-83)|BRCA - Breast invasive adenocarcinoma(9;0.0294)					Mis			melanoma 			Hereditary_Melanoma				---	---	---	---
CYP27B1	1594	broad.mit.edu	37	12	58156675	58156675	+	3'UTR	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:58156675delG	uc001spz.1	-	9					CYP27B1_uc001sqa.1_3'UTR	NM_000785	NP_000776			cytochrome P450, family 27, subfamily B,						bone mineralization|calcium ion homeostasis|calcium ion transport|decidualization|G1 to G0 transition|hormone biosynthetic process|negative regulation of calcidiol 1-monooxygenase activity|negative regulation of cell growth|negative regulation of cell proliferation|positive regulation of keratinocyte differentiation|positive regulation of vitamin D 24-hydroxylase activity|positive regulation of vitamin D receptor signaling pathway|regulation of bone mineralization|response to estrogen stimulus|response to interferon-gamma|response to lipopolysaccharide|response to tumor necrosis factor|response to vitamin D|vitamin D biosynthetic process|xenobiotic metabolic process	mitochondrial outer membrane	calcidiol 1-monooxygenase activity|electron carrier activity|heme binding			central_nervous_system(3)	3	all_cancers(7;8.09e-80)|Lung NSC(6;2.26e-27)|all_lung(6;1.99e-25)|all_epithelial(6;3.62e-18)|Glioma(12;6.95e-05)|all_neural(12;0.00016)|Melanoma(17;0.122)		GBM - Glioblastoma multiforme(5;1.97e-113)|all cancers(5;1.54e-78)|BRCA - Breast invasive adenocarcinoma(9;0.0294)		Calcidiol(DB00146)|Calcitriol(DB00136)|Ergocalciferol(DB00153)													---	---	---	---
Unknown	0	broad.mit.edu	37	12	58942477	58942478	+	IGR	INS	-	AG	AG			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:58942477_58942478insAG								XRCC6BP1 (591426 upstream) : LRIG3 (323460 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	59252083	59252084	+	IGR	DEL	TC	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:59252083_59252084delTC								XRCC6BP1 (901032 upstream) : LRIG3 (13854 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	59372266	59372266	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:59372266delT								LRIG3 (58004 upstream) : SLC16A7 (617582 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	59560765	59560765	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:59560765delT								LRIG3 (246503 upstream) : SLC16A7 (429083 downstream)																																			---	---	---	---
SLC16A7	9194	broad.mit.edu	37	12	60027426	60027428	+	Intron	DEL	AAA	-	-	rs74920411		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:60027426_60027428delAAA	uc001sqs.2	+						SLC16A7_uc001sqt.2_Intron	NM_004731	NP_004722			solute carrier family 16, member 7							integral to plasma membrane|membrane fraction	pyruvate secondary active transmembrane transporter activity|secondary active monocarboxylate transmembrane transporter activity|symporter activity			ovary(1)	1				GBM - Glioblastoma multiforme(3;0.0303)	Pyruvic acid(DB00119)													---	---	---	---
Unknown	0	broad.mit.edu	37	12	60441257	60441258	+	IGR	DEL	TT	-	-	rs56955641		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:60441257_60441258delTT								SLC16A7 (265850 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	61006629	61006630	+	IGR	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:61006629_61006630delTT								SLC16A7 (831222 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	61097733	61097733	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:61097733delT								SLC16A7 (922326 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	61423509	61423511	+	IGR	DEL	TCT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:61423509_61423511delTCT								None (None upstream) : FAM19A2 (678532 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	61423676	61423676	+	IGR	DEL	T	-	-	rs74790740		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:61423676delT								None (None upstream) : FAM19A2 (678367 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	61498814	61498814	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:61498814delT								None (None upstream) : FAM19A2 (603229 downstream)																																			---	---	---	---
FAM19A2	338811	broad.mit.edu	37	12	62568096	62568096	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:62568096delA	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)														---	---	---	---
MON2	23041	broad.mit.edu	37	12	62960236	62960236	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:62960236delT	uc001sre.2	+						MON2_uc009zqj.2_Intron|MON2_uc010ssl.1_Intron|MON2_uc010ssm.1_Intron|MON2_uc010ssn.1_Intron|MON2_uc001srf.2_Intron|MON2_uc001srg.2_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)														---	---	---	---
PPM1H	57460	broad.mit.edu	37	12	63298022	63298023	+	Intron	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:63298022_63298023delTT	uc001srk.3	-							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	63891879	63891879	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:63891879delT								AVPR1A (345289 upstream) : DPY19L2 (60814 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	63894261	63894262	+	IGR	INS	-	AG	AG			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:63894261_63894262insAG								AVPR1A (347671 upstream) : DPY19L2 (58431 downstream)																																			---	---	---	---
DPY19L2	283417	broad.mit.edu	37	12	63964390	63964390	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:63964390delT	uc001srp.1	-						DPY19L2_uc010sso.1_Intron	NM_173812	NP_776173			dpy-19-like 2						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)														---	---	---	---
TMEM5	10329	broad.mit.edu	37	12	64202392	64202392	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:64202392delT	uc001srq.1	+						TMEM5_uc001srr.1_Intron|TMEM5_uc001srs.1_Intron	NM_014254	NP_055069			transmembrane protein 5							integral to plasma membrane					0		Myeloproliferative disorder(1001;0.0255)	BRCA - Breast invasive adenocarcinoma(9;0.0985)	GBM - Glioblastoma multiforme(28;9e-08)|BRCA - Breast invasive adenocarcinoma(357;0.000175)														---	---	---	---
SRGAP1	57522	broad.mit.edu	37	12	64251964	64251965	+	Intron	DEL	GT	-	-	rs113728268		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:64251964_64251965delGT	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)														---	---	---	---
Unknown	0	broad.mit.edu	37	12	64551680	64551680	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:64551680delT								SRGAP1 (10067 upstream) : C12orf66 (34740 downstream)																																			---	---	---	---
C12orf56	115749	broad.mit.edu	37	12	64662060	64662060	+	Intron	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:64662060delG	uc001ssa.3	-						uc001srx.2_Intron|C12orf56_uc001sry.2_Intron|C12orf56_uc001srz.2_Intron	NM_001099676	NP_001093146			hypothetical protein LOC115749												0			GBM - Glioblastoma multiforme(3;0.000582)	GBM - Glioblastoma multiforme(28;0.0259)														---	---	---	---
C12orf56	115749	broad.mit.edu	37	12	64779498	64779498	+	Intron	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:64779498delC	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)														---	---	---	---
Unknown	0	broad.mit.edu	37	12	64901154	64901154	+	IGR	DEL	G	-	-	rs7956852	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:64901154delG								TBK1 (5263 upstream) : RASSF3 (103139 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	64990854	64990855	+	IGR	INS	-	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:64990854_64990855insT								TBK1 (94963 upstream) : RASSF3 (13438 downstream)																																			---	---	---	---
RASSF3	283349	broad.mit.edu	37	12	65035529	65035530	+	Intron	DEL	TT	-	-	rs72288285		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:65035529_65035530delTT	uc001ssd.2	+						RASSF3_uc009zqn.2_Intron|RASSF3_uc001sse.2_Intron	NM_178169	NP_835463			Ras association (RalGDS/AF-6) domain family						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)														---	---	---	---
RASSF3	283349	broad.mit.edu	37	12	65046140	65046141	+	Intron	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:65046140_65046141delTT	uc001ssd.2	+						RASSF3_uc009zqn.2_Intron|RASSF3_uc001sse.2_Intron	NM_178169	NP_835463			Ras association (RalGDS/AF-6) domain family						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)														---	---	---	---
RASSF3	283349	broad.mit.edu	37	12	65049467	65049467	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:65049467delA	uc001ssd.2	+						RASSF3_uc009zqn.2_Intron|RASSF3_uc001sse.2_Intron	NM_178169	NP_835463			Ras association (RalGDS/AF-6) domain family						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)														---	---	---	---
Unknown	0	broad.mit.edu	37	12	65325061	65325061	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:65325061delT	uc001ssj.1	+											Homo sapiens cDNA FLJ41278 fis, clone BRAMY2037147.																														---	---	---	---
Unknown	0	broad.mit.edu	37	12	65369246	65369247	+	RNA	INS	-	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:65369246_65369247insT	uc001ssj.1	+	3		c.1110_1111insT								Homo sapiens cDNA FLJ41278 fis, clone BRAMY2037147.																														---	---	---	---
Unknown	0	broad.mit.edu	37	12	65404030	65404030	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:65404030delT								GNS (250804 upstream) : WIF1 (40377 downstream)																																			---	---	---	---
MSRB3	253827	broad.mit.edu	37	12	65762704	65762706	+	Intron	DEL	CCC	-	-	rs67548266		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:65762704_65762706delCCC	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	65957440	65957442	+	IGR	DEL	GAA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:65957440_65957442delGAA								MSRB3 (96760 upstream) : RPSAP52 (194361 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	66498687	66498688	+	IGR	DEL	TC	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:66498687_66498688delTC								HMGA2 (138619 upstream) : LLPH (18162 downstream)																																			---	---	---	---
LLPH	84298	broad.mit.edu	37	12	66517615	66517616	+	3'UTR	DEL	AG	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:66517615_66517616delAG	uc010ssw.1	-	3					LLPH_uc010ssx.1_RNA	NM_032338	NP_115714			LLP homolog												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	12	66672750	66672750	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:66672750delT								IRAK3 (24358 upstream) : HELB (23606 downstream)																																			---	---	---	---
GRIP1	23426	broad.mit.edu	37	12	66917609	66917610	+	Intron	INS	-	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:66917609_66917610insA	uc001stk.2	-						GRIP1_uc010sta.1_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)														---	---	---	---
Unknown	0	broad.mit.edu	37	12	67537968	67537968	+	IGR	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:67537968delC								GRIP1 (340074 upstream) : CAND1 (125093 downstream)																																			---	---	---	---
RAP1B	5908	broad.mit.edu	37	12	69020555	69020555	+	Intron	DEL	T	-	-	rs74812051		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:69020555delT	uc001sub.2	+						RAP1B_uc010ste.1_Intron|RAP1B_uc001suc.2_Intron|RAP1B_uc010stf.1_Intron|RAP1B_uc010stg.1_Intron|RAP1B_uc010sth.1_Intron|RAP1B_uc010sti.1_Intron	NM_001089704	NP_001083173			SubName: Full=Ras-related protein Rap-1A; SubName: Full=cDNA FLJ75985, highly similar to Homo sapiens RAP1A, member of RAS oncogene family (RAP1A), transcript variant 2, mRNA; SubName: Full=RAP1A, member of RAS oncogene family;						blood coagulation|energy reserve metabolic process|regulation of establishment of cell polarity|regulation of insulin secretion	cell-cell junction|cytosol	GDP binding|GTP binding|GTPase activity|protein binding				0	Breast(13;1.24e-05)		Lung(24;0.000131)|LUAD - Lung adenocarcinoma(15;0.00107)|STAD - Stomach adenocarcinoma(21;0.00694)	GBM - Glioblastoma multiforme(7;0.000306)														---	---	---	---
RAP1B	5908	broad.mit.edu	37	12	69044168	69044168	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:69044168delT	uc001sub.2	+						RAP1B_uc010ste.1_Intron|RAP1B_uc001suc.2_Intron|RAP1B_uc010stf.1_Intron|RAP1B_uc010stg.1_Intron|RAP1B_uc010sth.1_Intron|RAP1B_uc010sti.1_Intron	NM_001089704	NP_001083173			SubName: Full=Ras-related protein Rap-1A; SubName: Full=cDNA FLJ75985, highly similar to Homo sapiens RAP1A, member of RAS oncogene family (RAP1A), transcript variant 2, mRNA; SubName: Full=RAP1A, member of RAS oncogene family;						blood coagulation|energy reserve metabolic process|regulation of establishment of cell polarity|regulation of insulin secretion	cell-cell junction|cytosol	GDP binding|GTP binding|GTPase activity|protein binding				0	Breast(13;1.24e-05)		Lung(24;0.000131)|LUAD - Lung adenocarcinoma(15;0.00107)|STAD - Stomach adenocarcinoma(21;0.00694)	GBM - Glioblastoma multiforme(7;0.000306)														---	---	---	---
NUP107	57122	broad.mit.edu	37	12	69126366	69126367	+	Intron	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:69126366_69126367delAA	uc001suf.2	+						NUP107_uc001sug.2_Intron|NUP107_uc010stj.1_Intron	NM_020401	NP_065134			nucleoporin 107kDa						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)															---	---	---	---
Unknown	0	broad.mit.edu	37	12	69489277	69489277	+	IGR	DEL	A	-	-	rs72350707		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:69489277delA								CPM (132257 upstream) : CPSF6 (144040 downstream)																																			---	---	---	---
CPSF6	11052	broad.mit.edu	37	12	69667594	69667594	+	3'UTR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:69667594delA	uc001sut.3	+	10					CPSF6_uc001suu.3_3'UTR|CPSF6_uc010stk.1_3'UTR|MIR1279_hsa-mir-1279|MI0006426_5'Flank	NM_007007	NP_008938			cleavage and polyadenylation specific factor 6,						mRNA polyadenylation|protein tetramerization	mRNA cleavage factor complex|paraspeckles|ribonucleoprotein complex	mRNA binding|nucleotide binding|protein binding				0	all_epithelial(5;2.47e-36)|Lung NSC(4;1.1e-32)|all_lung(4;6.26e-31)|Breast(13;1.59e-06)|Esophageal squamous(21;0.187)		Epithelial(6;4.89e-17)|BRCA - Breast invasive adenocarcinoma(5;8.5e-10)|Lung(24;6.04e-05)|LUAD - Lung adenocarcinoma(15;0.00107)|STAD - Stomach adenocarcinoma(21;0.0151)|LUSC - Lung squamous cell carcinoma(43;0.171)|Kidney(9;0.241)															---	---	---	---
Unknown	0	broad.mit.edu	37	12	69718327	69718328	+	IGR	DEL	AA	-	-	rs67474159		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:69718327_69718328delAA								CPSF6 (50190 upstream) : LYZ (23806 downstream)																																			---	---	---	---
FRS2	10818	broad.mit.edu	37	12	69894953	69894956	+	Intron	DEL	AAAA	-	-	rs34578711		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:69894953_69894956delAAAA	uc001suy.2	+						FRS2_uc001suz.2_Intron|FRS2_uc009zrj.2_Intron|FRS2_uc009zrk.2_Intron	NM_006654	NP_006645			fibroblast growth factor receptor substrate 2						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)															---	---	---	---
Unknown	0	broad.mit.edu	37	12	70230823	70230823	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:70230823delA								RAB3IP (13841 upstream) : CNOT2 (405954 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	70423182	70423182	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:70423182delA								RAB3IP (206200 upstream) : CNOT2 (213595 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	70528138	70528138	+	IGR	DEL	A	-	-	rs149351648		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:70528138delA								RAB3IP (311156 upstream) : CNOT2 (108639 downstream)																																			---	---	---	---
CNOT2	4848	broad.mit.edu	37	12	70739865	70739865	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:70739865delT	uc001svv.2	+						CNOT2_uc009zro.2_Intron|CNOT2_uc009zrp.2_Intron|CNOT2_uc009zrq.2_Intron	NM_014515	NP_055330			CCR4-NOT transcription complex, subunit 2						nuclear-transcribed mRNA poly(A) tail shortening|regulation of transcription from RNA polymerase II promoter	cytosol|nucleus	protein binding|RNA polymerase II transcription cofactor activity				0	Renal(347;0.236)		GBM - Glioblastoma multiforme(1;4.77e-09)|Lung(24;0.000636)|OV - Ovarian serous cystadenocarcinoma(12;0.00243)|STAD - Stomach adenocarcinoma(21;0.0118)															---	---	---	---
KCNMB4	27345	broad.mit.edu	37	12	70780378	70780381	+	Intron	DEL	TTTT	-	-	rs11355226		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:70780378_70780381delTTTT	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)															---	---	---	---
Unknown	0	broad.mit.edu	37	12	70897885	70897886	+	Intron	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:70897885_70897886delTT	uc001svz.2	+											Homo sapiens cDNA clone IMAGE:4823238.																														---	---	---	---
Unknown	0	broad.mit.edu	37	12	71468031	71468031	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:71468031delT								PTPRR (153447 upstream) : TSPAN8 (50846 downstream)																																			---	---	---	---
ZFC3H1	196441	broad.mit.edu	37	12	72038162	72038162	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:72038162delA	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																		---	---	---	---
TRHDE	29953	broad.mit.edu	37	12	72774642	72774643	+	Intron	DEL	TC	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:72774642_72774643delTC	uc001sxa.2	+							NM_013381	NP_037513			thyrotropin-releasing hormone degrading enzyme						cell-cell signaling|proteolysis|signal transduction	integral to plasma membrane	aminopeptidase activity|metallopeptidase activity|zinc ion binding			ovary(2)|skin(1)	3																		---	---	---	---
Unknown	0	broad.mit.edu	37	12	73690989	73690994	+	IGR	DEL	ACACAC	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:73690989_73690994delACACAC								TRHDE (631568 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	73736196	73736196	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:73736196delT								TRHDE (676775 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	74549875	74549875	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:74549875delA	uc009zrx.1	-											Homo sapiens cDNA clone IMAGE:3926153, partial cds.																														---	---	---	---
Unknown	0	broad.mit.edu	37	12	75090661	75090662	+	IGR	DEL	AC	-	-	rs146346383		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:75090661_75090662delAC								ATXN7L3B (155438 upstream) : KCNC2 (343235 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	75180123	75180123	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:75180123delT								ATXN7L3B (244900 upstream) : KCNC2 (253774 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	75194418	75194419	+	IGR	INS	-	TAGT	TAGT	rs143201785	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:75194418_75194419insTAGT								ATXN7L3B (259195 upstream) : KCNC2 (239478 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	75868326	75868326	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:75868326delA								GLIPR1L2 (42735 upstream) : GLIPR1 (6187 downstream)																																			---	---	---	---
NAP1L1	4673	broad.mit.edu	37	12	76460254	76460254	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:76460254delA	uc001sxw.2	-						NAP1L1_uc001sxv.2_Intron|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	76806012	76806012	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:76806012delA	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																		---	---	---	---
OSBPL8	114882	broad.mit.edu	37	12	76913482	76913482	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:76913482delA	uc001sye.1	-						OSBPL8_uc001syf.1_Intron|OSBPL8_uc001syg.1_Intron	NM_020841	NP_065892			oxysterol-binding protein-like protein 8 isoform						lipid transport		lipid binding			ovary(1)	1																		---	---	---	---
ZDHHC17	23390	broad.mit.edu	37	12	77206097	77206097	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:77206097delT	uc001syk.1	+						ZDHHC17_uc001syi.1_Intron|ZDHHC17_uc001syj.2_Intron	NM_015336	NP_056151			huntingtin interacting protein 14						lipoprotein transport|positive regulation of I-kappaB kinase/NF-kappaB cascade	Golgi-associated vesicle membrane|integral to membrane	magnesium ion transmembrane transporter activity|protein binding|protein-cysteine S-palmitoleyltransferase activity|signal transducer activity|zinc ion binding				0																		---	---	---	---
ZDHHC17	23390	broad.mit.edu	37	12	77211125	77211125	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:77211125delT	uc001syk.1	+						ZDHHC17_uc001syi.1_Intron|ZDHHC17_uc001syj.2_Intron	NM_015336	NP_056151			huntingtin interacting protein 14						lipoprotein transport|positive regulation of I-kappaB kinase/NF-kappaB cascade	Golgi-associated vesicle membrane|integral to membrane	magnesium ion transmembrane transporter activity|protein binding|protein-cysteine S-palmitoleyltransferase activity|signal transducer activity|zinc ion binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	12	77300484	77300484	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:77300484delT								CSRP2 (27685 upstream) : E2F7 (114543 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	78073326	78073326	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:78073326delA								E2F7 (613966 upstream) : NAV3 (151743 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	78973549	78973550	+	IGR	DEL	CA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:78973549_78973550delCA								NAV3 (366761 upstream) : SYT1 (284223 downstream)																																			---	---	---	---
PAWR	5074	broad.mit.edu	37	12	80023377	80023378	+	Intron	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:80023377_80023378delAA	uc001syx.2	-							NM_002583	NP_002574			PRKC, apoptosis, WT1, regulator						actin filament bundle assembly|apoptosis|induction of apoptosis|negative regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	cytoplasm|nucleus|plasma membrane	actin binding|enzyme binding|leucine zipper domain binding|transcription corepressor activity				0																		---	---	---	---
PAWR	5074	broad.mit.edu	37	12	80077595	80077595	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:80077595delA	uc001syx.2	-							NM_002583	NP_002574			PRKC, apoptosis, WT1, regulator						actin filament bundle assembly|apoptosis|induction of apoptosis|negative regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	cytoplasm|nucleus|plasma membrane	actin binding|enzyme binding|leucine zipper domain binding|transcription corepressor activity				0																		---	---	---	---
PPP1R12A	4659	broad.mit.edu	37	12	80286524	80286524	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:80286524delA	uc001syz.2	-						PPP1R12A_uc010suc.1_Intron|PPP1R12A_uc001sza.2_Intron|PPP1R12A_uc010sud.1_Intron|PPP1R12A_uc001szb.2_Intron|PPP1R12A_uc001szc.2_Intron	NM_002480	NP_002471			protein phosphatase 1, regulatory (inhibitor)							contractile fiber	protein binding|signal transducer activity			ovary(2)|breast(2)|large_intestine(1)|central_nervous_system(1)|skin(1)	7																		---	---	---	---
Unknown	0	broad.mit.edu	37	12	80648804	80648804	+	IGR	DEL	T	-	-	rs80186622		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:80648804delT								PPP1R12A (319569 upstream) : PTPRQ (189322 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	80656010	80656011	+	IGR	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:80656010_80656011delTT								PPP1R12A (326775 upstream) : PTPRQ (182115 downstream)																																			---	---	---	---
PTPRQ	374462	broad.mit.edu	37	12	81063246	81063246	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:81063246delA	uc001sze.2	+							NM_001145026	NP_001138498			protein tyrosine phosphatase, receptor type, Q												0																		---	---	---	---
MYF5	4617	broad.mit.edu	37	12	81110516	81110516	+	5'Flank	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:81110516delA	uc001szg.2	+							NM_005593	NP_005584			myogenic factor 5						muscle cell fate commitment|positive regulation of muscle cell differentiation|skeletal muscle tissue development	nucleoplasm	DNA binding|protein heterodimerization activity|sequence-specific enhancer binding RNA polymerase II transcription factor activity			ovary(1)	1																		---	---	---	---
PPFIA2	8499	broad.mit.edu	37	12	81669906	81669906	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:81669906delA	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																		---	---	---	---
PPFIA2	8499	broad.mit.edu	37	12	82019991	82019991	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:82019991delA	uc001szo.1	-						PPFIA2_uc010suj.1_Intron|PPFIA2_uc009zsi.1_Intron	NM_003625	NP_003616			PTPRF interacting protein alpha 2											ovary(3)|lung(2)|pancreas(1)	6																		---	---	---	---
PPFIA2	8499	broad.mit.edu	37	12	82092543	82092544	+	Intron	DEL	AC	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:82092543_82092544delAC	uc001szo.1	-						PPFIA2_uc010suj.1_Intron|PPFIA2_uc009zsi.1_Intron	NM_003625	NP_003616			PTPRF interacting protein alpha 2											ovary(3)|lung(2)|pancreas(1)	6																		---	---	---	---
PPFIA2	8499	broad.mit.edu	37	12	82115232	82115233	+	Intron	DEL	AC	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:82115232_82115233delAC	uc001szo.1	-						PPFIA2_uc010suj.1_Intron|PPFIA2_uc009zsi.1_Intron	NM_003625	NP_003616			PTPRF interacting protein alpha 2											ovary(3)|lung(2)|pancreas(1)	6																		---	---	---	---
Unknown	0	broad.mit.edu	37	12	82919050	82919050	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:82919050delA								C12orf26 (46109 upstream) : TMTC2 (161884 downstream)																																			---	---	---	---
TMTC2	160335	broad.mit.edu	37	12	83424456	83424456	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:83424456delT	uc001szt.2	+						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	83696286	83696286	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:83696286delA								TMTC2 (168223 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	83819070	83819070	+	IGR	DEL	T	-	-	rs35598327		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:83819070delT								TMTC2 (291007 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	83971710	83971710	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:83971710delA								TMTC2 (443647 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	84290241	84290241	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:84290241delA								TMTC2 (762178 upstream) : SLC6A15 (963028 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	84428924	84428925	+	IGR	DEL	GC	-	-	rs140112318		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:84428924_84428925delGC								TMTC2 (900861 upstream) : SLC6A15 (824344 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	85108021	85108023	+	IGR	DEL	AAA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:85108021_85108023delAAA								None (None upstream) : SLC6A15 (145246 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	85357834	85357834	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:85357834delT								SLC6A15 (51228 upstream) : TSPAN19 (50261 downstream)																																			---	---	---	---
LRRIQ1	84125	broad.mit.edu	37	12	85506271	85506271	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:85506271delT	uc001tac.2	+						LRRIQ1_uc001tab.1_Intron	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	85529968	85529969	+	Intron	INS	-	CA	CA	rs142662115	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-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-4200-01A-01D-1126-08	TCGA-BR-4200-11A-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)														---	---	---	---
Unknown	0	broad.mit.edu	37	12	85902091	85902091	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:85902091delA								ALX1 (206532 upstream) : RASSF9 (296240 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	86360076	86360076	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:86360076delT								NTS (83313 upstream) : MGAT4C (12963 downstream)																																			---	---	---	---
MGAT4C	25834	broad.mit.edu	37	12	86374168	86374168	+	Frame_Shift_Del	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:86374168delT	uc001tai.3	-	8	1586	c.336delA	c.(334-336)AAAfs	p.K112fs	MGAT4C_uc001tal.3_Frame_Shift_Del_p.K112fs|MGAT4C_uc001taj.3_Frame_Shift_Del_p.K112fs|MGAT4C_uc001tak.3_Frame_Shift_Del_p.K112fs|MGAT4C_uc010sum.1_Frame_Shift_Del_p.K136fs|MGAT4C_uc001tah.3_Frame_Shift_Del_p.K112fs	NM_013244	NP_037376	Q9UBM8	MGT4C_HUMAN	alpha-1,3-mannosyl-glycoprotein	112	Lumenal (Potential).				post-translational protein modification|protein N-linked glycosylation via asparagine	Golgi membrane|integral to membrane	alpha-1,3-mannosylglycoprotein 4-beta-N-acetylglucosaminyltransferase activity|metal ion binding			ovary(3)	3																		---	---	---	---
Unknown	0	broad.mit.edu	37	12	87826193	87826193	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:87826193delA								MGAT4C (593512 upstream) : C12orf50 (547623 downstream)																																			---	---	---	---
CEP290	80184	broad.mit.edu	37	12	88448067	88448067	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-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																		---	---	---	---
CEP290	80184	broad.mit.edu	37	12	88524079	88524079	+	Frame_Shift_Del	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:88524079delT	uc001tar.2	-	9	979	c.635delA	c.(634-636)AACfs	p.N212fs	CEP290_uc001tat.2_5'Flank|CEP290_uc009zsl.1_RNA	NM_025114	NP_079390	O15078	CE290_HUMAN	centrosomal protein 290kDa	212	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																		---	---	---	---
CEP290	80184	broad.mit.edu	37	12	88525006	88525007	+	Intron	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:88525006_88525007delAA	uc001tar.2	-						CEP290_uc001tat.2_5'Flank|CEP290_uc009zsl.1_Intron	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																		---	---	---	---
Unknown	0	broad.mit.edu	37	12	88833081	88833081	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:88833081delA								TMTC3 (239418 upstream) : KITLG (53488 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	89254927	89254928	+	IGR	DEL	TT	-	-	rs111460498		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:89254927_89254928delTT								KITLG (280689 upstream) : DUSP6 (486911 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	90085956	90085956	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:90085956delA								ATP2B1 (36112 upstream) : LOC338758 (16776 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	90484023	90484023	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:90484023delT								LOC338758 (378295 upstream) : C12orf12 (861970 downstream)																																			---	---	---	---
DCN	1634	broad.mit.edu	37	12	91547102	91547102	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:91547102delT	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	92192464	92192464	+	IGR	DEL	A	-	-	rs35187158		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:92192464delA								DCN (615658 upstream) : BTG1 (186402 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	92372845	92372846	+	IGR	DEL	CA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:92372845_92372846delCA								DCN (796039 upstream) : BTG1 (6020 downstream)																																			---	---	---	---
CLLU1	574028	broad.mit.edu	37	12	92822429	92822430	+	Intron	INS	-	CCTT	CCTT			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:92822429_92822430insCCTT	uc001tcc.2	+						CLLU1OS_uc001tcb.1_5'Flank|CLLU1_uc001tcd.2_Intron|CLLU1_uc001tce.1_Intron|CLLU1_uc001tcf.2_Intron	NR_027932				Synthetic construct DNA, clone: pF1KB7210, Homo sapiens CLLU1 gene for chronic lymphocytic leukemia up-regulated 1, without stop codon, in Flexi system.											ovary(1)	1																		---	---	---	---
CLLU1	574028	broad.mit.edu	37	12	92845858	92845859	+	Intron	INS	-	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:92845858_92845859insA	uc001tce.1	+											Homo sapiens mRNA for non-coding transcript (CLLU1 gene), splice variant 1.											ovary(1)	1																		---	---	---	---
EEA1	8411	broad.mit.edu	37	12	93254660	93254661	+	Intron	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:93254660_93254661delAA	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	93477467	93477467	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:93477467delA								EEA1 (154360 upstream) : NUDT4 (294234 downstream)																																			---	---	---	---
MRPL42	28977	broad.mit.edu	37	12	93873154	93873154	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:93873154delT	uc001tcr.2	+						MRPL42_uc001tcq.2_Intron|MRPL42_uc001tcs.2_Intron|MRPL42_uc001tct.2_Intron	NM_172177	NP_751917			mitochondrial ribosomal protein L42 isoform a						translation	mitochondrial small ribosomal subunit	structural constituent of ribosome			ovary(2)	2																		---	---	---	---
CRADD	8738	broad.mit.edu	37	12	94227599	94227599	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:94227599delT	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																		---	---	---	---
Unknown	0	broad.mit.edu	37	12	94914713	94914713	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:94914713delT								LOC144486 (58371 upstream) : TMCC3 (46187 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	95084059	95084059	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:95084059delT								TMCC3 (39735 upstream) : MIR492 (144115 downstream)																																			---	---	---	---
NR2C1	7181	broad.mit.edu	37	12	95456235	95456235	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:95456235delT	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	95505574	95505575	+	Intron	INS	-	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:95505574_95505575insA	uc001tdp.3	-						FGD6_uc009zsx.2_Intron|FGD6_uc001tdq.1_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																		---	---	---	---
FGD6	55785	broad.mit.edu	37	12	95565220	95565220	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:95565220delA	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	95650969	95650969	+	Frame_Shift_Del	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:95650969delT	uc001tdz.2	+	3	317	c.212delT	c.(211-213)ATTfs	p.I71fs	VEZT_uc009zsy.1_Intron|VEZT_uc001tdr.2_Intron|VEZT_uc001tds.2_Frame_Shift_Del_p.I23fs|VEZT_uc001tdt.2_Frame_Shift_Del_p.I23fs|VEZT_uc009zsz.1_Frame_Shift_Del_p.I71fs|VEZT_uc001tdv.2_Frame_Shift_Del_p.I40fs|VEZT_uc001tdw.1_Frame_Shift_Del_p.I23fs|VEZT_uc009zta.1_Frame_Shift_Del_p.I23fs	NM_017599	NP_060069	Q9HBM0	VEZA_HUMAN	vezatin, adherens junctions transmembrane	71						acrosomal vesicle|adherens junction|integral to membrane|nucleus				ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	12	95825591	95825595	+	IGR	DEL	AAAAA	-	-	rs34264065		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:95825591_95825595delAAAAA								MIR331 (123302 upstream) : METAP2 (42227 downstream)																																			---	---	---	---
NTN4	59277	broad.mit.edu	37	12	96104938	96104938	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:96104938delT	uc001tei.2	-						NTN4_uc009ztf.2_Intron|NTN4_uc009ztg.2_Intron	NM_021229	NP_067052			netrin 4 precursor						axon guidance	basement membrane|plasma membrane				upper_aerodigestive_tract(1)|ovary(1)	2																		---	---	---	---
NTN4	59277	broad.mit.edu	37	12	96120918	96120919	+	Intron	INS	-	A	A	rs142625354	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:96120918_96120919insA	uc001tei.2	-						NTN4_uc009ztf.2_Intron|NTN4_uc009ztg.2_Intron	NM_021229	NP_067052			netrin 4 precursor						axon guidance	basement membrane|plasma membrane				upper_aerodigestive_tract(1)|ovary(1)	2																		---	---	---	---
SNRPF	6636	broad.mit.edu	37	12	96256480	96256480	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:96256480delT	uc001tej.2	+							NM_003095	NP_003086			small nuclear ribonucleoprotein polypeptide F						histone mRNA metabolic process|ncRNA metabolic process|spliceosomal snRNP assembly|termination of RNA polymerase II transcription	catalytic step 2 spliceosome|cytosol|nucleoplasm|U12-type spliceosomal complex|U7 snRNP	protein binding|RNA binding				0																		---	---	---	---
HAL	3034	broad.mit.edu	37	12	96369937	96369937	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:96369937delT	uc001tem.1	-						HAL_uc009zti.1_Intron|HAL_uc010suw.1_Intron|HAL_uc010sux.1_Intron	NM_002108	NP_002099			histidine ammonia-lyase						biosynthetic process|histidine catabolic process	cytosol	histidine ammonia-lyase activity			ovary(2)|skin(1)	3					L-Histidine(DB00117)													---	---	---	---
Unknown	0	broad.mit.edu	37	12	96537133	96537134	+	IGR	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:96537133_96537134delAA								LTA4H (99835 upstream) : ELK3 (51073 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	96553240	96553241	+	IGR	INS	-	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:96553240_96553241insA								LTA4H (115942 upstream) : ELK3 (34966 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	96927779	96927779	+	Intron	DEL	T	-	-	rs5800251		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:96927779delT	uc009ztl.1	+						uc001teq.2_Intron					RecName: Full=Uncharacterized protein C12orf55;																														---	---	---	---
Unknown	0	broad.mit.edu	37	12	96935066	96935069	+	Intron	DEL	TTTT	-	-	rs72392488		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:96935066_96935069delTTTT	uc001ter.1	+											Homo sapiens cDNA FLJ31514 fis, clone NT2RI1000164.																														---	---	---	---
C12orf63	374467	broad.mit.edu	37	12	97082938	97082938	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:97082938delT	uc001tet.1	+							NM_198520	NP_940922			hypothetical protein LOC374467											skin(6)|ovary(1)	7																		---	---	---	---
C12orf63	374467	broad.mit.edu	37	12	97124984	97124984	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:97124984delA	uc001tet.1	+							NM_198520	NP_940922			hypothetical protein LOC374467											skin(6)|ovary(1)	7																		---	---	---	---
Unknown	0	broad.mit.edu	37	12	97561261	97561262	+	IGR	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:97561261_97561262delTT								NEDD1 (213800 upstream) : RMST (297537 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	97702391	97702391	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:97702391delT								NEDD1 (354930 upstream) : RMST (156408 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	98621827	98621828	+	IGR	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:98621827_98621828delTT								RMST (663034 upstream) : LOC100128191 (284925 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	98836903	98836905	+	IGR	DEL	AAA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:98836903_98836905delAAA								RMST (878110 upstream) : LOC100128191 (69848 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	98872998	98872998	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:98872998delA								RMST (914205 upstream) : LOC100128191 (33755 downstream)																																			---	---	---	---
APAF1	317	broad.mit.edu	37	12	99043979	99043979	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:99043979delT	uc001tfz.2	+						APAF1_uc001tfy.2_Intron|APAF1_uc001tga.2_Intron|APAF1_uc001tgb.2_Intron|APAF1_uc001tgc.2_Intron	NM_181861	NP_863651			apoptotic peptidase activating factor 1 isoform						activation of caspase activity by cytochrome c|defense response|induction of apoptosis by intracellular signals|nervous system development	cytosol|Golgi apparatus|nucleus	ATP binding|caspase activator activity|protein binding			ovary(2)|lung(1)	3					Adenosine triphosphate(DB00171)													---	---	---	---
APAF1	317	broad.mit.edu	37	12	99106462	99106462	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:99106462delT	uc001tfz.2	+						APAF1_uc001tfy.2_Intron|APAF1_uc001tga.2_Intron|APAF1_uc001tgb.2_Intron|APAF1_uc001tgc.2_Intron|APAF1_uc009zto.2_Intron	NM_181861	NP_863651			apoptotic peptidase activating factor 1 isoform						activation of caspase activity by cytochrome c|defense response|induction of apoptosis by intracellular signals|nervous system development	cytosol|Golgi apparatus|nucleus	ATP binding|caspase activator activity|protein binding			ovary(2)|lung(1)	3					Adenosine triphosphate(DB00171)													---	---	---	---
ANKS1B	56899	broad.mit.edu	37	12	99279821	99279822	+	Intron	DEL	GA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:99279821_99279822delGA	uc001tge.1	-						ANKS1B_uc001tgf.1_Intron|ANKS1B_uc001tgk.2_Intron|ANKS1B_uc010svd.1_Intron|ANKS1B_uc001tgd.1_Intron|ANKS1B_uc010sve.1_Intron|ANKS1B_uc001tgh.3_Intron|ANKS1B_uc001tgi.2_Intron|ANKS1B_uc009ztr.2_Intron|ANKS1B_uc001tgj.2_Intron|ANKS1B_uc009ztp.2_Intron|ANKS1B_uc010svf.1_Intron|ANKS1B_uc001tgg.3_Intron|ANKS1B_uc010svg.1_Intron|ANKS1B_uc009zts.1_Intron|ANKS1B_uc001tgm.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	99306903	99306903	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:99306903delT	uc001tge.1	-						ANKS1B_uc001tgf.1_Intron|ANKS1B_uc001tgk.2_Intron|ANKS1B_uc001tgd.1_Intron|ANKS1B_uc001tgi.2_Intron|ANKS1B_uc009ztr.2_Intron|ANKS1B_uc001tgj.2_Intron|ANKS1B_uc001tgg.3_Intron|ANKS1B_uc010svg.1_Intron|ANKS1B_uc009zts.1_Intron|ANKS1B_uc001tgm.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)														---	---	---	---
UHRF1BP1L	23074	broad.mit.edu	37	12	100444276	100444277	+	Intron	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:100444276_100444277delAA	uc001tgq.2	-						UHRF1BP1L_uc001tgp.2_Intron	NM_015054	NP_055869			UHRF1 (ICBP90) binding protein 1-like isoform a											ovary(2)	2																		---	---	---	---
GOLGA2B	55592	broad.mit.edu	37	12	100560481	100560481	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:100560481delA	uc001tgu.2	-						GOLGA2B_uc001tgy.3_Intron|GOLGA2B_uc001tgz.3_Intron	NM_017600	NP_060070			golgi autoantigen, golgin subfamily a, 2-like 1												0																		---	---	---	---
GAS2L3	283431	broad.mit.edu	37	12	100983118	100983119	+	Intron	DEL	AA	-	-	rs112590509		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:100983118_100983119delAA	uc001thu.2	+						GAS2L3_uc009zty.2_Intron	NM_174942	NP_777602			growth arrest-specific 2 like 3						cell cycle arrest					skin(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	12	101085951	101085951	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:101085951delT								GAS2L3 (67268 upstream) : ANO4 (25353 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	101088680	101088683	+	IGR	DEL	TCTT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:101088680_101088683delTCTT								GAS2L3 (69997 upstream) : ANO4 (22621 downstream)																																			---	---	---	---
UTP20	27340	broad.mit.edu	37	12	101689237	101689237	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:101689237delT	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	101700374	101700374	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-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-4200-01A-01D-1126-08	TCGA-BR-4200-11A-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																		---	---	---	---
UTP20	27340	broad.mit.edu	37	12	101750320	101750321	+	Intron	INS	-	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:101750320_101750321insG	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																		---	---	---	---
Unknown	0	broad.mit.edu	37	12	101815131	101815131	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:101815131delA								ARL1 (13559 upstream) : SPIC (54068 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	101859711	101859711	+	IGR	DEL	A	-	-	rs113650778		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:101859711delA								ARL1 (58139 upstream) : SPIC (9488 downstream)																																			---	---	---	---
SYCP3	50511	broad.mit.edu	37	12	102128683	102128683	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:102128683delA	uc001tiq.2	-						SYCP3_uc001tir.2_Intron|SYCP3_uc001tis.2_Intron	NM_153694	NP_710161			synaptonemal complex protein 3						cell division|male meiosis I|spermatogenesis, exchange of chromosomal proteins	nucleus	DNA binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	12	102328957	102328957	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:102328957delT								DRAM1 (11558 upstream) : CCDC53 (77761 downstream)																																			---	---	---	---
NUP37	79023	broad.mit.edu	37	12	102468961	102468961	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-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																		---	---	---	---
Unknown	0	broad.mit.edu	37	12	102947394	102947395	+	IGR	DEL	TT	-	-	rs62667061		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:102947394_102947395delTT								IGF1 (73016 upstream) : PAH (284709 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	103170181	103170182	+	IGR	DEL	TC	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:103170181_103170182delTC								IGF1 (295803 upstream) : PAH (61922 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	103191065	103191065	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:103191065delT								IGF1 (316687 upstream) : PAH (41039 downstream)																																			---	---	---	---
STAB2	55576	broad.mit.edu	37	12	104067117	104067117	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:104067117delT	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																		---	---	---	---
STAB2	55576	broad.mit.edu	37	12	104127181	104127181	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:104127181delT	uc001tjw.2	+						STAB2_uc009zug.2_Intron	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	104134268	104134268	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:104134268delA	uc001tjw.2	+						STAB2_uc009zug.2_Intron	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																		---	---	---	---
TDG	6996	broad.mit.edu	37	12	104367963	104367963	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:104367963delT	uc001tkg.2	+						TDG_uc010swh.1_Intron|TDG_uc009zuk.2_Intron|TDG_uc010swi.1_Intron	NM_003211	NP_003202			thymine-DNA glycosylase						depyrimidination|mismatch repair	nucleoplasm	damaged DNA binding|mismatched DNA binding|protein binding|pyrimidine-specific mismatch base pair DNA N-glycosylase activity			ovary(3)|lung(3)	6				BRCA - Breast invasive adenocarcinoma(302;0.00114)									BER_DNA_glycosylases					---	---	---	---
Unknown	0	broad.mit.edu	37	12	104535366	104535368	+	IGR	DEL	AAA	-	-	rs77302409		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:104535366_104535368delAAA								NFYB (3326 upstream) : TXNRD1 (71120 downstream)																																			---	---	---	---
CHST11	50515	broad.mit.edu	37	12	104983085	104983085	+	Intron	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:104983085delG	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	105203151	105203152	+	Intron	INS	-	AACA	AACA	rs146662824	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:105203151_105203152insAACA	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																		---	---	---	---
SLC41A2	84102	broad.mit.edu	37	12	105249769	105249770	+	Intron	INS	-	A	A	rs146454307	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:105249769_105249770insA	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	105353249	105353249	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:105353249delT								SLC41A2 (30777 upstream) : C12orf45 (26849 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	105362811	105362812	+	IGR	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:105362811_105362812delTT								SLC41A2 (40339 upstream) : C12orf45 (17286 downstream)																																			---	---	---	---
ALDH1L2	160428	broad.mit.edu	37	12	105471855	105471855	+	Intron	DEL	C	-	-	rs5800648		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:105471855delC	uc001tlc.2	-						ALDH1L2_uc009zup.2_Intron	NM_001034173	NP_001029345			aldehyde dehydrogenase 1 family, member L2						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																		---	---	---	---
Unknown	0	broad.mit.edu	37	12	105870286	105870286	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:105870286delT								C12orf75 (104991 upstream) : NUAK1 (586839 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	106117882	106117882	+	IGR	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:106117882delC								C12orf75 (352587 upstream) : NUAK1 (339243 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	106664023	106664023	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:106664023delT								CKAP4 (22310 upstream) : TCP11L2 (32558 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	106939549	106939550	+	IGR	INS	-	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:106939549_106939550insA								POLR3B (35575 upstream) : RFX4 (37483 downstream)																																			---	---	---	---
RFX4	5992	broad.mit.edu	37	12	107141706	107141707	+	Intron	DEL	AA	-	-	rs34730173		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:107141706_107141707delAA	uc001tlr.2	+						RFX4_uc001tlt.2_Intron|RFX4_uc001tlv.2_Intron	NM_213594	NP_998759			regulatory factor X4 isoform c						transcription, DNA-dependent	nucleus	DNA binding			upper_aerodigestive_tract(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	12	107325049	107325049	+	IGR	DEL	A	-	-	rs66531971		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:107325049delA								RIC8B (41957 upstream) : C12orf23 (24495 downstream)																																			---	---	---	---
BTBD11	121551	broad.mit.edu	37	12	107717397	107717397	+	Intron	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:107717397delG	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	107874480	107874481	+	Intron	DEL	TG	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:107874480_107874481delTG	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	108008029	108008029	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:108008029delT	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																		---	---	---	---
Unknown	0	broad.mit.edu	37	12	108122033	108122033	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:108122033delA								PWP1 (15776 upstream) : PRDM4 (4611 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	108221502	108221503	+	IGR	INS	-	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:108221502_108221503insG								ASCL4 (51082 upstream) : WSCD2 (302008 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	108318623	108318624	+	IGR	DEL	AA	-	-	rs35544291		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:108318623_108318624delAA								ASCL4 (148203 upstream) : WSCD2 (204887 downstream)																																			---	---	---	---
CMKLR1	1240	broad.mit.edu	37	12	108703314	108703315	+	Intron	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:108703314_108703315delAA	uc009zuw.2	-						CMKLR1_uc001tmw.2_Intron|CMKLR1_uc001tmv.2_Intron|CMKLR1_uc009zuv.2_Intron	NM_001142345	NP_001135817			chemokine-like receptor 1 isoform a						chemotaxis|immune response|negative regulation of interleukin-12 production|negative regulation of NF-kappaB transcription factor activity|positive regulation of macrophage chemotaxis|regulation of calcium-mediated signaling|skeletal system development	integral to plasma membrane	chemokine receptor activity			lung(3)|ovary(1)|pancreas(1)	5																		---	---	---	---
TMEM119	338773	broad.mit.edu	37	12	108984473	108984473	+	3'UTR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:108984473delA	uc001tng.2	-	2					TMEM119_uc001tnf.2_Intron	NM_181724	NP_859075			transmembrane protein 119 precursor							integral to membrane				ovary(1)	1																		---	---	---	---
SVOP	55530	broad.mit.edu	37	12	109308348	109308348	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:109308348delT	uc010sxh.1	-							NM_018711	NP_061181			SV2 related protein							cell junction|integral to membrane|synaptic vesicle membrane	ion transmembrane transporter activity				0																		---	---	---	---
ACACB	32	broad.mit.edu	37	12	109605086	109605086	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:109605086delA	uc001tob.2	+						ACACB_uc001toc.2_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	109673803	109673804	+	Intron	INS	-	AA	AA			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:109673803_109673804insAA	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	110098176	110098176	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:110098176delA								MVK (63106 upstream) : C12orf34 (54014 downstream)																																			---	---	---	---
IFT81	28981	broad.mit.edu	37	12	110571432	110571432	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:110571432delA	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																		---	---	---	---
ANAPC7	51434	broad.mit.edu	37	12	110833403	110833406	+	Intron	DEL	TTTT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:110833403_110833406delTTTT	uc001tqo.2	-						ANAPC7_uc001tqp.3_Intron	NM_016238	NP_057322			anaphase-promoting complex subunit 7 isoform a						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	protein phosphatase binding				0																		---	---	---	---
RAD9B	144715	broad.mit.edu	37	12	110961743	110961745	+	Intron	DEL	ATC	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:110961743_110961745delATC	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																		---	---	---	---
HVCN1	84329	broad.mit.edu	37	12	111115012	111115014	+	Intron	DEL	AAA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:111115012_111115014delAAA	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																		---	---	---	---
HVCN1	84329	broad.mit.edu	37	12	111123478	111123478	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:111123478delT	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																		---	---	---	---
Unknown	0	broad.mit.edu	37	12	111194410	111194410	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:111194410delA								PPP1CC (13653 upstream) : CCDC63 (90401 downstream)																																			---	---	---	---
CUX2	23316	broad.mit.edu	37	12	111595284	111595284	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:111595284delA	uc001tsa.1	+						CUX2_uc001tsb.1_Intron	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																		---	---	---	---
CUX2	23316	broad.mit.edu	37	12	111775846	111775848	+	Intron	DEL	AAA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:111775846_111775848delAAA	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																		---	---	---	---
ATXN2	6311	broad.mit.edu	37	12	111937494	111937494	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:111937494delA	uc001tsj.2	-						ATXN2_uc001tsh.2_Intron|ATXN2_uc001tsi.2_Intron|ATXN2_uc001tsk.2_Intron	NM_002973	NP_002964			ataxin 2						cell death|cytoplasmic mRNA processing body assembly|regulation of translation|RNA metabolic process|RNA transport|stress granule assembly	nucleus|perinuclear region of cytoplasm|polysome|stress granule|trans-Golgi network	protein C-terminus binding|RNA binding			ovary(1)|breast(1)	2																		---	---	---	---
ATXN2	6311	broad.mit.edu	37	12	111987180	111987180	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:111987180delA	uc001tsj.2	-						ATXN2_uc001tsh.2_Intron|ATXN2_uc001tsi.2_Intron|ATXN2_uc001tsk.2_Intron|ATXN2_uc001tsm.1_Intron	NM_002973	NP_002964			ataxin 2						cell death|cytoplasmic mRNA processing body assembly|regulation of translation|RNA metabolic process|RNA transport|stress granule assembly	nucleus|perinuclear region of cytoplasm|polysome|stress granule|trans-Golgi network	protein C-terminus binding|RNA binding			ovary(1)|breast(1)	2																		---	---	---	---
BRAP	8315	broad.mit.edu	37	12	112096441	112096441	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:112096441delA	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																		---	---	---	---
ACAD10	80724	broad.mit.edu	37	12	112154012	112154013	+	Intron	INS	-	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:112154012_112154013insC	uc001tsq.2	+						ACAD10_uc001tso.3_Intron|ACAD10_uc001tsp.2_Intron|ACAD10_uc009zvx.2_Intron|ACAD10_uc001tsr.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																		---	---	---	---
ACAD10	80724	broad.mit.edu	37	12	112190083	112190085	+	Intron	DEL	TTG	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:112190083_112190085delTTG	uc001tsq.2	+						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																		---	---	---	---
C12orf47	51275	broad.mit.edu	37	12	112278286	112278286	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:112278286delA	uc001tsv.2	-						MAPKAPK5_uc001tsz.2_5'Flank|MAPKAPK5_uc001tta.2_5'Flank|C12orf47_uc001tsy.2_Intron|C12orf47_uc001tsu.1_Intron|C12orf47_uc001tsw.2_Intron|C12orf47_uc001tsx.2_Intron					Homo sapiens cDNA FLJ39616 fis, clone SMINT2000541.												0																		---	---	---	---
NAA25	80018	broad.mit.edu	37	12	112491341	112491341	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:112491341delA	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	112511089	112511090	+	Intron	INS	-	ACAT	ACAT	rs58427842		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:112511089_112511090insACAT	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																		---	---	---	---
C12orf51	283450	broad.mit.edu	37	12	112672449	112672449	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:112672449delA	uc009zwc.2	-							NM_001109662	NP_001103132			chromosome 12 open reading frame 51											ovary(1)|lung(1)	2																		---	---	---	---
PTPN11	5781	broad.mit.edu	37	12	112870670	112870670	+	Intron	DEL	T	-	-	rs117399332		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:112870670delT	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				---	---	---	---
RASAL1	8437	broad.mit.edu	37	12	113540535	113540535	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:113540535delA	uc001tum.1	-						RASAL1_uc010syp.1_Intron|RASAL1_uc001tul.2_Intron|RASAL1_uc001tun.1_Intron	NM_004658	NP_004649			RAS protein activator like 1						intracellular signal transduction|negative regulation of Ras protein signal transduction	cytoplasm|intrinsic to internal side of plasma membrane	metal ion binding|phospholipid binding|Ras GTPase activator activity			ovary(2)|skin(2)	4																		---	---	---	---
SLC24A6	80024	broad.mit.edu	37	12	113742712	113742713	+	Intron	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:113742712_113742713delAA	uc001tvc.2	-						SLC24A6_uc001tuz.2_Intron|SLC24A6_uc001tva.2_Intron|SLC24A6_uc001tvb.2_Intron	NM_024959	NP_079235			solute carrier family 24 member 6 precursor						response to stimulus|sodium ion transport	integral to membrane|plasma membrane	calcium:cation antiporter activity			central_nervous_system(1)	1																		---	---	---	---
SLC24A6	80024	broad.mit.edu	37	12	113748006	113748006	+	Intron	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:113748006delC	uc001tvc.2	-						SLC24A6_uc001tuz.2_Intron|SLC24A6_uc001tva.2_Intron|SLC24A6_uc001tvb.2_Intron	NM_024959	NP_079235			solute carrier family 24 member 6 precursor						response to stimulus|sodium ion transport	integral to membrane|plasma membrane	calcium:cation antiporter activity			central_nervous_system(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	12	114062902	114062903	+	IGR	DEL	TT	-	-	rs141948715		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:114062902_114062903delTT								LHX5 (153025 upstream) : RBM19 (191640 downstream)																																			---	---	---	---
RBM19	9904	broad.mit.edu	37	12	114322247	114322248	+	Intron	INS	-	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:114322247_114322248insT	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)																	---	---	---	---
RBM19	9904	broad.mit.edu	37	12	114343207	114343207	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:114343207delA	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	114454474	114454474	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:114454474delA								RBM19 (50298 upstream) : TBX5 (337262 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	114623986	114623986	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:114623986delT								RBM19 (219810 upstream) : TBX5 (167750 downstream)																																			---	---	---	---
TBX5	6910	broad.mit.edu	37	12	114804304	114804304	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:114804304delA	uc001tvo.2	-						TBX5_uc001tvp.2_Intron|TBX5_uc001tvq.2_Intron|TBX5_uc010syv.1_Intron	NM_181486	NP_852259			T-box 5 isoform 1						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)														---	---	---	---
Unknown	0	broad.mit.edu	37	12	114900673	114900673	+	IGR	DEL	A	-	-	rs11307568		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:114900673delA								TBX5 (54426 upstream) : TBX3 (207386 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	115076362	115076362	+	IGR	DEL	T	-	-	rs139053433	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:115076362delT								TBX5 (230115 upstream) : TBX3 (31697 downstream)																																			---	---	---	---
TBX3	6926	broad.mit.edu	37	12	115115335	115115335	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:115115335delA	uc001tvt.1	-						TBX3_uc001tvu.1_Intron	NM_016569	NP_057653			T-box 3 protein isoform 2						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)														---	---	---	---
Unknown	0	broad.mit.edu	37	12	115234038	115234040	+	IGR	DEL	TTT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:115234038_115234040delTTT								TBX3 (112069 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	116095618	116095633	+	IGR	DEL	TCCTCCTTCTTCCTCG	-	-	rs61218591	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:116095618_116095633delTCCTCCTTCTTCCTCG								TBX3 (973649 upstream) : MED13L (300750 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	116121788	116121789	+	IGR	INS	-	ATGA	ATGA			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:116121788_116121789insATGA								TBX3 (999819 upstream) : MED13L (274594 downstream)																																			---	---	---	---
MED13L	23389	broad.mit.edu	37	12	116406919	116406919	+	Intron	DEL	A	-	-	rs35517594		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:116406919delA	uc001tvw.2	-							NM_015335	NP_056150			mediator complex subunit 13-like						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	116614201	116614203	+	Intron	DEL	CAT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:116614201_116614203delCAT	uc001tvw.2	-							NM_015335	NP_056150			mediator complex subunit 13-like						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	116711373	116711373	+	Intron	DEL	A	-	-	rs35774076		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:116711373delA	uc001tvw.2	-							NM_015335	NP_056150			mediator complex subunit 13-like						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)														---	---	---	---
RNFT2	84900	broad.mit.edu	37	12	117193148	117193148	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:117193148delT	uc009zwn.2	+						RNFT2_uc001twb.3_Intron|RNFT2_uc001twa.3_Intron	NM_001109903	NP_001103373			transmembrane protein 118 isoform 1							integral to membrane	zinc ion binding				0	all_neural(191;0.117)|Medulloblastoma(191;0.163)			BRCA - Breast invasive adenocarcinoma(302;0.034)														---	---	---	---
RNFT2	84900	broad.mit.edu	37	12	117223700	117223700	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:117223700delA	uc009zwn.2	+						RNFT2_uc001twb.3_Intron|RNFT2_uc001twa.3_Intron|RNFT2_uc001twc.3_Intron	NM_001109903	NP_001103373			transmembrane protein 118 isoform 1							integral to membrane	zinc ion binding				0	all_neural(191;0.117)|Medulloblastoma(191;0.163)			BRCA - Breast invasive adenocarcinoma(302;0.034)														---	---	---	---
RNFT2	84900	broad.mit.edu	37	12	117289549	117289549	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:117289549delA	uc009zwn.2	+						RNFT2_uc001twb.3_Intron|RNFT2_uc001twa.3_Intron|RNFT2_uc001twc.3_Intron|RNFT2_uc001twd.2_RNA	NM_001109903	NP_001103373			transmembrane protein 118 isoform 1							integral to membrane	zinc ion binding				0	all_neural(191;0.117)|Medulloblastoma(191;0.163)			BRCA - Breast invasive adenocarcinoma(302;0.034)														---	---	---	---
Unknown	0	broad.mit.edu	37	12	117323079	117323080	+	IGR	DEL	AA	-	-	rs35613881		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:117323079_117323080delAA								HRK (3847 upstream) : FBXW8 (25681 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	117339003	117339003	+	IGR	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:117339003delG								HRK (19771 upstream) : FBXW8 (9758 downstream)																																			---	---	---	---
FBXW8	26259	broad.mit.edu	37	12	117369200	117369200	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:117369200delT	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)														---	---	---	---
FBXW8	26259	broad.mit.edu	37	12	117467419	117467420	+	3'UTR	INS	-	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:117467419_117467420insT	uc001twg.1	+	11					FBXW8_uc001twf.1_3'UTR|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)														---	---	---	---
Unknown	0	broad.mit.edu	37	12	117572866	117572866	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:117572866delT								TESC (35615 upstream) : FBXO21 (8720 downstream)																																			---	---	---	---
FBXO21	23014	broad.mit.edu	37	12	117603583	117603583	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:117603583delA	uc001twk.2	-						FBXO21_uc001twj.2_Intron|FBXO21_uc009zwq.2_Intron|FBXO21_uc001twl.1_Intron	NM_033624	NP_296373			F-box only protein 21 isoform 1						ubiquitin-dependent protein catabolic process	ubiquitin ligase complex	ubiquitin-protein ligase activity			kidney(1)	1	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)			BRCA - Breast invasive adenocarcinoma(302;0.0291)														---	---	---	---
NOS1	4842	broad.mit.edu	37	12	117766373	117766373	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:117766373delT	uc001twm.1	-							NM_000620	NP_000611			nitric oxide synthase 1, neuronal						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	118329222	118329222	+	Intron	DEL	A	-	-	rs147563190		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:118329222delA	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	118459446	118459447	+	Intron	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:118459446_118459447delAA	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)																	---	---	---	---
VSIG10	54621	broad.mit.edu	37	12	118511707	118511707	+	Frame_Shift_Del	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:118511707delG	uc001tws.2	-	5	1350	c.1016delC	c.(1015-1017)CCTfs	p.P339fs		NM_019086	NP_061959	Q8N0Z9	VSI10_HUMAN	V-set and immunoglobulin domain containing 10	339	Ig-like C2-type 4.|Extracellular (Potential).					integral to membrane					0																		---	---	---	---
Unknown	0	broad.mit.edu	37	12	118570605	118570605	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:118570605delA								VSIG10 (28795 upstream) : PEBP1 (3265 downstream)																																			---	---	---	---
TAOK3	51347	broad.mit.edu	37	12	118607979	118607980	+	Intron	DEL	TT	-	-	rs66588313		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:118607979_118607980delTT	uc001twx.2	-						TAOK3_uc001twv.2_Intron|TAOK3_uc001tww.2_Intron|TAOK3_uc001twy.3_Intron	NM_016281	NP_057365			TAO kinase 3						MAPKKK cascade|negative regulation of JNK cascade|positive regulation of JNK cascade|protein autophosphorylation	mitochondrion|plasma membrane	ATP binding|protein kinase inhibitor activity|protein serine/threonine kinase activity			lung(5)|central_nervous_system(1)	6	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)																	---	---	---	---
Unknown	0	broad.mit.edu	37	12	119290755	119290756	+	IGR	DEL	GA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:119290755_119290756delGA								SUDS3 (434916 upstream) : SRRM4 (128640 downstream)																																			---	---	---	---
HSPB8	26353	broad.mit.edu	37	12	119615781	119615781	+	5'Flank	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:119615781delA	uc001txb.2	+						HSPB8_uc001txc.2_5'Flank	NM_014365	NP_055180			heat shock 22kDa protein 8						cell death|response to heat	cytoplasm|nucleus	identical protein binding|protein serine/threonine kinase activity			central_nervous_system(1)|skin(1)	2	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)																	---	---	---	---
CCDC60	160777	broad.mit.edu	37	12	119805958	119805960	+	Intron	DEL	AAG	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:119805958_119805960delAAG	uc001txe.2	+							NM_178499	NP_848594			coiled-coil domain containing 60											ovary(2)|upper_aerodigestive_tract(1)	3	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)			BRCA - Breast invasive adenocarcinoma(302;0.207)														---	---	---	---
CCDC60	160777	broad.mit.edu	37	12	119891804	119891804	+	Intron	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:119891804delC	uc001txe.2	+						uc001txf.2_Intron	NM_178499	NP_848594			coiled-coil domain containing 60											ovary(2)|upper_aerodigestive_tract(1)	3	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)			BRCA - Breast invasive adenocarcinoma(302;0.207)														---	---	---	---
CIT	11113	broad.mit.edu	37	12	120165728	120165731	+	Intron	DEL	AAAA	-	-	rs113396996		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:120165728_120165731delAAAA	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	120348470	120348470	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:120348470delA								CIT (33378 upstream) : CCDC64 (79178 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	120387973	120387973	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:120387973delT								CIT (72881 upstream) : CCDC64 (39675 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	120706717	120706718	+	IGR	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:120706717_120706718delAA								PXN (3154 upstream) : NME2P1 (13222 downstream)																																			---	---	---	---
COQ5	84274	broad.mit.edu	37	12	120960838	120960838	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:120960838delA	uc001tyn.2	-						COQ5_uc001tyo.2_Intron|COQ5_uc010szj.1_Intron	NM_032314	NP_115690			coenzyme Q5 homolog, methyltransferase						ubiquinone biosynthetic process	mitochondrion	methyltransferase activity			ovary(1)	1	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)																	---	---	---	---
Unknown	0	broad.mit.edu	37	12	121054889	121054889	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:121054889delT								POP5 (35688 upstream) : CABP1 (23533 downstream)																																			---	---	---	---
SPPL3	121665	broad.mit.edu	37	12	121216341	121216342	+	Intron	INS	-	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:121216341_121216342insT	uc001tzd.2	-						SPPL3_uc009zwz.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)																	---	---	---	---
SPPL3	121665	broad.mit.edu	37	12	121318595	121318595	+	Intron	DEL	A	-	-	rs487943	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:121318595delA	uc001tzd.2	-						SPPL3_uc009zwz.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)																	---	---	---	---
HNF1A	6927	broad.mit.edu	37	12	121428560	121428560	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:121428560delA	uc001tzg.2	+						HNF1A_uc001tze.1_Intron|HNF1A_uc001tzf.2_Intron|HNF1A_uc010szn.1_Intron	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				---	---	---	---
P2RX4	5025	broad.mit.edu	37	12	121656286	121656286	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:121656286delA	uc001tzr.2	+						P2RX4_uc010szr.1_Intron|P2RX4_uc010szs.1_Intron|P2RX4_uc009zxc.2_Intron|P2RX4_uc001tzs.2_Intron|P2RX4_uc009zxb.2_Intron|P2RX4_uc010szt.1_Intron	NM_002560	NP_002551			purinergic receptor P2X4						endothelial cell activation|negative regulation of cardiac muscle hypertrophy|positive regulation of calcium ion transport into cytosol|positive regulation of calcium-mediated signaling|positive regulation of nitric oxide biosynthetic process|positive regulation of prostaglandin secretion|regulation of apoptosis|regulation of blood pressure|regulation of sodium ion transport|relaxation of cardiac muscle|response to ATP|response to fluid shear stress|sensory perception of pain|tissue homeostasis	cell junction|perinuclear region of cytoplasm	cadherin binding|copper ion binding|extracellular ATP-gated cation channel activity|protein homodimerization activity|purinergic nucleotide receptor activity|receptor binding|zinc ion binding				0	all_neural(191;0.0684)|Medulloblastoma(191;0.0922)																	---	---	---	---
KDM2B	84678	broad.mit.edu	37	12	121880228	121880228	+	Frame_Shift_Del	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:121880228delG	uc001uat.2	-	19	3120	c.3016delC	c.(3016-3018)CGGfs	p.R1006fs	KDM2B_uc001uaq.2_Frame_Shift_Del_p.R446fs|KDM2B_uc010szy.1_Frame_Shift_Del_p.R446fs|KDM2B_uc001uar.2_Frame_Shift_Del_p.R597fs|KDM2B_uc001uas.2_Frame_Shift_Del_p.R937fs|KDM2B_uc001uau.2_Intron|KDM2B_uc001uao.2_Frame_Shift_Del_p.R254fs|KDM2B_uc010szx.1_Frame_Shift_Del_p.R254fs|KDM2B_uc001uap.2_RNA	NM_032590	NP_115979	Q8NHM5	KDM2B_HUMAN	F-box and leucine-rich repeat protein 10 isoform	1006					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																		---	---	---	---
Unknown	0	broad.mit.edu	37	12	122053502	122053502	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:122053502delT								KDM2B (34582 upstream) : ORAI1 (10953 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	122140894	122140894	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:122140894delA								MORN3 (30357 upstream) : TMEM120B (9764 downstream)																																			---	---	---	---
CLIP1	6249	broad.mit.edu	37	12	122758720	122758720	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:122758720delA	uc001ucg.1	-						CLIP1_uc001uch.1_Intron|CLIP1_uc001uci.1_Intron|CLIP1_uc001ucf.1_5'Flank	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)														---	---	---	---
Unknown	0	broad.mit.edu	37	12	122954809	122954809	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:122954809delT								CLIP1 (47693 upstream) : ZCCHC8 (2627 downstream)																																			---	---	---	---
ZCCHC8	55596	broad.mit.edu	37	12	122967784	122967784	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:122967784delA	uc001ucn.2	-						ZCCHC8_uc001ucm.2_5'Flank|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)														---	---	---	---
KNTC1	9735	broad.mit.edu	37	12	123036082	123036082	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:123036082delT	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	123120404	123120404	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:123120404delT	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	123150946	123150946	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:123150946delA	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)														---	---	---	---
CCDC62	84660	broad.mit.edu	37	12	123308533	123308533	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:123308533delA	uc001udc.2	+						CCDC62_uc010tah.1_Intron|CCDC62_uc001udf.2_Intron|CCDC62_uc001ude.2_Intron	NM_201435	NP_958843			coiled-coil domain containing 62 isoform b							cytoplasm|nucleus				ovary(2)|large_intestine(1)|pancreas(1)|skin(1)	5	all_neural(191;0.0837)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;6.51e-06)|Epithelial(86;2.65e-05)|BRCA - Breast invasive adenocarcinoma(302;0.206)														---	---	---	---
PITPNM2	57605	broad.mit.edu	37	12	123549297	123549297	+	Intron	DEL	A	-	-	rs34701888		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:123549297delA	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)														---	---	---	---
PITPNM2	57605	broad.mit.edu	37	12	123558474	123558474	+	Intron	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:123558474delC	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)														---	---	---	---
MPHOSPH9	10198	broad.mit.edu	37	12	123699789	123699789	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:123699789delA	uc001uel.2	-						MPHOSPH9_uc010tal.1_Intron|MPHOSPH9_uc010tam.1_Intron|MPHOSPH9_uc001uem.2_Intron	NM_022782	NP_073619			M-phase phosphoprotein 9						M phase of mitotic cell cycle	centriole|Golgi membrane					0	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000182)|Epithelial(86;0.00046)|BRCA - Breast invasive adenocarcinoma(302;0.169)														---	---	---	---
MPHOSPH9	10198	broad.mit.edu	37	12	123702779	123702780	+	Intron	INS	-	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:123702779_123702780insA	uc001uel.2	-						MPHOSPH9_uc010tal.1_Intron|MPHOSPH9_uc010tam.1_Intron|MPHOSPH9_uc001uem.2_Intron	NM_022782	NP_073619			M-phase phosphoprotein 9						M phase of mitotic cell cycle	centriole|Golgi membrane					0	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000182)|Epithelial(86;0.00046)|BRCA - Breast invasive adenocarcinoma(302;0.169)														---	---	---	---
SNRNP35	11066	broad.mit.edu	37	12	123944513	123944515	+	Intron	DEL	CTC	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:123944513_123944515delCTC	uc001ufb.1	+						SNRNP35_uc010tar.1_Intron|SNRNP35_uc009zxz.2_Intron|SNRNP35_uc001ufc.1_Intron	NM_022717	NP_073208			small nuclear ribonucleoprotein 35kDa (U11/U12)						mRNA processing	U12-type spliceosomal complex	nucleotide binding|RNA binding				0																		---	---	---	---
RILPL1	353116	broad.mit.edu	37	12	123966107	123966108	+	Intron	DEL	TT	-	-	rs113872165		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:123966107_123966108delTT	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	123971857	123971857	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:123971857delT	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	123984482	123984482	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:123984482delT	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)														---	---	---	---
Unknown	0	broad.mit.edu	37	12	124036764	124036764	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:124036764delA								RILPL1 (18499 upstream) : TMED2 (32312 downstream)																																			---	---	---	---
TMED2	10959	broad.mit.edu	37	12	124074533	124074534	+	Intron	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:124074533_124074534delAA	uc001ufg.2	+							NM_006815	NP_006806			coated vesicle membrane protein precursor						protein transport|vesicle-mediated transport	COPI coated vesicle membrane|ER-Golgi intermediate compartment|integral to membrane|microsome|zymogen granule membrane	protein binding				0	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000138)|Epithelial(86;0.000613)|all cancers(50;0.00745)														---	---	---	---
NCOR2	9612	broad.mit.edu	37	12	124924035	124924036	+	Intron	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:124924035_124924036delAA	uc010tba.1	-						NCOR2_uc010tay.1_Intron|NCOR2_uc010taz.1_Intron|NCOR2_uc010tbb.1_Intron|NCOR2_uc010tbc.1_Intron|NCOR2_uc001ugj.1_Intron|NCOR2_uc001ugk.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)														---	---	---	---
NCOR2	9612	broad.mit.edu	37	12	125024254	125024254	+	Intron	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:125024254delC	uc001ugj.1	-							NM_006312	NP_006303			nuclear receptor co-repressor 2 isoform 1						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	125383709	125383709	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:125383709delA								SCARB1 (35190 upstream) : UBC (12485 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	125717002	125717002	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:125717002delT								AACS (89130 upstream) : TMEM132B (94160 downstream)																																			---	---	---	---
TMEM132B	114795	broad.mit.edu	37	12	125958522	125958522	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:125958522delT	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)														---	---	---	---
TMEM132B	114795	broad.mit.edu	37	12	126075567	126075568	+	Intron	DEL	GT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:126075567_126075568delGT	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	126610643	126610644	+	IGR	DEL	GA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:126610643_126610644delGA								TMEM132B (467054 upstream) : LOC100128554 (316383 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	126827058	126827058	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:126827058delA								TMEM132B (683469 upstream) : LOC100128554 (99969 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	127432391	127432391	+	Intron	DEL	T	-	-	rs72192691		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:127432391delT	uc001uho.2	-											Homo sapiens cDNA clone IMAGE:4829480.																														---	---	---	---
Unknown	0	broad.mit.edu	37	12	127814584	127814585	+	IGR	DEL	GT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:127814584_127814585delGT								LOC100128554 (857254 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	128229337	128229337	+	IGR	DEL	T	-	-	rs72428574		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:128229337delT								None (None upstream) : TMEM132C (669954 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	128454739	128454740	+	IGR	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:128454739_128454740delTT								None (None upstream) : TMEM132C (444551 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	128494350	128494350	+	IGR	DEL	A	-	-	rs34492447		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:128494350delA								None (None upstream) : TMEM132C (404941 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	128612885	128612886	+	IGR	INS	-	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:128612885_128612886insT								None (None upstream) : TMEM132C (286405 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	128673243	128673244	+	IGR	DEL	GA	-	-	rs67308748		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:128673243_128673244delGA								None (None upstream) : TMEM132C (226047 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	128718895	128718896	+	IGR	INS	-	TG	TG			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:128718895_128718896insTG								None (None upstream) : TMEM132C (180395 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	128866787	128866787	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:128866787delT								None (None upstream) : TMEM132C (32504 downstream)																																			---	---	---	---
TMEM132C	92293	broad.mit.edu	37	12	128996630	128996630	+	Intron	DEL	T	-	-	rs113131064		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:128996630delT	uc001uhs.3	+							NM_001136103	NP_001129575			transmembrane protein 132C							integral to membrane				central_nervous_system(1)	1																		---	---	---	---
TMEM132C	92293	broad.mit.edu	37	12	129000380	129000383	+	Intron	DEL	AAAA	-	-	rs78214520		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:129000380_129000383delAAAA	uc001uhs.3	+							NM_001136103	NP_001129575			transmembrane protein 132C							integral to membrane				central_nervous_system(1)	1																		---	---	---	---
SLC15A4	121260	broad.mit.edu	37	12	129311025	129311026	+	5'Flank	INS	-	TATG	TATG	rs149213503	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:129311025_129311026insTATG	uc001uhu.2	-						SLC15A4_uc001uhv.2_5'Flank	NM_145648	NP_663623			solute carrier family 15, member 4						oligopeptide transport|protein transport	integral to membrane|lysosomal membrane	peptide:hydrogen symporter activity				0	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;1.69e-06)|Epithelial(86;1.17e-05)|all cancers(50;5.07e-05)														---	---	---	---
TMEM132D	121256	broad.mit.edu	37	12	129652797	129652797	+	Intron	DEL	T	-	-	rs35876106		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:129652797delT	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	129883380	129883383	+	Intron	DEL	CATC	-	-	rs144105630		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:129883380_129883383delCATC	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	130184534	130184534	+	Frame_Shift_Del	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:130184534delG	uc009zyl.1	-	2	1117	c.789delC	c.(787-789)CCCfs	p.P263fs		NM_133448	NP_597705	Q14C87	T132D_HUMAN	transmembrane protein 132D precursor	263	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)														---	---	---	---
Unknown	0	broad.mit.edu	37	12	130619397	130619398	+	IGR	DEL	GT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:130619397_130619398delGT								LOC100190940 (92510 upstream) : FZD10 (27634 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	130732478	130732479	+	IGR	INS	-	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:130732478_130732479insA								FZD10 (82194 upstream) : PIWIL1 (90135 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	130739945	130739945	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:130739945delT								FZD10 (89661 upstream) : PIWIL1 (82669 downstream)																																			---	---	---	---
PIWIL1	9271	broad.mit.edu	37	12	130838925	130838925	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:130838925delA	uc001uik.2	+						PIWIL1_uc001uij.1_Intron	NM_004764	NP_004755			piwi-like 1						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	130919596	130919599	+	Intron	DEL	TTTT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:130919596_130919599delTTTT	uc001uil.2	-						RIMBP2_uc001uim.2_Intron|RIMBP2_uc001uin.1_Intron	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)														---	---	---	---
STX2	2054	broad.mit.edu	37	12	131314704	131314704	+	Intron	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:131314704delC	uc001uio.2	-						STX2_uc001uip.2_Intron|STX2_uc010tbj.1_Intron	NM_194356	NP_919337			syntaxin 2 isoform 2						acrosome reaction|ectoderm development|intracellular protein transport|organ morphogenesis|signal transduction	basolateral plasma membrane|integral to membrane|microsome|soluble fraction	calcium-dependent protein binding|SNAP receptor activity				0	all_neural(191;0.0982)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;2.79e-06)|all cancers(50;5.27e-05)|Epithelial(86;5.29e-05)														---	---	---	---
Unknown	0	broad.mit.edu	37	12	131707797	131707798	+	IGR	INS	-	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:131707797_131707798insC								LOC116437 (10322 upstream) : SFRS8 (487837 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	131792640	131792640	+	IGR	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:131792640delC								LOC116437 (95165 upstream) : SFRS8 (402995 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	132066360	132066361	+	IGR	DEL	TG	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:132066360_132066361delTG								LOC116437 (368885 upstream) : SFRS8 (129274 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	132145103	132145103	+	IGR	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:132145103delC								LOC116437 (447628 upstream) : SFRS8 (50532 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	132178015	132178015	+	IGR	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:132178015delC								LOC116437 (480540 upstream) : SFRS8 (17620 downstream)																																			---	---	---	---
EP400	57634	broad.mit.edu	37	12	132558005	132558007	+	Intron	DEL	TTT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:132558005_132558007delTTT	uc001ujn.2	+						EP400_uc001ujl.2_Intron|EP400_uc001ujm.2_Intron|EP400_uc001ujp.2_Intron|EP400_uc010tbo.1_5'Flank	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)														---	---	---	---
NOC4L	79050	broad.mit.edu	37	12	132635357	132635357	+	Intron	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:132635357delC	uc001ujz.1	+							NM_024078	NP_076983			nucleolar complex associated 4 homolog						rRNA processing	integral to membrane|nuclear membrane|nucleolus	protein binding				0	all_neural(191;0.0982)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;7.2e-08)|Epithelial(86;3.34e-07)|all cancers(50;1.97e-05)														---	---	---	---
GALNT9	50614	broad.mit.edu	37	12	132853621	132853622	+	Intron	DEL	AC	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:132853621_132853622delAC	uc001ukc.3	-						GALNT9_uc001ukb.2_Intron|GALNT9_uc009zys.2_Intron|uc001ukd.1_5'Flank|LOC100130238_uc010tbp.1_Intron	NM_001122636	NP_001116108			UDP-N-acetyl-alpha-D-galactosamine:polypeptide						protein O-linked glycosylation	Golgi membrane|integral to membrane	polypeptide N-acetylgalactosaminyltransferase activity|sugar binding				0	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	all_epithelial(31;0.241)		OV - Ovarian serous cystadenocarcinoma(86;7.49e-08)|Epithelial(86;3.55e-07)|all cancers(50;2.09e-05)														---	---	---	---
ZNF268	10795	broad.mit.edu	37	12	133723432	133723432	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:133723432delA	uc010tbv.1	+						ZNF10_uc009zzb.2_Intron|ZNF10_uc001ulq.2_Intron					RecName: Full=Zinc finger protein 268; AltName: Full=Zinc finger protein 3; AltName: Full=HZF3;							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)														---	---	---	---
ZNF268	10795	broad.mit.edu	37	12	133750026	133750026	+	Intron	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:133750026delC	uc010tbv.1	+											RecName: Full=Zinc finger protein 268; AltName: Full=Zinc finger protein 3; AltName: Full=HZF3;							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)														---	---	---	---
ZNF268	10795	broad.mit.edu	37	12	133764791	133764791	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:133764791delT	uc010tcf.1	+						ZNF268_uc010tbv.1_Intron|ZNF268_uc010tbw.1_Intron|ZNF268_uc010tbx.1_Intron|ZNF268_uc010tby.1_Intron|ZNF268_uc010tbz.1_Intron|ZNF268_uc010tca.1_Intron|ZNF268_uc010tcb.1_Intron|ZNF268_uc010tcc.1_Intron|ZNF268_uc010tcd.1_Intron|ZNF268_uc010tce.1_Intron|ZNF268_uc010tcg.1_Intron|ZNF268_uc010tch.1_Intron	NM_003415	NP_003406			zinc finger protein 268 isoform a							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)														---	---	---	---
Unknown	0	broad.mit.edu	37	13	19320620	19320620	+	5'Flank	DEL	T	-	-	rs113823012		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:19320620delT	uc001ulv.1	-											DQ586768																														---	---	---	---
Unknown	0	broad.mit.edu	37	13	19513266	19513267	+	IGR	DEL	AA	-	-	rs75101356		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:19513266_19513267delAA								LOC284232 (67157 upstream) : LOC348021 (69132 downstream)																																			---	---	---	---
TPTE2	93492	broad.mit.edu	37	13	19997315	19997315	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:19997315delA	uc001umd.2	-						TPTE2_uc009zzk.2_Intron|TPTE2_uc009zzl.2_Intron|TPTE2_uc001ume.2_Intron|TPTE2_uc009zzm.2_Intron|TPTE2_uc010tcm.1_Intron|TPTE2_uc010tcl.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	20366565	20366566	+	IGR	INS	-	T	T	rs145889444		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:20366565_20366566insT								PSPC1 (9482 upstream) : ZMYM5 (31058 downstream)																																			---	---	---	---
ZMYM5	9205	broad.mit.edu	37	13	20399839	20399839	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:20399839delA	uc010tcn.1	-						ZMYM5_uc001umm.1_Intron	NM_001142684	NP_001136156			zinc finger protein 237 isoform 3							nucleus	zinc ion binding				0		all_cancers(29;2.96e-22)|all_epithelial(30;3.76e-20)|all_lung(29;4.38e-20)|Lung NSC(5;5.8e-17)|Lung SC(185;0.0262)|Ovarian(182;0.162)		all cancers(112;1.61e-05)|Epithelial(112;4.89e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00171)|Lung(94;0.00942)|LUSC - Lung squamous cell carcinoma(192;0.0431)														---	---	---	---
ZMYM2	7750	broad.mit.edu	37	13	20601286	20601286	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:20601286delA	uc001umr.2	+						ZMYM2_uc001ums.2_Intron|ZMYM2_uc001umt.2_Intron|ZMYM2_uc010tco.1_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	20626552	20626552	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:20626552delT	uc001umr.2	+						ZMYM2_uc001ums.2_Intron|ZMYM2_uc001umt.2_Intron|ZMYM2_uc010tco.1_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	20684271	20684272	+	IGR	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:20684271_20684272delTT								ZMYM2 (23333 upstream) : GJA3 (28123 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	20685475	20685475	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:20685475delA								ZMYM2 (24537 upstream) : GJA3 (26920 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	20704144	20704151	+	IGR	DEL	GATACACT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:20704144_20704151delGATACACT								ZMYM2 (43206 upstream) : GJA3 (8244 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	20944893	20944894	+	IGR	DEL	AA	-	-	rs75742896		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:20944893_20944894delAA								GJB6 (138359 upstream) : CRYL1 (32915 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	21116634	21116634	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:21116634delT								CRYL1 (16622 upstream) : IFT88 (24574 downstream)																																			---	---	---	---
IFT88	8100	broad.mit.edu	37	13	21146366	21146366	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:21146366delT	uc001unh.2	+						IFT88_uc001uni.2_Intron|IFT88_uc001unj.2_Intron|IFT88_uc010tcq.1_Intron	NM_175605	NP_783195			intraflagellar transport 88 homolog isoform 1						cilium morphogenesis	centriole|intraflagellar transport particle B|microtubule basal body|microtubule-based flagellum	protein binding			ovary(1)	1		all_cancers(29;5.79e-25)|all_epithelial(30;2.57e-20)|all_lung(29;3.13e-16)|Lung SC(185;0.0262)|Ovarian(182;0.0825)|Hepatocellular(188;0.244)		all cancers(112;0.000667)|Epithelial(112;0.00119)|OV - Ovarian serous cystadenocarcinoma(117;0.0141)|Lung(94;0.0183)|LUSC - Lung squamous cell carcinoma(192;0.0528)														---	---	---	---
N6AMT2	221143	broad.mit.edu	37	13	21303477	21303477	+	Intron	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:21303477delG	uc001uno.1	-						uc001unn.1_5'Flank|N6AMT2_uc009zzr.1_Intron|N6AMT2_uc001unp.2_Intron	NM_174928	NP_777588			N-6 adenine-specific DNA methyltransferase 2								methyltransferase activity|nucleic acid binding				0		all_cancers(29;5.91e-19)|all_epithelial(30;1.42e-15)|all_lung(29;5.9e-14)|Lung SC(185;0.0367)		all cancers(112;0.000234)|Epithelial(112;0.000471)|OV - Ovarian serous cystadenocarcinoma(117;0.0111)|Lung(94;0.0161)|LUSC - Lung squamous cell carcinoma(192;0.0431)														---	---	---	---
N6AMT2	221143	broad.mit.edu	37	13	21340960	21340961	+	Intron	INS	-	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:21340960_21340961insA	uc001uno.1	-						N6AMT2_uc009zzr.1_Intron|N6AMT2_uc001unp.2_Intron	NM_174928	NP_777588			N-6 adenine-specific DNA methyltransferase 2								methyltransferase activity|nucleic acid binding				0		all_cancers(29;5.91e-19)|all_epithelial(30;1.42e-15)|all_lung(29;5.9e-14)|Lung SC(185;0.0367)		all cancers(112;0.000234)|Epithelial(112;0.000471)|OV - Ovarian serous cystadenocarcinoma(117;0.0111)|Lung(94;0.0161)|LUSC - Lung squamous cell carcinoma(192;0.0431)														---	---	---	---
XPO4	64328	broad.mit.edu	37	13	21479764	21479764	+	5'Flank	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:21479764delA	uc001unq.3	-						XPO4_uc010tcr.1_5'Flank	NM_022459	NP_071904			exportin 4						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)														---	---	---	---
Unknown	0	broad.mit.edu	37	13	21701305	21701307	+	IGR	DEL	TTT	-	-	rs76702376		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:21701305_21701307delTTT								LATS2 (65583 upstream) : SAP18 (13346 downstream)																																			---	---	---	---
SAP18	10284	broad.mit.edu	37	13	21721082	21721082	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:21721082delT	uc001uns.2	+							NM_005870	NP_005861			Sin3A-associated protein, 18kDa						regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	cytoplasm|histone deacetylase complex|plasma membrane	protein binding|transcription corepressor activity				0		all_cancers(29;2.16e-20)|all_epithelial(30;2.97e-18)|all_lung(29;4.58e-16)|Lung SC(185;0.0262)|Breast(139;0.147)		all cancers(112;9.79e-05)|Epithelial(112;0.000292)|OV - Ovarian serous cystadenocarcinoma(117;0.00276)|Lung(94;0.0941)														---	---	---	---
ZDHHC20	253832	broad.mit.edu	37	13	21988036	21988036	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:21988036delA	uc001uob.2	-						ZDHHC20_uc001uod.2_Intron|ZDHHC20_uc001uoc.2_Intron|ZDHHC20_uc001uoe.2_Intron|ZDHHC20_uc010tcs.1_Intron	NM_153251	NP_694983			zinc finger, DHHC-type containing 20							integral to membrane	acyltransferase activity|zinc ion binding			ovary(1)	1		all_cancers(29;8.1e-16)|all_epithelial(30;3.63e-14)|all_lung(29;2.04e-13)|Lung SC(185;0.0367)		all cancers(112;0.000268)|Epithelial(112;0.000735)|OV - Ovarian serous cystadenocarcinoma(117;0.00517)|Lung(94;0.171)														---	---	---	---
ZDHHC20	253832	broad.mit.edu	37	13	22009335	22009335	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:22009335delT	uc001uob.2	-						ZDHHC20_uc001uod.2_Intron|ZDHHC20_uc001uoc.2_Intron|ZDHHC20_uc001uoe.2_Intron|ZDHHC20_uc010tcs.1_Intron	NM_153251	NP_694983			zinc finger, DHHC-type containing 20							integral to membrane	acyltransferase activity|zinc ion binding			ovary(1)	1		all_cancers(29;8.1e-16)|all_epithelial(30;3.63e-14)|all_lung(29;2.04e-13)|Lung SC(185;0.0367)		all cancers(112;0.000268)|Epithelial(112;0.000735)|OV - Ovarian serous cystadenocarcinoma(117;0.00517)|Lung(94;0.171)														---	---	---	---
Unknown	0	broad.mit.edu	37	13	22208250	22208251	+	IGR	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:22208250_22208251delTT								EFHA1 (29943 upstream) : FGF9 (36964 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	22526403	22526403	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:22526403delA								FGF9 (247763 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	23105629	23105629	+	IGR	DEL	A	-	-	rs35508353		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:23105629delA								FGF9 (826989 upstream) : SGCG (649431 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	23443551	23443551	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:23443551delT								None (None upstream) : SGCG (311509 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	23571254	23571254	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:23571254delA								None (None upstream) : SGCG (183806 downstream)																																			---	---	---	---
SGCG	6445	broad.mit.edu	37	13	23798805	23798806	+	Intron	DEL	AC	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:23798805_23798806delAC	uc001uom.2	+						SGCG_uc009zzv.2_Intron|SGCG_uc009zzw.2_Intron	NM_000231	NP_000222			gamma sarcoglycan						cytoskeleton organization|muscle organ development	cytoplasm|cytoskeleton|integral to membrane|sarcoglycan complex|sarcolemma					0		all_cancers(29;4.34e-23)|all_epithelial(30;4.4e-19)|all_lung(29;2.45e-18)|Lung SC(185;0.0228)|Breast(139;0.188)		all cancers(112;0.00255)|Epithelial(112;0.0129)|OV - Ovarian serous cystadenocarcinoma(117;0.0365)|Lung(94;0.205)														---	---	---	---
Unknown	0	broad.mit.edu	37	13	24065304	24065305	+	IGR	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:24065304_24065305delAA								SACS (57463 upstream) : TNFRSF19 (79418 downstream)																																			---	---	---	---
SPATA13	221178	broad.mit.edu	37	13	24562975	24562975	+	Intron	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:24562975delC	uc001upd.1	+						C1QTNF9_uc001upe.2_Intron|uc001upc.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)														---	---	---	---
SPATA13	221178	broad.mit.edu	37	13	24835080	24835080	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:24835080delT	uc001upg.1	+						SPATA13_uc001upd.1_Intron|C1QTNF9_uc001upe.2_Intron|SPATA13_uc010tcy.1_Intron|SPATA13_uc010tcz.1_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	24893518	24893519	+	Intron	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:24893518_24893519delAA	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)														---	---	---	---
PARP4	143	broad.mit.edu	37	13	25049930	25049931	+	Intron	DEL	TT	-	-	rs72497561		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:25049930_25049931delTT	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	25327909	25327910	+	IGR	INS	-	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:25327909_25327910insT								ATP12A (41992 upstream) : RNF17 (10391 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	25568569	25568569	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:25568569delA								TPTE2P1 (25962 upstream) : PABPC3 (101707 downstream)																																			---	---	---	---
ATP8A2	51761	broad.mit.edu	37	13	26404324	26404324	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:26404324delT	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	26455752	26455753	+	Intron	DEL	AG	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:26455752_26455753delAG	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)														---	---	---	---
Unknown	0	broad.mit.edu	37	13	27861374	27861376	+	IGR	DEL	TTG	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:27861374_27861376delTTG								RASL11A (13547 upstream) : GTF3A (137305 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	28045033	28045033	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:28045033delT								MTIF3 (20322 upstream) : LNX2 (75019 downstream)																																			---	---	---	---
LNX2	222484	broad.mit.edu	37	13	28133855	28133856	+	Intron	INS	-	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:28133855_28133856insT	uc001url.3	-						LNX2_uc001urm.1_Intron	NM_153371	NP_699202			ligand of numb-protein X 2								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)														---	---	---	---
Unknown	0	broad.mit.edu	37	13	28343815	28343815	+	IGR	DEL	A	-	-	rs34395395		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:28343815delA								POLR1D (102268 upstream) : GSX1 (22965 downstream)																																			---	---	---	---
FLT3	2322	broad.mit.edu	37	13	28663876	28663876	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:28663876delT	uc001urw.2	-						FLT3_uc010aao.2_Intron|FLT3_uc010tdn.1_Intron	NM_004119	NP_004110			fms-related tyrosine kinase 3 precursor						positive regulation of cell proliferation	integral to plasma membrane	ATP binding|vascular endothelial growth factor receptor activity			haematopoietic_and_lymphoid_tissue(8536)|lung(7)|ovary(3)|stomach(1)|central_nervous_system(1)|skin(1)	8549	Acute lymphoblastic leukemia(6;0.04)	Lung SC(185;0.0156)|Ovarian(182;0.0392)	Colorectal(13;0.000157)|READ - Rectum adenocarcinoma(15;0.105)	OV - Ovarian serous cystadenocarcinoma(117;0.00154)|all cancers(112;0.00459)|GBM - Glioblastoma multiforme(144;0.00562)|Epithelial(112;0.0959)|Lung(94;0.212)	Sorafenib(DB00398)|Sunitinib(DB01268)			Mis|O		AML|ALL								---	---	---	---
PAN3	255967	broad.mit.edu	37	13	28804192	28804192	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:28804192delT	uc001urz.2	+						PAN3_uc010tdo.1_Intron|PAN3_uc001ury.2_Intron|PAN3_uc001urx.2_Intron	NM_175854	NP_787050			PABP1-dependent poly A-specific ribonuclease						nuclear-transcribed mRNA catabolic process, nonsense-mediated decay|nuclear-transcribed mRNA poly(A) tail shortening	centrosome|cytosol	ATP binding|protein kinase activity			ovary(1)	1	Acute lymphoblastic leukemia(6;0.04)	Lung SC(185;0.0262)	Colorectal(13;0.000334)	all cancers(112;0.0102)|Epithelial(112;0.0803)|GBM - Glioblastoma multiforme(144;0.121)|OV - Ovarian serous cystadenocarcinoma(117;0.13)|Lung(94;0.174)														---	---	---	---
Unknown	0	broad.mit.edu	37	13	29088667	29088669	+	IGR	DEL	AAA	-	-	rs113095059		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:29088667_29088669delAAA								FLT1 (19402 upstream) : POMP (144572 downstream)																																			---	---	---	---
SLC46A3	283537	broad.mit.edu	37	13	29286810	29286810	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:29286810delA	uc001usi.2	-						SLC46A3_uc001usg.2_Intron|SLC46A3_uc001usj.2_Intron|SLC46A3_uc001ush.2_Intron|SLC46A3_uc001usk.2_Frame_Shift_Del_p.F281fs	NM_181785	NP_861450			solute carrier family 46, member 3 isoform a						transmembrane transport	integral to membrane				central_nervous_system(1)|skin(1)	2		Lung SC(185;0.0367)		all cancers(112;0.159)														---	---	---	---
Unknown	0	broad.mit.edu	37	13	29301317	29301317	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:29301317delT								SLC46A3 (8167 upstream) : MTUS2 (297431 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	29322746	29322746	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:29322746delA								SLC46A3 (29596 upstream) : MTUS2 (276002 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	29337148	29337151	+	IGR	DEL	TGTG	-	-	rs74414616		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:29337148_29337151delTGTG								SLC46A3 (43998 upstream) : MTUS2 (261597 downstream)																																			---	---	---	---
MTUS2	23281	broad.mit.edu	37	13	29688294	29688294	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:29688294delT	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	29949064	29949064	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:29949064delA	uc001usl.3	+							NM_001033602	NP_001028774			hypothetical protein LOC23281 isoform a							cytoplasm|microtubule	microtubule binding|protein homodimerization activity				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	13	30255760	30255763	+	IGR	DEL	AAAA	-	-	rs35880937		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:30255760_30255763delAAAA								SLC7A1 (85935 upstream) : UBL3 (82783 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	30447579	30447579	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:30447579delA								UBL3 (22759 upstream) : KATNAL1 (329189 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	30475566	30475566	+	IGR	DEL	A	-	-	rs67160997		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:30475566delA								UBL3 (50746 upstream) : KATNAL1 (301202 downstream)																																			---	---	---	---
KATNAL1	84056	broad.mit.edu	37	13	30782951	30782951	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:30782951delA	uc001uss.2	-						KATNAL1_uc001ust.2_Intron	NM_001014380	NP_001014402			katanin p60 subunit A-like 1							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	30803283	30803283	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:30803283delA	uc001uss.2	-						KATNAL1_uc001ust.2_Intron	NM_001014380	NP_001014402			katanin p60 subunit A-like 1							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)														---	---	---	---
LOC100188949	100188949	broad.mit.edu	37	13	30926345	30926346	+	Intron	DEL	AA	-	-	rs75946445		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:30926345_30926346delAA	uc001usu.2	-							NR_024464				full-length cDNA clone CS0DG007YC17 of B cells (Ramos cell line) of Homo sapiens (human).												0																		---	---	---	---
USPL1	10208	broad.mit.edu	37	13	31220493	31220493	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:31220493delT	uc001utc.2	+						USPL1_uc001utb.2_Intron|USPL1_uc001utd.2_Intron|USPL1_uc001ute.1_Intron	NM_005800	NP_005791			ubiquitin specific peptidase like 1						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)														---	---	---	---
USPL1	10208	broad.mit.edu	37	13	31226101	31226101	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:31226101delA	uc001utc.2	+						USPL1_uc001utd.2_Intron|USPL1_uc001ute.1_Intron	NM_005800	NP_005791			ubiquitin specific peptidase like 1						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)														---	---	---	---
ALOX5AP	241	broad.mit.edu	37	13	31335046	31335046	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:31335046delA	uc001utf.1	+						ALOX5AP_uc010tdr.1_Intron	NM_001629	NP_001620			arachidonate 5-lipoxygenase-activating protein						cellular response to calcium ion|leukotriene biosynthetic process|leukotriene production involved in inflammatory response|protein homotrimerization	endoplasmic reticulum membrane|integral to membrane|microsome|nuclear membrane	arachidonic acid binding|protein N-terminus binding				0		Lung SC(185;0.0257)|Breast(139;0.203)		all cancers(112;0.0187)|Epithelial(112;0.0803)|OV - Ovarian serous cystadenocarcinoma(117;0.0864)														---	---	---	---
Unknown	0	broad.mit.edu	37	13	31342909	31342910	+	IGR	DEL	GA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:31342909_31342910delGA								ALOX5AP (4353 upstream) : C13orf33 (137402 downstream)																																			---	---	---	---
B3GALTL	145173	broad.mit.edu	37	13	31811263	31811263	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:31811263delA	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	31959648	31959648	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:31959648delT								B3GALTL (53239 upstream) : RXFP2 (354031 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	31967917	31967917	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:31967917delT								B3GALTL (61508 upstream) : RXFP2 (345762 downstream)																																			---	---	---	---
EEF1DP3	196549	broad.mit.edu	37	13	32514692	32514692	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:32514692delA	uc001utu.2	+						EEF1DP3_uc010tdv.1_Intron					Homo sapiens similar to hypothetical protein FLJ20897, mRNA (cDNA clone IMAGE:5267252).												0																		---	---	---	---
EEF1DP3	196549	broad.mit.edu	37	13	32531744	32531749	+	Intron	DEL	AGAAGA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:32531744_32531749delAGAAGA	uc010tdv.1	+							NR_027062				Homo sapiens similar to hypothetical protein FLJ20897, mRNA (cDNA clone IMAGE:5267252).												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	13	32571212	32571212	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:32571212delA								EEF1DP3 (37492 upstream) : FRY (34225 downstream)																																			---	---	---	---
FRY	10129	broad.mit.edu	37	13	32647682	32647685	+	Intron	DEL	GTGT	-	-	rs35631279		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:32647682_32647685delGTGT	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	32673954	32673954	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-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	32836660	32836660	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:32836660delA	uc001utx.2	+						FRY_uc010tdw.1_Intron|FRY_uc001uty.2_Intron|FRY_uc001utz.2_Intron|FRY_uc010tdx.1_5'Flank	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)														---	---	---	---
N4BP2L1	90634	broad.mit.edu	37	13	32994519	32994519	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:32994519delT	uc001uuc.2	-						N4BP2L1_uc001uud.2_Intron|N4BP2L1_uc010tdy.1_Intron|N4BP2L1_uc001uuf.2_Intron	NM_052818	NP_438169			NEDD4 binding protein 2-like 1 isoform 1						cell killing		ATP binding			ovary(1)	1		Lung SC(185;0.0262)		all cancers(112;6.3e-06)|Epithelial(112;3.51e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00607)|BRCA - Breast invasive adenocarcinoma(63;0.0171)														---	---	---	---
PDS5B	23047	broad.mit.edu	37	13	33197633	33197634	+	Intron	INS	-	TTAAAG	TTAAAG	rs140262741	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:33197633_33197634insTTAAAG	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	33273827	33273827	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:33273827delA	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)														---	---	---	---
STARD13	90627	broad.mit.edu	37	13	33844381	33844382	+	Intron	INS	-	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:33844381_33844382insA	uc001uuw.2	-						STARD13_uc001uux.2_Intron|STARD13_uc010tec.1_Intron|STARD13_uc010abh.1_Intron	NM_178006	NP_821074			StAR-related lipid transfer (START) domain						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)														---	---	---	---
STARD13	90627	broad.mit.edu	37	13	34023888	34023888	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:34023888delA	uc001uux.2	-							NM_052851	NP_443083			StAR-related lipid transfer (START) domain						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)														---	---	---	---
RFC3	5983	broad.mit.edu	37	13	34398063	34398063	+	Frame_Shift_Del	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-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	34571054	34571054	+	IGR	DEL	T	-	-	rs75346854	byFrequency;by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:34571054delT								RFC3 (30360 upstream) : NBEA (945402 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	34828063	34828063	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:34828063delA								RFC3 (287369 upstream) : NBEA (688393 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	35322253	35322254	+	IGR	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:35322253_35322254delTT								RFC3 (781559 upstream) : NBEA (194202 downstream)																																			---	---	---	---
NBEA	26960	broad.mit.edu	37	13	36242470	36242470	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:36242470delT	uc001uvb.2	+						NBEA_uc010abi.2_Intron|NBEA_uc010tef.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	36276534	36276535	+	IGR	DEL	GA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:36276534_36276535delGA								NBEA (29662 upstream) : DCLK1 (66588 downstream)																																			---	---	---	---
DCLK1	9201	broad.mit.edu	37	13	36468279	36468279	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:36468279delA	uc001uvf.2	-						uc001uvi.1_Intron	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)														---	---	---	---
DCLK1	9201	broad.mit.edu	37	13	36480729	36480729	+	Intron	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:36480729delC	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)														---	---	---	---
C13orf36	400120	broad.mit.edu	37	13	37246585	37246585	+	5'Flank	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:37246585delC	uc001uvt.3	+							NM_203451	NP_982276			hypothetical protein LOC400120							integral to membrane				skin(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	13	37639117	37639118	+	IGR	DEL	TG	-	-	rs5802855		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:37639117_37639118delTG								FAM48A (5267 upstream) : CSNK1A1L (38279 downstream)																																			---	---	---	---
TRPC4	7223	broad.mit.edu	37	13	38418423	38418423	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:38418423delT	uc001uws.2	-						TRPC4_uc001uwt.2_Intron|TRPC4_uc010tey.1_Intron|TRPC4_uc010abw.2_Intron|TRPC4_uc010abx.2_Intron|TRPC4_uc010aby.2_Intron	NM_016179	NP_057263			transient receptor potential cation channel,						axon guidance|calcium ion import	basolateral plasma membrane|calcium channel complex|cell surface|cortical cytoskeleton	beta-catenin binding|cadherin binding|store-operated calcium channel activity			ovary(3)|skin(2)|breast(1)	6				all cancers(112;1.92e-08)|Epithelial(112;5.04e-06)|OV - Ovarian serous cystadenocarcinoma(117;0.000677)|GBM - Glioblastoma multiforme(144;0.00623)|BRCA - Breast invasive adenocarcinoma(63;0.0126)														---	---	---	---
Unknown	0	broad.mit.edu	37	13	38567784	38567785	+	IGR	INS	-	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:38567784_38567785insT								TRPC4 (123845 upstream) : UFM1 (356157 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	38968291	38968293	+	IGR	DEL	TTT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:38968291_38968293delTTT								UFM1 (31149 upstream) : FREM2 (292880 downstream)																																			---	---	---	---
FREM2	341640	broad.mit.edu	37	13	39289741	39289742	+	Intron	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:39289741_39289742delTT	uc001uwv.2	+							NM_207361	NP_997244			FRAS1-related extracellular matrix protein 2						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)														---	---	---	---
FREM2	341640	broad.mit.edu	37	13	39452808	39452808	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:39452808delA	uc001uwv.2	+							NM_207361	NP_997244			FRAS1-related extracellular matrix protein 2						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)														---	---	---	---
Unknown	0	broad.mit.edu	37	13	39468883	39468883	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:39468883delA								FREM2 (7618 upstream) : STOML3 (71180 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	39649970	39649972	+	IGR	DEL	AAA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:39649970_39649972delAAA								NHLRC3 (25728 upstream) : LHFP (267058 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	39743614	39743614	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:39743614delA								NHLRC3 (119372 upstream) : LHFP (173416 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	39798430	39798430	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:39798430delA								NHLRC3 (174188 upstream) : LHFP (118600 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	39915299	39915306	+	IGR	DEL	AAAAAAAA	-	-	rs34824244		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:39915299_39915306delAAAAAAAA								NHLRC3 (291057 upstream) : LHFP (1724 downstream)																																			---	---	---	---
COG6	57511	broad.mit.edu	37	13	40252213	40252213	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:40252213delT	uc001uxh.2	+						COG6_uc001uxi.2_Intron|COG6_uc010acb.2_Intron	NM_020751	NP_065802			component of oligomeric golgi complex 6 isoform						protein transport	Golgi membrane|Golgi transport complex				kidney(1)|skin(1)	2		Lung NSC(96;0.000124)|Breast(139;0.0199)|Prostate(109;0.0233)|Lung SC(185;0.0367)		all cancers(112;6.03e-09)|Epithelial(112;7e-07)|OV - Ovarian serous cystadenocarcinoma(117;0.00015)|BRCA - Breast invasive adenocarcinoma(63;0.00438)|GBM - Glioblastoma multiforme(144;0.0168)														---	---	---	---
Unknown	0	broad.mit.edu	37	13	40419663	40419664	+	IGR	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:40419663_40419664delTT								COG6 (53861 upstream) : LOC646982 (501609 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	41294440	41294440	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:41294440delT								FOXO1 (53706 upstream) : MIR320D-1 (7524 downstream)																																			---	---	---	---
ELF1	1997	broad.mit.edu	37	13	41528373	41528373	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:41528373delA	uc001uxs.2	-						ELF1_uc010tfc.1_Intron|ELF1_uc010acd.2_Intron	NM_172373	NP_758961			E74-like factor 1 (ets domain transcription						positive regulation of transcription from RNA polymerase II promoter	cytoplasm|nucleus	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			ovary(1)	1		Lung NSC(96;8.3e-05)|Prostate(109;0.0233)|Breast(139;0.0296)|Lung SC(185;0.0367)		all cancers(112;1.87e-08)|Epithelial(112;8.45e-06)|OV - Ovarian serous cystadenocarcinoma(117;0.000202)|GBM - Glioblastoma multiforme(144;0.00266)|BRCA - Breast invasive adenocarcinoma(63;0.072)														---	---	---	---
Unknown	0	broad.mit.edu	37	13	41629993	41629993	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:41629993delT								ELF1 (36485 upstream) : WBP4 (5704 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	41674497	41674497	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:41674497delA								WBP4 (16360 upstream) : KBTBD6 (27212 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	41720052	41720053	+	Intron	INS	-	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:41720052_41720053insT	uc001uxv.1	+											Homo sapiens cDNA FLJ31620 fis, clone NT2RI2003184.																														---	---	---	---
Unknown	0	broad.mit.edu	37	13	42062786	42062787	+	IGR	INS	-	TTTCT	TTTCT	rs151234723	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:42062786_42062787insTTTCT								C13orf15 (17773 upstream) : KIAA0564 (78175 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	42088450	42088450	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:42088450delA								C13orf15 (43437 upstream) : KIAA0564 (52512 downstream)																																			---	---	---	---
KIAA0564	23078	broad.mit.edu	37	13	42249231	42249231	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:42249231delA	uc001uyj.2	-							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)														---	---	---	---
KIAA0564	23078	broad.mit.edu	37	13	42333537	42333537	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:42333537delT	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	42682987	42682988	+	Intron	INS	-	AAGGA	AAGGA	rs140473533	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:42682987_42682988insAAGGA	uc001uyl.1	+						DGKH_uc010tfh.1_Intron|DGKH_uc001uym.1_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	43053766	43053766	+	IGR	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:43053766delG								AKAP11 (156364 upstream) : TNFSF11 (83106 downstream)																																			---	---	---	---
TNFSF11	8600	broad.mit.edu	37	13	43151670	43151671	+	Intron	DEL	TG	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:43151670_43151671delTG	uc001uyu.2	+						TNFSF11_uc001uyt.2_Intron	NM_003701	NP_003692			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)														---	---	---	---
Unknown	0	broad.mit.edu	37	13	43189422	43189424	+	IGR	DEL	TTT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:43189422_43189424delTTT								TNFSF11 (7273 upstream) : C13orf30 (166262 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	43712761	43712761	+	IGR	DEL	T	-	-	rs74646391		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:43712761delT								DNAJC15 (29457 upstream) : ENOX1 (74919 downstream)																																			---	---	---	---
ENOX1	55068	broad.mit.edu	37	13	43838889	43838889	+	Intron	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:43838889delG	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	43903836	43903836	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:43903836delT	uc001uza.3	-						ENOX1_uc001uzb.3_Intron|ENOX1_uc001uzc.3_Intron|ENOX1_uc001uyz.3_Intron|ENOX1_uc010tfm.1_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	43947306	43947306	+	Intron	DEL	A	-	-	rs72056475		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:43947306delA	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)														---	---	---	---
C13orf31	144811	broad.mit.edu	37	13	44464090	44464090	+	Intron	DEL	C	-	-	rs7989857	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:44464090delC	uc010acg.2	+						C13orf31_uc001uzf.3_Intron	NM_001128303	NP_001121775			hypothetical protein LOC144811												0		Lung NSC(96;0.000163)|all_hematologic(4;0.0127)|Prostate(109;0.0233)|Hepatocellular(98;0.0268)|Breast(139;0.0364)|Lung SC(185;0.0367)|Acute lymphoblastic leukemia(4;0.138)		GBM - Glioblastoma multiforme(144;0.000573)|BRCA - Breast invasive adenocarcinoma(63;0.121)														---	---	---	---
C13orf31	144811	broad.mit.edu	37	13	44464520	44464520	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:44464520delA	uc010acg.2	+						C13orf31_uc001uzf.3_Intron	NM_001128303	NP_001121775			hypothetical protein LOC144811												0		Lung NSC(96;0.000163)|all_hematologic(4;0.0127)|Prostate(109;0.0233)|Hepatocellular(98;0.0268)|Breast(139;0.0364)|Lung SC(185;0.0367)|Acute lymphoblastic leukemia(4;0.138)		GBM - Glioblastoma multiforme(144;0.000573)|BRCA - Breast invasive adenocarcinoma(63;0.121)														---	---	---	---
Unknown	0	broad.mit.edu	37	13	44540612	44540613	+	IGR	DEL	TC	-	-	rs71759424		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:44540612_44540613delTC								C13orf31 (72545 upstream) : LOC121838 (55858 downstream)																																			---	---	---	---
TSC22D1	8848	broad.mit.edu	37	13	45020879	45020879	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:45020879delA	uc001uzn.3	-						TSC22D1_uc001uzo.1_Intron	NM_183422	NP_904358			TSC22 domain family, member 1 isoform 1						transcription from RNA polymerase II promoter	cytoplasm|nucleus	protein binding|sequence-specific DNA binding transcription factor activity				0		all_hematologic(4;8.74e-08)|Acute lymphoblastic leukemia(4;1.78e-07)|Lung NSC(96;2.21e-05)|Breast(139;0.000625)|Prostate(109;0.000947)|Hepatocellular(98;0.0202)|Lung SC(185;0.0262)		GBM - Glioblastoma multiforme(144;0.000522)|BRCA - Breast invasive adenocarcinoma(63;0.118)														---	---	---	---
TSC22D1	8848	broad.mit.edu	37	13	45039400	45039401	+	Intron	INS	-	A	A	rs112528555		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:45039400_45039401insA	uc001uzn.3	-						TSC22D1_uc001uzo.1_Intron	NM_183422	NP_904358			TSC22 domain family, member 1 isoform 1						transcription from RNA polymerase II promoter	cytoplasm|nucleus	protein binding|sequence-specific DNA binding transcription factor activity				0		all_hematologic(4;8.74e-08)|Acute lymphoblastic leukemia(4;1.78e-07)|Lung NSC(96;2.21e-05)|Breast(139;0.000625)|Prostate(109;0.000947)|Hepatocellular(98;0.0202)|Lung SC(185;0.0262)		GBM - Glioblastoma multiforme(144;0.000522)|BRCA - Breast invasive adenocarcinoma(63;0.118)														---	---	---	---
TSC22D1	8848	broad.mit.edu	37	13	45130517	45130517	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:45130517delA	uc001uzn.3	-						TSC22D1_uc001uzo.1_Intron	NM_183422	NP_904358			TSC22 domain family, member 1 isoform 1						transcription from RNA polymerase II promoter	cytoplasm|nucleus	protein binding|sequence-specific DNA binding transcription factor activity				0		all_hematologic(4;8.74e-08)|Acute lymphoblastic leukemia(4;1.78e-07)|Lung NSC(96;2.21e-05)|Breast(139;0.000625)|Prostate(109;0.000947)|Hepatocellular(98;0.0202)|Lung SC(185;0.0262)		GBM - Glioblastoma multiforme(144;0.000522)|BRCA - Breast invasive adenocarcinoma(63;0.118)														---	---	---	---
Unknown	0	broad.mit.edu	37	13	45190301	45190301	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:45190301delT								TSC22D1 (39600 upstream) : NUFIP1 (323083 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	45199251	45199251	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:45199251delT								TSC22D1 (48550 upstream) : NUFIP1 (314133 downstream)																																			---	---	---	---
KIAA1704	55425	broad.mit.edu	37	13	45578723	45578723	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:45578723delT	uc001uzq.2	+						KIAA1704_uc010tfo.1_Intron|KIAA1704_uc001uzr.1_Intron|KIAA1704_uc001uzs.2_Intron|KIAA1704_uc001uzt.2_5'Flank	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)														---	---	---	---
Unknown	0	broad.mit.edu	37	13	45651588	45651588	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:45651588delA								KIAA1704 (43846 upstream) : GTF2F2 (43043 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	45860822	45860822	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:45860822delT								GTF2F2 (2585 upstream) : TPT1 (50482 downstream)																																			---	---	---	---
LOC100190939	100190939	broad.mit.edu	37	13	45942015	45942015	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:45942015delT	uc010tfr.1	+						LOC100190939_uc001vac.2_Intron	NR_024458				Homo sapiens pp13759 mRNA, complete cds.												0																		---	---	---	---
SLC25A30	253512	broad.mit.edu	37	13	45980812	45980813	+	Intron	INS	-	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:45980812_45980813insC	uc001vag.2	-						SLC25A30_uc010tfs.1_Intron|SLC25A30_uc001vah.2_Intron|SLC25A30_uc010tft.1_Intron|SLC25A30_uc001vaf.2_5'Flank	NM_001010875	NP_001010875			solute carrier family 25, member 30						mitochondrial transport	integral to membrane|mitochondrial inner membrane	binding			breast(1)	1		Lung NSC(96;0.00227)|Prostate(109;0.00578)|Breast(56;0.0192)|Lung SC(185;0.0367)|Hepatocellular(98;0.0556)	KIRC - Kidney renal clear cell carcinoma(16;0.234)	GBM - Glioblastoma multiforme(144;7.95e-05)														---	---	---	---
Unknown	0	broad.mit.edu	37	13	46003972	46003972	+	IGR	DEL	A	-	-	rs113181141		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:46003972delA								SLC25A30 (11456 upstream) : COG3 (35099 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	46249436	46249436	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:46249436delT								FAM194B (59562 upstream) : SPERT (27010 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	46336966	46336966	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:46336966delT								SPERT (48273 upstream) : SIAH3 (17452 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	46447619	46447619	+	IGR	DEL	A	-	-	rs75712135		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:46447619delA								SIAH3 (21773 upstream) : ZC3H13 (82186 downstream)																																			---	---	---	---
ZC3H13	23091	broad.mit.edu	37	13	46587184	46587186	+	Intron	DEL	AAG	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:46587184_46587186delAAG	uc010tfw.1	-						ZC3H13_uc001vas.1_Intron|ZC3H13_uc001vat.1_Intron	NM_015070	NP_055885			zinc finger CCCH-type containing 13								nucleic acid binding|zinc ion binding			ovary(1)|lung(1)	2		Lung NSC(96;7.26e-05)|Breast(56;0.000118)|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;4.18e-05)														---	---	---	---
ZC3H13	23091	broad.mit.edu	37	13	46619244	46619244	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:46619244delA	uc010tfw.1	-						ZC3H13_uc001vas.1_Intron|ZC3H13_uc001vat.1_Intron	NM_015070	NP_055885			zinc finger CCCH-type containing 13								nucleic acid binding|zinc ion binding			ovary(1)|lung(1)	2		Lung NSC(96;7.26e-05)|Breast(56;0.000118)|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;4.18e-05)														---	---	---	---
CPB2	1361	broad.mit.edu	37	13	46638395	46638395	+	Intron	DEL	A	-	-	rs74342011		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:46638395delA	uc001vaw.2	-						uc001vau.1_Intron|uc001vav.1_Intron|CPB2_uc001vax.2_Intron	NM_001872	NP_001863			plasma carboxypeptidase B2 isoform a						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)														---	---	---	---
Unknown	0	broad.mit.edu	37	13	46765151	46765151	+	IGR	DEL	T	-	-	rs71717069		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:46765151delT								LCP1 (8692 upstream) : C13orf18 (150988 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	46894739	46894739	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:46894739delA								LCP1 (138280 upstream) : C13orf18 (21400 downstream)																																			---	---	---	---
C13orf18	80183	broad.mit.edu	37	13	46919832	46919832	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:46919832delT	uc010acl.2	-						C13orf18_uc010tfy.1_Intron|C13orf18_uc001vbf.3_Intron|C13orf18_uc001vbg.3_Intron|C13orf18_uc010tfz.1_Intron|C13orf18_uc010acm.2_Intron|C13orf18_uc010acn.2_Intron|C13orf18_uc001vbe.3_Intron|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	47529361	47529361	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:47529361delT								HTR2A (58311 upstream) : SUCLA2 (987431 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	47896549	47896549	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:47896549delA								HTR2A (425499 upstream) : SUCLA2 (620243 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	47998336	47998338	+	IGR	DEL	TTT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:47998336_47998338delTTT								HTR2A (527286 upstream) : SUCLA2 (518454 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	48102463	48102463	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:48102463delA								HTR2A (631413 upstream) : SUCLA2 (414329 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	48247493	48247493	+	IGR	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:48247493delG								HTR2A (776443 upstream) : SUCLA2 (269299 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	48340720	48340722	+	IGR	DEL	TTT	-	-	rs112736233		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:48340720_48340722delTTT								HTR2A (869670 upstream) : SUCLA2 (176070 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	48461673	48461673	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:48461673delT								HTR2A (990623 upstream) : SUCLA2 (55119 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	48471123	48471124	+	IGR	DEL	CT	-	-	rs72450872		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:48471123_48471124delCT								None (None upstream) : SUCLA2 (45668 downstream)																																			---	---	---	---
SUCLA2	8803	broad.mit.edu	37	13	48518192	48518192	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:48518192delA	uc001vbs.2	-						SUCLA2_uc010tgb.1_Intron|SUCLA2_uc010tgc.1_Intron|SUCLA2_uc010tgd.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)													---	---	---	---
RB1	5925	broad.mit.edu	37	13	48937186	48937186	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:48937186delT	uc001vcb.2	+						RB1_uc010act.1_Intron	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.?(5)		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	49177394	49177394	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:49177394delA								RCBTB2 (67276 upstream) : CYSLTR2 (50471 downstream)																																			---	---	---	---
CYSLTR2	57105	broad.mit.edu	37	13	49236136	49236136	+	Intron	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:49236136delC	uc010acx.1	+						CYSLTR2_uc010acy.1_Intron|CYSLTR2_uc010acz.1_Intron|CYSLTR2_uc010ada.1_Intron|CYSLTR2_uc010adb.1_Intron|CYSLTR2_uc010adc.1_Intron|CYSLTR2_uc010add.1_Intron|CYSLTR2_uc010acw.1_Intron	NM_020377	NP_065110			cysteinyl leukotriene receptor 2						immune response	integral to membrane|plasma membrane				lung(2)	2		all_cancers(8;1.66e-53)|all_epithelial(8;1.96e-19)|all_lung(13;9.94e-09)|all_hematologic(8;7.13e-07)|Lung NSC(96;1.72e-06)|Breast(56;1.53e-05)|Acute lymphoblastic leukemia(8;6.86e-05)|Prostate(109;0.00174)|Myeloproliferative disorder(33;0.0179)|Hepatocellular(98;0.0207)|all_neural(104;0.0416)|Lung SC(185;0.0787)		GBM - Glioblastoma multiforme(99;1.19e-09)	Nedocromil(DB00716)													---	---	---	---
Unknown	0	broad.mit.edu	37	13	49449351	49449351	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:49449351delT								CYSLTR2 (165853 upstream) : FNDC3A (100697 downstream)																																			---	---	---	---
PHF11	51131	broad.mit.edu	37	13	50077026	50077027	+	Intron	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:50077026_50077027delTT	uc001vdb.2	+						PHF11_uc010tgl.1_Intron|PHF11_uc001vdc.2_Intron|PHF11_uc001vdd.2_Intron	NM_001040443	NP_001035533			PHD finger protein 11 isoform a						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	zinc ion binding				0		Lung NSC(96;2.1e-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;2.38e-09)														---	---	---	---
KPNA3	3839	broad.mit.edu	37	13	50338890	50338891	+	Intron	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:50338890_50338891delAA	uc001vdj.2	-							NM_002267	NP_002258			karyopherin alpha 3						interspecies interaction between organisms|NLS-bearing substrate import into nucleus|protein complex assembly	cytoplasm|nuclear pore	nuclear localization sequence binding|protein transporter activity				0		Lung NSC(96;2.46e-05)|Breast(56;9.7e-05)|Prostate(109;0.00174)|Hepatocellular(98;0.0207)|Myeloproliferative disorder(33;0.163)|Lung SC(185;0.187)|all_neural(104;0.19)		GBM - Glioblastoma multiforme(99;1.42e-09)														---	---	---	---
Unknown	0	broad.mit.edu	37	13	50428238	50428241	+	IGR	DEL	AAAA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:50428238_50428241delAAAA								KPNA3 (61181 upstream) : LOC220429 (36304 downstream)																																			---	---	---	---
DLEU2	8847	broad.mit.edu	37	13	50559522	50559522	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:50559522delT	uc001vdn.1	-						DLEU2_uc001vdo.1_Intron	NR_002612				Homo sapiens BCMS-upstream neighbor (BCMSUN) mRNA, partial sequence.												0																		---	---	---	---
DLEU2	8847	broad.mit.edu	37	13	50611042	50611043	+	Intron	DEL	AC	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:50611042_50611043delAC	uc001vdn.1	-						DLEU2_uc001vdo.1_Intron	NR_002612				Homo sapiens BCMS-upstream neighbor (BCMSUN) mRNA, partial sequence.												0																		---	---	---	---
DLEU2	8847	broad.mit.edu	37	13	50618819	50618819	+	RNA	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:50618819delT	uc001vdn.1	-	5		c.567delA			DLEU2_uc001vdo.1_RNA|DLEU2_uc001vdv.2_RNA|DLEU2_uc001vdw.2_RNA|DLEU2_uc001vdx.2_RNA|DLEU2_uc001vdy.2_RNA|DLEU2_uc001vdz.2_RNA	NR_002612				Homo sapiens BCMS-upstream neighbor (BCMSUN) mRNA, partial sequence.												0																		---	---	---	---
DLEU2	8847	broad.mit.edu	37	13	50646353	50646353	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:50646353delA	uc001vdn.1	-						DLEU2_uc001vdo.1_Intron|DLEU2_uc001vdx.2_Intron|DLEU2_uc001vdy.2_Intron|DLEU2_uc001vdz.2_Intron|DLEU2_uc001veb.1_Intron	NR_002612				Homo sapiens BCMS-upstream neighbor (BCMSUN) mRNA, partial sequence.												0																		---	---	---	---
DLEU1	10301	broad.mit.edu	37	13	50822422	50822423	+	Intron	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:50822422_50822423delTT	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|uc001vek.1_Intron|uc001vel.1_Intron|uc001vem.1_Intron|uc001ven.1_Intron					Homo sapiens XTP6 (XTP6) mRNA, complete cds.												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	13	51195502	51195502	+	Intron	DEL	A	-	-	rs78253016		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:51195502delA	uc001vet.1	+											Homo sapiens mRNA for B-cell neoplasia associated transcript, (BCMS gene), splice variant D, non coding transcript.																														---	---	---	---
WDFY2	115825	broad.mit.edu	37	13	52298196	52298196	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:52298196delT	uc001vfp.2	+						WDFY2_uc010ads.1_Intron|WDFY2_uc010adt.1_Intron	NM_052950	NP_443182			WD repeat and FYVE domain containing 2								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	52509214	52509214	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:52509214delT	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|ATP7B_uc001vfv.2_Intron|ATP7B_uc010tgs.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				---	---	---	---
VPS36	51028	broad.mit.edu	37	13	53011191	53011192	+	Intron	DEL	TT	-	-	rs76746430		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:53011191_53011192delTT	uc001vgs.2	-						VPS36_uc001vgq.2_Intron	NM_016075	NP_057159			vacuolar protein sorting 36						cellular membrane organization|endosome transport|protein transport|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytosol|late endosome|membrane|nucleus	lipid binding			skin(1)	1		Breast(56;0.000207)|Lung NSC(96;0.00212)|Hepatocellular(98;0.065)|Prostate(109;0.0771)|all_neural(104;0.173)		GBM - Glioblastoma multiforme(99;3.14e-08)														---	---	---	---
CKAP2	26586	broad.mit.edu	37	13	53047434	53047435	+	Intron	INS	-	T	T	rs143621118	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:53047434_53047435insT	uc001vgv.2	+						CKAP2_uc001vgu.2_Intron|CKAP2_uc010tha.1_Intron	NM_001098525	NP_001091995			cytoskeleton associated protein 2 isoform 2						apoptosis|cell cycle	centrosome|microtubule|spindle pole				ovary(1)|skin(1)	2		Breast(56;0.000207)|Lung NSC(96;0.00212)|Hepatocellular(98;0.065)|Prostate(109;0.0771)|all_neural(104;0.173)		GBM - Glioblastoma multiforme(99;2.6e-08)														---	---	---	---
TPTE2P3	220115	broad.mit.edu	37	13	53109216	53109217	+	Intron	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:53109216_53109217delAA	uc001vgw.2	+							NR_002793				Homo sapiens TPTE and PTEN homologous inositol lipid phosphatase pseudogene, mRNA (cDNA clone IMAGE:5298506), with apparent retained intron.												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	13	53545971	53545973	+	IGR	DEL	TTT	-	-	rs150548276		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:53545971_53545973delTTT								PCDH8 (123197 upstream) : OLFM4 (56999 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	53557411	53557411	+	IGR	DEL	T	-	-	rs63660160		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:53557411delT								PCDH8 (134637 upstream) : OLFM4 (45561 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	54272603	54272603	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:54272603delA								OLFM4 (646417 upstream) : MIR1297 (613504 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	54616506	54616507	+	IGR	INS	-	AAC	AAC			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:54616506_54616507insAAC								OLFM4 (990320 upstream) : MIR1297 (269600 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	55671033	55671034	+	IGR	DEL	AG	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:55671033_55671034delAG								MIR1297 (784850 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	57120640	57120640	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:57120640delA								None (None upstream) : PRR20C (594412 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	57429723	57429723	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:57429723delA								None (None upstream) : PRR20C (285329 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	57747907	57747907	+	IGR	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:57747907delC								PRR20B (3555 upstream) : PCDH17 (457882 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	57929358	57929359	+	IGR	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:57929358_57929359delTT								PRR20B (185006 upstream) : PCDH17 (276430 downstream)																																			---	---	---	---
PCDH17	27253	broad.mit.edu	37	13	58205278	58205279	+	5'Flank	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:58205278_58205279delAA	uc001vhq.1	+						PCDH17_uc010aec.1_5'Flank	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	58979497	58979497	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:58979497delT								PCDH17 (676432 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	59922015	59922015	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:59922015delA								None (None upstream) : DIAPH3 (317710 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	60035437	60035437	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:60035437delA								None (None upstream) : DIAPH3 (204288 downstream)																																			---	---	---	---
DIAPH3	81624	broad.mit.edu	37	13	60240802	60240803	+	Frame_Shift_Ins	INS	-	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:60240802_60240803insT	uc001vht.2	-	28	3716_3717	c.3497_3498insA	c.(3496-3498)AAGfs	p.K1166fs	DIAPH3_uc001vhs.2_RNA	NM_001042517	NP_001035982	Q9NSV4	DIAP3_HUMAN	diaphanous homolog 3 isoform a	1166					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	60309247	60309247	+	Intron	DEL	T	-	-	rs141064680		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:60309247delT	uc001vht.2	-						DIAPH3_uc001vhs.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)														---	---	---	---
DIAPH3	81624	broad.mit.edu	37	13	60420749	60420749	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:60420749delA	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)														---	---	---	---
DIAPH3	81624	broad.mit.edu	37	13	60485737	60485737	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:60485737delA	uc001vht.2	-						DIAPH3_uc001vhu.2_Intron|DIAPH3_uc001vhv.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)														---	---	---	---
TDRD3	81550	broad.mit.edu	37	13	61057789	61057789	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:61057789delT	uc001via.2	+						TDRD3_uc010aef.2_Intron|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	61150942	61150942	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:61150942delA								TDRD3 (2930 upstream) : PCDH20 (832879 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	61239914	61239914	+	IGR	DEL	T	-	-	rs35384296		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:61239914delT								TDRD3 (91902 upstream) : PCDH20 (743907 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	61682623	61682624	+	IGR	DEL	AA	-	-	rs66477258		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:61682623_61682624delAA								TDRD3 (534611 upstream) : PCDH20 (301197 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	62528707	62528708	+	IGR	INS	-	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:62528707_62528708insT								PCDH20 (526628 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	63021514	63021517	+	IGR	DEL	CAGT	-	-	rs71727128		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:63021514_63021517delCAGT								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	63324333	63324333	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:63324333delT								None (None upstream) : OR7E156P (987235 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	64618632	64618632	+	Intron	DEL	A	-	-	rs35745716		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:64618632delA	uc001vii.1	-											Homo sapiens cDNA FLJ32909 fis, clone TESTI2006007.																														---	---	---	---
Unknown	0	broad.mit.edu	37	13	64932141	64932141	+	IGR	DEL	A	-	-	rs77370805		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:64932141delA								OR7E156P (615440 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	65234918	65234918	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:65234918delT								OR7E156P (918217 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	65638566	65638566	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:65638566delT								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	65738349	65738349	+	IGR	DEL	T	-	-	rs76595117		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:65738349delT								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	65983422	65983422	+	IGR	DEL	A	-	-	rs144937469		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:65983422delA								None (None upstream) : PCDH9 (893545 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	66293744	66293744	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:66293744delA								None (None upstream) : PCDH9 (583223 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	66491605	66491605	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:66491605delA								None (None upstream) : PCDH9 (385362 downstream)																																			---	---	---	---
PCDH9	5101	broad.mit.edu	37	13	67573465	67573465	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:67573465delA	uc001vik.2	-						PCDH9_uc001vil.2_Intron|PCDH9_uc010thl.1_Intron	NM_203487	NP_982354			protocadherin 9 isoform 1 precursor						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)														---	---	---	---
Unknown	0	broad.mit.edu	37	13	68290734	68290735	+	IGR	DEL	AG	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:68290734_68290735delAG								PCDH9 (486266 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	69285427	69285427	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:69285427delT								None (None upstream) : KLHL1 (989299 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	69701924	69701924	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:69701924delT								None (None upstream) : KLHL1 (572802 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	71471477	71471477	+	IGR	DEL	T	-	-	rs77083756		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:71471477delT								ATXN8OS (757592 upstream) : DACH1 (540621 downstream)																																			---	---	---	---
DACH1	1602	broad.mit.edu	37	13	72431594	72431595	+	Intron	DEL	GT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:72431594_72431595delGT	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	73209136	73209136	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:73209136delT								DACH1 (767806 upstream) : C13orf37 (73359 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	73255990	73255990	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:73255990delT								DACH1 (814660 upstream) : C13orf37 (26505 downstream)																																			---	---	---	---
C13orf34	79866	broad.mit.edu	37	13	73302918	73302918	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-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	73337441	73337441	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:73337441delA	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)			---	---	---	---
KLF5	688	broad.mit.edu	37	13	73650112	73650112	+	3'UTR	DEL	C	-	-	rs9573097	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:73650112delC	uc001vje.2	+	4					KLF5_uc001vjd.2_3'UTR	NM_001730	NP_001721			Kruppel-like factor 5						transcription from RNA polymerase II promoter	nucleus	DNA binding|zinc ion binding			large_intestine(1)|ovary(1)|pancreas(1)	3		Prostate(6;0.00187)|Breast(118;0.0735)		GBM - Glioblastoma multiforme(99;0.0011)														---	---	---	---
Unknown	0	broad.mit.edu	37	13	73806840	73806840	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:73806840delT								KLF5 (155165 upstream) : KLF12 (453310 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	73838082	73838082	+	IGR	DEL	A	-	-	rs34618281		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:73838082delA								KLF5 (186407 upstream) : KLF12 (422068 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	73842327	73842328	+	IGR	DEL	GT	-	-	rs111628699		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:73842327_73842328delGT								KLF5 (190652 upstream) : KLF12 (417822 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	73902942	73902943	+	IGR	INS	-	AT	AT	rs149103444	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:73902942_73902943insAT								KLF5 (251267 upstream) : KLF12 (357207 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	74038806	74038806	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:74038806delA								KLF5 (387131 upstream) : KLF12 (221344 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	74174982	74174982	+	IGR	DEL	T	-	-	rs68146351		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:74174982delT								KLF5 (523307 upstream) : KLF12 (85168 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	75146312	75146312	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:75146312delT								KLF12 (437918 upstream) : LOC647288 (665578 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	75516947	75516947	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:75516947delA								KLF12 (808553 upstream) : LOC647288 (294943 downstream)																																			---	---	---	---
TBC1D4	9882	broad.mit.edu	37	13	75863376	75863376	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:75863376delA	uc001vjl.1	-						TBC1D4_uc010tht.1_Intron|TBC1D4_uc010thu.1_Intron|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	75894317	75894317	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-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	75913724	75913726	+	Intron	DEL	TTT	-	-	rs71811439		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:75913724_75913726delTTT	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	76096534	76096534	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:76096534delT								TBC1D4 (40284 upstream) : COMMD6 (2816 downstream)																																			---	---	---	---
COMMD6	170622	broad.mit.edu	37	13	76113931	76113931	+	5'Flank	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:76113931delA	uc001vjo.1	-						COMMD6_uc001vjn.1_5'Flank|COMMD6_uc010aet.1_5'Flank|COMMD6_uc001vjp.1_5'Flank	NM_203495	NP_987091			COMM domain containing 6 isoform b							cytoplasm|nucleus	protein binding				0		Breast(118;0.0979)|Prostate(6;0.122)		GBM - Glioblastoma multiforme(99;0.0104)														---	---	---	---
UCHL3	7347	broad.mit.edu	37	13	76179846	76179846	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:76179846delT	uc001vjq.2	+						UCHL3_uc001vjr.2_Intron	NM_006002	NP_005993			ubiquitin carboxyl-terminal esterase L3						ubiquitin-dependent protein catabolic process	cytoplasm	cysteine-type peptidase activity|ubiquitin binding|ubiquitin thiolesterase activity				0				GBM - Glioblastoma multiforme(99;0.0125)														---	---	---	---
LMO7	4008	broad.mit.edu	37	13	76207560	76207560	+	Intron	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:76207560delC	uc010thv.1	+						LMO7_uc001vjt.1_5'Flank	NM_005358	NP_005349			LIM domain only 7 isoform 1							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)														---	---	---	---
LMO7	4008	broad.mit.edu	37	13	76224276	76224276	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:76224276delT	uc010thv.1	+						LMO7_uc001vjt.1_Intron	NM_005358	NP_005349			LIM domain only 7 isoform 1							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)														---	---	---	---
Unknown	0	broad.mit.edu	37	13	77046685	77046685	+	IGR	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:77046685delG								LMO7 (612681 upstream) : KCTD12 (407619 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	77392314	77392314	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:77392314delT								LMO7 (958310 upstream) : KCTD12 (61990 downstream)																																			---	---	---	---
MYCBP2	23077	broad.mit.edu	37	13	77760328	77760329	+	Intron	INS	-	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:77760328_77760329insT	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)														---	---	---	---
MYCBP2	23077	broad.mit.edu	37	13	77820808	77820808	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:77820808delA	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	78059564	78059564	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:78059564delT								MYCBP2 (158387 upstream) : SCEL (50245 downstream)																																			---	---	---	---
SCEL	8796	broad.mit.edu	37	13	78184275	78184275	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:78184275delT	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)														---	---	---	---
EDNRB	1910	broad.mit.edu	37	13	78475114	78475115	+	Intron	INS	-	ATC	ATC			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:78475114_78475115insATC	uc001vko.2	-						EDNRB_uc001vkq.1_Intron|uc001vkn.1_Intron|EDNRB_uc010aez.1_Intron|EDNRB_uc001vkp.1_Intron	NM_001122659	NP_001116131			endothelin receptor type B isoform 1 precursor						activation of phospholipase C activity by G-protein coupled receptor protein signaling pathway coupled to IP3 second messenger|enteric nervous system development|enteric smooth muscle cell differentiation|macrophage chemotaxis|negative regulation of adenylate cyclase activity|negative regulation of cellular protein metabolic process|negative regulation of neuron maturation|negative regulation of transcription from RNA polymerase II promoter|vein smooth muscle contraction	integral to plasma membrane	endothelin-B receptor activity|peptide hormone binding				0		Acute lymphoblastic leukemia(28;0.0279)|Breast(118;0.037)		GBM - Glioblastoma multiforme(99;0.0933)	Bosentan(DB00559)													---	---	---	---
EDNRB	1910	broad.mit.edu	37	13	78490855	78490855	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:78490855delT	uc001vko.2	-						uc001vks.2_5'Flank|EDNRB_uc001vkq.1_Intron|EDNRB_uc010aez.1_Intron|EDNRB_uc001vkp.1_Intron	NM_001122659	NP_001116131			endothelin receptor type B isoform 1 precursor						activation of phospholipase C activity by G-protein coupled receptor protein signaling pathway coupled to IP3 second messenger|enteric nervous system development|enteric smooth muscle cell differentiation|macrophage chemotaxis|negative regulation of adenylate cyclase activity|negative regulation of cellular protein metabolic process|negative regulation of neuron maturation|negative regulation of transcription from RNA polymerase II promoter|vein smooth muscle contraction	integral to plasma membrane	endothelin-B receptor activity|peptide hormone binding				0		Acute lymphoblastic leukemia(28;0.0279)|Breast(118;0.037)		GBM - Glioblastoma multiforme(99;0.0933)	Bosentan(DB00559)													---	---	---	---
Unknown	0	broad.mit.edu	37	13	79267521	79267523	+	IGR	DEL	CAA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:79267521_79267523delCAA								RNF219 (32821 upstream) : RBM26 (626577 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	79287119	79287119	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:79287119delT								RNF219 (52419 upstream) : RBM26 (606981 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	79335843	79335843	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:79335843delA								RNF219 (101143 upstream) : RBM26 (558257 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	79344296	79344296	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:79344296delA								RNF219 (109596 upstream) : RBM26 (549804 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	79789894	79789895	+	IGR	DEL	CT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:79789894_79789895delCT								RNF219 (555194 upstream) : RBM26 (104205 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	80670848	80670849	+	IGR	DEL	AA	-	-	rs67062790		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:80670848_80670849delAA								NDFIP2 (540643 upstream) : SPRY2 (239265 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	80822395	80822395	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:80822395delA								NDFIP2 (692190 upstream) : SPRY2 (87719 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	80864162	80864163	+	IGR	DEL	AA	-	-	rs139790769		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:80864162_80864163delAA								NDFIP2 (733957 upstream) : SPRY2 (45951 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	81029718	81029719	+	IGR	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:81029718_81029719delAA								SPRY2 (114632 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	81166452	81166452	+	IGR	DEL	A	-	-	rs148429702	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:81166452delA								SPRY2 (251366 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	81168658	81168659	+	IGR	DEL	TG	-	-	rs114082715	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:81168658_81168659delTG								SPRY2 (253572 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	81192075	81192075	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:81192075delA								SPRY2 (276989 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	81335477	81335478	+	IGR	DEL	GA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:81335477_81335478delGA								SPRY2 (420391 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	81699915	81699915	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:81699915delT								SPRY2 (784829 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	81742464	81742464	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:81742464delT								SPRY2 (827378 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	82505362	82505363	+	IGR	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:82505362_82505363delTT								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	82676339	82676341	+	IGR	DEL	TTT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:82676339_82676341delTTT								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	82726351	82726351	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:82726351delA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	82941746	82941746	+	IGR	DEL	A	-	-	rs145279152	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:82941746delA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	83575393	83575393	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:83575393delT								None (None upstream) : SLITRK1 (875951 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	83697711	83697711	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:83697711delA								None (None upstream) : SLITRK1 (753633 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	83715105	83715105	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:83715105delT								None (None upstream) : SLITRK1 (736239 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	85021809	85021809	+	IGR	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:85021809delG								SLITRK1 (565281 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	85096593	85096593	+	IGR	DEL	A	-	-	rs8001685	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:85096593delA								SLITRK1 (640065 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	85501472	85501472	+	IGR	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:85501472delG								None (None upstream) : SLITRK6 (865450 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	86113432	86113432	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:86113432delT								None (None upstream) : SLITRK6 (253490 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	86917008	86917009	+	IGR	DEL	TG	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:86917008_86917009delTG								SLITRK6 (543525 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	87864427	87864427	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:87864427delA								None (None upstream) : SLITRK5 (460443 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	88012964	88012965	+	IGR	DEL	TT	-	-	rs144474071		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:88012964_88012965delTT								None (None upstream) : SLITRK5 (311905 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	88133335	88133335	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:88133335delT	uc001vlm.1	-											Homo sapiens clone IMAGE:32106, mRNA sequence.																														---	---	---	---
Unknown	0	broad.mit.edu	37	13	88675845	88675845	+	IGR	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-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	88724007	88724008	+	IGR	INS	-	ATG	ATG	rs144648139	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:88724007_88724008insATG								SLITRK5 (392139 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	88900597	88900598	+	IGR	INS	-	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:88900597_88900598insG								SLITRK5 (568729 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	89273111	89273111	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:89273111delT								SLITRK5 (941243 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	89359063	89359064	+	IGR	DEL	TT	-	-	rs149336318		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:89359063_89359064delTT								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	90598157	90598158	+	IGR	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:90598157_90598158delTT								None (None upstream) : MIR622 (285278 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	91265768	91265769	+	IGR	DEL	CT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:91265768_91265769delCT								MIR622 (382237 upstream) : LOC144776 (277439 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	91709896	91709896	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:91709896delA								LOC144776 (131045 upstream) : MIR17HG (290178 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	92015351	92015352	+	IGR	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:92015351_92015352delAA								MIR17HG (8522 upstream) : GPC5 (35583 downstream)																																			---	---	---	---
GPC5	2262	broad.mit.edu	37	13	92381024	92381026	+	Intron	DEL	AAA	-	-	rs76178251		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:92381024_92381026delAAA	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	93058036	93058036	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:93058036delA	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	93429869	93429870	+	Intron	INS	-	CAAAA	CAAAA	rs150232674	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:93429869_93429870insCAAAA	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	93839891	93839892	+	IGR	INS	-	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:93839891_93839892insC								GPC5 (320406 upstream) : GPC6 (39186 downstream)																																			---	---	---	---
GPC6	10082	broad.mit.edu	37	13	93982096	93982096	+	Intron	DEL	A	-	-	rs34309783		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:93982096delA	uc001vlt.2	+						GPC6_uc010tig.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	94051314	94051315	+	Intron	INS	-	ACAC	ACAC	rs145491780	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:94051314_94051315insACAC	uc001vlt.2	+						GPC6_uc010tig.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	94101492	94101493	+	Intron	INS	-	T	T	rs148581333	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:94101492_94101493insT	uc001vlt.2	+						GPC6_uc010tig.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	94197839	94197842	+	Intron	DEL	TTTT	-	-	rs34963201		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:94197839_94197842delTTTT	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	94502120	94502120	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:94502120delT	uc001vlt.2	+						GPC6_uc010tig.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	94595874	94595874	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:94595874delA	uc001vlt.2	+						GPC6_uc010tig.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	94864303	94864303	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:94864303delT	uc001vlt.2	+						GPC6_uc010tig.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	94867505	94867505	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:94867505delT	uc001vlt.2	+						GPC6_uc010tig.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	94908316	94908316	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:94908316delA	uc001vlt.2	+						GPC6_uc010tig.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)																---	---	---	---
TGDS	23483	broad.mit.edu	37	13	95244716	95244716	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:95244716delT	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)																	---	---	---	---
Unknown	0	broad.mit.edu	37	13	95498138	95498138	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:95498138delT	uc001vmc.2	+											Homo sapiens, clone IMAGE:5728875, mRNA.																														---	---	---	---
Unknown	0	broad.mit.edu	37	13	95626213	95626213	+	IGR	DEL	T	-	-	rs11330706		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:95626213delT								SOX21 (261824 upstream) : ABCC4 (45871 downstream)																																			---	---	---	---
ABCC4	10257	broad.mit.edu	37	13	95711896	95711896	+	Intron	DEL	T	-	-	rs67361662		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:95711896delT	uc001vmd.3	-						ABCC4_uc010afj.2_Intron|ABCC4_uc010afk.2_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	95863780	95863780	+	Intron	DEL	A	-	-	rs1678400	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:95863780delA	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)													---	---	---	---
Unknown	0	broad.mit.edu	37	13	95984623	95984626	+	IGR	DEL	AAAA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:95984623_95984626delAAAA								ABCC4 (30936 upstream) : CLDN10 (101227 downstream)																																			---	---	---	---
DZIP1	22873	broad.mit.edu	37	13	96292823	96292823	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:96292823delA	uc001vmk.2	-						DZIP1_uc001vml.2_Intron|DZIP1_uc001vmn.2_Intron	NM_198968	NP_945319			DAZ interacting protein 1 isoform 2						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)															---	---	---	---
DNAJC3	5611	broad.mit.edu	37	13	96373895	96373895	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:96373895delT	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	96743853	96743853	+	Intron	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:96743853delC	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	96880974	96880974	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:96880974delA	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	96922867	96922868	+	Intron	INS	-	GTATATA	GTATATA	rs145408885	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:96922867_96922868insGTATATA	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	97064269	97064269	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:97064269delT	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	97126370	97126371	+	Intron	INS	-	T	T	rs147495722	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:97126370_97126371insT	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	97128503	97128503	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:97128503delT	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	97200132	97200132	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:97200132delT	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	97238557	97238557	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:97238557delT	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	98017439	98017439	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:98017439delT	uc010aft.2	+						MBNL2_uc001vmz.2_Intron|MBNL2_uc001vna.2_Intron|MBNL2_uc001vnb.2_Intron|MBNL2_uc010tij.1_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	98552833	98552834	+	IGR	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:98552833_98552834delAA								RAP2A (432582 upstream) : IPO5 (53095 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	98580265	98580265	+	IGR	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:98580265delG								RAP2A (460014 upstream) : IPO5 (25664 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	98679693	98679694	+	IGR	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:98679693_98679694delTT								IPO5 (3144 upstream) : FARP1 (115122 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	98709696	98709696	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:98709696delA								IPO5 (33147 upstream) : FARP1 (85120 downstream)																																			---	---	---	---
STK24	8428	broad.mit.edu	37	13	99141376	99141378	+	Intron	DEL	ACA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:99141376_99141378delACA	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	99502312	99502312	+	Frame_Shift_Del	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:99502312delA	uc001vnt.2	-	36	4060	c.4005delT	c.(4003-4005)TTTfs	p.F1335fs	DOCK9_uc001vnw.2_Frame_Shift_Del_p.F1334fs|DOCK9_uc001vnv.1_RNA|DOCK9_uc010tir.1_Frame_Shift_Del_p.F1335fs|DOCK9_uc001vnr.2_5'Flank|DOCK9_uc010tin.1_5'Flank|DOCK9_uc001vns.2_5'Flank|DOCK9_uc010tio.1_Frame_Shift_Del_p.F4fs|DOCK9_uc010tip.1_Frame_Shift_Del_p.F22fs|DOCK9_uc001vnu.1_5'Flank|DOCK9_uc010tiq.1_Frame_Shift_Del_p.F313fs	NM_015296	NP_056111	Q9BZ29	DOCK9_HUMAN	dedicator of cytokinesis 9 isoform a	1335					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)																	---	---	---	---
DOCK9	23348	broad.mit.edu	37	13	99530752	99530752	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:99530752delT	uc001vnt.2	-						DOCK9_uc001vnw.2_Intron|DOCK9_uc001vnv.1_Intron|DOCK9_uc010tir.1_Intron|DOCK9_uc010tis.1_Intron|DOCK9_uc010tit.1_Intron|DOCK9_uc010afu.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)																	---	---	---	---
DOCK9	23348	broad.mit.edu	37	13	99644379	99644381	+	Intron	DEL	AAA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:99644379_99644381delAAA	uc001vnt.2	-						DOCK9_uc001vnv.1_Intron|DOCK9_uc010tir.1_Intron|DOCK9_uc010tit.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)																	---	---	---	---
Unknown	0	broad.mit.edu	37	13	99776479	99776479	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:99776479delT								DOCK9 (37819 upstream) : UBAC2 (76200 downstream)																																			---	---	---	---
UBAC2	337867	broad.mit.edu	37	13	99899775	99899775	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:99899775delT	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	99926590	99926591	+	Intron	INS	-	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:99926590_99926591insT	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-4200-01A-01D-1126-08	TCGA-BR-4200-11A-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	100041901	100041901	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:100041901delA								UBAC2 (3150 upstream) : TM9SF2 (111827 downstream)																																			---	---	---	---
CLYBL	171425	broad.mit.edu	37	13	100295038	100295038	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:100295038delT	uc001vok.2	+						CLYBL_uc010tix.1_Intron|CLYBL_uc010tiy.1_Intron|hsa-mir-4306|MI0015836_5'Flank	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)																	---	---	---	---
Unknown	0	broad.mit.edu	37	13	100653356	100653356	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:100653356delT								ZIC2 (14338 upstream) : PCCA (87981 downstream)																																			---	---	---	---
PCCA	5095	broad.mit.edu	37	13	100764388	100764388	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:100764388delT	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	100768947	100768947	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:100768947delT	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	100779049	100779049	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:100779049delT	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	100854740	100854741	+	Intron	INS	-	T	T	rs80124111		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:100854740_100854741insT	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	100885683	100885683	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:100885683delT	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	100940858	100940859	+	Intron	DEL	TG	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:100940858_100940859delTG	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	101095704	101095706	+	Intron	DEL	AAA	-	-	rs75144360		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:101095704_101095706delAAA	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)													---	---	---	---
PCCA	5095	broad.mit.edu	37	13	101107962	101107962	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:101107962delT	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)													---	---	---	---
PCCA	5095	broad.mit.edu	37	13	101168019	101168019	+	Intron	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:101168019delC	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)													---	---	---	---
A2LD1	87769	broad.mit.edu	37	13	101199718	101199719	+	Intron	INS	-	A	A	rs148512970	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:101199718_101199719insA	uc001vor.2	-							NM_033110	NP_149101			AIG2-like domain 1						cellular modified amino acid catabolic process		acyltransferase activity|gamma-glutamylcyclotransferase activity				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	13	101453162	101453162	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:101453162delA								TMTC4 (126059 upstream) : NALCN (252968 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	101492650	101492651	+	IGR	DEL	AA	-	-	rs35369205		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:101492650_101492651delAA								TMTC4 (165547 upstream) : NALCN (213479 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	101543749	101543749	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:101543749delA								TMTC4 (216646 upstream) : NALCN (162381 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	101591768	101591768	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:101591768delT								TMTC4 (264665 upstream) : NALCN (114362 downstream)																																			---	---	---	---
NALCN	259232	broad.mit.edu	37	13	101952773	101952773	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:101952773delT	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	102109267	102109267	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:102109267delA	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	102173769	102173769	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:102173769delT	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	102662024	102662024	+	Intron	DEL	A	-	-	rs78419873		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:102662024delA	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	102665502	102665503	+	Intron	DEL	CA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:102665502_102665503delCA	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	102849308	102849308	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:102849308delT	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)																	---	---	---	---
TPP2	7174	broad.mit.edu	37	13	103249495	103249495	+	Frame_Shift_Del	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:103249495delG	uc001vpi.3	+	1	210	c.107delG	c.(106-108)CGGfs	p.R36fs		NM_003291	NP_003282	P29144	TPP2_HUMAN	tripeptidyl peptidase II	36					proteolysis	cytoplasm|nucleus	aminopeptidase activity|serine-type endopeptidase activity|tripeptidyl-peptidase activity			upper_aerodigestive_tract(1)|ovary(1)	2	all_neural(89;0.0438)|Medulloblastoma(90;0.163)|Lung SC(71;0.184)																	---	---	---	---
LOC643677	643677	broad.mit.edu	37	13	103381996	103381996	+	Frame_Shift_Del	DEL	A	-	-	rs34874700		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:103381996delA	uc001vpm.2	-	4	21191	c.21051delT	c.(21049-21051)TTTfs	p.F7017fs		NM_001146197	NP_001139669			hypothetical protein LOC643677												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	13	103415342	103415342	+	IGR	DEL	A	-	-	rs77558849		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:103415342delA								LOC643677 (3920 upstream) : C13orf27 (3123 downstream)																																			---	---	---	---
LOC121952	121952	broad.mit.edu	37	13	103542438	103542439	+	Intron	DEL	AC	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:103542438_103542439delAC	uc001vpx.1	+							NR_026965				Homo sapiens cDNA FLJ39105 fis, clone NTONG2004806.												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	13	103630453	103630453	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:103630453delT								LOC121952 (82070 upstream) : SLC10A2 (65897 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	104030985	104030985	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:104030985delA								SLC10A2 (311789 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	104614829	104614829	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:104614829delT								SLC10A2 (895633 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	104617607	104617607	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:104617607delT								SLC10A2 (898411 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	105029993	105029993	+	IGR	DEL	C	-	-	rs9519312		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:105029993delC								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	105475655	105475656	+	IGR	DEL	TC	-	-	rs71870003		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:105475655_105475656delTC								None (None upstream) : DAOA (642560 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	105929662	105929662	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:105929662delA								None (None upstream) : DAOA (188554 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	106163083	106163084	+	IGR	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:106163083_106163084delTT								DAOA (19701 upstream) : EFNB2 (979014 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	106207467	106207467	+	IGR	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:106207467delC								DAOA (64085 upstream) : EFNB2 (934631 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	106389314	106389314	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:106389314delA	uc001vqf.1	+											Homo sapiens cDNA FLJ25324 fis, clone TST00330.																														---	---	---	---
Unknown	0	broad.mit.edu	37	13	106659521	106659521	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:106659521delA								DAOA (516139 upstream) : EFNB2 (482577 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	106833024	106833024	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:106833024delT								DAOA (689642 upstream) : EFNB2 (309074 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	107140340	107140340	+	IGR	DEL	T	-	-	rs141267177		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:107140340delT								DAOA (996958 upstream) : EFNB2 (1758 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	107279769	107279769	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:107279769delT								ARGLU1 (59255 upstream) : FAM155A (541111 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	107534287	107534287	+	IGR	DEL	A	-	-	rs35812570		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:107534287delA								ARGLU1 (313773 upstream) : FAM155A (286593 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	107535378	107535379	+	IGR	DEL	AA	-	-	rs72661246	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:107535378_107535379delAA								ARGLU1 (314864 upstream) : FAM155A (285501 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	107725904	107725904	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:107725904delT								ARGLU1 (505390 upstream) : FAM155A (94976 downstream)																																			---	---	---	---
FAM155A	728215	broad.mit.edu	37	13	107836323	107836323	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:107836323delT	uc001vql.2	-							NM_001080396	NP_001073865			family with sequence similarity 155, member A							integral to membrane	binding			skin(1)	1																		---	---	---	---
FAM155A	728215	broad.mit.edu	37	13	107900573	107900573	+	Intron	DEL	A	-	-	rs34226155		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:107900573delA	uc001vql.2	-							NM_001080396	NP_001073865			family with sequence similarity 155, member A							integral to membrane	binding			skin(1)	1																		---	---	---	---
FAM155A	728215	broad.mit.edu	37	13	108150373	108150373	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:108150373delA	uc001vql.2	-							NM_001080396	NP_001073865			family with sequence similarity 155, member A							integral to membrane	binding			skin(1)	1																		---	---	---	---
FAM155A	728215	broad.mit.edu	37	13	108174291	108174292	+	Intron	DEL	AC	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:108174291_108174292delAC	uc001vql.2	-							NM_001080396	NP_001073865			family with sequence similarity 155, member A							integral to membrane	binding			skin(1)	1																		---	---	---	---
FAM155A	728215	broad.mit.edu	37	13	108217414	108217420	+	Intron	DEL	AAAAAAA	-	-	rs71754551		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:108217414_108217420delAAAAAAA	uc001vql.2	-							NM_001080396	NP_001073865			family with sequence similarity 155, member A							integral to membrane	binding			skin(1)	1																		---	---	---	---
LIG4	3981	broad.mit.edu	37	13	108863511	108863511	+	Frame_Shift_Del	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:108863511delT	uc001vqn.2	-	2	379	c.106delA	c.(106-108)ATCfs	p.I36fs	LIG4_uc001vqo.2_Frame_Shift_Del_p.I36fs|LIG4_uc010agg.1_5'UTR|LIG4_uc010agf.2_Frame_Shift_Del_p.I36fs|LIG4_uc001vqp.2_Frame_Shift_Del_p.I36fs	NM_002312	NP_002303	P49917	DNLI4_HUMAN	DNA ligase IV	36					cell cycle|cell division|cell proliferation|central nervous system development|chromosome organization|DNA ligation involved in DNA recombination|DNA ligation involved in DNA repair|DNA replication|double-strand break repair via nonhomologous end joining|in utero embryonic development|initiation of viral infection|isotype switching|negative regulation of neuron apoptosis|neuron apoptosis|nucleotide-excision repair, DNA gap filling|positive regulation of fibroblast proliferation|positive regulation of neurogenesis|pro-B cell differentiation|provirus integration|response to gamma radiation|response to X-ray|single strand break repair|somatic stem cell maintenance|T cell differentiation in thymus|T cell receptor V(D)J recombination	condensed chromosome|cytoplasm|DNA ligase IV complex|DNA-dependent protein kinase-DNA ligase 4 complex|focal adhesion|nucleoplasm	ATP binding|DNA binding|DNA ligase (ATP) activity|metal ion binding|protein C-terminus binding				0	all_lung(23;0.000238)|all_neural(89;0.00256)|Lung NSC(43;0.0056)|Medulloblastoma(90;0.00596)|Lung SC(71;0.104)												NHEJ					---	---	---	---
Unknown	0	broad.mit.edu	37	13	108920716	108920716	+	IGR	DEL	T	-	-	rs112704561		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:108920716delT								ABHD13 (34114 upstream) : TNFSF13B (1261 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	109040198	109040198	+	IGR	DEL	G	-	-	rs34514127		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:109040198delG								TNFSF13B (80834 upstream) : MYO16 (208302 downstream)																																			---	---	---	---
MYO16	23026	broad.mit.edu	37	13	109680807	109680807	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:109680807delA	uc001vqt.1	+						MYO16_uc010agk.1_Intron|MYO16_uc001vqu.1_Intron|MYO16_uc010tjh.1_Intron	NM_015011	NP_055826			myosin heavy chain Myr 8						cerebellum development|negative regulation of cell proliferation|negative regulation of S phase of mitotic cell cycle	myosin complex|nucleoplasm|perinuclear region of cytoplasm|plasma membrane	actin filament binding|ATP binding|motor activity			ovary(6)|large_intestine(1)|kidney(1)|breast(1)|central_nervous_system(1)	10	all_lung(23;0.000332)|all_neural(89;0.00294)|Medulloblastoma(90;0.00596)|Lung NSC(43;0.00751)|Lung SC(71;0.104)		BRCA - Breast invasive adenocarcinoma(86;0.19)|all cancers(43;0.201)															---	---	---	---
MYO16	23026	broad.mit.edu	37	13	109700636	109700636	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:109700636delA	uc001vqt.1	+						MYO16_uc010agk.1_Intron|MYO16_uc001vqu.1_Intron|MYO16_uc010tjh.1_Intron	NM_015011	NP_055826			myosin heavy chain Myr 8						cerebellum development|negative regulation of cell proliferation|negative regulation of S phase of mitotic cell cycle	myosin complex|nucleoplasm|perinuclear region of cytoplasm|plasma membrane	actin filament binding|ATP binding|motor activity			ovary(6)|large_intestine(1)|kidney(1)|breast(1)|central_nervous_system(1)	10	all_lung(23;0.000332)|all_neural(89;0.00294)|Medulloblastoma(90;0.00596)|Lung NSC(43;0.00751)|Lung SC(71;0.104)		BRCA - Breast invasive adenocarcinoma(86;0.19)|all cancers(43;0.201)															---	---	---	---
MYO16	23026	broad.mit.edu	37	13	109737087	109737087	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:109737087delT	uc001vqt.1	+						MYO16_uc010agk.1_Intron|MYO16_uc010tjh.1_Intron	NM_015011	NP_055826			myosin heavy chain Myr 8						cerebellum development|negative regulation of cell proliferation|negative regulation of S phase of mitotic cell cycle	myosin complex|nucleoplasm|perinuclear region of cytoplasm|plasma membrane	actin filament binding|ATP binding|motor activity			ovary(6)|large_intestine(1)|kidney(1)|breast(1)|central_nervous_system(1)	10	all_lung(23;0.000332)|all_neural(89;0.00294)|Medulloblastoma(90;0.00596)|Lung NSC(43;0.00751)|Lung SC(71;0.104)		BRCA - Breast invasive adenocarcinoma(86;0.19)|all cancers(43;0.201)															---	---	---	---
MYO16	23026	broad.mit.edu	37	13	109793111	109793111	+	Frame_Shift_Del	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:109793111delC	uc001vqt.1	+	32	4611	c.4485delC	c.(4483-4485)TTCfs	p.F1495fs	MYO16_uc010agk.1_Frame_Shift_Del_p.F1517fs	NM_015011	NP_055826	Q9Y6X6	MYO16_HUMAN	myosin heavy chain Myr 8	1495	Pro-rich.				cerebellum development|negative regulation of cell proliferation|negative regulation of S phase of mitotic cell cycle	myosin complex|nucleoplasm|perinuclear region of cytoplasm|plasma membrane	actin filament binding|ATP binding|motor activity			ovary(6)|large_intestine(1)|kidney(1)|breast(1)|central_nervous_system(1)	10	all_lung(23;0.000332)|all_neural(89;0.00294)|Medulloblastoma(90;0.00596)|Lung NSC(43;0.00751)|Lung SC(71;0.104)		BRCA - Breast invasive adenocarcinoma(86;0.19)|all cancers(43;0.201)															---	---	---	---
Unknown	0	broad.mit.edu	37	13	109974686	109974686	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:109974686delA								MYO16 (114331 upstream) : IRS2 (431500 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	110223076	110223076	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:110223076delT								MYO16 (362721 upstream) : IRS2 (183110 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	110308605	110308605	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:110308605delA								MYO16 (448250 upstream) : IRS2 (97581 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	110521900	110521901	+	IGR	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:110521900_110521901delAA								IRS2 (82986 upstream) : COL4A1 (279410 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	111451470	111451470	+	IGR	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:111451470delG								ING1 (78050 upstream) : C13orf29 (64864 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	111462856	111462856	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:111462856delA								ING1 (89436 upstream) : C13orf29 (53478 downstream)																																			---	---	---	---
ANKRD10	55608	broad.mit.edu	37	13	111536253	111536253	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:111536253delA	uc001vrn.2	-						ANKRD10_uc001vrm.2_Intron|ANKRD10_uc001vrl.2_5'Flank	NM_017664	NP_060134			ankyrin repeat domain 10											central_nervous_system(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)		all cancers(43;0.0882)|BRCA - Breast invasive adenocarcinoma(86;0.188)|Lung(89;0.208)															---	---	---	---
ARHGEF7	8874	broad.mit.edu	37	13	111804528	111804531	+	Intron	DEL	AATT	-	-	rs77264894		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:111804528_111804531delAATT	uc001vrs.2	+						ARHGEF7_uc001vrr.2_Intron|ARHGEF7_uc001vrt.2_Intron|ARHGEF7_uc010tjn.1_5'Flank|ARHGEF7_uc001vru.1_5'Flank|ARHGEF7_uc001vrv.3_5'Flank|ARHGEF7_uc001vrw.3_5'Flank	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	112220395	112220396	+	IGR	DEL	AT	-	-	rs67112505		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:112220395_112220396delAT								C13orf16 (223802 upstream) : SOX1 (501517 downstream)																																			---	---	---	---
ATP11A	23250	broad.mit.edu	37	13	113473961	113473961	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:113473961delA	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)																---	---	---	---
TFDP1	7027	broad.mit.edu	37	13	114289228	114289229	+	Intron	DEL	GT	-	-	rs4150800	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:114289228_114289229delGT	uc001vtw.2	+						TFDP1_uc010tkd.1_Intron|TFDP1_uc010tke.1_Intron|TFDP1_uc001vty.3_Intron|TFDP1_uc001vtx.2_Intron	NM_007111	NP_009042			transcription factor Dp-1						cell proliferation|G1 phase of mitotic cell cycle|G1/S transition of mitotic cell cycle|regulation of transcription from RNA polymerase II promoter	transcription factor complex	DNA binding|protein domain specific binding|sequence-specific DNA binding transcription factor activity|transcription coactivator activity|transcription factor binding			lung(4)|ovary(2)|skin(1)	7	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;0.132)|all_epithelial(44;0.0731)|all_lung(25;0.149)|Breast(118;0.153)	all cancers(43;0.0576)												TSP Lung(29;0.18)			---	---	---	---
RASA3	22821	broad.mit.edu	37	13	114884653	114884653	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:114884653delA	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)															---	---	---	---
UPF3A	65110	broad.mit.edu	37	13	115057211	115057211	+	Frame_Shift_Del	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:115057211delA	uc001vup.2	+	7	827	c.790delA	c.(790-792)AAAfs	p.K264fs	UPF3A_uc001vuq.2_Frame_Shift_Del_p.K231fs|UPF3A_uc001vus.2_RNA|UPF3A_uc001vur.2_RNA|UPF3A_uc001vut.2_Frame_Shift_Del_p.K63fs|UPF3A_uc001vuu.2_5'UTR	NM_023011	NP_075387	Q9H1J1	REN3A_HUMAN	UPF3 regulator of nonsense transcripts homolog A	264					mRNA transport|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay|positive regulation of translation	cytoplasm|nucleus|plasma membrane	nucleocytoplasmic transporter activity|nucleotide binding|protein binding|RNA binding			skin(1)	1	Lung NSC(43;0.00299)|all_neural(89;0.0337)|Medulloblastoma(90;0.163)|Lung SC(71;0.218)	all_cancers(25;0.0191)|all_epithelial(44;0.00716)|all_lung(25;0.0173)|Lung NSC(25;0.0634)|Breast(118;0.238)	BRCA - Breast invasive adenocarcinoma(86;0.0886)	OV - Ovarian serous cystadenocarcinoma(48;0.195)|Epithelial(10;0.2)														---	---	---	---
Unknown	0	broad.mit.edu	37	13	115109319	115109320	+	IGR	DEL	AT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:115109319_115109320delAT								ZNF828 (16517 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	19034958	19034958	+	IGR	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:19034958delG								None (None upstream) : OR11H12 (342636 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	19052832	19052832	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:19052832delA								None (None upstream) : OR11H12 (324762 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	19106110	19106110	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:19106110delA								None (None upstream) : OR11H12 (271484 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	19432658	19432658	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:19432658delA								OR11H12 (54086 upstream) : POTEG (120707 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	19635412	19635413	+	Intron	INS	-	T	T	rs139189873	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:19635412_19635413insT	uc001vvi.2	+											Homo sapiens prostate-specific P775P mRNA sequence.																														---	---	---	---
Unknown	0	broad.mit.edu	37	14	19656071	19656071	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:19656071delT	uc001vvk.1	+						uc001vvl.3_Intron					Homo sapiens cDNA FLJ12852 fis, clone NT2RP2003445.																														---	---	---	---
Unknown	0	broad.mit.edu	37	14	19747418	19747418	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:19747418delA								POTEG (162476 upstream) : P704P (236536 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	19930412	19930412	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:19930412delA								POTEG (345470 upstream) : P704P (53542 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	20716748	20716748	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:20716748delA								OR11H4 (4824 upstream) : TTC5 (40555 downstream)																																			---	---	---	---
PARP2	10038	broad.mit.edu	37	14	20820570	20820570	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:20820570delA	uc001vxc.2	+						PARP2_uc001vxd.2_Intron|PARP2_uc001vxb.1_Intron|PARP2_uc010tle.1_5'Flank	NM_005484	NP_005475			poly (ADP-ribose) polymerase family, member 2						protein ADP-ribosylation	nucleolus|nucleoplasm	DNA binding|NAD+ ADP-ribosyltransferase activity			ovary(1)|pancreas(1)	2	all_cancers(95;0.00092)	all_lung(585;0.235)	Epithelial(56;5.34e-07)|all cancers(55;3.7e-06)	GBM - Glioblastoma multiforme(265;0.00888)|READ - Rectum adenocarcinoma(17;0.0649)									Direct_reversal_of_damage|PARP_enzymes_that_bind_to_DNA					---	---	---	---
Unknown	0	broad.mit.edu	37	14	21130877	21130879	+	IGR	DEL	TTT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:21130877_21130879delTTT								OR6S1 (21027 upstream) : ANG (21457 downstream)																																			---	---	---	---
ZNF219	51222	broad.mit.edu	37	14	21561604	21561604	+	Intron	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:21561604delG	uc001vzr.2	-						ZNF219_uc001vzs.2_Intron|ZNF219_uc010aik.1_Intron	NM_016423	NP_057507			zinc finger protein 219						negative regulation of transcription, DNA-dependent	integral to membrane|nucleus	DNA binding|histamine receptor activity|protein binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			central_nervous_system(1)	1	all_cancers(95;0.00185)		OV - Ovarian serous cystadenocarcinoma(11;9.86e-11)|Epithelial(56;1.27e-08)|all cancers(55;6.06e-08)	GBM - Glioblastoma multiforme(265;0.0191)												OREG0022565	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	21750402	21750403	+	IGR	DEL	TT	-	-	rs113876880		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:21750402_21750403delTT								HNRNPC (12764 upstream) : RPGRIP1 (5733 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	22046138	22046138	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:22046138delA								OR10G3 (7263 upstream) : OR10G2 (55929 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	22231865	22231865	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:22231865delA	uc010tmf.1	+											SubName: Full=Putative uncharacterized protein ENSP00000374943;																														---	---	---	---
Unknown	0	broad.mit.edu	37	14	22409538	22409540	+	Intron	DEL	TCT	-	-	rs2178778		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:22409538_22409540delTCT	uc001wbw.2	+						uc010tmg.1_Intron|uc010tmh.1_Intron|uc010aiv.1_Intron|uc010tmi.1_Intron|uc010tmj.1_Intron|uc010aja.1_Intron|uc010ajb.1_Intron|uc001wck.2_Intron					SubName: Full=Alpha-chain C region; Flags: Fragment;																														---	---	---	---
Unknown	0	broad.mit.edu	37	14	22467730	22467730	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:22467730delT	uc001wbw.2	+						uc010tmh.1_Intron|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|uc010ajd.1_Intron					SubName: Full=Alpha-chain C region; Flags: Fragment;																														---	---	---	---
Unknown	0	broad.mit.edu	37	14	22771930	22771930	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:22771930delA	uc001wbw.2	+						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|uc001wdf.2_Intron|uc010ajk.1_Intron|uc001wdg.1_Intron|uc010ajl.1_Intron|uc001wdj.2_Intron|uc010ajo.1_Intron|uc010ajp.1_Intron|uc010ajq.1_5'UTR					SubName: Full=Alpha-chain C region; Flags: Fragment;																														---	---	---	---
Unknown	0	broad.mit.edu	37	14	23083079	23083079	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:23083079delT								ABHD4 (1822 upstream) : OXA1L (152652 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	23362131	23362141	+	IGR	DEL	CCAGCCCCTGC	-	-	rs3830997		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:23362131_23362141delCCAGCCCCTGC								REM2 (5242 upstream) : RBM23 (7714 downstream)																																			---	---	---	---
HAUS4	54930	broad.mit.edu	37	14	23415991	23415998	+	Intron	DEL	TTTTTTTT	-	-	rs147170987		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:23415991_23415998delTTTTTTTT	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	23678967	23678969	+	IGR	DEL	AAC	-	-	rs111496824		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:23678967_23678969delAAC								SLC7A8 (26118 upstream) : HOMEZ (63875 downstream)																																			---	---	---	---
HOMEZ	57594	broad.mit.edu	37	14	23768659	23768661	+	5'UTR	DEL	CTT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:23768659_23768661delCTT	uc001wjb.2	-	1					PPP1R3E_uc001wjc.2_RNA	NM_020834	NP_065885			homeodomain leucine zipper protein							nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity				0	all_cancers(95;5.54e-06)			GBM - Glioblastoma multiforme(265;0.00643)														---	---	---	---
PABPN1	8106	broad.mit.edu	37	14	23794352	23794352	+	Intron	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:23794352delC	uc001wjk.2	+						PABPN1_uc001wjh.3_Intron|PABPN1_uc001wjj.2_3'UTR	NM_004643	NP_004634			poly(A) binding protein, nuclear 1						modification by virus of host mRNA processing|mRNA 3'-end processing|muscle contraction|nuclear mRNA splicing, via spliceosome|poly(A)+ mRNA export from nucleus|termination of RNA polymerase II transcription|viral infectious cycle	cytoplasm|nucleoplasm|ribonucleoprotein complex	nucleotide binding|protein binding|RNA binding			ovary(2)	2	all_cancers(95;6.69e-06)			GBM - Glioblastoma multiforme(265;0.00643)														---	---	---	---
Unknown	0	broad.mit.edu	37	14	24075879	24075880	+	IGR	INS	-	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:24075879_24075880insA								JPH4 (27870 upstream) : DHRS2 (23444 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	24219150	24219150	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:24219150delA								DHRS2 (104304 upstream) : C14orf165 (172309 downstream)																																			---	---	---	---
NRL	4901	broad.mit.edu	37	14	24580356	24580356	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:24580356delT	uc001wlq.2	-							NM_006177	NP_006168			neural retina leucine zipper						response to stimulus|transcription from RNA polymerase II promoter|visual perception	nucleus	leucine zipper domain binding|sequence-specific DNA binding				0				GBM - Glioblastoma multiforme(265;0.0181)														---	---	---	---
TM9SF1	10548	broad.mit.edu	37	14	24667820	24667820	+	5'Flank	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:24667820delT	uc001wnb.1	-						TM9SF1_uc010toa.1_5'Flank|TM9SF1_uc001wna.1_5'Flank|TM9SF1_uc010tob.1_Intron|TM9SF1_uc001wnc.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)														---	---	---	---
Unknown	0	broad.mit.edu	37	14	24751086	24751086	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:24751086delT								RABGGTA (10283 upstream) : DHRS1 (8720 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	25073263	25073264	+	IGR	DEL	AC	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:25073263_25073264delAC								CTSG (27797 upstream) : GZMH (2429 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	26489584	26489584	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:26489584delT								STXBP6 (970413 upstream) : NOVA1 (425506 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	27124679	27124679	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:27124679delT								NOVA1 (57719 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	28206092	28206092	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:28206092delT								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	28361122	28361123	+	IGR	DEL	TA	-	-	rs113460368		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:28361122_28361123delTA								None (None upstream) : FOXG1 (875164 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	28573017	28573017	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:28573017delA								None (None upstream) : FOXG1 (663270 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	28772957	28772958	+	IGR	DEL	GA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:28772957_28772958delGA								None (None upstream) : FOXG1 (463329 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	29188035	29188038	+	IGR	DEL	AATA	-	-	rs66474621		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:29188035_29188038delAATA								None (None upstream) : FOXG1 (48249 downstream)																																			---	---	---	---
PRKD1	5587	broad.mit.edu	37	14	30276935	30276935	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:30276935delT	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	30729662	30729663	+	IGR	DEL	AC	-	-	rs34923007		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:30729662_30729663delAC								PRKD1 (332763 upstream) : G2E3 (298666 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	30801074	30801074	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:30801074delT								PRKD1 (404175 upstream) : G2E3 (227255 downstream)																																			---	---	---	---
G2E3	55632	broad.mit.edu	37	14	31056997	31056998	+	Intron	DEL	AG	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:31056997_31056998delAG	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																		---	---	---	---
Unknown	0	broad.mit.edu	37	14	31239005	31239005	+	IGR	DEL	A	-	-	rs71443389		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:31239005delA								SCFD1 (33987 upstream) : COCH (104736 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	31309660	31309661	+	IGR	DEL	GA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:31309660_31309661delGA								SCFD1 (104642 upstream) : COCH (34080 downstream)																																			---	---	---	---
STRN3	29966	broad.mit.edu	37	14	31420163	31420163	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:31420163delA	uc001wqu.2	-						STRN3_uc001wqv.2_Intron|STRN3_uc010tpj.1_Intron	NM_001083893	NP_001077362			nuclear autoantigen isoform 1						negative regulation of estrogen receptor signaling pathway|negative regulation of transcription from RNA polymerase II promoter|positive regulation of transcription from RNA polymerase II promoter|response to estradiol stimulus	cytoplasm|dendrite|Golgi apparatus|neuronal cell body|nucleoplasm|nucleus|plasma membrane|protein complex	armadillo repeat domain binding|calmodulin binding|protein complex binding|protein phosphatase 2A binding|sequence-specific DNA binding transcription factor activity				0	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;0.0124)														---	---	---	---
HECTD1	25831	broad.mit.edu	37	14	31641344	31641344	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:31641344delA	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)														---	---	---	---
HECTD1	25831	broad.mit.edu	37	14	31669989	31669991	+	Intron	DEL	AAA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:31669989_31669991delAAA	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	31936084	31936084	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:31936084delT								HEATR5A (9404 upstream) : NUBPL (94507 downstream)																																			---	---	---	---
NUBPL	80224	broad.mit.edu	37	14	32059466	32059467	+	Intron	INS	-	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:32059466_32059467insA	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	32562766	32562766	+	Frame_Shift_Del	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:32562766delT	uc001wrl.2	+	2	3130	c.2891delT	c.(2890-2892)GTTfs	p.V964fs	ARHGAP5_uc001wrm.2_Frame_Shift_Del_p.V964fs|ARHGAP5_uc001wrn.2_Frame_Shift_Del_p.V964fs|ARHGAP5_uc001wro.2_Intron|ARHGAP5_uc001wrp.2_Intron	NM_001173	NP_001025226	Q13017	RHG05_HUMAN	Rho GTPase activating protein 5 isoform b	964					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	32647328	32647328	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:32647328delT								ARHGAP5 (18396 upstream) : AKAP6 (151151 downstream)																																			---	---	---	---
AKAP6	9472	broad.mit.edu	37	14	33198481	33198481	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:33198481delA	uc001wrq.2	+						AKAP6_uc010aml.2_Intron	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)														---	---	---	---
AKAP6	9472	broad.mit.edu	37	14	33294194	33294194	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-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	33855719	33855719	+	Intron	DEL	T	-	-	rs150733697		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:33855719delT	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	34568474	34568474	+	IGR	DEL	T	-	-	rs113211934		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:34568474delT								EGLN3 (148187 upstream) : C14orf147 (333671 downstream)																																			---	---	---	---
EAPP	55837	broad.mit.edu	37	14	34985336	34985336	+	3'UTR	DEL	A	-	-	rs144603764		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:34985336delA	uc001wsd.1	-	6						NM_018453	NP_060923			E2F-associated phosphoprotein						negative regulation of transcription elongation from RNA polymerase II promoter|positive regulation of cell proliferation|positive regulation of transcription elongation from RNA polymerase II promoter	Golgi apparatus|nucleus|plasma membrane				ovary(1)	1	Breast(36;0.0473)|Hepatocellular(127;0.158)		LUAD - Lung adenocarcinoma(48;0.00169)|Lung(238;0.00342)|Epithelial(34;0.18)	GBM - Glioblastoma multiforme(112;0.0196)														---	---	---	---
SNX6	58533	broad.mit.edu	37	14	35065424	35065424	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:35065424delA	uc001wsf.1	-						SNX6_uc001wse.1_Intron|SNX6_uc010tpm.1_Intron|SNX6_uc010amm.1_Intron	NM_152233	NP_689419			sorting nexin 6 isoform b						cell communication|intracellular protein transport|negative regulation of epidermal growth factor receptor activity|negative regulation of transcription, DNA-dependent|negative regulation of transforming growth factor beta receptor signaling pathway|retrograde transport, endosome to Golgi	cytoplasmic vesicle membrane|early endosome membrane|nucleus	phosphatidylinositol binding|protein homodimerization activity				0	Breast(36;0.0473)|Hepatocellular(127;0.158)		LUAD - Lung adenocarcinoma(48;0.00169)|Lung(238;0.00199)|Epithelial(34;0.187)	GBM - Glioblastoma multiforme(112;0.0245)														---	---	---	---
SNX6	58533	broad.mit.edu	37	14	35092481	35092481	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:35092481delA	uc001wsf.1	-						SNX6_uc001wse.1_Intron|SNX6_uc010tpm.1_Intron|SNX6_uc010amm.1_Intron	NM_152233	NP_689419			sorting nexin 6 isoform b						cell communication|intracellular protein transport|negative regulation of epidermal growth factor receptor activity|negative regulation of transcription, DNA-dependent|negative regulation of transforming growth factor beta receptor signaling pathway|retrograde transport, endosome to Golgi	cytoplasmic vesicle membrane|early endosome membrane|nucleus	phosphatidylinositol binding|protein homodimerization activity				0	Breast(36;0.0473)|Hepatocellular(127;0.158)		LUAD - Lung adenocarcinoma(48;0.00169)|Lung(238;0.00199)|Epithelial(34;0.187)	GBM - Glioblastoma multiforme(112;0.0245)														---	---	---	---
BAZ1A	11177	broad.mit.edu	37	14	35294239	35294239	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:35294239delT	uc001wsk.2	-						BAZ1A_uc001wsl.2_Intron|BAZ1A_uc001wsm.1_Intron	NM_013448	NP_038476			bromodomain adjacent to zinc finger domain, 1A						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)														---	---	---	---
SRP54	6729	broad.mit.edu	37	14	35468028	35468028	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:35468028delA	uc001wso.2	+						SRP54_uc010tpp.1_Intron|SRP54_uc010tpq.1_Intron	NM_003136	NP_003127			signal recognition particle 54kDa isoform 1						GTP catabolic process|response to drug|SRP-dependent cotranslational protein targeting to membrane, signal sequence recognition|SRP-dependent cotranslational protein targeting to membrane, translocation	cytosol|nuclear speck|signal recognition particle, endoplasmic reticulum targeting	7S RNA binding|drug binding|endoplasmic reticulum signal peptide binding|GDP binding|GTP binding|nucleoside-triphosphatase activity|ribonucleoprotein binding			ovary(1)	1	Breast(36;0.0545)|Hepatocellular(127;0.158)		LUAD - Lung adenocarcinoma(48;2.48e-05)|Lung(238;3.13e-05)|Epithelial(34;0.0314)|all cancers(34;0.0797)|BRCA - Breast invasive adenocarcinoma(188;0.243)	GBM - Glioblastoma multiforme(112;0.0396)														---	---	---	---
SRP54	6729	broad.mit.edu	37	14	35470316	35470316	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:35470316delT	uc001wso.2	+						SRP54_uc010tpp.1_Intron|SRP54_uc010tpq.1_Intron	NM_003136	NP_003127			signal recognition particle 54kDa isoform 1						GTP catabolic process|response to drug|SRP-dependent cotranslational protein targeting to membrane, signal sequence recognition|SRP-dependent cotranslational protein targeting to membrane, translocation	cytosol|nuclear speck|signal recognition particle, endoplasmic reticulum targeting	7S RNA binding|drug binding|endoplasmic reticulum signal peptide binding|GDP binding|GTP binding|nucleoside-triphosphatase activity|ribonucleoprotein binding			ovary(1)	1	Breast(36;0.0545)|Hepatocellular(127;0.158)		LUAD - Lung adenocarcinoma(48;2.48e-05)|Lung(238;3.13e-05)|Epithelial(34;0.0314)|all cancers(34;0.0797)|BRCA - Breast invasive adenocarcinoma(188;0.243)	GBM - Glioblastoma multiforme(112;0.0396)														---	---	---	---
KIAA0391	9692	broad.mit.edu	37	14	35594078	35594079	+	Intron	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:35594078_35594079delTT	uc001wsy.1	+						KIAA0391_uc010tps.1_Intron|KIAA0391_uc001wsz.1_Intron|KIAA0391_uc001wta.2_Intron|KIAA0391_uc001wtb.1_Intron|KIAA0391_uc001wtc.1_Intron|PPP2R3C_uc001wss.2_5'Flank|PPP2R3C_uc001wst.2_5'Flank|PPP2R3C_uc010tpr.1_5'Flank|PPP2R3C_uc001wsu.2_5'Flank|PPP2R3C_uc010amn.1_5'Flank|PPP2R3C_uc001wsw.2_5'Flank|PPP2R3C_uc001wsx.1_5'Flank	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)														---	---	---	---
Unknown	0	broad.mit.edu	37	14	35943645	35943647	+	IGR	DEL	CTT	-	-	rs4595711		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:35943645_35943647delCTT								NFKBIA (69685 upstream) : INSM2 (59601 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	35951649	35951651	+	IGR	DEL	TTT	-	-	rs67001606		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:35951649_35951651delTTT								NFKBIA (77689 upstream) : INSM2 (51597 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	35986421	35986421	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:35986421delA								NFKBIA (112461 upstream) : INSM2 (16827 downstream)																																			---	---	---	---
RALGAPA1	253959	broad.mit.edu	37	14	36191820	36191822	+	Intron	DEL	AAA	-	-	rs74584343		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:36191820_36191822delAAA	uc001wti.2	-						RALGAPA1_uc001wtj.2_Intron|RALGAPA1_uc010tpv.1_Intron|RALGAPA1_uc010tpw.1_Intron|RALGAPA1_uc001wtk.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																		---	---	---	---
BRMS1L	84312	broad.mit.edu	37	14	36328321	36328322	+	Intron	INS	-	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:36328321_36328322insT	uc001wtl.2	+						BRMS1L_uc010tpx.1_Intron	NM_032352	NP_115728			breast cancer metastasis-suppressor 1-like						regulation of growth|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus				skin(1)	1	Breast(36;0.137)|Hepatocellular(127;0.158)		Lung(8;1.7e-07)|LUAD - Lung adenocarcinoma(9;3e-07)|Epithelial(34;0.00467)|all cancers(34;0.0157)|BRCA - Breast invasive adenocarcinoma(188;0.158)	GBM - Glioblastoma multiforme(112;0.0333)														---	---	---	---
Unknown	0	broad.mit.edu	37	14	36705881	36705881	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:36705881delA								BRMS1L (364713 upstream) : MBIP (61883 downstream)																																			---	---	---	---
SLC25A21	89874	broad.mit.edu	37	14	37637080	37637080	+	Intron	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:37637080delC	uc001wtz.1	-							NM_030631	NP_085134			solute carrier family 25 (mitochondrial						lysine catabolic process	integral to membrane|mitochondrial inner membrane	alpha-ketoglutarate transmembrane transporter activity|binding			skin(1)	1	Esophageal squamous(585;0.164)|Breast(36;0.179)|Hepatocellular(127;0.213)		Lung(8;2.16e-08)|LUAD - Lung adenocarcinoma(9;2.16e-07)|Epithelial(34;0.0112)|all cancers(34;0.0274)|LUSC - Lung squamous cell carcinoma(13;0.149)	GBM - Glioblastoma multiforme(112;0.00204)														---	---	---	---
MIPOL1	145282	broad.mit.edu	37	14	37785724	37785724	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:37785724delT	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	38030814	38030817	+	IGR	DEL	GTGT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:38030814_38030817delGTGT								MIPOL1 (13949 upstream) : FOXA1 (28376 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	38338849	38338849	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:38338849delT	uc001wug.2	+											Homo sapiens chromosome 14 open reading frame 25, mRNA (cDNA clone IMAGE:5268731), partial cds.																														---	---	---	---
Unknown	0	broad.mit.edu	37	14	38416151	38416152	+	Intron	INS	-	G	G	rs149839863	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:38416151_38416152insG	uc001wug.2	+											Homo sapiens chromosome 14 open reading frame 25, mRNA (cDNA clone IMAGE:5268731), partial cds.																														---	---	---	---
Unknown	0	broad.mit.edu	37	14	38798779	38798779	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:38798779delT								CLEC14A (73205 upstream) : SEC23A (702344 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	39082628	39082629	+	IGR	DEL	TT	-	-	rs79955671		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:39082628_39082629delTT								CLEC14A (357054 upstream) : SEC23A (418494 downstream)																																			---	---	---	---
SEC23A	10484	broad.mit.edu	37	14	39573672	39573672	+	5'Flank	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:39573672delA	uc001wup.1	-						SEC23A_uc010tqa.1_5'Flank|SEC23A_uc010tqb.1_5'Flank	NM_006364	NP_006355			SEC23-related protein A						COPII vesicle coating|intracellular protein transport|post-translational protein modification|protein N-linked glycosylation via asparagine	COPII vesicle coat|cytosol|Golgi membrane|smooth endoplasmic reticulum membrane	protein binding|zinc ion binding			ovary(4)|upper_aerodigestive_tract(1)	5	Hepatocellular(127;0.213)		Lung(238;0.00047)|LUAD - Lung adenocarcinoma(48;0.000565)	GBM - Glioblastoma multiforme(112;0.0151)														---	---	---	---
SIP1	8487	broad.mit.edu	37	14	39583926	39583926	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:39583926delT	uc001wuq.2	+						SIP1_uc001wur.2_Intron|SIP1_uc001wus.2_Intron|SIP1_uc010amx.2_Intron	NM_003616	NP_003607			SMN-interacting protein 1 isoform alpha						ncRNA metabolic process|spliceosomal snRNP assembly|spliceosome assembly	Cajal body|cytosol|spliceosomal complex	protein binding				0	Hepatocellular(127;0.213)		Lung(238;0.00047)|LUAD - Lung adenocarcinoma(48;0.000565)	GBM - Glioblastoma multiforme(112;0.0121)														---	---	---	---
TRAPPC6B	122553	broad.mit.edu	37	14	39623315	39623315	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:39623315delA	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	39696613	39696614	+	IGR	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:39696613_39696614delAA								PNN (44192 upstream) : MIA2 (6511 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	39834690	39834690	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:39834690delT								CTAGE5 (14295 upstream) : FBXO33 (32188 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	40688527	40688527	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:40688527delT								FBXO33 (786823 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	40816930	40816931	+	IGR	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:40816930_40816931delTT								FBXO33 (915226 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	41006198	41006198	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:41006198delA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	41066221	41066222	+	IGR	DEL	TG	-	-	rs3031149		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:41066221_41066222delTG								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	41301361	41301361	+	IGR	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:41301361delC								None (None upstream) : LRFN5 (775403 downstream)																																			---	---	---	---
LRFN5	145581	broad.mit.edu	37	14	42322574	42322574	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:42322574delA	uc001wvm.2	+						LRFN5_uc010ana.2_Intron	NM_152447	NP_689660			leucine rich repeat and fibronectin type III							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)			---	---	---	---
Unknown	0	broad.mit.edu	37	14	42525924	42525924	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:42525924delA								LRFN5 (152174 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	43521362	43521362	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:43521362delT								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	43809170	43809170	+	IGR	DEL	A	-	-	rs72297218		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:43809170delA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	43809432	43809432	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:43809432delT								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	44195626	44195626	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:44195626delA								None (None upstream) : FSCB (777729 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	44622908	44622908	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:44622908delA								None (None upstream) : FSCB (350447 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	44760816	44760816	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:44760816delA								None (None upstream) : FSCB (212539 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	44843365	44843365	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:44843365delA								None (None upstream) : FSCB (129990 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	44989468	44989468	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:44989468delT								FSCB (12969 upstream) : C14orf28 (377039 downstream)																																			---	---	---	---
FAM179B	23116	broad.mit.edu	37	14	45444979	45444979	+	Intron	DEL	T	-	-	rs113316910		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:45444979delT	uc001wvv.2	+						FAM179B_uc001wvw.2_Intron|FAM179B_uc010anc.2_Intron|FAM179B_uc010anb.1_Intron|FAM179B_uc001wvu.2_Intron	NM_015091	NP_055906			hypothetical protein LOC23116								binding			skin(2)|upper_aerodigestive_tract(1)	3																		---	---	---	---
FAM179B	23116	broad.mit.edu	37	14	45467006	45467007	+	Intron	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:45467006_45467007delAA	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																		---	---	---	---
PRPF39	55015	broad.mit.edu	37	14	45564346	45564346	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:45564346delT	uc001wvz.3	+						PRPF39_uc001wvy.3_Intron|PRPF39_uc010and.2_Intron	NM_017922	NP_060392			PRP39 pre-mRNA processing factor 39 homolog						mRNA processing|RNA splicing	nucleus	binding			ovary(1)|breast(1)	2																		---	---	---	---
FANCM	57697	broad.mit.edu	37	14	45609820	45609820	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:45609820delT	uc001wwd.3	+						FANCM_uc001wwc.2_Intron|FANCM_uc010anf.2_Intron	NM_020937	NP_065988			Fanconi anemia, complementation group M						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				---	---	---	---
Unknown	0	broad.mit.edu	37	14	46712481	46712481	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:46712481delT								C14orf106 (989876 upstream) : RPL10L (407741 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	46873068	46873068	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:46873068delA								None (None upstream) : RPL10L (247154 downstream)																																			---	---	---	---
MDGA2	161357	broad.mit.edu	37	14	47415597	47415598	+	Intron	DEL	AA	-	-	rs76308236		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:47415597_47415598delAA	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																		---	---	---	---
MDGA2	161357	broad.mit.edu	37	14	47776895	47776895	+	Intron	DEL	A	-	-	rs113956118		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:47776895delA	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																		---	---	---	---
MDGA2	161357	broad.mit.edu	37	14	47888516	47888516	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:47888516delT	uc001wwj.3	-						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																		---	---	---	---
Unknown	0	broad.mit.edu	37	14	49303305	49303305	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:49303305delA								None (None upstream) : SDCCAG1 (729722 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	49414438	49414447	+	IGR	DEL	GTGTGTGTGT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:49414438_49414447delGTGTGTGTGT								None (None upstream) : SDCCAG1 (618580 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	49426342	49426343	+	IGR	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:49426342_49426343delAA								None (None upstream) : SDCCAG1 (606684 downstream)																																			---	---	---	---
SDCCAG1	9147	broad.mit.edu	37	14	50308824	50308824	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:50308824delA	uc001wxc.2	-						SDCCAG1_uc010anj.1_Intron|SDCCAG1_uc010tqi.1_Intron|SDCCAG1_uc001wxe.2_Intron|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)														---	---	---	---
C14orf182	283551	broad.mit.edu	37	14	50470550	50470551	+	Intron	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:50470550_50470551delTT	uc001wxi.1	-						uc010tqj.1_5'Flank	NM_001012706	NP_001012724			hypothetical protein LOC283551												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	14	50487481	50487481	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:50487481delT								C14orf182 (13243 upstream) : C14orf183 (62889 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	50511087	50511087	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:50511087delT								C14orf182 (36849 upstream) : C14orf183 (39283 downstream)																																			---	---	---	---
SOS2	6655	broad.mit.edu	37	14	50670810	50670810	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:50670810delT	uc001wxs.3	-						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)																	---	---	---	---
NIN	51199	broad.mit.edu	37	14	51227156	51227166	+	Intron	DEL	TTTTTTTTTTT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:51227156_51227166delTTTTTTTTTTT	uc001wym.2	-						NIN_uc001wyi.2_Intron|NIN_uc001wyj.2_Intron|NIN_uc001wyk.2_Intron|NIN_uc010tqp.1_Intron|NIN_uc001wyo.2_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	51764060	51764060	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:51764060delA								TMX1 (39690 upstream) : FRMD6 (191795 downstream)																																			---	---	---	---
FRMD6	122786	broad.mit.edu	37	14	52132127	52132127	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:52132127delT	uc001wzd.2	+						FRMD6_uc001wzb.2_Intron|FRMD6_uc001wzc.2_Intron	NM_152330	NP_689543			FERM domain containing 6							cytoskeleton|mitochondrion|plasma membrane	binding			ovary(1)|breast(1)|central_nervous_system(1)	3	all_epithelial(31;0.0163)|Breast(41;0.089)																	---	---	---	---
C14orf166	51637	broad.mit.edu	37	14	52455393	52455394	+	5'Flank	DEL	CT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:52455393_52455394delCT	uc010aod.2	+							NM_016039	NP_057123			homeobox prox 1							microtubule organizing center|nucleus|perinuclear region of cytoplasm|tRNA-splicing ligase complex	identical protein binding				0	Breast(41;0.0639)|all_epithelial(31;0.101)																	---	---	---	---
Unknown	0	broad.mit.edu	37	14	52761455	52761455	+	IGR	DEL	T	-	-	rs78616910		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:52761455delT								PTGDR (18014 upstream) : PTGER2 (19561 downstream)																																			---	---	---	---
GPR137C	283554	broad.mit.edu	37	14	53101641	53101641	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:53101641delT	uc001wzu.3	+						GPR137C_uc001wzt.3_Intron	NM_001099652	NP_001093122			G protein-coupled receptor 137C							integral to membrane					0	Breast(41;0.0716)																	---	---	---	---
Unknown	0	broad.mit.edu	37	14	53278319	53278322	+	IGR	DEL	TTTT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:53278319_53278322delTTTT								GNPNAT1 (19933 upstream) : FERMT2 (45668 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	53941031	53941031	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:53941031delT								DDHD1 (320985 upstream) : BMP4 (475426 downstream)																																			---	---	---	---
SAMD4A	23034	broad.mit.edu	37	14	55118023	55118023	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:55118023delT	uc001xbb.2	+						SAMD4A_uc001xba.2_Intron|SAMD4A_uc001xbc.2_Intron	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	55207413	55207413	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:55207413delT	uc001xbb.2	+						SAMD4A_uc001xbc.2_Intron	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																		---	---	---	---
WDHD1	11169	broad.mit.edu	37	14	55408168	55408168	+	3'UTR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:55408168delA	uc001xbm.1	-	26					WDHD1_uc010aom.1_3'UTR|WDHD1_uc001xbn.1_3'UTR	NM_007086	NP_009017			WD repeat and HMG-box DNA binding protein 1							cytoplasm|nucleoplasm	DNA binding			skin(1)	1																		---	---	---	---
WDHD1	11169	broad.mit.edu	37	14	55445883	55445883	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:55445883delT	uc001xbm.1	-						WDHD1_uc010aom.1_Intron|WDHD1_uc001xbn.1_Intron	NM_007086	NP_009017			WD repeat and HMG-box DNA binding protein 1							cytoplasm|nucleoplasm	DNA binding			skin(1)	1																		---	---	---	---
WDHD1	11169	broad.mit.edu	37	14	55473950	55473954	+	Intron	DEL	AAAAA	-	-	rs9806068		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:55473950_55473954delAAAAA	uc001xbm.1	-						WDHD1_uc001xbn.1_Intron	NM_007086	NP_009017			WD repeat and HMG-box DNA binding protein 1							cytoplasm|nucleoplasm	DNA binding			skin(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	14	55701368	55701368	+	IGR	DEL	T	-	-	rs139671626	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:55701368delT								DLGAP5 (42972 upstream) : FBXO34 (36653 downstream)																																			---	---	---	---
KIAA0831	22863	broad.mit.edu	37	14	55837364	55837364	+	Intron	DEL	T	-	-	rs72140162		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:55837364delT	uc001xbx.1	-						FBXO34_uc001xbv.2_Intron|KIAA0831_uc001xbw.1_Intron	NM_014924	NP_055739			Barkor						autophagic vacuole assembly|positive regulation of autophagy	autophagic vacuole|endoplasmic reticulum|pre-autophagosomal structure membrane	protein binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	14	55936578	55936578	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:55936578delT								TBPL2 (29315 upstream) : C14orf33 (88112 downstream)																																			---	---	---	---
C14orf33	100129075	broad.mit.edu	37	14	56044659	56044660	+	Intron	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:56044659_56044660delTT	uc001xbz.2	-						KTN1_uc001xce.2_5'Flank|KTN1_uc001xcb.2_5'Flank|KTN1_uc001xcc.2_5'Flank|KTN1_uc001xcd.2_5'Flank|KTN1_uc010trb.1_5'Flank|C14orf33_uc001xca.2_Intron|C14orf33_uc010aop.2_Intron					Homo sapiens cDNA FLJ42937 fis, clone BRSSN2014556.												0																		---	---	---	---
KTN1	3895	broad.mit.edu	37	14	56048160	56048161	+	Intron	DEL	GG	-	-	rs149329005	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:56048160_56048161delGG	uc001xcb.2	+						KTN1_uc001xce.2_Intron|KTN1_uc001xcc.2_Intron|KTN1_uc001xcd.2_Intron|KTN1_uc010trb.1_Intron|C14orf33_uc001xbz.2_5'Flank|C14orf33_uc001xca.2_5'Flank|C14orf33_uc010aop.2_5'Flank	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								---	---	---	---
KTN1	3895	broad.mit.edu	37	14	56150981	56150981	+	3'UTR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:56150981delA	uc001xcb.2	+	46					KTN1_uc001xce.2_3'UTR|KTN1_uc001xcc.2_3'UTR|KTN1_uc001xcd.2_3'UTR|KTN1_uc010trb.1_3'UTR|KTN1_uc010aoq.2_3'UTR|KTN1_uc010trc.1_3'UTR|KTN1_uc001xcg.2_3'UTR	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								---	---	---	---
Unknown	0	broad.mit.edu	37	14	56218133	56218134	+	IGR	DEL	TT	-	-	rs111626121		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:56218133_56218134delTT								KTN1 (66832 upstream) : RPL13AP3 (14829 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	56416477	56416477	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:56416477delA								C14orf34 (153085 upstream) : PELI2 (168616 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	56513992	56513992	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:56513992delT								C14orf34 (250600 upstream) : PELI2 (71101 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	56519958	56519958	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:56519958delA								C14orf34 (256566 upstream) : PELI2 (65135 downstream)																																			---	---	---	---
PELI2	57161	broad.mit.edu	37	14	56594792	56594792	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:56594792delA	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	56834744	56834745	+	IGR	INS	-	T	T	rs148758748	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:56834744_56834745insT								PELI2 (66714 upstream) : C14orf101 (211593 downstream)																																			---	---	---	---
EXOC5	10640	broad.mit.edu	37	14	57689192	57689192	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:57689192delT	uc001xct.2	-						EXOC5_uc001xcs.2_Intron|EXOC5_uc010trg.1_Intron|EXOC5_uc010trh.1_Intron	NM_006544	NP_006535			SEC10 protein						exocytosis|post-Golgi vesicle-mediated transport|protein transport|vesicle docking	cytoplasm				ovary(2)|breast(1)	3																		---	---	---	---
Unknown	0	broad.mit.edu	37	14	58078970	58078970	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:58078970delA								SLC35F4 (15355 upstream) : C14orf37 (391839 downstream)																																			---	---	---	---
C14orf37	145407	broad.mit.edu	37	14	58698763	58698763	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:58698763delT	uc010tro.1	-						ACTR10_uc001xdf.2_Intron|ACTR10_uc001xdg.2_Intron|ACTR10_uc001xdh.2_Intron|ACTR10_uc010trp.1_Intron|ACTR10_uc010apc.2_Intron	NM_001001872	NP_001001872			hypothetical protein LOC145407 precursor							integral to membrane	binding				0																		---	---	---	---
KIAA0586	9786	broad.mit.edu	37	14	58959015	58959015	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:58959015delT	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	59076822	59076822	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:59076822delT								KIAA0586 (61274 upstream) : DACT1 (23964 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	59140791	59140791	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:59140791delT								DACT1 (25755 upstream) : DAAM1 (514608 downstream)																																			---	---	---	---
DAAM1	23002	broad.mit.edu	37	14	59717300	59717300	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:59717300delT	uc001xdz.1	+						DAAM1_uc001xea.1_Intron|DAAM1_uc001xeb.1_Intron|DAAM1_uc001xdy.2_Intron	NM_014992	NP_055807			dishevelled-associated activator of						actin cytoskeleton organization	cytoplasm|plasma membrane	actin binding|Rho GTPase binding			ovary(1)	1				OV - Ovarian serous cystadenocarcinoma(108;0.165)														---	---	---	---
C14orf149	112849	broad.mit.edu	37	14	59945122	59945123	+	Intron	INS	-	AC	AC	rs141101470	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:59945122_59945123insAC	uc001xee.1	-							NM_144581	NP_653182			proline racemase-like								proline racemase activity			ovary(1)	1				OV - Ovarian serous cystadenocarcinoma(108;0.14)	L-Proline(DB00172)													---	---	---	---
C14orf135	64430	broad.mit.edu	37	14	60581403	60581403	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:60581403delT	uc001xer.3	+						C14orf135_uc001xeq.2_Intron	NM_022495	NP_071940			hepatitis C virus F protein-binding protein 2							integral to membrane				ovary(2)	2		Myeloproliferative disorder(585;0.163)		OV - Ovarian serous cystadenocarcinoma(108;0.127)														---	---	---	---
Unknown	0	broad.mit.edu	37	14	60707768	60707768	+	RNA	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:60707768delA	uc001xev.1	-	2		c.1927delT								Homo sapiens cDNA clone IMAGE:5266689.																														---	---	---	---
C14orf39	317761	broad.mit.edu	37	14	60950600	60950600	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:60950600delA	uc001xez.3	-						C14orf39_uc010apo.2_Intron	NM_174978	NP_777638			hypothetical protein LOC317761											ovary(2)|haematopoietic_and_lymphoid_tissue(1)|skin(1)	4				OV - Ovarian serous cystadenocarcinoma(108;0.0448)														---	---	---	---
Unknown	0	broad.mit.edu	37	14	61165213	61165213	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:61165213delA								SIX1 (49058 upstream) : SIX4 (11043 downstream)																																			---	---	---	---
MNAT1	4331	broad.mit.edu	37	14	61206873	61206873	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:61206873delA	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					---	---	---	---
Unknown	0	broad.mit.edu	37	14	61612788	61612789	+	IGR	DEL	AC	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:61612788_61612789delAC								SLC38A6 (62338 upstream) : PRKCH (41498 downstream)																																			---	---	---	---
PRKCH	5583	broad.mit.edu	37	14	61901168	61901168	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:61901168delA	uc001xfn.2	+						PRKCH_uc010tsa.1_Intron	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)														---	---	---	---
PRKCH	5583	broad.mit.edu	37	14	61927747	61927747	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:61927747delA	uc001xfn.2	+						PRKCH_uc010tsa.1_Intron	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	62072005	62072005	+	Intron	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:62072005delG	uc001xfp.2	+											Homo sapiens cDNA: FLJ22447 fis, clone HRC09479.																														---	---	---	---
Unknown	0	broad.mit.edu	37	14	62727540	62727543	+	IGR	DEL	TACC	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:62727540_62727543delTACC								FLJ43390 (130308 upstream) : KCNH5 (446404 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	63090298	63090302	+	IGR	DEL	TTTTT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:63090298_63090302delTTTTT								FLJ43390 (493066 upstream) : KCNH5 (83645 downstream)																																			---	---	---	---
KCNH5	27133	broad.mit.edu	37	14	63357504	63357504	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:63357504delA	uc001xfx.2	-						KCNH5_uc001xfy.2_Intron|KCNH5_uc001xfz.1_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)														---	---	---	---
KCNH5	27133	broad.mit.edu	37	14	63362053	63362056	+	Intron	DEL	TTTT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:63362053_63362056delTTTT	uc001xfx.2	-						KCNH5_uc001xfy.2_Intron|KCNH5_uc001xfz.1_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)														---	---	---	---
KCNH5	27133	broad.mit.edu	37	14	63444990	63444990	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:63444990delA	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)														---	---	---	---
KCNH5	27133	broad.mit.edu	37	14	63527137	63527138	+	Intron	INS	-	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:63527137_63527138insA	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	63806125	63806125	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:63806125delA								GPHB5 (21562 upstream) : PPP2R5E (35230 downstream)																																			---	---	---	---
PPP2R5E	5529	broad.mit.edu	37	14	63860444	63860444	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:63860444delA	uc001xgd.1	-						PPP2R5E_uc010tsf.1_Intron|PPP2R5E_uc010tsg.1_Intron|PPP2R5E_uc001xge.2_Intron|PPP2R5E_uc010tsh.1_Intron|PPP2R5E_uc001xgf.1_Intron	NM_006246	NP_006237			epsilon isoform of regulatory subunit B56,						signal transduction	cytoplasm|intracellular membrane-bounded organelle|protein phosphatase type 2A complex	protein binding|protein phosphatase type 2A regulator activity			ovary(1)	1				OV - Ovarian serous cystadenocarcinoma(108;0.00197)|all cancers(60;0.0153)|BRCA - Breast invasive adenocarcinoma(234;0.128)														---	---	---	---
PPP2R5E	5529	broad.mit.edu	37	14	63920609	63920609	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:63920609delA	uc001xgd.1	-						PPP2R5E_uc010tsf.1_Intron|PPP2R5E_uc010tsg.1_Intron|PPP2R5E_uc001xge.2_Intron|PPP2R5E_uc010tsh.1_Intron|PPP2R5E_uc001xgf.1_Intron|PPP2R5E_uc001xgg.3_Intron	NM_006246	NP_006237			epsilon isoform of regulatory subunit B56,						signal transduction	cytoplasm|intracellular membrane-bounded organelle|protein phosphatase type 2A complex	protein binding|protein phosphatase type 2A regulator activity			ovary(1)	1				OV - Ovarian serous cystadenocarcinoma(108;0.00197)|all cancers(60;0.0153)|BRCA - Breast invasive adenocarcinoma(234;0.128)														---	---	---	---
Unknown	0	broad.mit.edu	37	14	64287075	64287075	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:64287075delA								SGPP1 (92319 upstream) : SYNE2 (32608 downstream)																																			---	---	---	---
SYNE2	23224	broad.mit.edu	37	14	64407136	64407136	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:64407136delA	uc001xgm.2	+						SYNE2_uc001xgk.2_Intron|SYNE2_uc001xgl.2_Intron	NM_015180	NP_055995			spectrin repeat containing, nuclear envelope 2						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)														---	---	---	---
SYNE2	23224	broad.mit.edu	37	14	64641649	64641649	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:64641649delT	uc001xgm.2	+						SYNE2_uc001xgl.2_Intron|SYNE2_uc010apy.2_Intron|SYNE2_uc001xgn.2_Intron|SYNE2_uc001xgo.2_Intron|SYNE2_uc010aqa.2_Intron|SYNE2_uc001xgq.2_Intron	NM_015180	NP_055995			spectrin repeat containing, nuclear envelope 2						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	64786814	64786814	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:64786814delA	uc001xgv.2	-						ESR2_uc001xgw.2_Intron|ESR2_uc001xgx.2_Intron	NM_001040276	NP_001035366			estrogen receptor beta isoform 2						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)													---	---	---	---
MTHFD1	4522	broad.mit.edu	37	14	64867679	64867679	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:64867679delT	uc001xhb.2	+						MTHFD1_uc010aqe.2_Intron|MTHFD1_uc010aqf.2_Intron	NM_005956	NP_005947			methylenetetrahydrofolate dehydrogenase 1						folic acid metabolic process|folic acid-containing compound biosynthetic process|histidine biosynthetic process|methionine biosynthetic process|one-carbon metabolic process|purine nucleotide biosynthetic process	cytosol|mitochondrion	ATP binding|formate-tetrahydrofolate ligase activity|methenyltetrahydrofolate cyclohydrolase activity|methylenetetrahydrofolate dehydrogenase (NADP+) activity|methylenetetrahydrofolate dehydrogenase|protein binding			ovary(2)	2				OV - Ovarian serous cystadenocarcinoma(108;8.7e-12)|all cancers(60;3.29e-11)|BRCA - Breast invasive adenocarcinoma(234;0.0488)	NADH(DB00157)|Tetrahydrofolic acid(DB00116)													---	---	---	---
MTHFD1	4522	broad.mit.edu	37	14	64888697	64888697	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:64888697delT	uc001xhb.2	+						MTHFD1_uc010aqe.2_Intron|MTHFD1_uc010aqf.2_Intron	NM_005956	NP_005947			methylenetetrahydrofolate dehydrogenase 1						folic acid metabolic process|folic acid-containing compound biosynthetic process|histidine biosynthetic process|methionine biosynthetic process|one-carbon metabolic process|purine nucleotide biosynthetic process	cytosol|mitochondrion	ATP binding|formate-tetrahydrofolate ligase activity|methenyltetrahydrofolate cyclohydrolase activity|methylenetetrahydrofolate dehydrogenase (NADP+) activity|methylenetetrahydrofolate dehydrogenase|protein binding			ovary(2)	2				OV - Ovarian serous cystadenocarcinoma(108;8.7e-12)|all cancers(60;3.29e-11)|BRCA - Breast invasive adenocarcinoma(234;0.0488)	NADH(DB00157)|Tetrahydrofolic acid(DB00116)													---	---	---	---
MTHFD1	4522	broad.mit.edu	37	14	64896336	64896337	+	Intron	INS	-	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:64896336_64896337insT	uc001xhb.2	+						MTHFD1_uc010aqe.2_Intron|MTHFD1_uc010aqf.2_Intron	NM_005956	NP_005947			methylenetetrahydrofolate dehydrogenase 1						folic acid metabolic process|folic acid-containing compound biosynthetic process|histidine biosynthetic process|methionine biosynthetic process|one-carbon metabolic process|purine nucleotide biosynthetic process	cytosol|mitochondrion	ATP binding|formate-tetrahydrofolate ligase activity|methenyltetrahydrofolate cyclohydrolase activity|methylenetetrahydrofolate dehydrogenase (NADP+) activity|methylenetetrahydrofolate dehydrogenase|protein binding			ovary(2)	2				OV - Ovarian serous cystadenocarcinoma(108;8.7e-12)|all cancers(60;3.29e-11)|BRCA - Breast invasive adenocarcinoma(234;0.0488)	NADH(DB00157)|Tetrahydrofolic acid(DB00116)													---	---	---	---
Unknown	0	broad.mit.edu	37	14	65093142	65093142	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:65093142delT								C14orf50 (37046 upstream) : PLEKHG3 (78051 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	65130046	65130048	+	IGR	DEL	TTT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:65130046_65130048delTTT								C14orf50 (73950 upstream) : PLEKHG3 (41145 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	65370390	65370390	+	IGR	DEL	A	-	-	rs11308429		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:65370390delA								SPTB (23789 upstream) : CHURC1 (10750 downstream)																																			---	---	---	---
CHURC1	91612	broad.mit.edu	37	14	65399360	65399360	+	3'UTR	DEL	A	-	-	rs71695415		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:65399360delA	uc001xhw.1	+	4					CHURC1_uc010tsj.1_Intron|CHURC1_uc010tsk.1_Intron|FNTB_uc010tsl.1_Intron|FNTB_uc010tsm.1_Intron|CHURC1_uc001xhv.1_3'UTR	NM_145165	NP_660148			churchill domain containing 1						multicellular organismal development|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent		zinc ion binding			pancreas(1)	1				all cancers(60;0.00119)|OV - Ovarian serous cystadenocarcinoma(108;0.0056)|BRCA - Breast invasive adenocarcinoma(234;0.00976)														---	---	---	---
Unknown	0	broad.mit.edu	37	14	65836043	65836043	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:65836043delT								MAX (266816 upstream) : LOC645431 (41270 downstream)																																			---	---	---	---
FUT8	2530	broad.mit.edu	37	14	65904987	65904987	+	Intron	DEL	T	-	-	rs66475337		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:65904987delT	uc001xin.2	+						FUT8_uc001xio.2_Intron|FUT8_uc010tsp.1_Intron|FUT8_uc001xir.3_Intron|FUT8_uc001xip.2_Intron|FUT8_uc001xiq.2_Intron	NM_178155	NP_835368			fucosyltransferase 8 isoform a						in utero embryonic development|L-fucose catabolic process|N-glycan processing|oligosaccharide biosynthetic process|post-translational protein modification|protein glycosylation in Golgi|protein N-linked glycosylation via asparagine	Golgi cisterna membrane|integral to membrane	glycoprotein 6-alpha-L-fucosyltransferase activity|SH3 domain binding			ovary(1)	1				all cancers(60;0.00109)|OV - Ovarian serous cystadenocarcinoma(108;0.00242)|BRCA - Breast invasive adenocarcinoma(234;0.0114)														---	---	---	---
FUT8	2530	broad.mit.edu	37	14	65948167	65948167	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:65948167delT	uc001xin.2	+						FUT8_uc001xio.2_Intron|FUT8_uc010tsp.1_Intron|FUT8_uc001xir.3_Intron|FUT8_uc001xip.2_Intron|FUT8_uc001xiq.2_Intron	NM_178155	NP_835368			fucosyltransferase 8 isoform a						in utero embryonic development|L-fucose catabolic process|N-glycan processing|oligosaccharide biosynthetic process|post-translational protein modification|protein glycosylation in Golgi|protein N-linked glycosylation via asparagine	Golgi cisterna membrane|integral to membrane	glycoprotein 6-alpha-L-fucosyltransferase activity|SH3 domain binding			ovary(1)	1				all cancers(60;0.00109)|OV - Ovarian serous cystadenocarcinoma(108;0.00242)|BRCA - Breast invasive adenocarcinoma(234;0.0114)														---	---	---	---
Unknown	0	broad.mit.edu	37	14	66276236	66276236	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:66276236delT								FUT8 (66275 upstream) : C14orf53 (676873 downstream)																																			---	---	---	---
C14orf53	440184	broad.mit.edu	37	14	66956097	66956098	+	Intron	INS	-	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:66956097_66956098insT	uc001xiu.3	+						C14orf53_uc010tsq.1_Intron|C14orf53_uc001xiv.3_Intron	NR_024338				Homo sapiens similar to CG32662-PA, mRNA (cDNA clone IMAGE:5163906).												0																		---	---	---	---
FAM71D	161142	broad.mit.edu	37	14	67683885	67683885	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:67683885delT	uc001xja.1	+						FAM71D_uc010aqn.1_Intron	NM_173526	NP_775797			hypothetical protein LOC161142											ovary(1)	1		all_hematologic(31;0.0116)		all cancers(60;0.00107)|BRCA - Breast invasive adenocarcinoma(234;0.00993)|OV - Ovarian serous cystadenocarcinoma(108;0.012)														---	---	---	---
MPP5	64398	broad.mit.edu	37	14	67754024	67754025	+	Intron	DEL	TT	-	-	rs66994334		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:67754024_67754025delTT	uc001xjc.2	+						MPP5_uc001xjd.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)														---	---	---	---
MPP5	64398	broad.mit.edu	37	14	67786932	67786932	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-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)														---	---	---	---
Unknown	0	broad.mit.edu	37	14	68079851	68079851	+	IGR	DEL	T	-	-	rs35284636		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:68079851delT								PIGH (12834 upstream) : ARG2 (6728 downstream)																																			---	---	---	---
RAD51L1	5890	broad.mit.edu	37	14	68449453	68449453	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:68449453delT	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	69037633	69037634	+	Intron	DEL	CA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:69037633_69037634delCA	uc001xkf.1	+						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					---	---	---	---
Unknown	0	broad.mit.edu	37	14	70185641	70185642	+	IGR	DEL	AG	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:70185641_70185642delAG								KIAA0247 (3782 upstream) : SFRS5 (7977 downstream)																																			---	---	---	---
SFRS5	6430	broad.mit.edu	37	14	70237110	70237110	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:70237110delT	uc001xll.2	+						SFRS5_uc001xlm.2_RNA|SFRS5_uc001xln.1_3'UTR|SFRS5_uc001xlo.2_Intron|SFRS5_uc001xlp.2_Intron|SFRS5_uc001xlq.2_Intron	NM_006925	NP_008856			splicing factor, arginine/serine-rich 5						mRNA 3'-end processing|mRNA export from nucleus|mRNA splice site selection|termination of RNA polymerase II transcription	nuclear speck	nucleotide binding|protein binding|RNA binding				0				all cancers(60;0.00144)|BRCA - Breast invasive adenocarcinoma(234;0.0132)|OV - Ovarian serous cystadenocarcinoma(108;0.0154)														---	---	---	---
SLC8A3	6547	broad.mit.edu	37	14	70510962	70510962	+	3'UTR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:70510962delT	uc001xly.2	-	8					SLC8A3_uc001xlu.2_3'UTR|SLC8A3_uc001xlv.2_3'UTR|SLC8A3_uc001xlw.2_3'UTR|SLC8A3_uc001xlx.2_3'UTR|SLC8A3_uc001xlz.2_3'UTR|SLC8A3_uc010ara.2_RNA	NM_183002	NP_892114			solute carrier family 8 (sodium/calcium						cell communication|platelet activation	integral to membrane|plasma membrane	calcium:sodium antiporter activity|calmodulin binding			skin(3)|ovary(2)|breast(2)	7				BRCA - Breast invasive adenocarcinoma(234;0.0079)|all cancers(60;0.0102)|OV - Ovarian serous cystadenocarcinoma(108;0.0555)														---	---	---	---
SLC8A3	6547	broad.mit.edu	37	14	70562602	70562602	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:70562602delT	uc001xly.2	-						SLC8A3_uc001xlw.2_Intron|SLC8A3_uc001xlx.2_Intron|SLC8A3_uc001xlz.2_Intron|SLC8A3_uc010ara.2_Intron	NM_183002	NP_892114			solute carrier family 8 (sodium/calcium						cell communication|platelet activation	integral to membrane|plasma membrane	calcium:sodium antiporter activity|calmodulin binding			skin(3)|ovary(2)|breast(2)	7				BRCA - Breast invasive adenocarcinoma(234;0.0079)|all cancers(60;0.0102)|OV - Ovarian serous cystadenocarcinoma(108;0.0555)														---	---	---	---
Unknown	0	broad.mit.edu	37	14	70787358	70787366	+	IGR	DEL	TTTTTTTTT	-	-	rs35053640		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:70787358_70787366delTTTTTTTTT								ADAM21P1 (72840 upstream) : COX16 (4433 downstream)																																			---	---	---	---
COX16	51241	broad.mit.edu	37	14	70813395	70813395	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:70813395delT	uc001xmb.2	-							NM_016468	NP_057552			COX16 cytochrome c oxidase assembly homolog							integral to membrane|mitochondrial membrane					0																		---	---	---	---
SYNJ2BP	55333	broad.mit.edu	37	14	70841923	70841924	+	Intron	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:70841923_70841924delTT	uc001xmc.3	-						SYNJ2BP_uc010arc.2_Intron	NM_018373	NP_060843			synaptojanin 2 binding protein							integral to membrane|mitochondrial outer membrane					0				all cancers(60;0.00367)|BRCA - Breast invasive adenocarcinoma(234;0.00716)|OV - Ovarian serous cystadenocarcinoma(108;0.0377)														---	---	---	---
Unknown	0	broad.mit.edu	37	14	70901949	70901949	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:70901949delA								SYNJ2BP (18142 upstream) : ADAM21 (22268 downstream)																																			---	---	---	---
MAP3K9	4293	broad.mit.edu	37	14	71207814	71207814	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:71207814delT	uc001xmm.2	-						MAP3K9_uc010ttk.1_Intron|MAP3K9_uc001xmk.2_Intron|MAP3K9_uc001xml.2_Intron	NM_033141	NP_149132			mitogen-activated protein kinase kinase kinase						activation of JUN kinase activity|protein autophosphorylation		ATP binding|JUN kinase kinase kinase activity|MAP kinase kinase activity|protein homodimerization activity			stomach(2)|lung(1)|central_nervous_system(1)|skin(1)	5				all cancers(60;0.00779)|BRCA - Breast invasive adenocarcinoma(234;0.00884)|OV - Ovarian serous cystadenocarcinoma(108;0.08)														---	---	---	---
PCNX	22990	broad.mit.edu	37	14	71419299	71419299	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:71419299delT	uc001xmo.2	+						PCNX_uc001xmn.3_Intron|PCNX_uc010are.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)														---	---	---	---
PCNX	22990	broad.mit.edu	37	14	71576040	71576040	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:71576040delT	uc001xmo.2	+						PCNX_uc010are.1_Intron|PCNX_uc010arf.1_Intron|PCNX_uc001xmp.2_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)														---	---	---	---
PCNX	22990	broad.mit.edu	37	14	71581398	71581399	+	3'UTR	INS	-	T	T	rs150040848	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:71581398_71581399insT	uc001xmo.2	+	36					PCNX_uc010are.1_3'UTR|PCNX_uc010arf.1_3'UTR|PCNX_uc001xmp.2_3'UTR	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	71672941	71672941	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:71672941delA								PCNX (90842 upstream) : SNORD56B (192113 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	71896967	71896967	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:71896967delT								SNORD56B (31844 upstream) : SIPA1L1 (36935 downstream)																																			---	---	---	---
RGS6	9628	broad.mit.edu	37	14	72584379	72584379	+	Intron	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:72584379delG	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	72939405	72939405	+	Intron	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:72939405delG	uc001xna.3	+						RGS6_uc010ttn.1_Intron|RGS6_uc001xmx.3_Intron|RGS6_uc010tto.1_Intron|RGS6_uc001xmy.3_Intron|RGS6_uc010ttp.1_Intron|RGS6_uc001xmz.1_Intron|RGS6_uc010arg.2_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	73130499	73130500	+	Intron	INS	-	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:73130499_73130500insA	uc001xnc.2	-						DPF3_uc001xnd.1_Intron|DPF3_uc001xnf.2_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)														---	---	---	---
DPF3	8110	broad.mit.edu	37	14	73360602	73360602	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:73360602delA	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)														---	---	---	---
PSEN1	5663	broad.mit.edu	37	14	73623378	73623378	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:73623378delT	uc001xnr.2	+						PSEN1_uc001xnv.2_Intron|PSEN1_uc010ark.2_Intron|PSEN1_uc001xnt.1_Intron|PSEN1_uc001xnu.2_Intron|PSEN1_uc001xnq.3_Intron	NM_000021	NP_000012			presenilin 1 isoform I-467						amyloid precursor protein catabolic process|anti-apoptosis|beta-amyloid metabolic process|cell-cell adhesion|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|smooth endoplasmic reticulum calcium ion homeostasis	apical plasma membrane|axon|cell cortex|cell surface|centrosome|ciliary rootlet|dendritic shaft|endoplasmic reticulum membrane|gamma-secretase complex|Golgi membrane|growth cone|integral to plasma membrane|kinetochore|lysosomal membrane|membrane raft|mitochondrial inner membrane|neuromuscular junction|neuronal cell body|nuclear outer membrane|perinuclear region of cytoplasm|rough endoplasmic reticulum|smooth endoplasmic reticulum|Z disc	aspartic-type endopeptidase activity|beta-catenin binding|cadherin binding|calcium channel activity|PDZ domain binding			breast(1)|kidney(1)	2				BRCA - Breast invasive adenocarcinoma(234;0.00394)|OV - Ovarian serous cystadenocarcinoma(108;0.075)														---	---	---	---
NUMB	8650	broad.mit.edu	37	14	73769292	73769292	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:73769292delT	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)														---	---	---	---
NUMB	8650	broad.mit.edu	37	14	73898687	73898687	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:73898687delA	uc001xny.1	-						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)														---	---	---	---
DNAL1	83544	broad.mit.edu	37	14	74121532	74121533	+	Intron	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:74121532_74121533delTT	uc001xoq.3	+						DNAL1_uc010aru.2_Intron|DNAL1_uc010arv.2_Intron	NM_031427	NP_113615			axonemal dynein light chain 1												0				BRCA - Breast invasive adenocarcinoma(234;0.00384)|KIRC - Kidney renal clear cell carcinoma(182;0.095)														---	---	---	---
DNAL1	83544	broad.mit.edu	37	14	74153808	74153808	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:74153808delA	uc001xoq.3	+						DNAL1_uc010aru.2_Intron|DNAL1_uc010arv.2_Intron	NM_031427	NP_113615			axonemal dynein light chain 1												0				BRCA - Breast invasive adenocarcinoma(234;0.00384)|KIRC - Kidney renal clear cell carcinoma(182;0.095)														---	---	---	---
DNAL1	83544	broad.mit.edu	37	14	74161248	74161248	+	Intron	DEL	T	-	-	rs34869338		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:74161248delT	uc001xoq.3	+						DNAL1_uc010aru.2_Intron|DNAL1_uc010arv.2_Intron	NM_031427	NP_113615			axonemal dynein light chain 1												0				BRCA - Breast invasive adenocarcinoma(234;0.00384)|KIRC - Kidney renal clear cell carcinoma(182;0.095)														---	---	---	---
C14orf43	91748	broad.mit.edu	37	14	74205773	74205773	+	Frame_Shift_Del	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:74205773delG	uc001xot.2	-	2	1722	c.939delC	c.(937-939)CCCfs	p.P313fs	C14orf43_uc001xou.2_Frame_Shift_Del_p.P313fs|C14orf43_uc010tud.1_Frame_Shift_Del_p.P313fs|C14orf43_uc010arw.2_RNA	NM_194278	NP_919254	Q6PJG2	CN043_HUMAN	hypothetical protein LOC91748	313	Pro-rich.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding			ovary(4)|central_nervous_system(1)	5				BRCA - Breast invasive adenocarcinoma(234;0.00358)|KIRC - Kidney renal clear cell carcinoma(182;0.0878)|OV - Ovarian serous cystadenocarcinoma(108;0.115)														---	---	---	---
FCF1	51077	broad.mit.edu	37	14	75190167	75190168	+	Intron	INS	-	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:75190167_75190168insG	uc001xqh.2	+						FCF1_uc001xqf.1_Intron|FCF1_uc001xqg.2_Intron|FCF1_uc001xqi.2_Intron	NM_015962	NP_057046			FCF1 small subunit						rRNA processing	nucleolus				ovary(1)	1				BRCA - Breast invasive adenocarcinoma(234;0.0037)														---	---	---	---
RPS6KL1	83694	broad.mit.edu	37	14	75383387	75383388	+	Intron	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-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)														---	---	---	---
NEK9	91754	broad.mit.edu	37	14	75570708	75570708	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:75570708delA	uc001xrl.2	-						NEK9_uc001xrk.2_Intron	NM_033116	NP_149107			NIMA-related kinase 9						cell division|mitosis	mitochondrion|nucleus	ATP binding|metal ion binding|protein kinase binding|protein serine/threonine kinase activity			lung(2)|stomach(2)|ovary(1)	5				BRCA - Breast invasive adenocarcinoma(234;0.00718)														---	---	---	---
NEK9	91754	broad.mit.edu	37	14	75585642	75585642	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:75585642delA	uc001xrl.2	-						NEK9_uc001xrk.2_5'Flank	NM_033116	NP_149107			NIMA-related kinase 9						cell division|mitosis	mitochondrion|nucleus	ATP binding|metal ion binding|protein kinase binding|protein serine/threonine kinase activity			lung(2)|stomach(2)|ovary(1)	5				BRCA - Breast invasive adenocarcinoma(234;0.00718)														---	---	---	---
TMED10	10972	broad.mit.edu	37	14	75614507	75614508	+	Intron	INS	-	GCCT	GCCT			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:75614507_75614508insGCCT	uc001xrm.1	-						TMED10_uc010ash.1_Intron|TMED10_uc010asg.1_5'Flank|TMED10_uc010tuz.1_Intron	NM_006827	NP_006818			transmembrane emp24 domain-containing protein 10						protein transport|regulated secretory pathway|vesicle targeting, to, from or within Golgi	cis-Golgi network|ER-Golgi intermediate compartment|Golgi membrane|integral to membrane|melanosome|microsome|zymogen granule membrane	protein binding				0				BRCA - Breast invasive adenocarcinoma(234;0.0126)														---	---	---	---
Unknown	0	broad.mit.edu	37	14	75812513	75812514	+	IGR	DEL	GT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:75812513_75812514delGT								FOS (63578 upstream) : JDP2 (81995 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	75951173	75951174	+	IGR	DEL	AC	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:75951173_75951174delAC								JDP2 (11771 upstream) : BATF (37610 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	76016363	76016363	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:76016363delT								BATF (3036 upstream) : FLVCR2 (28577 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	76018328	76018330	+	IGR	DEL	TTT	-	-	rs58666200		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:76018328_76018330delTTT								BATF (5001 upstream) : FLVCR2 (26610 downstream)																																			---	---	---	---
FLVCR2	55640	broad.mit.edu	37	14	76100278	76100280	+	Intron	DEL	TTT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:76100278_76100280delTTT	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)														---	---	---	---
C14orf179	112752	broad.mit.edu	37	14	76548390	76548390	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:76548390delA	uc010asm.1	+						C14orf179_uc001xsf.2_Intron|C14orf179_uc010asl.1_Intron|C14orf179_uc001xsg.2_Intron|C14orf179_uc010tve.1_Intron	NM_001102564	NP_001096034			hypothetical protein LOC112752 isoform 2						cilium morphogenesis|intraflagellar retrograde transport						0				BRCA - Breast invasive adenocarcinoma(234;0.0199)														---	---	---	---
Unknown	0	broad.mit.edu	37	14	76755908	76755909	+	IGR	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:76755908_76755909delAA								C14orf118 (86775 upstream) : ESRRB (81781 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	77156904	77156904	+	IGR	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:77156904delG								ESRRB (188726 upstream) : VASH1 (71331 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	77550121	77550121	+	5'Flank	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:77550121delT	uc001xsz.2	-						uc001xtb.1_Intron					Homo sapiens cDNA clone IMAGE:5271982.																														---	---	---	---
TMEM63C	57156	broad.mit.edu	37	14	77717922	77717923	+	Intron	INS	-	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:77717922_77717923insT	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)														---	---	---	---
C14orf174	161394	broad.mit.edu	37	14	77846656	77846656	+	Intron	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:77846656delC	uc001xtq.1	+							NM_001010860	NP_001010860			hypothetical protein LOC161394												0			Kidney(204;0.164)	BRCA - Breast invasive adenocarcinoma(234;0.0278)														---	---	---	---
C14orf148	122945	broad.mit.edu	37	14	77865641	77865641	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:77865641delA	uc001xtr.2	-							NM_001113475	NP_001106946			hypothetical protein LOC122945 isoform 1						proline biosynthetic process		binding|pyrroline-5-carboxylate reductase activity				0			Kidney(204;0.164)	BRCA - Breast invasive adenocarcinoma(234;0.0277)														---	---	---	---
C14orf148	122945	broad.mit.edu	37	14	77874561	77874561	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:77874561delT	uc001xtr.2	-						C14orf148_uc010tvi.1_Intron	NM_001113475	NP_001106946			hypothetical protein LOC122945 isoform 1						proline biosynthetic process		binding|pyrroline-5-carboxylate reductase activity				0			Kidney(204;0.164)	BRCA - Breast invasive adenocarcinoma(234;0.0277)														---	---	---	---
NRXN3	9369	broad.mit.edu	37	14	78643722	78643722	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:78643722delT	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	78646685	78646685	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:78646685delA	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	78672896	78672896	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:78672896delA	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	78693692	78693692	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:78693692delA	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	78717617	78717617	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-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	78923391	78923391	+	Intron	DEL	G	-	-	rs8010016		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:78923391delG	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	79235353	79235353	+	Intron	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:79235353delG	uc001xun.2	+						NRXN3_uc001xum.1_Intron|NRXN3_uc010asv.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	79271944	79271947	+	Intron	DEL	AAAA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:79271944_79271947delAAAA	uc001xun.2	+						NRXN3_uc001xum.1_Intron|NRXN3_uc010asv.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	79470611	79470611	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:79470611delT	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	79545618	79545619	+	Intron	INS	-	TTTG	TTTG	rs143480628	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:79545618_79545619insTTTG	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	79943460	79943460	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:79943460delT	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)														---	---	---	---
NRXN3	9369	broad.mit.edu	37	14	79959888	79959889	+	Intron	INS	-	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:79959888_79959889insA	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	80581716	80581716	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:80581716delT								NRXN3 (250958 upstream) : DIO2 (82154 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	80942211	80942213	+	IGR	DEL	CAA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:80942211_80942213delCAA								DIO2 (244814 upstream) : C14orf145 (1119 downstream)																																			---	---	---	---
C14orf145	145508	broad.mit.edu	37	14	81034291	81034292	+	Intron	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:81034291_81034292delAA	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	81198641	81198641	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:81198641delA	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	81251990	81251990	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:81251990delA	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	81372527	81372528	+	Intron	INS	-	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:81372527_81372528insC	uc001xux.2	-						C14orf145_uc001xuz.2_Intron|C14orf145_uc001xva.1_Intron|C14orf145_uc010ata.1_Intron|C14orf145_uc001xuy.1_5'Flank	NM_152446	NP_689659			hypothetical protein LOC145508							centriole|spindle pole					0				BRCA - Breast invasive adenocarcinoma(234;0.0586)														---	---	---	---
GTF2A1	2957	broad.mit.edu	37	14	81652018	81652018	+	Intron	DEL	A	-	-	rs71931712		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:81652018delA	uc001xvf.1	-						GTF2A1_uc010atb.1_Intron|GTF2A1_uc001xvg.1_Intron	NM_015859	NP_056943			TFIIA alpha, p55 isoform 1						regulation of transcription, DNA-dependent|transcription elongation from RNA polymerase II promoter|transcription initiation from RNA polymerase II promoter|viral reproduction	cytoplasm|transcription factor TFIIA complex	DNA binding|protein binding|protein heterodimerization activity|TBP-class protein binding|transcription coactivator activity			breast(1)	1				BRCA - Breast invasive adenocarcinoma(234;0.0287)														---	---	---	---
STON2	85439	broad.mit.edu	37	14	81729046	81729046	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:81729046delT	uc001xvk.1	-							NM_033104	NP_149095			stonin 2						endocytosis|intracellular protein transport|regulation of endocytosis	clathrin adaptor complex|nucleolus	protein binding			skin(3)|pancreas(2)	5				BRCA - Breast invasive adenocarcinoma(234;0.0348)														---	---	---	---
STON2	85439	broad.mit.edu	37	14	81799173	81799173	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:81799173delT	uc010tvu.1	-						STON2_uc001xvk.1_Intron	NM_033104	NP_149095			stonin 2						endocytosis|intracellular protein transport|regulation of endocytosis	clathrin adaptor complex|nucleolus	protein binding			skin(3)|pancreas(2)	5				BRCA - Breast invasive adenocarcinoma(234;0.0348)														---	---	---	---
SEL1L	6400	broad.mit.edu	37	14	81945757	81945757	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:81945757delA	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)														---	---	---	---
SEL1L	6400	broad.mit.edu	37	14	81951796	81951798	+	Intron	DEL	TTT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:81951796_81951798delTTT	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)														---	---	---	---
SEL1L	6400	broad.mit.edu	37	14	81964078	81964078	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:81964078delT	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	82180854	82180855	+	IGR	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:82180854_82180855delTT								SEL1L (180649 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	82299573	82299573	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:82299573delT								SEL1L (299368 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	82729550	82729551	+	IGR	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:82729550_82729551delTT								SEL1L (729345 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	82988471	82988471	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:82988471delA								SEL1L (988266 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	83191287	83191288	+	IGR	DEL	GT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:83191287_83191288delGT								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	83355859	83355860	+	IGR	DEL	TG	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:83355859_83355860delTG								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	83502859	83502860	+	IGR	DEL	AG	-	-	rs75378802	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:83502859_83502860delAG								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	84392285	84392285	+	IGR	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:84392285delG								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	84621670	84621671	+	IGR	DEL	TC	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:84621670_84621671delTC								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	85365937	85365937	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:85365937delA								None (None upstream) : FLRT2 (630551 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	85466459	85466459	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:85466459delT								None (None upstream) : FLRT2 (530029 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	85526493	85526493	+	IGR	DEL	T	-	-	rs111344242		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:85526493delT								None (None upstream) : FLRT2 (469995 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	85839376	85839376	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:85839376delT								None (None upstream) : FLRT2 (157112 downstream)																																			---	---	---	---
FLRT2	23768	broad.mit.edu	37	14	86090075	86090076	+	3'UTR	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:86090075_86090076delAA	uc001xvr.2	+	2					FLRT2_uc010atd.2_3'UTR	NM_013231	NP_037363			fibronectin leucine rich transmembrane protein 2						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)														---	---	---	---
Unknown	0	broad.mit.edu	37	14	86558786	86558786	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:86558786delA								FLRT2 (464517 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	87545398	87545398	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:87545398delA								None (None upstream) : GALC (758766 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	87740626	87740627	+	IGR	INS	-	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:87740626_87740627insA								None (None upstream) : GALC (563537 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	88263834	88263834	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:88263834delA								None (None upstream) : GALC (40330 downstream)																																			---	---	---	---
PTPN21	11099	broad.mit.edu	37	14	88938803	88938803	+	Frame_Shift_Del	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:88938803delT	uc001xwv.3	-	15	2987	c.2656delA	c.(2656-2658)ATTfs	p.I886fs	PTPN21_uc010twc.1_Frame_Shift_Del_p.I682fs	NM_007039	NP_008970	Q16825	PTN21_HUMAN	protein tyrosine phosphatase, non-receptor type	886						cytoplasm|cytoskeleton	binding|protein tyrosine phosphatase activity			ovary(3)|skin(1)	4																		---	---	---	---
PTPN21	11099	broad.mit.edu	37	14	88952286	88952286	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:88952286delA	uc001xwv.3	-						PTPN21_uc010twc.1_Intron	NM_007039	NP_008970			protein tyrosine phosphatase, non-receptor type							cytoplasm|cytoskeleton	binding|protein tyrosine phosphatase activity			ovary(3)|skin(1)	4																		---	---	---	---
PTPN21	11099	broad.mit.edu	37	14	88974369	88974369	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:88974369delA	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																		---	---	---	---
EML5	161436	broad.mit.edu	37	14	89093477	89093477	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:89093477delA	uc001xxg.2	-						EML5_uc001xxf.2_Intron|EML5_uc001xxh.1_Intron	NM_183387	NP_899243			echinoderm microtubule associated protein like							cytoplasm|microtubule				ovary(3)	3																		---	---	---	---
FOXN3	1112	broad.mit.edu	37	14	89878534	89878534	+	Frame_Shift_Del	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:89878534delG	uc001xxo.3	-	2	424	c.287delC	c.(286-288)CCAfs	p.P96fs	FOXN3_uc001xxn.3_Frame_Shift_Del_p.P96fs|FOXN3_uc010atk.2_Frame_Shift_Del_p.P96fs|FOXN3_uc001xxp.2_Frame_Shift_Del_p.P96fs	NM_001085471	NP_001078940	O00409	FOXN3_HUMAN	checkpoint suppressor 1 isoform 1	96					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	89913548	89913550	+	Intron	DEL	AAA	-	-	rs78658665		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:89913548_89913550delAAA	uc001xxo.3	-						FOXN3_uc010atk.2_Intron|FOXN3_uc001xxp.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	90068633	90068633	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:90068633delA	uc001xxo.3	-						FOXN3_uc010atk.2_Intron|FOXN3_uc001xxp.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																		---	---	---	---
Unknown	0	broad.mit.edu	37	14	90113995	90113995	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:90113995delA								FOXN3 (28501 upstream) : C14orf143 (149476 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	90135140	90135141	+	IGR	DEL	AC	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:90135140_90135141delAC								FOXN3 (49646 upstream) : C14orf143 (128330 downstream)																																			---	---	---	---
TDP1	55775	broad.mit.edu	37	14	90458490	90458490	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:90458490delT	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_Intron|TDP1_uc001xyd.1_Intron	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					---	---	---	---
KCNK13	56659	broad.mit.edu	37	14	90602858	90602859	+	Intron	DEL	AA	-	-	rs113562814		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:90602858_90602859delAA	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)																---	---	---	---
C14orf159	80017	broad.mit.edu	37	14	91682990	91682991	+	Intron	DEL	AA	-	-	rs113958230		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:91682990_91682991delAA	uc001xzb.2	+						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_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)														---	---	---	---
Unknown	0	broad.mit.edu	37	14	92000775	92000775	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:92000775delA								SMEK1 (23962 upstream) : C14orf184 (38013 downstream)																																			---	---	---	---
FBLN5	10516	broad.mit.edu	37	14	92404816	92404817	+	Intron	INS	-	A	A	rs7143178		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:92404816_92404817insA	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)																---	---	---	---
TRIP11	9321	broad.mit.edu	37	14	92491854	92491854	+	Intron	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:92491854delC	uc001xzy.2	-							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	92596263	92596263	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:92596263delT	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)														---	---	---	---
CPSF2	53981	broad.mit.edu	37	14	92618218	92618218	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:92618218delA	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	92683351	92683351	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:92683351delA								CPSF2 (52808 upstream) : SLC24A4 (105574 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	92965867	92965867	+	RNA	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:92965867delT	uc001yao.2	+	1		c.890delT								Homo sapiens cDNA clone IMAGE:4818211.																														---	---	---	---
RIN3	79890	broad.mit.edu	37	14	93010365	93010365	+	Intron	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:93010365delC	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)																---	---	---	---
BTBD7	55727	broad.mit.edu	37	14	93720148	93720148	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:93720148delT	uc001ybo.2	-						BTBD7_uc010aur.2_Intron|BTBD7_uc010two.1_Intron|BTBD7_uc001ybp.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	93991796	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:93991796delA	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-4200-01A-01D-1126-08	TCGA-BR-4200-11A-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	94250689	94250689	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:94250689delT	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)														---	---	---	---
Unknown	0	broad.mit.edu	37	14	94314581	94314581	+	IGR	DEL	T	-	-	rs141420799	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:94314581delT								PRIMA1 (59815 upstream) : C14orf86 (56495 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	94454442	94454442	+	IGR	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:94454442delG								ASB2 (11366 upstream) : C14orf48 (9174 downstream)																																			---	---	---	---
DDX24	57062	broad.mit.edu	37	14	94521091	94521091	+	Intron	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:94521091delG	uc001ycj.2	-						DDX24_uc010twq.1_Intron|DDX24_uc010twr.1_Intron	NM_020414	NP_065147			DEAD (Asp-Glu-Ala-Asp) box polypeptide 24						RNA metabolic process	cytoplasm|nucleolus|nucleolus	ATP binding|ATP-dependent RNA helicase activity|protein binding|RNA binding			ovary(2)|kidney(1)|skin(1)	4		all_cancers(154;0.12)		Epithelial(152;0.114)|all cancers(159;0.19)|COAD - Colon adenocarcinoma(157;0.207)														---	---	---	---
DDX24	57062	broad.mit.edu	37	14	94531569	94531569	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:94531569delT	uc001ycj.2	-						DDX24_uc010twq.1_Intron|DDX24_uc010twr.1_Intron	NM_020414	NP_065147			DEAD (Asp-Glu-Ala-Asp) box polypeptide 24						RNA metabolic process	cytoplasm|nucleolus|nucleolus	ATP binding|ATP-dependent RNA helicase activity|protein binding|RNA binding			ovary(2)|kidney(1)|skin(1)	4		all_cancers(154;0.12)		Epithelial(152;0.114)|all cancers(159;0.19)|COAD - Colon adenocarcinoma(157;0.207)														---	---	---	---
SERPINA10	51156	broad.mit.edu	37	14	94759953	94759953	+	5'Flank	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:94759953delG	uc001yct.2	-						SERPINA10_uc001ycu.3_5'Flank	NM_016186	NP_057270			serine (or cysteine) proteinase inhibitor, clade						regulation of proteolysis	extracellular region	serine-type endopeptidase inhibitor activity			ovary(2)|skin(1)	3		all_cancers(154;0.105)		Epithelial(152;0.135)|COAD - Colon adenocarcinoma(157;0.207)|all cancers(159;0.221)														---	---	---	---
Unknown	0	broad.mit.edu	37	14	95130427	95130428	+	IGR	DEL	AA	-	-	rs67436818		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:95130427_95130428delAA								SERPINA13 (17097 upstream) : GSC (104133 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	95154155	95154155	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:95154155delT								SERPINA13 (40825 upstream) : GSC (80406 downstream)																																			---	---	---	---
CLMN	79789	broad.mit.edu	37	14	95676983	95676983	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:95676983delA	uc001yef.2	-							NM_024734	NP_079010			calmin							integral to membrane	actin binding				0				Epithelial(152;0.193)														---	---	---	---
CLMN	79789	broad.mit.edu	37	14	95741316	95741322	+	Intron	DEL	AAAAAAA	-	-	rs71674697		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:95741316_95741322delAAAAAAA	uc001yef.2	-							NM_024734	NP_079010			calmin							integral to membrane	actin binding				0				Epithelial(152;0.193)														---	---	---	---
Unknown	0	broad.mit.edu	37	14	96262129	96262131	+	IGR	DEL	TCT	-	-	rs143074378		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:96262129_96262131delTCT								TCL1A (81596 upstream) : C14orf132 (243531 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	96294324	96294328	+	IGR	DEL	AAAAA	-	-	rs71936557		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:96294324_96294328delAAAAA								TCL1A (113791 upstream) : C14orf132 (211334 downstream)																																			---	---	---	---
AK7	122481	broad.mit.edu	37	14	96873030	96873030	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:96873030delT	uc001yfn.2	+							NM_152327	NP_689540			adenylate kinase 7						cell projection organization	cytosol	adenylate kinase activity|ATP binding|cytidylate kinase activity			ovary(1)	1		all_cancers(154;0.0482)|all_epithelial(191;0.128)|Melanoma(154;0.155)		Epithelial(152;0.134)|COAD - Colon adenocarcinoma(157;0.228)														---	---	---	---
AK7	122481	broad.mit.edu	37	14	96926214	96926214	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:96926214delA	uc001yfn.2	+							NM_152327	NP_689540			adenylate kinase 7						cell projection organization	cytosol	adenylate kinase activity|ATP binding|cytidylate kinase activity			ovary(1)	1		all_cancers(154;0.0482)|all_epithelial(191;0.128)|Melanoma(154;0.155)		Epithelial(152;0.134)|COAD - Colon adenocarcinoma(157;0.228)														---	---	---	---
PAPOLA	10914	broad.mit.edu	37	14	96966566	96966566	+	5'Flank	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:96966566delT	uc001yfq.2	+						PAPOLA_uc001yfo.2_5'Flank|PAPOLA_uc001yfp.2_5'Flank|PAPOLA_uc001yfr.2_5'Flank|PAPOLA_uc010twv.1_5'Flank|PAPOLA_uc010avp.2_5'Flank	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)														---	---	---	---
PAPOLA	10914	broad.mit.edu	37	14	96987170	96987171	+	Intron	DEL	AG	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:96987170_96987171delAG	uc001yfq.2	+						PAPOLA_uc001yfo.2_Intron|PAPOLA_uc001yfp.2_Intron|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)														---	---	---	---
VRK1	7443	broad.mit.edu	37	14	97282225	97282225	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:97282225delA	uc001yft.2	+							NM_003384	NP_003375			vaccinia related kinase 1							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)														---	---	---	---
C14orf64	388011	broad.mit.edu	37	14	98427949	98427951	+	Intron	DEL	AAC	-	-	rs145892913	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:98427949_98427951delAAC	uc001yfw.2	-						C14orf64_uc001yfx.2_Intron|C14orf64_uc001yfy.2_Intron|C14orf64_uc010avq.2_Intron	NR_015430				Homo sapiens cDNA FLJ34349 fis, clone FEBRA2011063.												0																		---	---	---	---
C14orf64	388011	broad.mit.edu	37	14	98442416	98442417	+	Intron	DEL	GT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:98442416_98442417delGT	uc001yfw.2	-						C14orf64_uc001yfx.2_Intron|C14orf64_uc001yfy.2_Intron|C14orf64_uc010avq.2_Intron	NR_015430				Homo sapiens cDNA FLJ34349 fis, clone FEBRA2011063.												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	14	98681569	98681570	+	IGR	DEL	TT	-	-	rs113293793		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:98681569_98681570delTT								C14orf64 (237108 upstream) : C14orf177 (496380 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	99008147	99008148	+	IGR	DEL	CT	-	-	rs66635420		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:99008147_99008148delCT								C14orf64 (563686 upstream) : C14orf177 (169802 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	99059666	99059666	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:99059666delT								C14orf64 (615205 upstream) : C14orf177 (118284 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	99387952	99387952	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:99387952delA								C14orf177 (203855 upstream) : BCL11B (247675 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	99615284	99615285	+	IGR	DEL	GA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:99615284_99615285delGA								C14orf177 (431187 upstream) : BCL11B (20342 downstream)																																			---	---	---	---
SETD3	84193	broad.mit.edu	37	14	99881940	99881940	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:99881940delA	uc001ygc.2	-						SETD3_uc001ygd.2_Intron|SETD3_uc001ygf.2_Intron	NM_032233	NP_115609			SET domain containing 3 isoform a						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)																---	---	---	---
EML1	2009	broad.mit.edu	37	14	100326605	100326605	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:100326605delT	uc001ygs.2	+						EML1_uc010avt.1_Intron|EML1_uc010tww.1_Intron|EML1_uc001ygq.2_Intron|EML1_uc001ygr.2_Intron	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)																---	---	---	---
Unknown	0	broad.mit.edu	37	14	100696020	100696023	+	IGR	DEL	GTGT	-	-	rs35272708		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:100696020_100696023delGTGT								DEGS2 (70008 upstream) : YY1 (9079 downstream)																																			---	---	---	---
SLC25A29	123096	broad.mit.edu	37	14	100762766	100762766	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:100762766delA	uc001yha.2	-						SLC25A29_uc010avv.2_5'Flank|SLC25A29_uc010twx.1_Intron|SLC25A29_uc010avw.2_Intron	NM_001039355	NP_001034444			solute carrier family 25, member 29							integral to membrane|mitochondrial inner membrane	binding			ovary(1)	1		Melanoma(154;0.152)			L-Carnitine(DB00583)													---	---	---	---
Unknown	0	broad.mit.edu	37	14	101047048	101047049	+	IGR	DEL	TG	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:101047048_101047049delTG								BEGAIN (10917 upstream) : C14orf70 (76556 downstream)																																			---	---	---	---
MEG3	55384	broad.mit.edu	37	14	101314063	101314063	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:101314063delT	uc001yid.1	+						MEG3_uc001yhy.2_Intron|MEG3_uc010txb.1_Intron|MEG3_uc010txc.1_Intron|MEG3_uc001yib.2_Intron|MEG3_uc010txd.1_Intron|MEG3_uc010txe.1_Intron|MEG3_uc001yic.2_Intron|MEG3_uc010txf.1_Intron|MEG3_uc010avz.1_Intron|MEG3_uc001yhw.2_Intron|MEG3_uc001yie.2_Intron|MEG3_uc001yhx.2_Intron|MEG3_uc010txg.1_Intron|MEG3_uc001yhz.2_Intron|MEG3_uc001yia.2_Intron|MEG3_uc010txh.1_Intron					SubName: Full=HCG25025, isoform CRA_b; SubName: Full=Full-length cDNA clone CS0DI033YL14 of Placenta of Homo sapiens (human);												0																		---	---	---	---
RTL1	388015	broad.mit.edu	37	14	101347507	101347507	+	Frame_Shift_Del	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:101347507delG	uc010txj.1	-	1	3678	c.3619delC	c.(3619-3621)CAGfs	p.Q1207fs	MIR433_hsa-mir-433|MI0001723_5'Flank|uc001yig.3_5'Flank|MIR127_hsa-mir-127|MI0000472_5'Flank	NM_001134888	NP_001128360	A6NKG5	RTL1_HUMAN	retrotransposon-like 1	1207										pancreas(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	14	101757205	101757206	+	IGR	DEL	CT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:101757205_101757206delCT								MIR656 (224067 upstream) : DIO3OS (261354 downstream)																																			---	---	---	---
PPP2R5C	5527	broad.mit.edu	37	14	102229419	102229419	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:102229419delT	uc010txr.1	+						PPP2R5C_uc001ykj.3_Intron|PPP2R5C_uc001ykk.2_Intron	NM_001161725	NP_001155197			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																		---	---	---	---
WDR20	91833	broad.mit.edu	37	14	102681212	102681213	+	3'UTR	DEL	TT	-	-	rs78069694		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:102681212_102681213delTT	uc001ylc.2	+	4					WDR20_uc001yld.2_Intron|WDR20_uc001yle.2_Intron					SubName: Full=WDR20 protein;												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	14	102776627	102776627	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:102776627delA								RAGE (5096 upstream) : ZNF839 (7087 downstream)																																			---	---	---	---
TECPR2	9895	broad.mit.edu	37	14	102839526	102839526	+	Intron	DEL	T	-	-	rs10706672		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:102839526delT	uc001ylw.1	+						TECPR2_uc010txw.1_Intron|TECPR2_uc010awl.2_Intron|TECPR2_uc010txx.1_Intron	NM_014844	NP_055659			tectonin beta-propeller repeat containing 2								protein binding			lung(1)|central_nervous_system(1)|skin(1)	3																		---	---	---	---
Unknown	0	broad.mit.edu	37	14	103763706	103763706	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:103763706delT								TNFAIP2 (159930 upstream) : EIF5 (36787 downstream)																																			---	---	---	---
MARK3	4140	broad.mit.edu	37	14	103969166	103969167	+	Intron	DEL	AG	-	-	rs80337525	byFrequency;by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:103969166_103969167delAG	uc001ymz.3	+						MARK3_uc001ymx.3_Intron|MARK3_uc001ymw.3_Intron|MARK3_uc001yna.3_Intron|MARK3_uc001ymy.3_Intron|MARK3_uc010awp.2_Intron|MARK3_uc010tyb.1_Intron|MARK3_uc010awq.2_Intron|MARK3_uc001ynd.2_Intron	NM_001128918	NP_001122390			MAP/microtubule affinity-regulating kinase 3								ATP binding|protein binding|protein serine/threonine kinase activity			central_nervous_system(2)|ovary(1)|stomach(1)	4		Melanoma(154;0.155)	Epithelial(46;0.241)															---	---	---	---
Unknown	0	broad.mit.edu	37	14	104014214	104014215	+	IGR	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:104014214_104014215delTT								TRMT61A (10806 upstream) : BAG5 (8674 downstream)																																			---	---	---	---
TDRD9	122402	broad.mit.edu	37	14	104516267	104516267	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:104516267delA	uc001yom.3	+						TDRD9_uc001yon.3_Intron	NM_153046	NP_694591			tudor domain containing 9						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)																---	---	---	---
KIF26A	26153	broad.mit.edu	37	14	104636543	104636544	+	Intron	INS	-	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:104636543_104636544insA	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	104955735	104955735	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:104955735delA								KIF26A (308501 upstream) : C14orf180 (90321 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	105037888	105037890	+	IGR	DEL	TTT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:105037888_105037890delTTT								KIF26A (390654 upstream) : C14orf180 (8166 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	105131179	105131179	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:105131179delA								TMEM179 (60082 upstream) : INF2 (24764 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	105386107	105386108	+	IGR	DEL	TA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:105386107_105386108delTA								KIAA0284 (23021 upstream) : PLD4 (5079 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	105546884	105546884	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:105546884delT								GPR132 (15130 upstream) : JAG2 (61193 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	105601821	105601822	+	IGR	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:105601821_105601822delAA								GPR132 (70067 upstream) : JAG2 (6255 downstream)																																			---	---	---	---
BRF1	2972	broad.mit.edu	37	14	105694126	105694126	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:105694126delT	uc001yqp.2	-						BRF1_uc010tyo.1_Intron|BRF1_uc010typ.1_Intron|BRF1_uc001yql.2_Intron|BRF1_uc001yqo.2_Intron|BRF1_uc010axg.1_Intron|BRF1_uc001yqn.2_Intron|BRF1_uc010axh.1_Intron|BRF1_uc010axj.1_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)														---	---	---	---
ADAM6	8755	broad.mit.edu	37	14	106036932	106036933	+	Intron	DEL	AC	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:106036932_106036933delAC	uc010tyt.1	-											Parts of antibodies, mostly variable regions.												0																		---	---	---	---
ADAM6	8755	broad.mit.edu	37	14	106280784	106280784	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:106280784delA	uc010tyt.1	-						uc001yrs.2_Intron|uc001yrt.2_Intron|uc001yrw.1_Intron|uc001yrx.1_Intron|uc001yrz.1_Intron|uc001yse.2_Intron|uc001ysf.2_Intron					Parts of antibodies, mostly variable regions.												0																		---	---	---	---
ADAM6	8755	broad.mit.edu	37	14	106772128	106772128	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:106772128delA	uc010tyt.1	-											Parts of antibodies, mostly variable regions.												0																		---	---	---	---
ADAM6	8755	broad.mit.edu	37	14	106802196	106802197	+	Intron	INS	-	A	A	rs138774888	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:106802196_106802197insA	uc010tyt.1	-											Parts of antibodies, mostly variable regions.												0																		---	---	---	---
ADAM6	8755	broad.mit.edu	37	14	106804128	106804128	+	Intron	DEL	A	-	-	rs66645678		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:106804128delA	uc010tyt.1	-											Parts of antibodies, mostly variable regions.												0																		---	---	---	---
ADAM6	8755	broad.mit.edu	37	14	106853277	106853277	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:106853277delA	uc010tyt.1	-											Parts of antibodies, mostly variable regions.												0																		---	---	---	---
ADAM6	8755	broad.mit.edu	37	14	107235429	107235429	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:107235429delA	uc010tyt.1	-											Parts of antibodies, mostly variable regions.												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	15	20033695	20033695	+	IGR	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:20033695delC								None (None upstream) : GOLGA6L6 (703399 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	20139627	20139627	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:20139627delT								None (None upstream) : GOLGA6L6 (597467 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	20435366	20435366	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:20435366delA								None (None upstream) : GOLGA6L6 (301728 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	20439542	20439542	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:20439542delT								None (None upstream) : GOLGA6L6 (297552 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	20458728	20458728	+	IGR	DEL	T	-	-	rs4931924	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:20458728delT								None (None upstream) : GOLGA6L6 (278366 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	20589959	20589959	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:20589959delA	uc001ytg.2	-						uc010tyx.1_Intron					RecName: Full=Putative HERC2-like protein 3;																														---	---	---	---
Unknown	0	broad.mit.edu	37	15	20599326	20599326	+	Intron	DEL	T	-	-	rs60373366		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:20599326delT	uc001ytg.2	-						uc010tyx.1_Intron					RecName: Full=Putative HERC2-like protein 3;																														---	---	---	---
Unknown	0	broad.mit.edu	37	15	20608498	20608501	+	Intron	DEL	ATTG	-	-	rs141907926	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:20608498_20608501delATTG	uc001ytg.2	-						uc010tyx.1_Intron					RecName: Full=Putative HERC2-like protein 3;																														---	---	---	---
Unknown	0	broad.mit.edu	37	15	20616555	20616555	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:20616555delA	uc001ytg.2	-						uc010tyx.1_Intron|uc001yth.3_Intron					RecName: Full=Putative HERC2-like protein 3;																														---	---	---	---
Unknown	0	broad.mit.edu	37	15	20851184	20851184	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:20851184delT								GOLGA8C (70158 upstream) : BCL8 (18872 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	21150721	21150722	+	Intron	INS	-	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:21150721_21150722insT	uc001ytw.1	+											Homo sapiens hypothetical protein LOC348120, mRNA (cDNA clone IMAGE:4838061).																														---	---	---	---
Unknown	0	broad.mit.edu	37	15	21194928	21194929	+	Intron	DEL	TC	-	-	rs71455739	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:21194928_21194929delTC	uc001ytw.1	+											Homo sapiens hypothetical protein LOC348120, mRNA (cDNA clone IMAGE:4838061).																														---	---	---	---
Unknown	0	broad.mit.edu	37	15	21910170	21910170	+	IGR	DEL	T	-	-	rs142420042		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:21910170delT								NF1P1 (775545 upstream) : LOC646214 (22344 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	22463371	22463371	+	IGR	DEL	A	-	-	rs138556234		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:22463371delA								OR4N3P (48986 upstream) : MIR1268 (49858 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	22490836	22490836	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:22490836delT								OR4N3P (76451 upstream) : MIR1268 (22393 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	22534539	22534540	+	IGR	INS	-	AG	AG			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:22534539_22534540insAG								MIR1268 (21259 upstream) : GOLGA8DP (167745 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	22551671	22551671	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:22551671delT								MIR1268 (38391 upstream) : GOLGA8DP (150614 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	22671886	22671886	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:22671886delA								MIR1268 (158606 upstream) : GOLGA8DP (30399 downstream)																																			---	---	---	---
TUBGCP5	114791	broad.mit.edu	37	15	22862068	22862069	+	Intron	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-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	22870170	22870171	+	Intron	DEL	AA	-	-	rs35406170		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:22870170_22870171delAA	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	22902798	22902798	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:22902798delT	uc001yus.2	+						CYFIP1_uc001yut.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)														---	---	---	---
CYFIP1	23191	broad.mit.edu	37	15	22917513	22917514	+	Intron	INS	-	GGGCAGGAGAGGGGTT	GGGCAGGAGAGGGGTT	rs138137433	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:22917513_22917514insGGGCAGGAGAGGGGTT	uc001yus.2	+						CYFIP1_uc001yut.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)														---	---	---	---
CYFIP1	23191	broad.mit.edu	37	15	22950058	22950059	+	Intron	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:22950058_22950059delTT	uc001yus.2	+						CYFIP1_uc001yut.2_Intron|CYFIP1_uc010aya.1_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)														---	---	---	---
NIPA2	81614	broad.mit.edu	37	15	23005670	23005670	+	3'UTR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:23005670delT	uc001yux.2	-	8					NIPA2_uc001yuy.2_3'UTR|NIPA2_uc001yuz.2_3'UTR|NIPA2_uc001yva.2_3'UTR|NIPA2_uc001yvb.2_3'UTR|NIPA2_uc010ayb.2_3'UTR	NM_030922	NP_112184			non imprinted in Prader-Willi/Angelman syndrome							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)														---	---	---	---
NIPA2	81614	broad.mit.edu	37	15	23023674	23023675	+	Intron	INS	-	GAT	GAT	rs149309330	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:23023674_23023675insGAT	uc001yux.2	-						NIPA2_uc001yuy.2_Intron|NIPA2_uc001yuz.2_Intron|NIPA2_uc001yva.2_Intron|NIPA2_uc001yvb.2_Intron|NIPA2_uc010ayb.2_Intron	NM_030922	NP_112184			non imprinted in Prader-Willi/Angelman syndrome							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)														---	---	---	---
NIPA1	123606	broad.mit.edu	37	15	23060404	23060404	+	Intron	DEL	T	-	-	rs67975707		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:23060404delT	uc001yvc.2	-						NIPA1_uc001yvd.2_Intron|NIPA1_uc001yve.2_Intron	NM_144599	NP_653200			non-imprinted in Prader-Willi/Angelman syndrome						cell death	early endosome|integral to membrane|plasma membrane					0		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;4.18e-06)|Epithelial(43;3.97e-05)|BRCA - Breast invasive adenocarcinoma(123;0.00165)														---	---	---	---
Unknown	0	broad.mit.edu	37	15	23114116	23114116	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-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	23131706	23131706	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:23131706delA								NIPA1 (44863 upstream) : WHAMML1 (56025 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	23150868	23150868	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:23150868delT								NIPA1 (64025 upstream) : WHAMML1 (36863 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	24684137	24684137	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:24684137delT								PWRN2 (269042 upstream) : PWRN1 (94702 downstream)																																			---	---	---	---
SNRPN	6638	broad.mit.edu	37	15	25227367	25227367	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-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	25413631	25413631	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:25413631delT	uc001yyp.1	+						IPW_uc010aym.1_Intron|SNORD115-1_uc001yyq.1_5'Flank					Homo sapiens clone kid12 SNURF-SNRPN mRNA, downstream untranslated exons, alternatively spliced.												0																		---	---	---	---
UBE3A	7337	broad.mit.edu	37	15	25600932	25600932	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:25600932delT	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	25759126	25759127	+	IGR	DEL	TG	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:25759126_25759127delTG								UBE3A (74998 upstream) : ATP10A (164735 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	26248808	26248808	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:26248808delA								ATP10A (138491 upstream) : GABRB3 (539887 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	26625989	26625989	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:26625989delT								ATP10A (515672 upstream) : GABRB3 (162706 downstream)																																			---	---	---	---
GABRB3	2562	broad.mit.edu	37	15	26919667	26919668	+	Intron	DEL	TA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:26919667_26919668delTA	uc001zaz.2	-						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)													---	---	---	---
GABRB3	2562	broad.mit.edu	37	15	27040419	27040419	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:27040419delT	uc001zbb.2	-							NM_021912	NP_068712			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)													---	---	---	---
GABRB3	2562	broad.mit.edu	37	15	27050450	27050450	+	Intron	DEL	T	-	-	rs76313898		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:27050450delT	uc001zbb.2	-							NM_021912	NP_068712			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)													---	---	---	---
GABRB3	2562	broad.mit.edu	37	15	27156514	27156515	+	Intron	INS	-	CA	CA			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:27156514_27156515insCA	uc001zbb.2	-						GABRA5_uc001zbd.1_Intron	NM_021912	NP_068712			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)													---	---	---	---
OCA2	4948	broad.mit.edu	37	15	28042709	28042709	+	Intron	DEL	T	-	-	rs10706526		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:28042709delT	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	28388214	28388214	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:28388214delA	uc001zbj.2	-							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)														---	---	---	---
HERC2	8924	broad.mit.edu	37	15	28473276	28473279	+	Intron	DEL	AAAA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:28473276_28473279delAAAA	uc001zbj.2	-							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	28725822	28725822	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:28725822delT								GOLGA8G (88651 upstream) : WHAMML2 (256907 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	28962773	28962773	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:28962773delA								GOLGA8G (325602 upstream) : WHAMML2 (19956 downstream)																																			---	---	---	---
FAM189A1	23359	broad.mit.edu	37	15	29476192	29476192	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:29476192delT	uc010azk.1	-						FAM189A1_uc001zcn.2_Intron	NM_015307	NP_056122			hypothetical protein LOC23359							integral to membrane					0																		---	---	---	---
FAM189A1	23359	broad.mit.edu	37	15	29595767	29595769	+	Intron	DEL	GTT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:29595767_29595769delGTT	uc010azk.1	-							NM_015307	NP_056122			hypothetical protein LOC23359							integral to membrane					0																		---	---	---	---
Unknown	0	broad.mit.edu	37	15	30268868	30268869	+	IGR	INS	-	A	A	rs149191553	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:30268868_30268869insA								TJP1 (154162 upstream) : FAM7A3 (127066 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	30317957	30317957	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:30317957delT								TJP1 (203251 upstream) : FAM7A3 (77978 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	30318852	30318852	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:30318852delA								TJP1 (204146 upstream) : FAM7A3 (77083 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	30700365	30700365	+	5'Flank	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:30700365delG	uc001zeg.2	+											Homo sapiens mRNA for FLJ00278 protein.																														---	---	---	---
Unknown	0	broad.mit.edu	37	15	30736858	30736859	+	IGR	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:30736858_30736859delAA								CHRFAM7A (50994 upstream) : FAM7A2 (127899 downstream)																																			---	---	---	---
MTMR15	22909	broad.mit.edu	37	15	31230232	31230232	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:31230232delA	uc001zff.2	+						MTMR15_uc001zfe.2_Intron	NM_014967	NP_055782			myotubularin related protein 15 isoform a						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					---	---	---	---
TRPM1	4308	broad.mit.edu	37	15	31359898	31359898	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:31359898delT	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	31427208	31427208	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:31427208delA								TRPM1 (33284 upstream) : KLF13 (191875 downstream)																																			---	---	---	---
OTUD7A	161725	broad.mit.edu	37	15	32140650	32140650	+	Intron	DEL	T	-	-	rs9806670		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:32140650delT	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)														---	---	---	---
Unknown	0	broad.mit.edu	37	15	32312567	32312568	+	IGR	INS	-	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:32312567_32312568insC								OTUD7A (149575 upstream) : CHRNA7 (10158 downstream)																																			---	---	---	---
ARHGAP11A	9824	broad.mit.edu	37	15	32927960	32927960	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:32927960delT	uc001zgy.1	+						ARHGAP11A_uc010ubw.1_Intron|ARHGAP11A_uc001zgw.2_Intron|ARHGAP11A_uc001zgx.2_Intron|ARHGAP11A_uc010ubx.1_Intron	NM_014783	NP_055598			Rho GTPase activating protein 11A isoform 1						regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol	GTPase activator activity			skin(3)|breast(2)|urinary_tract(1)	6		all_lung(180;1.3e-11)		all cancers(64;3.34e-21)|Epithelial(43;2.64e-15)|GBM - Glioblastoma multiforme(186;5.17e-06)|BRCA - Breast invasive adenocarcinoma(123;0.00112)|Lung(196;0.227)														---	---	---	---
Unknown	0	broad.mit.edu	37	15	32990843	32990843	+	IGR	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:32990843delG								SCG5 (1545 upstream) : GREM1 (19362 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	33061212	33061213	+	IGR	INS	-	GAG	GAG	rs72521271	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:33061212_33061213insGAG								GREM1 (34346 upstream) : FMN1 (5134 downstream)																																			---	---	---	---
FMN1	342184	broad.mit.edu	37	15	33213881	33213881	+	Intron	DEL	T	-	-	rs113887412		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:33213881delT	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	33436028	33436028	+	IGR	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:33436028delC								FMN1 (75943 upstream) : RYR3 (167149 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	33456299	33456299	+	Intron	DEL	A	-	-	rs35591848		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:33456299delA	uc001zhh.2	-											RecName: Full=Formin-1; AltName: Full=Limb deformity protein homolog;																														---	---	---	---
RYR3	6263	broad.mit.edu	37	15	33706585	33706585	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:33706585delA	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)														---	---	---	---
CHRM5	1133	broad.mit.edu	37	15	34309335	34309336	+	Intron	DEL	GA	-	-	rs66703947		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:34309335_34309336delGA	uc001zhk.1	+						AVEN_uc001zhj.2_Intron|CHRM5_uc001zhl.1_5'Flank	NM_012125	NP_036257			cholinergic receptor, muscarinic 5						cell proliferation|inhibition of adenylate cyclase activity by muscarinic acetylcholine receptor signaling pathway	cell junction|integral to plasma membrane|postsynaptic membrane	muscarinic acetylcholine receptor activity|phosphatidylinositol phospholipase C activity			ovary(1)|central_nervous_system(1)	2		all_lung(180;1.76e-08)		all cancers(64;4.82e-17)|GBM - Glioblastoma multiforme(113;2.58e-06)|BRCA - Breast invasive adenocarcinoma(123;0.0262)	Atropine(DB00572)|Benzquinamide(DB00767)|Cryptenamine(DB00785)|Homatropine Methylbromide(DB00725)|Methotrimeprazine(DB01403)|Metixene(DB00340)|Olanzapine(DB00334)|Promazine(DB00420)|Promethazine(DB01069)|Propiomazine(DB00777)|Thiethylperazine(DB00372)													---	---	---	---
SLC12A6	9990	broad.mit.edu	37	15	34528550	34528551	+	Intron	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:34528550_34528551delTT	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_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)													---	---	---	---
SLC12A6	9990	broad.mit.edu	37	15	34543443	34543443	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:34543443delT	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)													---	---	---	---
AQR	9716	broad.mit.edu	37	15	35176362	35176362	+	Intron	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:35176362delC	uc001ziv.2	-							NM_014691	NP_055506			aquarius							catalytic step 2 spliceosome	RNA binding			large_intestine(1)	1		Lung NSC(122;8.7e-10)|all_lung(180;1.47e-08)		all cancers(64;4.34e-18)|GBM - Glioblastoma multiforme(113;4.59e-07)|BRCA - Breast invasive adenocarcinoma(123;0.0283)														---	---	---	---
AQR	9716	broad.mit.edu	37	15	35177037	35177037	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:35177037delA	uc001ziv.2	-							NM_014691	NP_055506			aquarius							catalytic step 2 spliceosome	RNA binding			large_intestine(1)	1		Lung NSC(122;8.7e-10)|all_lung(180;1.47e-08)		all cancers(64;4.34e-18)|GBM - Glioblastoma multiforme(113;4.59e-07)|BRCA - Breast invasive adenocarcinoma(123;0.0283)														---	---	---	---
Unknown	0	broad.mit.edu	37	15	35292399	35292400	+	IGR	DEL	TT	-	-	rs34550324		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:35292399_35292400delTT								ZNF770 (11945 upstream) : LOC723972 (237127 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	35610195	35610195	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:35610195delA								LOC723972 (79933 upstream) : ATPBD4 (52976 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	35981471	35981472	+	Intron	DEL	TT	-	-	rs78826251		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:35981471_35981472delTT	uc001zjc.2	+											Homo sapiens, Similar to LOC161538, clone IMAGE:5199550, mRNA.																														---	---	---	---
Unknown	0	broad.mit.edu	37	15	36252167	36252167	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:36252167delA								ATPBD4 (413763 upstream) : C15orf41 (619645 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	37129917	37129917	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:37129917delA								CSNK1A1P (19210 upstream) : LOC145845 (26727 downstream)																																			---	---	---	---
MEIS2	4212	broad.mit.edu	37	15	37360943	37360945	+	Intron	DEL	TTT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:37360943_37360945delTTT	uc001zjr.2	-						MEIS2_uc001zjl.2_Intron|MEIS2_uc010ucj.1_Intron|MEIS2_uc001zjm.2_Intron|MEIS2_uc001zjn.2_Intron|MEIS2_uc001zjo.2_Intron|MEIS2_uc001zjp.2_Intron|MEIS2_uc001zjs.2_Intron|MEIS2_uc001zju.2_Intron|MEIS2_uc001zjt.2_Intron	NM_170675	NP_733775			Meis homeobox 2 isoform c						negative regulation of transcription from RNA polymerase II promoter|transcription from RNA polymerase II promoter	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription corepressor activity			ovary(2)	2		all_epithelial(112;9.77e-14)|Lung NSC(122;1.42e-09)|all_lung(180;2.2e-08)|Ovarian(310;0.134)|Melanoma(134;0.155)		all cancers(64;9.33e-21)|GBM - Glioblastoma multiforme(113;1.71e-06)|BRCA - Breast invasive adenocarcinoma(123;0.0288)														---	---	---	---
Unknown	0	broad.mit.edu	37	15	37474358	37474358	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:37474358delT								MEIS2 (80858 upstream) : TMCO5A (752469 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	38278079	38278079	+	Intron	DEL	T	-	-	rs11284425		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:38278079delT	uc001zjx.1	+											Homo sapiens, clone IMAGE:5755094, mRNA.																														---	---	---	---
Unknown	0	broad.mit.edu	37	15	38394424	38394424	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:38394424delT								TMCO5A (134499 upstream) : SPRED1 (150628 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	38469504	38469505	+	Intron	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:38469504_38469505delTT	uc001zjy.2	-											Homo sapiens, clone IMAGE:3923347, mRNA.																														---	---	---	---
Unknown	0	broad.mit.edu	37	15	38913887	38913887	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-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	38914825	38914826	+	IGR	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:38914825_38914826delTT								RASGRP1 (57818 upstream) : C15orf53 (73973 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	39163810	39163810	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:39163810delT								C15orf53 (171571 upstream) : C15orf54 (379075 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	39645422	39645423	+	IGR	INS	-	A	A	rs139761941	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:39645422_39645423insA								C15orf54 (98374 upstream) : THBS1 (227857 downstream)																																			---	---	---	---
GPR176	11245	broad.mit.edu	37	15	40112505	40112506	+	Intron	DEL	AT	-	-	rs76658253		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:40112505_40112506delAT	uc001zkj.1	-						GPR176_uc010uck.1_Intron|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)														---	---	---	---
EIF2AK4	440275	broad.mit.edu	37	15	40224574	40224574	+	5'Flank	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:40224574delA	uc001zkm.1	+						EIF2AK4_uc001zkl.2_5'Flank	NM_001013703	NP_001013725			eukaryotic translation initiation factor 2 alpha						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)														---	---	---	---
BUB1B	701	broad.mit.edu	37	15	40509619	40509619	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:40509619delT	uc001zkx.3	+						PAK6_uc010bbl.2_5'Flank|PAK6_uc010bbm.2_5'Flank	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				---	---	---	---
RAD51	5888	broad.mit.edu	37	15	40985935	40985935	+	5'Flank	DEL	T	-	-	rs113848177		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:40985935delT	uc001zmi.3	+						RAD51_uc010bbw.2_5'Flank|RAD51_uc010bbx.2_5'Flank|RAD51_uc001zmk.3_5'Flank|RAD51_uc001zml.3_5'Flank	NM_002875	NP_002866			RAD51 homolog protein isoform 1						DNA recombinase assembly|DNA unwinding involved in replication|mitotic recombination|positive regulation of DNA ligation|protein homooligomerization|reciprocal meiotic recombination	mitochondrial matrix|nucleus|perinuclear region of cytoplasm|PML body	ATP binding|damaged DNA binding|double-stranded DNA binding|identical protein binding|protein C-terminus binding|single-stranded DNA binding|single-stranded DNA-dependent ATPase activity				0		all_cancers(109;1.19e-18)|all_epithelial(112;2.33e-15)|Lung NSC(122;5.34e-11)|all_lung(180;1.33e-09)|Melanoma(134;0.0574)|Ovarian(310;0.0822)|Colorectal(260;0.0946)		GBM - Glioblastoma multiforme(113;1.45e-05)|BRCA - Breast invasive adenocarcinoma(123;0.000421)|COAD - Colon adenocarcinoma(120;0.163)									Homologous_recombination					---	---	---	---
RTF1	23168	broad.mit.edu	37	15	41751574	41751574	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:41751574delA	uc001zny.2	+							NM_015138	NP_055953			Paf1/RNA polymerase II complex component						histone modification|regulation of transcription, DNA-dependent|transcription initiation, DNA-dependent	nucleoplasm	protein binding|single-stranded DNA binding			ovary(2)	2		all_cancers(109;1.79e-19)|all_epithelial(112;8.18e-17)|Lung NSC(122;3.16e-11)|all_lung(180;8.14e-10)|Melanoma(134;0.0179)|Colorectal(260;0.0946)|Ovarian(310;0.143)		OV - Ovarian serous cystadenocarcinoma(18;1.15e-16)|GBM - Glioblastoma multiforme(113;1.81e-06)|BRCA - Breast invasive adenocarcinoma(123;0.119)														---	---	---	---
RTF1	23168	broad.mit.edu	37	15	41756455	41756456	+	Intron	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:41756455_41756456delTT	uc001zny.2	+							NM_015138	NP_055953			Paf1/RNA polymerase II complex component						histone modification|regulation of transcription, DNA-dependent|transcription initiation, DNA-dependent	nucleoplasm	protein binding|single-stranded DNA binding			ovary(2)	2		all_cancers(109;1.79e-19)|all_epithelial(112;8.18e-17)|Lung NSC(122;3.16e-11)|all_lung(180;8.14e-10)|Melanoma(134;0.0179)|Colorectal(260;0.0946)|Ovarian(310;0.143)		OV - Ovarian serous cystadenocarcinoma(18;1.15e-16)|GBM - Glioblastoma multiforme(113;1.81e-06)|BRCA - Breast invasive adenocarcinoma(123;0.119)														---	---	---	---
MAPKBP1	23005	broad.mit.edu	37	15	42073937	42073937	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:42073937delT	uc001zok.3	+						MAPKBP1_uc001zoj.3_Intron|MAPKBP1_uc010bcj.2_Intron|MAPKBP1_uc010bci.2_Intron|MAPKBP1_uc010udb.1_Intron|MAPKBP1_uc010bck.2_Intron	NM_001128608	NP_001122080			mitogen-activated protein kinase binding protein											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)														---	---	---	---
Unknown	0	broad.mit.edu	37	15	42269443	42269446	+	IGR	DEL	ACAC	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:42269443_42269446delACAC								EHD4 (4688 upstream) : PLA2G4E (6506 downstream)																																			---	---	---	---
LRRC57	255252	broad.mit.edu	37	15	42836388	42836388	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:42836388delT	uc001zqd.1	-						LRRC57_uc001zqc.2_Intron	NM_153260	NP_694992			leucine rich repeat containing 57												0		all_cancers(109;1.99e-12)|all_epithelial(112;5.11e-11)|Lung NSC(122;4.53e-07)|all_lung(180;1.64e-06)|Melanoma(134;0.0262)		GBM - Glioblastoma multiforme(94;6.87e-07)														---	---	---	---
LRRC57	255252	broad.mit.edu	37	15	42837014	42837015	+	Intron	DEL	CA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:42837014_42837015delCA	uc001zqd.1	-						LRRC57_uc001zqc.2_Intron	NM_153260	NP_694992			leucine rich repeat containing 57												0		all_cancers(109;1.99e-12)|all_epithelial(112;5.11e-11)|Lung NSC(122;4.53e-07)|all_lung(180;1.64e-06)|Melanoma(134;0.0262)		GBM - Glioblastoma multiforme(94;6.87e-07)														---	---	---	---
HAUS2	55142	broad.mit.edu	37	15	42842875	42842875	+	Intron	DEL	T	-	-	rs11354771		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:42842875delT	uc001zqe.2	+						HAUS2_uc010udi.1_Intron|HAUS2_uc001zqf.2_Intron|LRRC57_uc001zqd.1_5'Flank|LRRC57_uc001zqc.2_5'Flank	NM_018097	NP_060567			centrosomal protein 27kDa isoform 1						cell division|centrosome organization|G2/M transition of mitotic cell cycle|mitosis|spindle assembly	centrosome|cytosol|HAUS complex|microtubule|spindle					0																		---	---	---	---
TGM5	9333	broad.mit.edu	37	15	43528260	43528262	+	Intron	DEL	TTC	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:43528260_43528262delTTC	uc001zrd.1	-						TGM5_uc001zrc.1_Intron|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)													---	---	---	---
Unknown	0	broad.mit.edu	37	15	43565956	43565956	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:43565956delT								TGM5 (6901 upstream) : TGM7 (2523 downstream)																																			---	---	---	---
TP53BP1	7158	broad.mit.edu	37	15	43705010	43705011	+	Intron	INS	-	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:43705010_43705011insA	uc001zrs.2	-						TP53BP1_uc010udp.1_Intron|TP53BP1_uc001zrq.3_Intron|TP53BP1_uc001zrr.3_Intron|TP53BP1_uc001zrp.2_Intron	NM_005657	NP_005648			tumor protein p53 binding protein 1 isoform 3						double-strand break repair via homologous recombination|positive regulation of transcription from RNA polymerase II promoter	condensed chromosome kinetochore|cytoplasm|nucleoplasm	p53 binding|RNA polymerase II activating transcription factor binding|RNA polymerase II transcription cofactor activity			ovary(2)|skin(2)|large_intestine(1)|pancreas(1)|kidney(1)	7		all_cancers(109;6.94e-11)|all_epithelial(112;2.69e-09)|Lung NSC(122;7.86e-07)|all_lung(180;7.84e-06)|Melanoma(134;0.0728)		GBM - Glioblastoma multiforme(94;1.59e-06)									Direct_reversal_of_damage|Other_conserved_DNA_damage_response_genes					---	---	---	---
PDIA3	2923	broad.mit.edu	37	15	44058333	44058337	+	Intron	DEL	AAAAA	-	-	rs34486889		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:44058333_44058337delAAAAA	uc001zsu.2	+						PDIA3_uc010bdp.2_Intron|PDIA3_uc010ued.1_Intron	NM_005313	NP_005304			protein disulfide-isomerase A3 precursor						cell redox homeostasis|glycerol ether metabolic process|post-translational protein modification|protein folding|protein import into nucleus|protein N-linked glycosylation via asparagine|protein retention in ER lumen|signal transduction	endoplasmic reticulum lumen|melanosome	cysteine-type endopeptidase activity|electron carrier activity|phospholipase C activity|protein binding|protein disulfide isomerase activity|protein disulfide oxidoreductase activity			ovary(1)|skin(1)	2		all_cancers(109;2.61e-15)|all_epithelial(112;1.12e-12)|Lung NSC(122;2.17e-08)|all_lung(180;2.45e-07)|Melanoma(134;0.027)|Colorectal(260;0.215)		GBM - Glioblastoma multiforme(94;9.48e-07)														---	---	---	---
ELL3	80237	broad.mit.edu	37	15	44077598	44077598	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:44077598delT	uc001zsx.1	-							NM_025165	NP_079441			elongation factor RNA polymerase II-like 3						positive regulation of transcription elongation, DNA-dependent|positive regulation of transcription from RNA polymerase II promoter|spermatogenesis|transcription elongation from RNA polymerase II promoter	transcription elongation factor complex				ovary(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;7.81e-07)														---	---	---	---
WDR76	79968	broad.mit.edu	37	15	44140281	44140281	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:44140281delA	uc001zti.1	+							NM_024908	NP_079184			WD repeat domain 76												0		all_cancers(109;3.26e-11)|all_epithelial(112;4.82e-09)|Lung NSC(122;1.61e-06)|all_lung(180;1.5e-05)|Melanoma(134;0.0417)		all cancers(107;3.78e-21)|GBM - Glioblastoma multiforme(94;5.04e-07)														---	---	---	---
CASC4	113201	broad.mit.edu	37	15	44665655	44665655	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:44665655delA	uc001zto.1	+						CASC4_uc001ztp.2_Intron|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)														---	---	---	---
CASC4	113201	broad.mit.edu	37	15	44697825	44697825	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:44697825delT	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	44741008	44741008	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:44741008delA	uc001ztr.2	+						CTDSPL2_uc001zts.2_Intron|CTDSPL2_uc001ztt.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	44776398	44776398	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:44776398delT	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	44796907	44796908	+	Intron	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:44796907_44796908delAA	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)														---	---	---	---
SPG11	80208	broad.mit.edu	37	15	44944222	44944222	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:44944222delA	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	45763487	45763487	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:45763487delA	uc001zvi.1	+											Homo sapiens cDNA FLJ32124 fis, clone PEBLM1000180.																														---	---	---	---
PLDN	26258	broad.mit.edu	37	15	45878428	45878428	+	5'Flank	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:45878428delT	uc001zvq.2	+						PLDN_uc001zvr.2_5'Flank|PLDN_uc001zvs.2_5'Flank	NM_012388	NP_036520			pallidin						post-Golgi vesicle-mediated transport|synaptic vesicle docking involved in exocytosis	BLOC-1 complex|endomembrane system|membrane	identical protein binding|syntaxin-13 binding			skin(1)	1		Lung NSC(122;1.6e-06)|all_lung(180;1.13e-05)|Melanoma(134;0.027)		all cancers(107;6.58e-18)|GBM - Glioblastoma multiforme(94;5.91e-07)														---	---	---	---
PLDN	26258	broad.mit.edu	37	15	45897794	45897794	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:45897794delT	uc001zvq.2	+						PLDN_uc001zvr.2_Intron|PLDN_uc001zvs.2_Intron	NM_012388	NP_036520			pallidin						post-Golgi vesicle-mediated transport|synaptic vesicle docking involved in exocytosis	BLOC-1 complex|endomembrane system|membrane	identical protein binding|syntaxin-13 binding			skin(1)	1		Lung NSC(122;1.6e-06)|all_lung(180;1.13e-05)|Melanoma(134;0.027)		all cancers(107;6.58e-18)|GBM - Glioblastoma multiforme(94;5.91e-07)														---	---	---	---
Unknown	0	broad.mit.edu	37	15	45902861	45902861	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:45902861delA								PLDN (953 upstream) : SQRDL (20485 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	45989733	45989735	+	IGR	DEL	TTA	-	-	rs71826377		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:45989733_45989735delTTA								SQRDL (6255 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	47361680	47361680	+	IGR	DEL	C	-	-	rs139409694	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:47361680delC								None (None upstream) : SEMA6D (114723 downstream)																																			---	---	---	---
SEMA6D	80031	broad.mit.edu	37	15	47687098	47687098	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:47687098delT	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)														---	---	---	---
SLC12A1	6557	broad.mit.edu	37	15	48526950	48526951	+	Intron	DEL	AA	-	-	rs77430774		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:48526950_48526951delAA	uc001zwn.3	+						SLC12A1_uc010uew.1_Intron|SLC12A1_uc010bem.2_Intron|SLC12A1_uc010uex.1_Intron|SLC12A1_uc001zwq.3_Intron|SLC12A1_uc001zwr.3_Intron	NM_000338	NP_000329			sodium potassium chloride cotransporter 2						potassium ion transport|sodium ion transport	integral to membrane|membrane fraction	sodium:potassium:chloride symporter activity			ovary(1)|central_nervous_system(1)	2		all_lung(180;0.00219)		all cancers(107;1.76e-09)|GBM - Glioblastoma multiforme(94;1.48e-06)	Bumetanide(DB00887)|Chlormerodrin(DB00534)|Chlorthalidone(DB00310)|Ethacrynic acid(DB00903)|Furosemide(DB00695)|Hydroflumethiazide(DB00774)|Methyclothiazide(DB00232)|Metolazone(DB00524)|Potassium Chloride(DB00761)|Torasemide(DB00214)|Trichlormethiazide(DB01021)													---	---	---	---
SLC12A1	6557	broad.mit.edu	37	15	48577440	48577440	+	Frame_Shift_Del	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:48577440delA	uc001zwn.3	+	21	2839	c.2623delA	c.(2623-2625)AAAfs	p.K875fs	SLC12A1_uc010uew.1_Frame_Shift_Del_p.K681fs|SLC12A1_uc001zwq.3_Frame_Shift_Del_p.K646fs|SLC12A1_uc001zwr.3_Frame_Shift_Del_p.K602fs	NM_000338	NP_000329	Q13621	S12A1_HUMAN	sodium potassium chloride cotransporter 2	875	Cytoplasmic (Potential).				potassium ion transport|sodium ion transport	integral to membrane|membrane fraction	sodium:potassium:chloride symporter activity			ovary(1)|central_nervous_system(1)	2		all_lung(180;0.00219)		all cancers(107;1.76e-09)|GBM - Glioblastoma multiforme(94;1.48e-06)	Bumetanide(DB00887)|Chlormerodrin(DB00534)|Chlorthalidone(DB00310)|Ethacrynic acid(DB00903)|Furosemide(DB00695)|Hydroflumethiazide(DB00774)|Methyclothiazide(DB00232)|Metolazone(DB00524)|Potassium Chloride(DB00761)|Torasemide(DB00214)|Trichlormethiazide(DB01021)													---	---	---	---
CEP152	22995	broad.mit.edu	37	15	49037009	49037009	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:49037009delA	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)														---	---	---	---
Unknown	0	broad.mit.edu	37	15	49115465	49115465	+	IGR	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:49115465delC								CEP152 (12281 upstream) : SHC4 (469 downstream)																																			---	---	---	---
C15orf33	196951	broad.mit.edu	37	15	49894363	49894363	+	Intron	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:49894363delG	uc001zxl.2	-						C15orf33_uc001zxm.2_Intron	NM_152647	NP_689860			hypothetical protein LOC196951											ovary(1)	1		all_lung(180;0.00187)		all cancers(107;3.45e-08)|GBM - Glioblastoma multiforme(94;0.000124)														---	---	---	---
Unknown	0	broad.mit.edu	37	15	50011497	50011497	+	IGR	DEL	T	-	-	rs67518496		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:50011497delT								DTWD1 (74165 upstream) : ATP8B4 (138939 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	50043825	50043825	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:50043825delA								DTWD1 (106493 upstream) : ATP8B4 (106611 downstream)																																			---	---	---	---
HDC	3067	broad.mit.edu	37	15	50556655	50556655	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:50556655delA	uc001zxz.2	-						HDC_uc010uff.1_Intron|HDC_uc010bet.1_Intron|HDC_uc010beu.1_Intron	NM_002112	NP_002103			histidine decarboxylase						catecholamine biosynthetic process|histidine metabolic process		histidine decarboxylase activity			large_intestine(2)|skin(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)	6		all_lung(180;0.0138)		all cancers(107;1.12e-06)|GBM - Glioblastoma multiforme(94;9.95e-05)	L-Histidine(DB00117)|Pyridoxal Phosphate(DB00114)													---	---	---	---
Unknown	0	broad.mit.edu	37	15	50684432	50684432	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:50684432delA								LOC100129387 (33931 upstream) : USP8 (32147 downstream)																																			---	---	---	---
TRPM7	54822	broad.mit.edu	37	15	50855784	50855784	+	Intron	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:50855784delG	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)														---	---	---	---
Unknown	0	broad.mit.edu	37	15	51301719	51301720	+	IGR	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:51301719_51301720delTT								AP4E1 (3622 upstream) : TNFAIP8L3 (47081 downstream)																																			---	---	---	---
TMOD3	29766	broad.mit.edu	37	15	52154828	52154828	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:52154828delT	uc002abm.2	+							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-4200-01A-01D-1126-08	TCGA-BR-4200-11A-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	52452149	52452150	+	Intron	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:52452149_52452150delTT	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)														---	---	---	---
MYO5C	55930	broad.mit.edu	37	15	52524296	52524296	+	Intron	DEL	A	-	-	rs72456983		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:52524296delA	uc010bff.2	-						MYO5C_uc010uga.1_Intron|MYO5C_uc010ugb.1_Intron	NM_018728	NP_061198			myosin VC							myosin complex	actin binding|ATP binding|calmodulin binding|motor activity			ovary(7)|central_nervous_system(3)|large_intestine(2)|skin(2)	14				all cancers(107;0.0137)														---	---	---	---
Unknown	0	broad.mit.edu	37	15	53164421	53164423	+	IGR	DEL	AAA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:53164421_53164423delAAA								ONECUT1 (82212 upstream) : WDR72 (641515 downstream)																																			---	---	---	---
WDR72	256764	broad.mit.edu	37	15	53957396	53957396	+	Intron	DEL	T	-	-	rs75991135		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:53957396delT	uc002acj.2	-						WDR72_uc010bfi.1_Intron	NM_182758	NP_877435			WD repeat domain 72											lung(1)|skin(1)	2				all cancers(107;0.0511)														---	---	---	---
WDR72	256764	broad.mit.edu	37	15	53961909	53961909	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:53961909delA	uc002acj.2	-						WDR72_uc010bfi.1_Intron	NM_182758	NP_877435			WD repeat domain 72											lung(1)|skin(1)	2				all cancers(107;0.0511)														---	---	---	---
UNC13C	440279	broad.mit.edu	37	15	54355711	54355711	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:54355711delT	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	54642192	54642193	+	Intron	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:54642192_54642193delTT	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)														---	---	---	---
Unknown	0	broad.mit.edu	37	15	54970024	54970024	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:54970024delA								UNC13C (49219 upstream) : RSL24D1 (503497 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	55028736	55028736	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:55028736delA								UNC13C (107931 upstream) : RSL24D1 (444785 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	55142418	55142418	+	IGR	DEL	A	-	-	rs34892940		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:55142418delA								UNC13C (221613 upstream) : RSL24D1 (331103 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	55472602	55472603	+	IGR	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:55472602_55472603delAA								UNC13C (551797 upstream) : RSL24D1 (918 downstream)																																			---	---	---	---
PIGB	9488	broad.mit.edu	37	15	55637455	55637455	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:55637455delA	uc002act.2	+						PIGB_uc010ugg.1_Intron	NM_004855	NP_004846			phosphatidylinositol glycan, class B						C-terminal protein lipidation|preassembly of GPI anchor in ER membrane	integral to membrane|intrinsic to endoplasmic reticulum membrane	glycolipid mannosyltransferase activity				0				all cancers(107;0.0255)														---	---	---	---
CCPG1	9236	broad.mit.edu	37	15	55784479	55784479	+	Intron	DEL	A	-	-	rs11312285		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:55784479delA	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)														---	---	---	---
PRTG	283659	broad.mit.edu	37	15	56010827	56010828	+	Intron	DEL	AA	-	-	rs142878423		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:56010827_56010828delAA	uc002adg.2	-							NM_173814	NP_776175			protogenin precursor						multicellular organismal development	integral to membrane				large_intestine(1)|ovary(1)|skin(1)	3				all cancers(107;0.00891)|GBM - Glioblastoma multiforme(80;0.135)														---	---	---	---
NEDD4	4734	broad.mit.edu	37	15	56242150	56242150	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:56242150delA	uc002adl.2	-							NM_006154	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	56315017	56315018	+	IGR	DEL	AA	-	-	rs2175103	by1000genomes;by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:56315017_56315018delAA								NEDD4 (29182 upstream) : RFX7 (64461 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	56324579	56324579	+	IGR	DEL	T	-	-	rs113161754		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:56324579delT								NEDD4 (38744 upstream) : RFX7 (54900 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	56851837	56851837	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:56851837delT	uc002ads.2	-											Homo sapiens cDNA clone IMAGE:5275275.																														---	---	---	---
ZNF280D	54816	broad.mit.edu	37	15	56983810	56983810	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:56983810delA	uc002adu.2	-						ZNF280D_uc002adv.2_Intron|ZNF280D_uc010bfq.2_Intron|ZNF280D_uc002adw.1_Intron|ZNF280D_uc010bfr.1_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)														---	---	---	---
ZNF280D	54816	broad.mit.edu	37	15	57170580	57170581	+	Intron	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:57170580_57170581delAA	uc002adw.1	-							NM_001002843	NP_001002843			suppressor of hairy wing homolog 4 isoform 2						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	57284307	57284308	+	Intron	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:57284307_57284308delAA	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								---	---	---	---
TCF12	6938	broad.mit.edu	37	15	57300160	57300161	+	Intron	DEL	TC	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:57300160_57300161delTC	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								---	---	---	---
CGNL1	84952	broad.mit.edu	37	15	57729189	57729190	+	Intron	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:57729189_57729190delAA	uc002aeg.2	+						CGNL1_uc010bfw.2_Intron	NM_032866	NP_116255			cingulin-like 1							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)														---	---	---	---
CGNL1	84952	broad.mit.edu	37	15	57767850	57767852	+	Intron	DEL	TCT	-	-	rs79013528		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:57767850_57767852delTCT	uc002aeg.2	+						CGNL1_uc010bfw.2_Intron	NM_032866	NP_116255			cingulin-like 1							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)														---	---	---	---
Unknown	0	broad.mit.edu	37	15	58139874	58139874	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:58139874delT								GCOM1 (130122 upstream) : ALDH1A2 (105754 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	58159186	58159186	+	IGR	DEL	T	-	-	rs145052074		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:58159186delT								GCOM1 (149434 upstream) : ALDH1A2 (86442 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	58662677	58662678	+	IGR	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:58662677_58662678delAA								ALDH1A2 (91215 upstream) : LIPC (40097 downstream)																																			---	---	---	---
FAM63B	54629	broad.mit.edu	37	15	59139120	59139120	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:59139120delA	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	59246177	59246179	+	IGR	DEL	AAA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:59246177_59246179delAAA								SLTM (20325 upstream) : RNF111 (33686 downstream)																																			---	---	---	---
MYO1E	4643	broad.mit.edu	37	15	59447604	59447604	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:59447604delT	uc002aga.2	-							NM_004998	NP_004989			myosin IE						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)														---	---	---	---
MYO1E	4643	broad.mit.edu	37	15	59660945	59660945	+	Intron	DEL	A	-	-	rs71996121		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:59660945delA	uc002aga.2	-							NM_004998	NP_004989			myosin IE						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)														---	---	---	---
Unknown	0	broad.mit.edu	37	15	59707021	59707021	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:59707021delT								MYO1E (41950 upstream) : FAM81A (23351 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	59817572	59817572	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:59817572delT								FAM81A (1821 upstream) : GCNT3 (86410 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	59826109	59826109	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:59826109delA								FAM81A (10358 upstream) : GCNT3 (77873 downstream)																																			---	---	---	---
BNIP2	663	broad.mit.edu	37	15	59970050	59970050	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:59970050delA	uc010uhc.1	-						BNIP2_uc010uhb.1_Intron	NM_004330	NP_004321			BCL2/adenovirus E1B 19kD interacting protein 2						anti-apoptosis|apoptosis|positive regulation of muscle cell differentiation	nuclear envelope|perinuclear region of cytoplasm	calcium ion binding|GTPase activator activity|protein binding			ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	15	60384176	60384176	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:60384176delA								FOXB1 (55768 upstream) : ANXA2 (255175 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	60487600	60487611	+	IGR	DEL	GAGGAGGAAGAC	-	-	rs71723521		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:60487600_60487611delGAGGAGGAAGAC								FOXB1 (159192 upstream) : ANXA2 (151740 downstream)																																			---	---	---	---
NARG2	79664	broad.mit.edu	37	15	60747651	60747651	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:60747651delA	uc002agp.2	-						NARG2_uc002ago.2_Intron|NARG2_uc002agq.3_5'Flank|NARG2_uc010bgk.2_Intron|NARG2_uc002agr.1_Intron	NM_024611	NP_078887			NMDA receptor regulated 2 isoform a							nucleus				ovary(1)|lung(1)	2																		---	---	---	---
RORA	6095	broad.mit.edu	37	15	60878655	60878656	+	Intron	DEL	GT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:60878655_60878656delGT	uc002agv.2	-						RORA_uc002agt.3_Intron|RORA_uc002agw.2_Intron|RORA_uc002agx.2_Intron	NM_134260	NP_599022			RAR-related orphan receptor A isoform b						positive regulation of transcription from RNA polymerase II promoter|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor	nucleoplasm	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|steroid hormone receptor activity|zinc ion binding			large_intestine(1)|ovary(1)	2																		---	---	---	---
RORA	6095	broad.mit.edu	37	15	61009600	61009601	+	Intron	INS	-	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:61009600_61009601insT	uc002agx.2	-							NM_134261	NP_599023			RAR-related orphan receptor A isoform a						positive regulation of transcription from RNA polymerase II promoter|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor	nucleoplasm	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|steroid hormone receptor activity|zinc ion binding			large_intestine(1)|ovary(1)	2																		---	---	---	---
RORA	6095	broad.mit.edu	37	15	61274034	61274034	+	Intron	DEL	T	-	-	rs112592138		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:61274034delT	uc002agx.2	-							NM_134261	NP_599023			RAR-related orphan receptor A isoform a						positive regulation of transcription from RNA polymerase II promoter|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor	nucleoplasm	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|steroid hormone receptor activity|zinc ion binding			large_intestine(1)|ovary(1)	2																		---	---	---	---
RORA	6095	broad.mit.edu	37	15	61375281	61375281	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:61375281delA	uc002agx.2	-							NM_134261	NP_599023			RAR-related orphan receptor A isoform a						positive regulation of transcription from RNA polymerase II promoter|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor	nucleoplasm	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|steroid hormone receptor activity|zinc ion binding			large_intestine(1)|ovary(1)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	15	61605861	61605861	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:61605861delT								RORA (84359 upstream) : VPS13C (538731 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	61882485	61882485	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:61882485delA								RORA (360983 upstream) : VPS13C (262107 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	62032912	62032912	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:62032912delT								RORA (511410 upstream) : VPS13C (111680 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	62110022	62110022	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:62110022delA								RORA (588520 upstream) : VPS13C (34570 downstream)																																			---	---	---	---
VPS13C	54832	broad.mit.edu	37	15	62254181	62254181	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:62254181delT	uc002agz.2	-						VPS13C_uc002aha.2_Intron|VPS13C_uc002ahb.1_Intron|VPS13C_uc002ahc.1_Intron	NM_020821	NP_065872			vacuolar protein sorting 13C protein isoform 2A						protein localization					ovary(2)	2																		---	---	---	---
VPS13C	54832	broad.mit.edu	37	15	62289068	62289069	+	Intron	DEL	AC	-	-	rs139662140		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:62289068_62289069delAC	uc002agz.2	-						VPS13C_uc002aha.2_Intron|VPS13C_uc002ahb.1_Intron|VPS13C_uc002ahc.1_Intron	NM_020821	NP_065872			vacuolar protein sorting 13C protein isoform 2A						protein localization					ovary(2)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	15	62507694	62507694	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:62507694delT								C2CD4B (50212 upstream) : MGC15885 (421677 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	62582781	62582781	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:62582781delA								C2CD4B (125299 upstream) : MGC15885 (346590 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	62837135	62837137	+	IGR	DEL	TTT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:62837135_62837137delTTT								C2CD4B (379653 upstream) : MGC15885 (92234 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	63235784	63235784	+	IGR	DEL	C	-	-	rs151303053	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:63235784delC								TLN2 (98957 upstream) : TPM1 (99054 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	63261483	63261483	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:63261483delT								TLN2 (124656 upstream) : TPM1 (73355 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	63463091	63463091	+	IGR	DEL	A	-	-	rs34908588		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:63463091delA								RPS27L (13350 upstream) : RAB8B (18637 downstream)																																			---	---	---	---
RAB8B	51762	broad.mit.edu	37	15	63547690	63547690	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:63547690delT	uc002alz.2	+						RAB8B_uc010uih.1_Intron	NM_016530	NP_057614			RAB8B, member RAS oncogene family						protein transport|small GTPase mediated signal transduction	plasma membrane	GTP binding|GTPase activity			ovary(1)|kidney(1)	2																		---	---	---	---
USP3	9960	broad.mit.edu	37	15	63835499	63835499	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:63835499delA	uc002amf.2	+						USP3_uc010uii.1_Intron|USP3_uc002amg.2_Intron|USP3_uc002amh.2_Intron|USP3_uc010uij.1_Intron|USP3_uc010uik.1_Intron|USP3_uc010bgs.2_Intron|USP3_uc002ami.2_Intron	NM_006537	NP_006528			ubiquitin thiolesterase 3						DNA repair|histone deubiquitination|mitotic cell cycle|regulation of protein stability|ubiquitin-dependent protein catabolic process	nuclear chromatin	histone binding|ubiquitin thiolesterase activity|ubiquitin-specific protease activity|zinc ion binding			lung(1)	1				GBM - Glioblastoma multiforme(80;0.0187)														---	---	---	---
USP3	9960	broad.mit.edu	37	15	63854986	63854986	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:63854986delT	uc002amf.2	+						USP3_uc010uii.1_Intron|USP3_uc002amg.2_Intron|USP3_uc002amh.2_Intron|USP3_uc010uij.1_Intron|USP3_uc010uik.1_Intron|USP3_uc010bgs.2_Intron|USP3_uc002ami.2_Intron	NM_006537	NP_006528			ubiquitin thiolesterase 3						DNA repair|histone deubiquitination|mitotic cell cycle|regulation of protein stability|ubiquitin-dependent protein catabolic process	nuclear chromatin	histone binding|ubiquitin thiolesterase activity|ubiquitin-specific protease activity|zinc ion binding			lung(1)	1				GBM - Glioblastoma multiforme(80;0.0187)														---	---	---	---
USP3	9960	broad.mit.edu	37	15	63869274	63869275	+	Intron	DEL	AT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:63869274_63869275delAT	uc002amf.2	+						USP3_uc002amg.2_Intron|USP3_uc002amh.2_Intron|USP3_uc010uij.1_Intron|USP3_uc010uik.1_Intron|USP3_uc010bgs.2_Intron|USP3_uc002ami.2_Intron	NM_006537	NP_006528			ubiquitin thiolesterase 3						DNA repair|histone deubiquitination|mitotic cell cycle|regulation of protein stability|ubiquitin-dependent protein catabolic process	nuclear chromatin	histone binding|ubiquitin thiolesterase activity|ubiquitin-specific protease activity|zinc ion binding			lung(1)	1				GBM - Glioblastoma multiforme(80;0.0187)														---	---	---	---
HERC1	8925	broad.mit.edu	37	15	64027312	64027313	+	Intron	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:64027312_64027313delAA	uc002amp.2	-						HERC1_uc010uil.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																		---	---	---	---
DAPK2	23604	broad.mit.edu	37	15	64293085	64293085	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:64293085delT	uc002amr.2	-						DAPK2_uc010uim.1_Intron|DAPK2_uc010bgu.1_Intron	NM_014326	NP_055141			death-associated kinase 2						apoptosis|induction of apoptosis|intracellular protein kinase cascade	cytoplasm	ATP binding|calmodulin binding|calmodulin-dependent protein kinase activity|identical protein binding			stomach(1)|central_nervous_system(1)	2				LUAD - Lung adenocarcinoma(2;0.215)														---	---	---	---
SNX1	6642	broad.mit.edu	37	15	64410941	64410941	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:64410941delT	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	65017914	65017914	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:65017914delA								OAZ2 (22452 upstream) : RBPMS2 (14184 downstream)																																			---	---	---	---
DPP8	54878	broad.mit.edu	37	15	65804975	65804975	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:65804975delA	uc002aov.2	-						DPP8_uc002aow.2_Intron|DPP8_uc010uiv.1_Intron|DPP8_uc002aox.2_Intron|DPP8_uc002aoy.2_Intron|DPP8_uc002aoz.2_Intron|DPP8_uc010bhj.2_Intron	NM_130434	NP_569118			dipeptidyl peptidase 8 isoform 1						immune response|proteolysis	cytoplasm|membrane|nucleus	aminopeptidase activity|dipeptidyl-peptidase activity|serine-type peptidase activity			ovary(1)	1																		---	---	---	---
PTPLAD1	51495	broad.mit.edu	37	15	65822157	65822158	+	5'Flank	INS	-	AAC	AAC			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:65822157_65822158insAAC	uc002apc.2	+						PTPLAD1_uc002apb.1_5'Flank|PTPLAD1_uc010uiw.1_5'Flank	NM_016395	NP_057479			protein tyrosine phosphatase-like A domain						activation of JUN kinase activity|fatty acid biosynthetic process|I-kappaB kinase/NF-kappaB cascade|Rac protein signal transduction	endoplasmic reticulum membrane|integral to membrane	GTPase activator activity|lyase activity|protein binding				0																		---	---	---	---
DENND4A	10260	broad.mit.edu	37	15	65957473	65957474	+	Intron	INS	-	A	A	rs28577871		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:65957473_65957474insA	uc002aph.2	-						DENND4A_uc002api.2_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	66476306	66476306	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:66476306delA	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																		---	---	---	---
TIPIN	54962	broad.mit.edu	37	15	66643826	66643827	+	Intron	INS	-	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:66643826_66643827insA	uc002apr.2	-						TIPIN_uc010ujn.1_Intron|TIPIN_uc010ujo.1_Intron	NM_017858	NP_060328			TIMELESS interacting protein						cell division|DNA replication checkpoint|intra-S DNA damage checkpoint|mitosis|positive regulation of cell proliferation|regulation of DNA replication involved in S phase|replication fork protection	cytoplasm|nuclear chromatin	protein binding			ovary(1)	1																		---	---	---	---
ZWILCH	55055	broad.mit.edu	37	15	66813068	66813068	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:66813068delT	uc002aqb.2	+						RPL4_uc002apx.2_Intron|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	67124676	67124679	+	IGR	DEL	TGTG	-	-	rs138525656	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:67124676_67124679delTGTG								SMAD6 (50341 upstream) : SMAD3 (233516 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	67323368	67323368	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:67323368delA								SMAD6 (249033 upstream) : SMAD3 (34827 downstream)																																			---	---	---	---
AAGAB	79719	broad.mit.edu	37	15	67496224	67496224	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:67496224delT	uc002aqk.3	-						AAGAB_uc002aql.2_Intron|AAGAB_uc010uju.1_Intron	NM_024666	NP_078942			alpha- and gamma-adaptin-binding protein p34						protein transport	cytoplasm					0																		---	---	---	---
AAGAB	79719	broad.mit.edu	37	15	67518473	67518473	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:67518473delT	uc002aqk.3	-						AAGAB_uc002aql.2_Intron|AAGAB_uc010uju.1_Intron	NM_024666	NP_078942			alpha- and gamma-adaptin-binding protein p34						protein transport	cytoplasm					0																		---	---	---	---
IQCH	64799	broad.mit.edu	37	15	67641339	67641339	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:67641339delT	uc002aqo.1	+						IQCH_uc010ujv.1_Intron|IQCH_uc002aqn.1_Intron|IQCH_uc002aqq.1_Intron|IQCH_uc002aqp.1_Intron	NM_001031715	NP_001026885			IQ motif containing H isoform 1											skin(3)|ovary(1)	4				Colorectal(3;0.0856)														---	---	---	---
MAP2K5	5607	broad.mit.edu	37	15	67920817	67920817	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:67920817delA	uc002aqu.2	+						MAP2K5_uc002aqt.1_Intron|MAP2K5_uc002aqv.2_Intron|MAP2K5_uc002aqw.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																		---	---	---	---
Unknown	0	broad.mit.edu	37	15	68308811	68308811	+	IGR	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:68308811delG								LBXCOR1 (182637 upstream) : PIAS1 (37761 downstream)																																			---	---	---	---
PIAS1	8554	broad.mit.edu	37	15	68473485	68473485	+	Intron	DEL	T	-	-	rs28455639		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:68473485delT	uc002aqz.2	+						PIAS1_uc002ara.2_Intron	NM_016166	NP_057250			protein inhibitor of activated STAT, 1						androgen receptor signaling pathway|interferon-gamma-mediated signaling pathway|JAK-STAT cascade|positive regulation of protein sumoylation|positive regulation of transcription, DNA-dependent|regulation of interferon-gamma-mediated signaling pathway|transcription, DNA-dependent	nuclear speck	androgen receptor binding|DNA binding|enzyme binding|SUMO ligase activity|transcription coactivator activity|transcription corepressor activity|zinc ion binding			ovary(1)|lung(1)	2																		---	---	---	---
CORO2B	10391	broad.mit.edu	37	15	69020047	69020047	+	3'UTR	DEL	T	-	-	rs71747415		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-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-4200-01A-01D-1126-08	TCGA-BR-4200-11A-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																		---	---	---	---
NOX5	79400	broad.mit.edu	37	15	69226959	69226959	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:69226959delA	uc002arp.1	+						NOX5_uc002arq.1_Intron|NOX5_uc010bid.1_Intron|NOX5_uc002aro.2_Intron|SPESP1_uc002arn.1_Intron	NM_024505	NP_078781			NADPH oxidase, EF-hand calcium binding domain 5						angiogenesis|angiogenesis|cytokine secretion|cytokinesis|electron transport chain|endothelial cell proliferation|induction of apoptosis|positive regulation of reactive oxygen species metabolic process|regulation of fusion of sperm to egg plasma membrane|regulation of proton transport|superoxide anion generation	endoplasmic reticulum|endoplasmic reticulum|integral to membrane	calcium ion binding|electron carrier activity|flavin adenine dinucleotide binding|heme binding|hydrogen ion channel activity|NADP binding|superoxide-generating NADPH oxidase activity			breast(1)|pancreas(1)	2																		---	---	---	---
GLCE	26035	broad.mit.edu	37	15	69484208	69484208	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:69484208delT	uc002ary.1	+						GLCE_uc002arw.2_Intron|GLCE_uc002arx.2_Intron	NM_015554	NP_056369			D-glucuronyl C5-epimerase						heparan sulfate proteoglycan biosynthetic process|heparin biosynthetic process	Golgi membrane|integral to membrane	UDP-glucuronate 5'-epimerase activity			ovary(2)	2																		---	---	---	---
LOC145837	145837	broad.mit.edu	37	15	69792353	69792358	+	Intron	DEL	CCCCAC	-	-	rs66470774		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:69792353_69792358delCCCCAC	uc002asf.1	+						LOC145837_uc002asg.1_Intron|LOC145837_uc010bij.1_Intron					Homo sapiens cDNA clone IMAGE:5189446.												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	15	70286001	70286001	+	IGR	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:70286001delC								C15orf50 (150696 upstream) : TLE3 (54542 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	70811726	70811727	+	IGR	DEL	AC	-	-	rs146449590		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:70811726_70811727delAC								TLE3 (421470 upstream) : UACA (135168 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	70920865	70920865	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:70920865delA								TLE3 (530609 upstream) : UACA (26030 downstream)																																			---	---	---	---
LRRC49	54839	broad.mit.edu	37	15	71235517	71235517	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:71235517delT	uc002asw.2	+						LRRC49_uc002asu.2_Intron|LRRC49_uc002asx.2_Intron|LRRC49_uc010ukf.1_Intron|LRRC49_uc002asy.2_Intron|LRRC49_uc002asz.2_Intron	NM_017691	NP_060161			leucine rich repeat containing 49							cytoplasm|microtubule				ovary(1)	1																		---	---	---	---
MYO9A	4649	broad.mit.edu	37	15	72347272	72347273	+	Intron	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:72347272_72347273delAA	uc002atl.3	-						MYO9A_uc010biq.2_Intron|MYO9A_uc002ato.2_Intron	NM_006901	NP_008832			myosin IXA						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																		---	---	---	---
GRAMD2	196996	broad.mit.edu	37	15	72475529	72475529	+	Intron	DEL	T	-	-	rs78583435		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:72475529delT	uc002atq.2	-						GRAMD2_uc010bis.2_Intron	NM_001012642	NP_001012660			GRAM domain containing 2							integral to membrane					0																		---	---	---	---
PKM2	5315	broad.mit.edu	37	15	72498895	72498895	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:72498895delA	uc002atx.1	-						PKM2_uc002ats.1_Intron|PKM2_uc002att.1_Intron|PKM2_uc002atu.1_Intron|PKM2_uc010bit.1_Intron|PKM2_uc010uki.1_Intron|PKM2_uc002atv.1_Intron|PKM2_uc002atw.1_Intron|PKM2_uc002aty.1_Intron|PKM2_uc010ukj.1_Intron|PKM2_uc010ukk.1_Intron|PKM2_uc010biu.1_Intron|PKM2_uc002atz.1_Intron	NM_182471	NP_872271			pyruvate kinase, muscle isoform M1						glycolysis|programmed cell death	cytosol|nucleus|plasma membrane	ATP binding|magnesium ion binding|potassium ion binding|protein binding|pyruvate kinase activity			breast(1)	1					Pyruvic acid(DB00119)													---	---	---	---
PKM2	5315	broad.mit.edu	37	15	72502386	72502386	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:72502386delT	uc002atx.1	-						PKM2_uc002att.1_5'Flank|PKM2_uc002atu.1_5'Flank|PKM2_uc010bit.1_Intron|PKM2_uc010uki.1_Intron|PKM2_uc002atv.1_Intron|PKM2_uc002atw.1_Intron|PKM2_uc002aty.1_Intron|PKM2_uc010ukj.1_Intron|PKM2_uc010ukk.1_Intron|PKM2_uc010biu.1_Intron|PKM2_uc002atz.1_Intron	NM_182471	NP_872271			pyruvate kinase, muscle isoform M1						glycolysis|programmed cell death	cytosol|nucleus|plasma membrane	ATP binding|magnesium ion binding|potassium ion binding|protein binding|pyruvate kinase activity			breast(1)	1					Pyruvic acid(DB00119)													---	---	---	---
PARP6	56965	broad.mit.edu	37	15	72550543	72550543	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:72550543delT	uc002auc.2	-						PARP6_uc002aua.2_Intron|PARP6_uc002aub.2_Intron|PARP6_uc002aud.3_Intron|PARP6_uc002auf.1_Intron	NM_020214	NP_064599			poly (ADP-ribose) polymerase family, member 6								NAD+ ADP-ribosyltransferase activity				0																		---	---	---	---
PARP6	56965	broad.mit.edu	37	15	72552656	72552656	+	Intron	DEL	A	-	-	rs79661791		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:72552656delA	uc002auc.2	-						PARP6_uc002aua.2_Intron|PARP6_uc002aub.2_Intron|PARP6_uc002aud.3_Intron|PARP6_uc002auf.1_Intron	NM_020214	NP_064599			poly (ADP-ribose) polymerase family, member 6								NAD+ ADP-ribosyltransferase activity				0																		---	---	---	---
GOLGA6B	55889	broad.mit.edu	37	15	72954509	72954516	+	Intron	DEL	TTTTTTTT	-	-	rs79734124		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:72954509_72954516delTTTTTTTT	uc010uks.1	+							NM_018652	NP_061122			golgi autoantigen, golgin subfamily a, 6B												0																		---	---	---	---
BBS4	585	broad.mit.edu	37	15	73003495	73003495	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:73003495delT	uc002avb.2	+						BBS4_uc010ukv.1_Intron|BBS4_uc002avc.2_Intron|BBS4_uc002avd.2_Intron	NM_033028	NP_149017			Bardet-Biedl syndrome 4						adult behavior|brain morphogenesis|cell cycle cytokinesis|centrosome organization|cerebral cortex development|convergent extension involved in gastrulation|dendrite development|fat cell differentiation|heart looping|hippocampus development|intracellular transport|maintenance of protein location in nucleus|melanosome transport|microtubule anchoring at centrosome|neural tube closure|nonmotile primary cilium assembly|photoreceptor cell maintenance|pigment granule aggregation in cell center|positive regulation of flagellum assembly|regulation of cilium beat frequency involved in ciliary motility|regulation of cytokinesis|regulation of lipid metabolic process|retina homeostasis|retinal rod cell development|sensory perception of smell|sensory processing|spermatid development|striatum development	BBSome|centriolar satellite|centriole|cilium membrane|microtubule basal body|motile cilium|nonmotile primary cilium|nucleus|pericentriolar material	alpha-tubulin binding|beta-tubulin binding|dynactin binding|microtubule motor activity				0														Bardet-Biedl_syndrome				---	---	---	---
Unknown	0	broad.mit.edu	37	15	73242963	73242964	+	IGR	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:73242963_73242964delAA								ADPGK (166296 upstream) : NEO1 (101911 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	73335233	73335233	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:73335233delA								ADPGK (258566 upstream) : NEO1 (9642 downstream)																																			---	---	---	---
NEO1	4756	broad.mit.edu	37	15	73461228	73461229	+	Intron	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:73461228_73461229delTT	uc002avm.3	+						NEO1_uc010ukx.1_Intron|NEO1_uc010uky.1_Intron|NEO1_uc010ukz.1_Intron|NEO1_uc002avn.3_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																		---	---	---	---
NEO1	4756	broad.mit.edu	37	15	73473126	73473126	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:73473126delT	uc002avm.3	+						NEO1_uc010ukx.1_Intron|NEO1_uc010uky.1_Intron|NEO1_uc010ukz.1_Intron|NEO1_uc002avn.3_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																		---	---	---	---
NEO1	4756	broad.mit.edu	37	15	73476098	73476098	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:73476098delA	uc002avm.3	+						NEO1_uc010ukx.1_Intron|NEO1_uc010uky.1_Intron|NEO1_uc010ukz.1_Intron|NEO1_uc002avn.3_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																		---	---	---	---
NEO1	4756	broad.mit.edu	37	15	73520739	73520740	+	Intron	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:73520739_73520740delTT	uc002avm.3	+						NEO1_uc010ukx.1_Intron|NEO1_uc010uky.1_Intron|NEO1_uc010ukz.1_Intron|NEO1_uc002avn.3_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	73751575	73751575	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:73751575delT	uc002avq.2	+						C15orf60_uc010bjb.2_Intron	NM_001042367	NP_001035826			hypothetical protein LOC283677											pancreas(1)	1																		---	---	---	---
NPTN	27020	broad.mit.edu	37	15	73889235	73889235	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:73889235delA	uc002avs.2	-						NPTN_uc010bjc.2_Intron|NPTN_uc002avt.2_Intron|NPTN_uc002avr.2_Intron|NPTN_uc010ula.1_Intron	NM_012428	NP_036560			neuroplastin isoform b precursor						elevation of cytosolic calcium ion concentration|homophilic cell adhesion|long-term synaptic potentiation|positive regulation of fibroblast growth factor receptor signaling pathway|positive regulation of long-term neuronal synaptic plasticity|positive regulation of neuron projection development|positive regulation of protein phosphorylation	integral to membrane|plasma membrane|presynaptic membrane	cell adhesion molecule binding|type 1 fibroblast growth factor receptor binding				0																		---	---	---	---
NPTN	27020	broad.mit.edu	37	15	73902426	73902426	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:73902426delT	uc002avs.2	-						NPTN_uc010bjc.2_Intron|NPTN_uc002avt.2_Intron|NPTN_uc002avr.2_Intron|NPTN_uc010ula.1_Intron	NM_012428	NP_036560			neuroplastin isoform b precursor						elevation of cytosolic calcium ion concentration|homophilic cell adhesion|long-term synaptic potentiation|positive regulation of fibroblast growth factor receptor signaling pathway|positive regulation of long-term neuronal synaptic plasticity|positive regulation of neuron projection development|positive regulation of protein phosphorylation	integral to membrane|plasma membrane|presynaptic membrane	cell adhesion molecule binding|type 1 fibroblast growth factor receptor binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	15	74155494	74155494	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:74155494delA								C15orf59 (111678 upstream) : TBC1D21 (10474 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	74262383	74262384	+	IGR	DEL	AC	-	-	rs113789852		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:74262383_74262384delAC								LOXL1 (17905 upstream) : STOML1 (13177 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	74404884	74404885	+	IGR	DEL	TG	-	-	rs6495088	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:74404884_74404885delTG								GOLGA6A (29993 upstream) : LOC283731 (13829 downstream)																																			---	---	---	---
CCDC33	80125	broad.mit.edu	37	15	74551861	74551861	+	Intron	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:74551861delC	uc002axo.2	+							NM_025055	NP_079331			coiled-coil domain containing 33 isoform 1								protein binding			ovary(3)|skin(2)	5																		---	---	---	---
UBL7	84993	broad.mit.edu	37	15	74745867	74745867	+	Intron	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:74745867delG	uc002axw.1	-						UBL7_uc002axx.1_Intron|UBL7_uc010bjr.1_Intron|UBL7_uc002axy.1_Intron|UBL7_uc002axz.1_Intron	NM_032907	NP_116296			ubiquitin-like 7								protein binding			ovary(1)	1																		---	---	---	---
CSK	1445	broad.mit.edu	37	15	75091438	75091438	+	Intron	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:75091438delG	uc010bkb.1	+						CSK_uc002ays.2_Intron|CSK_uc010bkc.1_5'Flank	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																		---	---	---	---
CSK	1445	broad.mit.edu	37	15	75095162	75095162	+	3'UTR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:75095162delT	uc010bkb.1	+	14					CSK_uc002ays.2_3'UTR|CSK_uc010bkc.1_3'UTR	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																		---	---	---	---
SCAMP2	10066	broad.mit.edu	37	15	75164407	75164407	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:75164407delA	uc002azb.1	-						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	75385154	75385154	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:75385154delA								PPCDC (42088 upstream) : C15orf39 (106079 downstream)																																			---	---	---	---
SIN3A	25942	broad.mit.edu	37	15	75706706	75706706	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:75706706delA	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																		---	---	---	---
PTPN9	5780	broad.mit.edu	37	15	75855298	75855298	+	Intron	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:75855298delG	uc002bal.2	-							NM_002833	NP_002824			protein tyrosine phosphatase, non-receptor type							cytoplasmic part	non-membrane spanning protein tyrosine phosphatase activity|protein binding			lung(1)|skin(1)	2																		---	---	---	---
SNUPN	10073	broad.mit.edu	37	15	75895122	75895122	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:75895122delT	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																		---	---	---	---
IMP3	55272	broad.mit.edu	37	15	75935957	75935958	+	Intron	DEL	AA	-	-	rs76404591		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:75935957_75935958delAA	uc002bat.2	-							NM_018285	NP_060755			IMP3, U3 small nucleolar ribonucleoprotein						rRNA processing	nucleolus|ribonucleoprotein complex	protein binding|rRNA binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	15	76039915	76039915	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:76039915delT								DNM1P35 (7413 upstream) : UBE2Q2 (95707 downstream)																																			---	---	---	---
UBE2Q2	92912	broad.mit.edu	37	15	76175815	76175815	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:76175815delT	uc002bbg.2	+						UBE2Q2_uc002bbh.2_Intron|UBE2Q2_uc010umn.1_Intron|UBE2Q2_uc002bbi.2_Intron	NM_173469	NP_775740			ubiquitin-conjugating enzyme E2Q 2 isoform 1						protein K48-linked ubiquitination	cytoplasm	ATP binding|ubiquitin-protein ligase activity			ovary(2)	2																		---	---	---	---
FBXO22	26263	broad.mit.edu	37	15	76210663	76210666	+	Intron	DEL	AAAA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:76210663_76210666delAAAA	uc002bbk.2	+						FBXO22_uc002bbj.1_Intron|FBXO22_uc002bbl.2_Intron	NM_147188	NP_671717			F-box only protein 22 isoform a						ubiquitin-dependent protein catabolic process		ubiquitin-protein ligase activity				0																		---	---	---	---
NRG4	145957	broad.mit.edu	37	15	76340332	76340332	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:76340332delA	uc010bko.2	-											Homo sapiens cDNA, FLJ97310.							extracellular region|integral to membrane|plasma membrane	growth factor activity				0																		---	---	---	---
ETFA	2108	broad.mit.edu	37	15	76577920	76577920	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-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																		---	---	---	---
SCAPER	49855	broad.mit.edu	37	15	76798449	76798449	+	Intron	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:76798449delG	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																		---	---	---	---
HMG20A	10363	broad.mit.edu	37	15	77757251	77757253	+	Intron	DEL	TTT	-	-	rs113381963		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:77757251_77757253delTTT	uc002bcr.2	+						HMG20A_uc002bcq.1_3'UTR|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	78089054	78089058	+	IGR	DEL	TTTTT	-	-	rs67293830		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:78089054_78089058delTTTTT								LINGO1 (100579 upstream) : LOC645752 (117501 downstream)																																			---	---	---	---
TBC1D2B	23102	broad.mit.edu	37	15	78310307	78310308	+	Intron	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:78310307_78310308delAA	uc002bcy.3	-						TBC1D2B_uc010bla.2_Intron|TBC1D2B_uc002bda.2_5'Flank	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	78438641	78438642	+	IGR	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:78438641_78438642delTT								CIB2 (14763 upstream) : IDH3A (3077 downstream)																																			---	---	---	---
CRABP1	1381	broad.mit.edu	37	15	78640474	78640474	+	3'UTR	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:78640474delC	uc002bdp.2	+	4						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)													---	---	---	---
IREB2	3658	broad.mit.edu	37	15	78758544	78758544	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:78758544delT	uc002bdr.2	+						IREB2_uc010unb.1_Intron|IREB2_uc002bdq.2_Intron	NM_004136	NP_004127			iron-responsive element binding protein 2								4 iron, 4 sulfur cluster binding|metal ion binding|protein binding				0				UCEC - Uterine corpus endometrioid carcinoma (272;0.232)														---	---	---	---
CHRNB4	1143	broad.mit.edu	37	15	78917039	78917040	+	3'UTR	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:78917039_78917040delAA	uc002bed.1	-	6					CHRNB4_uc002bee.1_3'UTR|uc002bef.1_5'Flank	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																		---	---	---	---
Unknown	0	broad.mit.edu	37	15	79026913	79026913	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:79026913delT								CHRNB4 (74039 upstream) : ADAMTS7 (24633 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	79196092	79196092	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:79196092delA								MORF4L1 (6020 upstream) : CTSH (18000 downstream)																																			---	---	---	---
RASGRF1	5923	broad.mit.edu	37	15	79268902	79268903	+	Intron	DEL	AC	-	-	rs111923447		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:79268902_79268903delAC	uc002beq.2	-						RASGRF1_uc002bep.2_Intron|RASGRF1_uc002beo.2_Intron	NM_002891	NP_002882			Ras protein-specific guanine						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	79296113	79296113	+	Intron	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:79296113delG	uc002beq.2	-						RASGRF1_uc002bep.2_Intron|RASGRF1_uc010blm.1_Intron|RASGRF1_uc002ber.3_Intron|RASGRF1_uc010unh.1_Intron|RASGRF1_uc002beo.2_Intron	NM_002891	NP_002882			Ras protein-specific guanine						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	79319752	79319752	+	Intron	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:79319752delC	uc002beq.2	-						RASGRF1_uc002bep.2_Intron|RASGRF1_uc010blm.1_Intron|RASGRF1_uc002ber.3_Intron	NM_002891	NP_002882			Ras protein-specific guanine						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																		---	---	---	---
Unknown	0	broad.mit.edu	37	15	80046088	80046088	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:80046088delT								KIAA1024 (281446 upstream) : MTHFS (91232 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	80093284	80093284	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:80093284delA								KIAA1024 (328642 upstream) : MTHFS (44036 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	80285007	80285007	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:80285007delA								BCL2A1 (21364 upstream) : ZFAND6 (67014 downstream)																																			---	---	---	---
ARNT2	9915	broad.mit.edu	37	15	80851520	80851523	+	Intron	DEL	CGGT	-	-	rs34979022		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:80851520_80851523delCGGT	uc002bfr.2	+						ARNT2_uc010unm.1_Intron|ARNT2_uc002bfs.2_Intron	NM_014862	NP_055677			aryl hydrocarbon receptor nuclear translocator						central nervous system development|in utero embryonic development|response to hypoxia		aryl hydrocarbon receptor binding|DNA binding|protein heterodimerization activity|sequence-specific DNA binding transcription factor activity|signal transducer activity			central_nervous_system(3)|ovary(1)|pancreas(1)	5			BRCA - Breast invasive adenocarcinoma(143;0.134)															---	---	---	---
Unknown	0	broad.mit.edu	37	15	81465142	81465142	+	IGR	DEL	A	-	-	rs68181044		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:81465142delA								C15orf26 (23627 upstream) : IL16 (9951 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	82011663	82011664	+	IGR	INS	-	TAT	TAT	rs141036355	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:82011663_82011664insTAT								TMC3 (345245 upstream) : MEX3B (322464 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	82016719	82016719	+	IGR	DEL	T	-	-	rs11351976		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:82016719delT								TMC3 (350301 upstream) : MEX3B (317409 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	82028847	82028847	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:82028847delA								TMC3 (362429 upstream) : MEX3B (305281 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	82089433	82089433	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:82089433delT								TMC3 (423015 upstream) : MEX3B (244695 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	82148855	82148856	+	IGR	DEL	TT	-	-	rs112707764		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:82148855_82148856delTT								TMC3 (482437 upstream) : MEX3B (185272 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	82258045	82258047	+	IGR	DEL	AAA	-	-	rs72056608		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:82258045_82258047delAAA								TMC3 (591627 upstream) : MEX3B (76081 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	82385421	82385421	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:82385421delT	uc002bgr.2	+											Homo sapiens cDNA clone IMAGE:5296580.																														---	---	---	---
AP3B2	8120	broad.mit.edu	37	15	83360356	83360356	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:83360356delA	uc010uoh.1	-						AP3B2_uc010uoi.1_Intron|AP3B2_uc010uoj.1_Intron|AP3B2_uc010uok.1_Intron	NM_004644	NP_004635			adaptor-related protein complex 3, beta 2						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)															---	---	---	---
TM6SF1	53346	broad.mit.edu	37	15	83790906	83790906	+	Intron	DEL	A	-	-	rs35354291		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:83790906delA	uc002bjp.2	+						TM6SF1_uc010bmq.2_Intron|TM6SF1_uc002bjq.2_Intron|TM6SF1_uc010bmr.2_Intron|TM6SF1_uc002bjr.2_Intron	NM_023003	NP_075379			transmembrane 6 superfamily member 1 isoform 1							integral to membrane				ovary(1)	1																		---	---	---	---
BNC1	646	broad.mit.edu	37	15	83935033	83935034	+	Intron	INS	-	AC	AC			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:83935033_83935034insAC	uc002bjt.1	-						BNC1_uc010uos.1_Intron	NM_001717	NP_001708			basonuclin 1						epidermis development|positive regulation of cell proliferation	cytoplasm|nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(3)	3																		---	---	---	---
ADAMTSL3	57188	broad.mit.edu	37	15	84690439	84690439	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:84690439delT	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	84773625	84773625	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:84773625delT								ADAMTSL3 (65034 upstream) : LOC388152 (93975 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	84790136	84790136	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:84790136delT								ADAMTSL3 (81545 upstream) : LOC388152 (77464 downstream)																																			---	---	---	---
ZNF592	9640	broad.mit.edu	37	15	85324002	85324004	+	Intron	DEL	TTG	-	-	rs112124713		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:85324002_85324004delTTG	uc002bld.2	+						ZNF592_uc010upb.1_Intron	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	85449886	85449887	+	Intron	DEL	TT	-	-	rs71397830		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:85449886_85449887delTT	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)															---	---	---	---
PDE8A	5151	broad.mit.edu	37	15	85635558	85635559	+	Intron	DEL	TG	-	-	rs12443441	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:85635558_85635559delTG	uc002blh.2	+						PDE8A_uc002bli.2_Intron|PDE8A_uc010bnc.2_Intron|PDE8A_uc010bnd.2_Intron|PDE8A_uc002blj.2_Intron|PDE8A_uc002blk.2_Intron	NM_002605	NP_002596			phosphodiesterase 8A 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			ovary(2)|pancreas(1)|skin(1)	4	Colorectal(223;0.227)		BRCA - Breast invasive adenocarcinoma(143;0.0608)															---	---	---	---
Unknown	0	broad.mit.edu	37	15	86366090	86366090	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:86366090delT								KLHL25 (27901 upstream) : AGBL1 (319152 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	86390332	86390332	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:86390332delA								KLHL25 (52143 upstream) : AGBL1 (294910 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	86675027	86675027	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:86675027delA								KLHL25 (336838 upstream) : AGBL1 (10215 downstream)																																			---	---	---	---
AGBL1	123624	broad.mit.edu	37	15	86796477	86796478	+	Intron	INS	-	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:86796477_86796478insT	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	87531267	87531267	+	Frame_Shift_Del	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:87531267delT	uc002blz.1	+	23	3213	c.3133delT	c.(3133-3135)TTTfs	p.F1045fs		NM_152336	NP_689549	Q96MI9	CBPC4_HUMAN	ATP/GTP binding protein-like 1	1045					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	87666428	87666429	+	IGR	INS	-	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:87666428_87666429insA								AGBL1 (94145 upstream) : NCRNA00052 (453731 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	87752924	87752924	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:87752924delA								AGBL1 (180641 upstream) : NCRNA00052 (367236 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	87890799	87890805	+	IGR	DEL	AAGGGTA	-	-	rs11278446		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:87890799_87890805delAAGGGTA								AGBL1 (318516 upstream) : NCRNA00052 (229355 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	88068080	88068088	+	IGR	DEL	AAAAAAAAA	-	-	rs71987976		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:88068080_88068088delAAAAAAAAA								AGBL1 (495797 upstream) : NCRNA00052 (52072 downstream)																																			---	---	---	---
NTRK3	4916	broad.mit.edu	37	15	88503607	88503607	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:88503607delT	uc002bme.1	-						NTRK3_uc002bmh.2_Intron|NTRK3_uc002bmf.1_Intron|NTRK3_uc010upl.1_Intron|NTRK3_uc010bnh.1_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	88509306	88509309	+	Intron	DEL	CAAA	-	-	rs145233033		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:88509306_88509309delCAAA	uc002bme.1	-						NTRK3_uc002bmh.2_Intron|NTRK3_uc002bmf.1_Intron|NTRK3_uc010upl.1_Intron|NTRK3_uc010bnh.1_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	88579006	88579007	+	Intron	DEL	AC	-	-	rs12440041	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:88579006_88579007delAC	uc002bme.1	-						NTRK3_uc002bmh.2_Intron|NTRK3_uc002bmf.1_Intron|NTRK3_uc010upl.1_Intron|NTRK3_uc010bnh.1_Intron|NTRK3_uc002bmg.2_Intron|NTRK3_uc010bni.2_5'Flank	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	89122935	89122935	+	IGR	DEL	A	-	-	rs34032513		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:89122935delA								DET1 (33023 upstream) : MIR1179 (28403 downstream)																																			---	---	---	---
FANCI	55215	broad.mit.edu	37	15	89801301	89801302	+	Intron	DEL	TT	-	-	rs113274691		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:89801301_89801302delTT	uc010bnp.1	+						FANCI_uc002bnm.1_Intron|FANCI_uc002bnn.1_Intron|FANCI_uc002bno.2_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				---	---	---	---
FANCI	55215	broad.mit.edu	37	15	89811935	89811935	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:89811935delT	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				---	---	---	---
FANCI	55215	broad.mit.edu	37	15	89857691	89857691	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:89857691delA	uc010bnp.1	+						FANCI_uc002bnm.1_Intron|FANCI_uc002bnn.1_Intron|FANCI_uc002bnp.1_Intron|FANCI_uc002bnq.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				---	---	---	---
POLG	5428	broad.mit.edu	37	15	89860991	89860993	+	Intron	DEL	TTT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:89860991_89860993delTTT	uc002bns.3	-						POLG_uc002bnr.3_Intron	NM_002693	NP_002684			DNA-directed DNA polymerase gamma						base-excision repair, gap-filling|cell death|DNA-dependent DNA replication	mitochondrial nucleoid	DNA binding|DNA-directed DNA polymerase activity|protease binding			ovary(1)|lung(1)	2	Lung NSC(78;0.0472)|all_lung(78;0.089)		STAD - Stomach adenocarcinoma(125;0.165)										DNA_polymerases_(catalytic_subunits)					---	---	---	---
KIF7	374654	broad.mit.edu	37	15	90199591	90199592	+	5'Flank	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:90199591_90199592delTT	uc002bof.2	-						KIF7_uc002bog.2_5'Flank	NM_198525	NP_940927			kinesin family member 7						microtubule-based movement|negative regulation of smoothened signaling pathway|positive regulation of smoothened signaling pathway	cilium	ATP binding|microtubule motor activity|protein binding			ovary(2)|lung(1)	3	Lung NSC(78;0.0237)|all_lung(78;0.0478)		BRCA - Breast invasive adenocarcinoma(143;0.128)															---	---	---	---
Unknown	0	broad.mit.edu	37	15	90288995	90288995	+	IGR	DEL	A	-	-	rs75395764		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:90288995delA								WDR93 (2127 upstream) : MESP1 (4105 downstream)																																			---	---	---	---
MESP2	145873	broad.mit.edu	37	15	90316108	90316108	+	Intron	DEL	T	-	-	rs36037316		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:90316108delT	uc010uqa.1	+											Homo sapiens mRNA full length insert cDNA clone EUROIMAGE 231282.						Notch signaling pathway	nucleus	DNA binding				0	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)															---	---	---	---
Unknown	0	broad.mit.edu	37	15	90648957	90648957	+	IGR	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:90648957delG								IDH2 (3249 upstream) : SEMA4B (79195 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	90825346	90825347	+	IGR	INS	-	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:90825346_90825347insT								TTLL13 (9903 upstream) : GABARAPL3 (64418 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	91214370	91214370	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:91214370delA								CRTC3 (25794 upstream) : BLM (46209 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	91406987	91406987	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:91406987delA								BLM (48303 upstream) : FURIN (4898 downstream)																																			---	---	---	---
VPS33B	26276	broad.mit.edu	37	15	91542549	91542550	+	Intron	DEL	TT	-	-	rs34013300		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:91542549_91542550delTT	uc002bqp.1	-						VPS33B_uc002bqq.1_Intron|VPS33B_uc010uqu.1_Intron	NM_018668	NP_061138			vacuolar protein sorting 33B (yeast homolog))						cellular membrane fusion|lysosome localization|melanosome localization|platelet alpha granule organization|protein transport|vesicle docking involved in exocytosis	late endosome membrane|lysosomal membrane|perinuclear region of cytoplasm|platelet alpha granule	protein binding			ovary(2)	2	Lung NSC(78;0.0987)|all_lung(78;0.175)																	---	---	---	---
SV2B	9899	broad.mit.edu	37	15	91701982	91701983	+	Intron	INS	-	CT	CT	rs150364044	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:91701982_91701983insCT	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)															---	---	---	---
SV2B	9899	broad.mit.edu	37	15	91769336	91769336	+	5'UTR	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:91769336delG	uc002bqv.2	+	1					SV2B_uc002bqt.2_5'UTR|SV2B_uc010uqv.1_Intron|SV2B_uc002bqu.3_RNA	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	92826332	92826333	+	IGR	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:92826332_92826333delAA								SLCO3A1 (110667 upstream) : ST8SIA2 (110807 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	92910153	92910153	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:92910153delT								SLCO3A1 (194488 upstream) : ST8SIA2 (26987 downstream)																																			---	---	---	---
ST8SIA2	8128	broad.mit.edu	37	15	92944951	92944952	+	Intron	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:92944951_92944952delTT	uc002bra.2	+						ST8SIA2_uc002brb.2_Intron	NM_006011	NP_006002			ST8 alpha-N-acetyl-neuraminide						axon guidance|N-glycan processing|oligosaccharide biosynthetic process|post-translational protein modification|protein N-linked glycosylation via asparagine	integral to Golgi membrane	alpha-N-acetylneuraminate alpha-2,8-sialyltransferase activity				0	Lung NSC(78;0.0893)|all_lung(78;0.125)		BRCA - Breast invasive adenocarcinoma(143;0.0355)|OV - Ovarian serous cystadenocarcinoma(32;0.203)															---	---	---	---
C15orf32	145858	broad.mit.edu	37	15	93033514	93033514	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:93033514delA	uc002brc.1	+						C15orf32_uc010bod.1_Intron	NM_153040	NP_694585			hypothetical protein LOC145858											ovary(1)	1	Lung NSC(78;0.0893)|all_lung(78;0.125)		BRCA - Breast invasive adenocarcinoma(143;0.0493)|OV - Ovarian serous cystadenocarcinoma(32;0.125)															---	---	---	---
Unknown	0	broad.mit.edu	37	15	93284821	93284821	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:93284821delA								FAM174B (7517 upstream) : CHD2 (144612 downstream)																																			---	---	---	---
CHD2	1106	broad.mit.edu	37	15	93486405	93486405	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:93486405delT	uc002bsp.2	+						CHD2_uc002bsm.1_3'UTR|CHD2_uc002bsn.2_Intron|CHD2_uc002bso.1_Intron|CHD2_uc010urb.1_Intron|CHD2_uc010bof.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)															---	---	---	---
CHD2	1106	broad.mit.edu	37	15	93496874	93496874	+	Intron	DEL	C	-	-	rs1371390	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:93496874delC	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)															---	---	---	---
CHD2	1106	broad.mit.edu	37	15	93558308	93558308	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:93558308delT	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	94119744	94119745	+	IGR	INS	-	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:94119744_94119745insT								RGMA (487311 upstream) : MCTP2 (655056 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	94239260	94239260	+	IGR	DEL	G	-	-	rs12916617	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:94239260delG								RGMA (606827 upstream) : MCTP2 (535541 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	94283723	94283723	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:94283723delA								RGMA (651290 upstream) : MCTP2 (491078 downstream)																																			---	---	---	---
MCTP2	55784	broad.mit.edu	37	15	94928849	94928849	+	Intron	DEL	A	-	-	rs28709064		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:94928849delA	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	95309300	95309300	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:95309300delT								MCTP2 (282120 upstream) : LOC145820 (667022 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	95953936	95953936	+	IGR	DEL	A	-	-	rs34063497		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:95953936delA								MCTP2 (926756 upstream) : LOC145820 (22386 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	96116269	96116269	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:96116269delA								LOC145820 (65195 upstream) : NR2F2 (752888 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	96237175	96237175	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:96237175delA								LOC145820 (186101 upstream) : NR2F2 (631982 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	96407507	96407507	+	IGR	DEL	A	-	-	rs142899577	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:96407507delA								LOC145820 (356433 upstream) : NR2F2 (461650 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	97455882	97455883	+	IGR	INS	-	AT	AT			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:97455882_97455883insAT								SPATA8 (127038 upstream) : LOC91948 (829963 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	97636510	97636513	+	IGR	DEL	TTTT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:97636510_97636513delTTTT								SPATA8 (307666 upstream) : LOC91948 (649333 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	97669864	97669864	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:97669864delT								SPATA8 (341020 upstream) : LOC91948 (615982 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	97690832	97690832	+	IGR	DEL	T	-	-	rs79770321		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:97690832delT								SPATA8 (361988 upstream) : LOC91948 (595014 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	98661645	98661645	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:98661645delT								ARRDC4 (144578 upstream) : FAM169B (318746 downstream)																																			---	---	---	---
FAM169B	283777	broad.mit.edu	37	15	98985187	98985187	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:98985187delA	uc002buk.1	-							NM_182562	NP_872368			hypothetical protein LOC283777												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	15	99061811	99061812	+	IGR	DEL	TT	-	-	rs67709732		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:99061811_99061812delTT								FAM169B (4200 upstream) : IGF1R (130949 downstream)																																			---	---	---	---
IGF1R	3480	broad.mit.edu	37	15	99232390	99232390	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:99232390delT	uc002bul.2	+						IGF1R_uc010urq.1_Intron|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)													---	---	---	---
IGF1R	3480	broad.mit.edu	37	15	99393975	99393975	+	Intron	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:99393975delG	uc002bul.2	+						IGF1R_uc010urq.1_Intron|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)													---	---	---	---
IGF1R	3480	broad.mit.edu	37	15	99407324	99407324	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:99407324delA	uc002bul.2	+						IGF1R_uc010urq.1_Intron|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)													---	---	---	---
PGPEP1L	145814	broad.mit.edu	37	15	99514409	99514410	+	Intron	INS	-	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:99514409_99514410insT	uc002bum.2	-						PGPEP1L_uc010bop.2_Intron|PGPEP1L_uc002bun.2_Intron	NM_001102612	NP_001096082			pyroglutamyl-peptidase 1-like protein						proteolysis		cysteine-type peptidase activity				0																		---	---	---	---
PGPEP1L	145814	broad.mit.edu	37	15	99518280	99518280	+	Intron	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:99518280delG	uc002bum.2	-						PGPEP1L_uc010bop.2_Intron|PGPEP1L_uc002bun.2_Intron	NM_001102612	NP_001096082			pyroglutamyl-peptidase 1-like protein						proteolysis		cysteine-type peptidase activity				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	15	99577805	99577805	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:99577805delT								PGPEP1L (26781 upstream) : SYNM (67481 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	99578382	99578383	+	IGR	INS	-	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:99578382_99578383insA								PGPEP1L (27358 upstream) : SYNM (66903 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	99619949	99619949	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:99619949delA								PGPEP1L (68925 upstream) : SYNM (25337 downstream)																																	OREG0023507	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
TTC23	64927	broad.mit.edu	37	15	99751835	99751836	+	Intron	INS	-	G	G	rs150922451	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:99751835_99751836insG	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)															---	---	---	---
Unknown	0	broad.mit.edu	37	15	100019400	100019401	+	IGR	INS	-	C	C	rs143243629	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:100019400_100019401insC								LRRC28 (92120 upstream) : MEF2A (86732 downstream)																																			---	---	---	---
MEF2A	4205	broad.mit.edu	37	15	100156535	100156535	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:100156535delT	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	100435445	100435446	+	IGR	DEL	TG	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:100435445_100435446delTG								C15orf51 (88313 upstream) : ADAMTS17 (76197 downstream)																																			---	---	---	---
ADAMTS17	170691	broad.mit.edu	37	15	100809181	100809183	+	Intron	DEL	CAT	-	-	rs147780806		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:100809181_100809183delCAT	uc002bvv.1	-						ADAMTS17_uc002bvx.1_Intron	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	101296633	101296633	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:101296633delT								ASB7 (104731 upstream) : ALDH1A3 (123376 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	101315278	101315278	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:101315278delT								ASB7 (123376 upstream) : ALDH1A3 (104731 downstream)																																			---	---	---	---
LRRK1	79705	broad.mit.edu	37	15	101562723	101562723	+	Frame_Shift_Del	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:101562723delC	uc002bwr.2	+	15	2307	c.1988delC	c.(1987-1989)GCCfs	p.A663fs	LRRK1_uc010usb.1_RNA|LRRK1_uc010usc.1_Intron	NM_024652	NP_078928	Q38SD2	LRRK1_HUMAN	leucine-rich repeat kinase 1	663	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)															---	---	---	---
CHSY1	22856	broad.mit.edu	37	15	101731952	101731952	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:101731952delT	uc002bwt.1	-							NM_014918	NP_055733			chondroitin sulfate synthase 1						chondroitin sulfate biosynthetic process	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				0	Lung NSC(78;0.00217)|all_lung(78;0.00271)|Melanoma(26;0.00505)		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	102097638	102097638	+	IGR	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:102097638delC								PCSK6 (67451 upstream) : TM2D3 (75542 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	102165580	102165580	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:102165580delA								PCSK6 (135393 upstream) : TM2D3 (7600 downstream)																																			---	---	---	---
TM2D3	80213	broad.mit.edu	37	15	102185369	102185369	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:102185369delA	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)															---	---	---	---
Unknown	0	broad.mit.edu	37	15	102283709	102283710	+	5'Flank	DEL	CT	-	-	rs111542757		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:102283709_102283710delCT	uc010usj.1	+											RecName: Full=Uncharacterized protein C15orf51.; Flags: Fragment;																														---	---	---	---
Unknown	0	broad.mit.edu	37	15	102521263	102521264	+	5'Flank	INS	-	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:102521263_102521264insT	uc010utv.1	-						uc002cds.2_5'Flank|uc010utw.1_5'Flank					SubName: Full=DEAD/H box polypeptide 11 like 9;																														---	---	---	---
NPRL3	8131	broad.mit.edu	37	16	159391	159392	+	Intron	DEL	CT	-	-	rs798608	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:159391_159392delCT	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																		---	---	---	---
Unknown	0	broad.mit.edu	37	16	192051	192051	+	IGR	DEL	T	-	-	rs78218306		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:192051delT								NPRL3 (3379 upstream) : HBZ (10803 downstream)																																			---	---	---	---
LUC7L	55692	broad.mit.edu	37	16	239633	239633	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:239633delA	uc002cgc.1	-						LUC7L_uc002cga.1_3'UTR|LUC7L_uc002cgd.1_Intron|LUC7L_uc002cge.1_Intron|LUC7L_uc002cgb.1_Intron	NM_201412	NP_958815			LUC7-like isoform b								metal ion binding			central_nervous_system(1)	1		all_cancers(16;1.1e-06)|all_epithelial(16;2.71e-06)|Hepatocellular(16;0.000105)|Lung NSC(18;0.0138)|all_lung(18;0.0306)																---	---	---	---
NARFL	64428	broad.mit.edu	37	16	779925	779925	+	3'UTR	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:779925delC	uc002cjr.2	-	11					NARFL_uc002cjp.2_3'UTR|NARFL_uc002cjq.2_3'UTR|NARFL_uc002cjs.2_3'UTR	NM_022493	NP_071938			nuclear prelamin A recognition factor-like						iron-sulfur cluster assembly|oxygen homeostasis|regulation of transcription, DNA-dependent|response to hypoxia		4 iron, 4 sulfur cluster binding|metal ion binding				0		Hepatocellular(780;0.0218)																---	---	---	---
LMF1	64788	broad.mit.edu	37	16	992686	992687	+	Intron	INS	-	CT	CT			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:992686_992687insCT	uc002ckj.2	-						LMF1_uc010brh.2_Intron|LMF1_uc010bri.2_Intron|LMF1_uc002ckk.2_Intron|LMF1_uc010uuu.1_Intron|LMF1_uc010uuv.1_Intron	NM_022773	NP_073610			lipase maturation factor 1							endoplasmic reticulum membrane|integral to membrane					0		Hepatocellular(780;0.00308)																---	---	---	---
Unknown	0	broad.mit.edu	37	16	1044462	1044462	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:1044462delA								SOX8 (7484 upstream) : LOC146336 (69622 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	1187964	1187965	+	IGR	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:1187964_1187965delTT								C1QTNF8 (41720 upstream) : CACNA1H (15276 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	1190814	1190814	+	IGR	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:1190814delC								C1QTNF8 (44570 upstream) : CACNA1H (12427 downstream)																																			---	---	---	---
IFT140	9742	broad.mit.edu	37	16	1633603	1633603	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:1633603delT	uc002cmb.2	-						IFT140_uc002clz.2_Intron	NM_014714	NP_055529			intraflagellar transport 140											ovary(3)|pancreas(1)|skin(1)	5		Hepatocellular(780;0.219)																---	---	---	---
PKD1	5310	broad.mit.edu	37	16	2171383	2171383	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:2171383delA	uc002cos.1	-						PKD1_uc002cot.1_Intron	NM_001009944	NP_001009944			polycystin 1 isoform 1 precursor						calcium-independent cell-matrix adhesion|homophilic cell adhesion|neuropeptide signaling pathway	basolateral plasma membrane|integral to plasma membrane	protein domain specific binding|sugar binding			central_nervous_system(2)|skin(1)	3																		---	---	---	---
ABCA3	21	broad.mit.edu	37	16	2370864	2370865	+	Intron	DEL	CT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:2370864_2370865delCT	uc002cpy.1	-						ABCA3_uc010bsk.1_Intron|ABCA3_uc010bsl.1_Intron	NM_001089	NP_001080			ATP-binding cassette, sub-family A member 3						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)																---	---	---	---
TBC1D24	57465	broad.mit.edu	37	16	2561020	2561020	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:2561020delT	uc002cqm.2	+						ATP6V0C_uc002cqn.2_5'Flank	NM_020705	NP_065756			TBC1 domain family, member 24						neuron projection development	cytoplasm	protein binding|Rab GTPase activator activity				0																		---	---	---	---
PRSS41	360226	broad.mit.edu	37	16	2847656	2847657	+	5'Flank	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:2847656_2847657delTT	uc010uwi.1	+							NM_001135086	NP_001128558			testis-specific serine protease 1 precursor						proteolysis	anchored to membrane|plasma membrane	serine-type endopeptidase activity				0																		---	---	---	---
PRSS21	10942	broad.mit.edu	37	16	2866730	2866732	+	5'Flank	DEL	AAA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:2866730_2866732delAAA	uc002crt.2	+						PRSS21_uc002crs.2_5'Flank|PRSS21_uc002crr.2_5'Flank	NM_006799	NP_006790			testisin isoform 1						proteolysis	anchored to membrane|cytoplasm|membrane fraction|plasma membrane	serine-type endopeptidase activity			ovary(1)|skin(1)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	16	3212351	3212351	+	IGR	DEL	T	-	-	rs113288349		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:3212351delT								ZNF213 (19547 upstream) : OR1F1 (41896 downstream)																																			---	---	---	---
ZNF263	10127	broad.mit.edu	37	16	3346792	3346792	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:3346792delA	uc002cur.2	+							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																		---	---	---	---
CLUAP1	23059	broad.mit.edu	37	16	3585113	3585113	+	Intron	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:3585113delG	uc002cvk.1	+						CLUAP1_uc002cvj.1_3'UTR|CLUAP1_uc002cvl.1_Intron|CLUAP1_uc002cvm.1_Intron|uc002cvn.1_5'Flank	NM_015041	NP_055856			clusterin associated protein 1 isoform 1							nucleus	protein binding			ovary(1)|breast(1)|pancreas(1)	3																		---	---	---	---
CREBBP	1387	broad.mit.edu	37	16	3786327	3786327	+	Intron	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:3786327delC	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				---	---	---	---
CREBBP	1387	broad.mit.edu	37	16	3823681	3823681	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:3823681delA	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				---	---	---	---
Unknown	0	broad.mit.edu	37	16	3942484	3942484	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:3942484delT								CREBBP (12363 upstream) : ADCY9 (70169 downstream)																																			---	---	---	---
ADCY9	115	broad.mit.edu	37	16	4027728	4027728	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:4027728delT	uc002cvx.2	-							NM_001116	NP_001107			adenylate cyclase 9						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 plasma membrane	adenylate cyclase activity|ATP binding|metal ion binding			ovary(4)|large_intestine(1)|central_nervous_system(1)	6																		---	---	---	---
TFAP4	7023	broad.mit.edu	37	16	4315079	4315079	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:4315079delT	uc010uxg.1	-							NM_003223	NP_003214			transcription factor AP-4 (activating enhancer						DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator|negative regulation by host of viral transcription|negative regulation of cell cycle arrest|negative regulation of cell proliferation|negative regulation of cyclin-dependent protein kinase activity|negative regulation of DNA binding|negative regulation of transcription, DNA-dependent|positive regulation by host of viral transcription|positive regulation of apoptosis|positive regulation of transcription from RNA polymerase II promoter|protein complex assembly|regulation of S phase of mitotic cell cycle	transcriptional repressor complex	E-box binding|histone deacetylase binding|protein homodimerization activity|sequence-specific DNA binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity			ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	16	4338681	4338681	+	IGR	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:4338681delC								TFAP4 (15680 upstream) : GLIS2 (43544 downstream)																																	OREG0023576	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
ANKS3	124401	broad.mit.edu	37	16	4769642	4769643	+	Intron	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:4769642_4769643delAA	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																		---	---	---	---
Unknown	0	broad.mit.edu	37	16	5466682	5466683	+	Intron	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:5466682_5466683delTT	uc002cyq.1	+											Homo sapiens cDNA clone IMAGE:5244947, **** WARNING: chimeric clone ****.																														---	---	---	---
Unknown	0	broad.mit.edu	37	16	5477039	5477040	+	Intron	INS	-	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:5477039_5477040insT	uc002cyq.1	+											Homo sapiens cDNA clone IMAGE:5244947, **** WARNING: chimeric clone ****.																														---	---	---	---
Unknown	0	broad.mit.edu	37	16	6028905	6028905	+	IGR	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:6028905delG								FAM86A (881116 upstream) : A2BP1 (40227 downstream)																																			---	---	---	---
A2BP1	54715	broad.mit.edu	37	16	6082313	6082313	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:6082313delA	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	6090018	6090019	+	Intron	DEL	GA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:6090018_6090019delGA	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	6195036	6195037	+	Intron	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:6195036_6195037delTT	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	6475605	6475605	+	Intron	DEL	T	-	-	rs113706495		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:6475605delT	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	6513219	6513220	+	Intron	INS	-	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:6513219_6513220insT	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	6982099	6982099	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:6982099delT	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)														---	---	---	---
A2BP1	54715	broad.mit.edu	37	16	7507821	7507822	+	Intron	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:7507821_7507822delAA	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|A2BP1_uc002cyw.2_Intron|A2BP1_uc002cyy.2_Intron|A2BP1_uc002cyx.2_Intron|A2BP1_uc010uyc.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	7695956	7695957	+	Intron	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:7695956_7695957delTT	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|A2BP1_uc002cyw.2_Intron|A2BP1_uc002cyy.2_Intron|A2BP1_uc002cyx.2_Intron|A2BP1_uc010uyc.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	8170026	8170026	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:8170026delT								A2BP1 (406686 upstream) : TMEM114 (449477 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	8366237	8366240	+	IGR	DEL	TTTT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:8366237_8366240delTTTT								A2BP1 (602897 upstream) : TMEM114 (253263 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	8464832	8464832	+	IGR	DEL	A	-	-	rs34971952		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:8464832delA								A2BP1 (701492 upstream) : TMEM114 (154671 downstream)																																			---	---	---	---
ABAT	18	broad.mit.edu	37	16	8777725	8777726	+	Intron	INS	-	ATTT	ATTT	rs146792826	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:8777725_8777726insATTT	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	9224900	9224900	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:9224900delA								C16orf72 (11355 upstream) : GRIN2A (622367 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	9265554	9265554	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:9265554delT								C16orf72 (52009 upstream) : GRIN2A (581713 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	9287360	9287360	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:9287360delT								C16orf72 (73815 upstream) : GRIN2A (559907 downstream)																																			---	---	---	---
GRIN2A	2903	broad.mit.edu	37	16	9919272	9919272	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:9919272delT	uc002czo.3	-						GRIN2A_uc010uym.1_Intron|GRIN2A_uc010uyn.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)													---	---	---	---
GRIN2A	2903	broad.mit.edu	37	16	10053829	10053830	+	Intron	INS	-	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:10053829_10053830insA	uc002czo.3	-						GRIN2A_uc010uym.1_Intron|GRIN2A_uc010uyn.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	10361898	10361898	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:10361898delA								GRIN2A (85287 upstream) : ATF7IP2 (118014 downstream)																																			---	---	---	---
ATF7IP2	80063	broad.mit.edu	37	16	10551547	10551547	+	Intron	DEL	T	-	-	rs57240502		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:10551547delT	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																		---	---	---	---
TEKT5	146279	broad.mit.edu	37	16	10727216	10727217	+	Intron	DEL	AA	-	-	rs78082805		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:10727216_10727217delAA	uc002czz.1	-							NM_144674	NP_653275			tektin 5						microtubule cytoskeleton organization	cilium axoneme|flagellar axoneme|microtubule				ovary(2)	2																		---	---	---	---
FAM18A	780776	broad.mit.edu	37	16	10864076	10864077	+	Intron	INS	-	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:10864076_10864077insT	uc010buo.1	-						FAM18A_uc010uyr.1_Intron|FAM18A_uc010uys.1_Intron|FAM18A_uc010uyt.1_Intron|FAM18A_uc010bun.2_Intron|FAM18A_uc010uyu.1_Intron|FAM18A_uc002dad.3_Intron|FAM18A_uc002daf.1_Intron|FAM18A_uc002dae.1_Intron	NM_001079512	NP_001072980			hypothetical protein LOC780776							integral to membrane					0																		---	---	---	---
CIITA	4261	broad.mit.edu	37	16	10993967	10993968	+	Intron	INS	-	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:10993967_10993968insA	uc002dai.3	+						CIITA_uc002daj.3_Intron|CIITA_uc002dak.3_Intron|CIITA_uc002dag.2_Intron|CIITA_uc002dah.2_Intron|CIITA_uc010bup.1_Intron	NM_000246	NP_000237			class II transactivator						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|								---	---	---	---
CLEC16A	23274	broad.mit.edu	37	16	11066725	11066725	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:11066725delT	uc002dao.2	+						CLEC16A_uc002dan.3_Intron	NM_015226	NP_056041			C-type lectin domain family 16, member A											ovary(1)|central_nervous_system(1)	2																		---	---	---	---
CLEC16A	23274	broad.mit.edu	37	16	11071363	11071363	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:11071363delT	uc002dao.2	+						CLEC16A_uc002dan.3_Intron	NM_015226	NP_056041			C-type lectin domain family 16, member A											ovary(1)|central_nervous_system(1)	2																		---	---	---	---
CLEC16A	23274	broad.mit.edu	37	16	11130148	11130148	+	Intron	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:11130148delC	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																		---	---	---	---
CLEC16A	23274	broad.mit.edu	37	16	11260792	11260792	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:11260792delT	uc002dao.2	+						CLEC16A_uc002dap.2_Intron	NM_015226	NP_056041			C-type lectin domain family 16, member A											ovary(1)|central_nervous_system(1)	2																		---	---	---	---
C16orf75	116028	broad.mit.edu	37	16	11444921	11444922	+	3'UTR	DEL	TC	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:11444921_11444922delTC	uc002daw.1	+	2					C16orf75_uc002daq.1_RNA	NM_152308	NP_689521			RecQ-mediated genome instability protein 2						DNA replication	nucleus	DNA binding				0								T	CIITA	PMBL|Hodgkin Lymphona|								---	---	---	---
LITAF	9516	broad.mit.edu	37	16	11678151	11678152	+	Intron	DEL	CT	-	-	rs140075569		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:11678151_11678152delCT	uc002daz.2	-						LITAF_uc002dba.2_Intron|LITAF_uc002dbb.2_Intron|LITAF_uc002dbc.2_Intron|LITAF_uc002dbd.2_Intron|LITAF_uc002dbe.3_Intron	NM_004862	NP_004853			lipopolysaccharide-induced TNF-alpha factor						apoptosis|positive regulation of I-kappaB kinase/NF-kappaB cascade|regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	Golgi apparatus|lysosomal membrane	signal transducer activity|WW domain binding			liver(1)	1																		---	---	---	---
TXNDC11	51061	broad.mit.edu	37	16	11811677	11811677	+	Intron	DEL	A	-	-	rs76311516		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:11811677delA	uc010buu.1	-						TXNDC11_uc002dbg.1_Intron	NM_015914	NP_056998			thioredoxin domain containing 11						cell redox homeostasis	endoplasmic reticulum membrane|integral to membrane					0																		---	---	---	---
TXNDC11	51061	broad.mit.edu	37	16	11817457	11817457	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:11817457delA	uc010buu.1	-						TXNDC11_uc002dbg.1_Intron	NM_015914	NP_056998			thioredoxin domain containing 11						cell redox homeostasis	endoplasmic reticulum membrane|integral to membrane					0																		---	---	---	---
ZC3H7A	29066	broad.mit.edu	37	16	11855927	11855927	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:11855927delT	uc002dbk.2	-						ZC3H7A_uc002dbj.2_Intron|ZC3H7A_uc002dbl.2_Intron|ZC3H7A_uc002dbm.1_Intron	NM_014153	NP_054872			zinc finger CCCH-type containing 7A							nucleus	nucleic acid binding|zinc ion binding			ovary(2)|pancreas(1)|skin(1)	4																		---	---	---	---
RUNDC2A	84127	broad.mit.edu	37	16	12082597	12082597	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:12082597delT	uc002dbw.1	+							NM_032167	NP_115543			RUN domain containing 2A											ovary(1)	1								T	CIITA	PMBL|Hodgkin Lymphona|								---	---	---	---
RUNDC2A	84127	broad.mit.edu	37	16	12089408	12089408	+	Intron	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:12089408delC	uc002dbw.1	+							NM_032167	NP_115543			RUN domain containing 2A											ovary(1)	1								T	CIITA	PMBL|Hodgkin Lymphona|								---	---	---	---
SNX29	92017	broad.mit.edu	37	16	12240120	12240123	+	Intron	DEL	TTTT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:12240120_12240123delTTTT	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	12439733	12439734	+	Intron	INS	-	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:12439733_12439734insT	uc002dby.3	+							NM_001080530	NP_001073999			sorting nexin 29						cell communication		phosphatidylinositol binding			ovary(1)	1																		---	---	---	---
CPPED1	55313	broad.mit.edu	37	16	12887899	12887899	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:12887899delA	uc002dca.3	-						CPPED1_uc002dcb.3_Intron	NM_018340	NP_060810			calcineurin-like phosphoesterase domain								hydrolase activity|metal ion binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	16	12971815	12971815	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:12971815delT								CPPED1 (74071 upstream) : SHISA9 (23662 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	13534785	13534786	+	IGR	DEL	AG	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:13534785_13534786delAG								SHISA9 (200513 upstream) : ERCC4 (479228 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	13642123	13642123	+	IGR	DEL	A	-	-	rs34517021		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:13642123delA								SHISA9 (307851 upstream) : ERCC4 (371891 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	13838274	13838274	+	IGR	DEL	T	-	-	rs76791387		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:13838274delT								SHISA9 (504002 upstream) : ERCC4 (175740 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	13848503	13848504	+	IGR	DEL	CT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:13848503_13848504delCT								SHISA9 (514231 upstream) : ERCC4 (165510 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	13854559	13854560	+	IGR	DEL	TC	-	-	rs117375310	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:13854559_13854560delTC								SHISA9 (520287 upstream) : ERCC4 (159454 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	13967906	13967906	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:13967906delA								SHISA9 (633634 upstream) : ERCC4 (46108 downstream)																																			---	---	---	---
MKL2	57496	broad.mit.edu	37	16	14312561	14312561	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-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	14312901	14312901	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:14312901delT	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																		---	---	---	---
PARN	5073	broad.mit.edu	37	16	14625578	14625578	+	Intron	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:14625578delC	uc010uzd.1	-						PARN_uc010uzc.1_Intron|PARN_uc010uze.1_Intron|PARN_uc010uzf.1_Intron	NM_002582	NP_002573			poly(A)-specific ribonuclease (deadenylation						female gamete generation|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay|nuclear-transcribed mRNA poly(A) tail shortening|RNA modification	cytosol|nucleolus	metal ion binding|mRNA 3'-UTR binding|nucleotide binding|poly(A)-specific ribonuclease activity|protein binding			ovary(2)	2																		---	---	---	---
PARN	5073	broad.mit.edu	37	16	14648695	14648695	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:14648695delA	uc010uzd.1	-						PARN_uc010uzc.1_Intron|PARN_uc010uze.1_Intron|PARN_uc010uzf.1_Intron	NM_002582	NP_002573			poly(A)-specific ribonuclease (deadenylation						female gamete generation|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay|nuclear-transcribed mRNA poly(A) tail shortening|RNA modification	cytosol|nucleolus	metal ion binding|mRNA 3'-UTR binding|nucleotide binding|poly(A)-specific ribonuclease activity|protein binding			ovary(2)	2																		---	---	---	---
PARN	5073	broad.mit.edu	37	16	14693890	14693890	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:14693890delA	uc010uzd.1	-						PARN_uc010uzc.1_Intron|PARN_uc010uze.1_Intron|PARN_uc010uzf.1_Intron|PARN_uc010uzg.1_Intron	NM_002582	NP_002573			poly(A)-specific ribonuclease (deadenylation						female gamete generation|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay|nuclear-transcribed mRNA poly(A) tail shortening|RNA modification	cytosol|nucleolus	metal ion binding|mRNA 3'-UTR binding|nucleotide binding|poly(A)-specific ribonuclease activity|protein binding			ovary(2)	2																		---	---	---	---
PARN	5073	broad.mit.edu	37	16	14721881	14721881	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:14721881delA	uc010uzd.1	-						PARN_uc010uzc.1_Intron|PARN_uc010uze.1_Intron|PARN_uc010uzf.1_Intron|PARN_uc010uzg.1_Intron	NM_002582	NP_002573			poly(A)-specific ribonuclease (deadenylation						female gamete generation|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay|nuclear-transcribed mRNA poly(A) tail shortening|RNA modification	cytosol|nucleolus	metal ion binding|mRNA 3'-UTR binding|nucleotide binding|poly(A)-specific ribonuclease activity|protein binding			ovary(2)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	16	15059045	15059045	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:15059045delT								NPIP (13115 upstream) : PDXDC1 (9554 downstream)																																			---	---	---	---
PDXDC1	23042	broad.mit.edu	37	16	15115242	15115242	+	Intron	DEL	A	-	-	rs79259340		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:15115242delA	uc002dda.3	+						PDXDC1_uc010uzl.1_Intron|PDXDC1_uc010uzm.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)													---	---	---	---
RRN3	54700	broad.mit.edu	37	16	15179349	15179349	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:15179349delT	uc002dde.2	-						PDXDC1_uc002ddc.2_Intron|RRN3_uc010uzp.1_Intron|RRN3_uc010uzq.1_Intron|RRN3_uc002ddf.1_Intron	NM_018427	NP_060897			RRN3 RNA polymerase I transcription factor						regulation of transcription, DNA-dependent|transcription initiation from RNA polymerase I promoter	nucleolus|nucleoplasm				ovary(1)	1																		---	---	---	---
RRN3	54700	broad.mit.edu	37	16	15186868	15186868	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:15186868delT	uc002dde.2	-						PDXDC1_uc002ddc.2_Intron|RRN3_uc010uzq.1_Intron|RRN3_uc002ddf.1_Intron|uc010bve.1_5'Flank	NM_018427	NP_060897			RRN3 RNA polymerase I transcription factor						regulation of transcription, DNA-dependent|transcription initiation from RNA polymerase I promoter	nucleolus|nucleoplasm				ovary(1)	1																		---	---	---	---
MYH11	4629	broad.mit.edu	37	16	15798090	15798090	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:15798090delT	uc002ddy.2	-						MYH11_uc002ddv.2_Intron|MYH11_uc002ddw.2_Intron|MYH11_uc002ddx.2_Intron|MYH11_uc010bvg.2_Intron|NDE1_uc010uzy.1_Intron|NDE1_uc002dds.2_Intron	NM_002474	NP_002465			smooth muscle myosin heavy chain 11 isoform						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								---	---	---	---
Unknown	0	broad.mit.edu	37	16	15958272	15958272	+	IGR	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:15958272delC								MYH11 (7385 upstream) : C16orf63 (1305 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	15989850	15989850	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:15989850delT								C16orf63 (7403 upstream) : ABCC1 (53584 downstream)																																			---	---	---	---
ABCC1	4363	broad.mit.edu	37	16	16151899	16151899	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:16151899delT	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)													---	---	---	---
Unknown	0	broad.mit.edu	37	16	16702855	16702855	+	IGR	DEL	A	-	-	rs71776191		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:16702855delA								LOC339047 (258418 upstream) : XYLT1 (493328 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	16734821	16734822	+	IGR	DEL	CT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:16734821_16734822delCT								LOC339047 (290384 upstream) : XYLT1 (461361 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	17082491	17082491	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:17082491delA								LOC339047 (638054 upstream) : XYLT1 (113692 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	17151195	17151195	+	IGR	DEL	T	-	-	rs76589971		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:17151195delT								LOC339047 (706758 upstream) : XYLT1 (44988 downstream)																																			---	---	---	---
XYLT1	64131	broad.mit.edu	37	16	17279866	17279867	+	Intron	DEL	AT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:17279866_17279867delAT	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	17721174	17721175	+	IGR	DEL	CA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:17721174_17721175delCA								XYLT1 (156436 upstream) : NOMO2 (790008 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	18093149	18093149	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:18093149delT								XYLT1 (528411 upstream) : NOMO2 (418034 downstream)																																			---	---	---	---
NOMO2	283820	broad.mit.edu	37	16	18531725	18531726	+	Intron	INS	-	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:18531725_18531726insA	uc002dfe.2	-						NOMO2_uc002dff.2_Intron|NOMO2_uc010bvx.2_Intron	NM_001004060	NP_001004060			nodal modulator 2 isoform 1							endoplasmic reticulum membrane|integral to membrane	carbohydrate binding|carboxypeptidase activity|protein binding			skin(1)	1																		---	---	---	---
SMG1	23049	broad.mit.edu	37	16	18897123	18897124	+	Intron	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:18897123_18897124delAA	uc002dfm.2	-						SMG1_uc010bwb.2_Intron	NM_015092	NP_055907			PI-3-kinase-related kinase SMG-1						DNA repair|mRNA export from nucleus|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay|peptidyl-serine phosphorylation|phosphatidylinositol phosphorylation|protein autophosphorylation	cytoplasm|nucleus	ATP binding|metal ion binding|protein binding|protein serine/threonine kinase activity			breast(5)|stomach(4)|lung(4)|kidney(2)|ovary(1)	16																		---	---	---	---
Unknown	0	broad.mit.edu	37	16	18989158	18989158	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:18989158delT								SMG1 (51432 upstream) : TMC7 (6098 downstream)																																			---	---	---	---
TMC7	79905	broad.mit.edu	37	16	19039185	19039186	+	Intron	DEL	AC	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:19039185_19039186delAC	uc002dfq.2	+						TMC7_uc010vao.1_Intron|TMC7_uc002dfp.2_Intron|TMC7_uc010vap.1_Intron	NM_024847	NP_079123			transmembrane channel-like 7 isoform a							integral to membrane				skin(2)|ovary(1)	3																		---	---	---	---
SYT17	51760	broad.mit.edu	37	16	19241727	19241727	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:19241727delA	uc002dfw.2	+						SYT17_uc002dfx.2_Intron|SYT17_uc002dfy.2_Intron|SYT17_uc002dfv.1_Intron	NM_016524	NP_057608			B/K protein							membrane|synaptic vesicle	transporter activity			ovary(1)	1																		---	---	---	---
SYT17	51760	broad.mit.edu	37	16	19269276	19269277	+	Intron	DEL	TT	-	-	rs66472231		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:19269276_19269277delTT	uc002dfw.2	+						SYT17_uc002dfx.2_Intron|SYT17_uc002dfy.2_Intron	NM_016524	NP_057608			B/K protein							membrane|synaptic vesicle	transporter activity			ovary(1)	1																		---	---	---	---
LOC728276	728276	broad.mit.edu	37	16	19309890	19309890	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:19309890delA	uc002dga.3	+						LOC728276_uc002dfz.3_Intron	NR_024436				RecName: Full=C-type lectin domain-containing protein UNQ5810/PRO19627; Flags: Precursor;												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	16	19320955	19320956	+	IGR	DEL	TT	-	-	rs75151911		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:19320955_19320956delTT								LOC728276 (5239 upstream) : TMC5 (100905 downstream)																																			---	---	---	---
TMC5	79838	broad.mit.edu	37	16	19501118	19501118	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:19501118delT	uc002dgc.3	+						TMC5_uc010vaq.1_Intron|TMC5_uc002dgb.3_Intron|TMC5_uc010var.1_Intron|TMC5_uc002dgd.1_Intron|TMC5_uc002dge.3_Intron|TMC5_uc002dgf.3_Intron|TMC5_uc002dgg.3_Intron	NM_001105248	NP_001098718			transmembrane channel-like 5 isoform a							integral to membrane				skin(1)	1																		---	---	---	---
C16orf62	57020	broad.mit.edu	37	16	19629582	19629582	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:19629582delA	uc002dgn.1	+						C16orf62_uc002dgo.1_Intron|C16orf62_uc002dgp.1_Intron	NM_020314	NP_064710			hypothetical protein LOC57020							integral to membrane				ovary(1)	1																		---	---	---	---
IQCK	124152	broad.mit.edu	37	16	19829668	19829669	+	Intron	INS	-	TG	TG	rs150424237		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:19829668_19829669insTG	uc002dgr.2	+						IQCK_uc002dgs.2_Intron|IQCK_uc010vat.1_Intron|IQCK_uc010bwc.2_Intron|IQCK_uc010vau.1_Intron	NM_153208	NP_694940			IQ motif containing K											skin(1)	1																		---	---	---	---
GPR139	124274	broad.mit.edu	37	16	20065902	20065903	+	Intron	INS	-	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:20065902_20065903insT	uc002dgu.1	-						GPR139_uc010vaw.1_Intron	NM_001002911	NP_001002911			G protein-coupled receptor 139							integral to membrane|plasma membrane				ovary(2)	2																		---	---	---	---
ACSM5	54988	broad.mit.edu	37	16	20429352	20429352	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:20429352delT	uc002dhe.2	+						ACSM5_uc002dhd.1_Intron	NM_017888	NP_060358			acyl-CoA synthetase medium-chain family member 5						fatty acid metabolic process	mitochondrial matrix	ATP binding|butyrate-CoA ligase activity|GTP binding|metal ion binding			ovary(2)	2																		---	---	---	---
ACSM5	54988	broad.mit.edu	37	16	20441396	20441396	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:20441396delA	uc002dhe.2	+							NM_017888	NP_060358			acyl-CoA synthetase medium-chain family member 5						fatty acid metabolic process	mitochondrial matrix	ATP binding|butyrate-CoA ligase activity|GTP binding|metal ion binding			ovary(2)	2																		---	---	---	---
DNAH3	55567	broad.mit.edu	37	16	20972391	20972391	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:20972391delA	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)														---	---	---	---
METTL9	51108	broad.mit.edu	37	16	21664118	21664118	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:21664118delT	uc002dje.2	+						uc002diq.3_Intron|METTL9_uc002djf.2_Intron|IGSF6_uc002djg.1_5'Flank|IGSF6_uc010vbi.1_5'Flank	NM_016025	NP_057109			methyltransferase like 9 isoform 1											ovary(1)	1				GBM - Glioblastoma multiforme(48;0.0759)														---	---	---	---
RRN3P1	730092	broad.mit.edu	37	16	21814060	21814060	+	Intron	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:21814060delG	uc010vbl.1	-						uc002diq.3_Intron	NR_003370				SubName: Full=Putative uncharacterized protein ENSP00000219758;												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	16	21890632	21890632	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:21890632delA	uc002djr.3	-						uc002djs.3_Intron|uc010vbo.1_RNA	NM_130464	NP_569731			nuclear pore complex interacting protein-like 3																														---	---	---	---
Unknown	0	broad.mit.edu	37	16	21902248	21902250	+	Intron	DEL	AAC	-	-	rs505863		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:21902248_21902250delAAC	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	21954174	21954174	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:21954174delA								RRN3P1 (122443 upstream) : UQCRC2 (10435 downstream)																																			---	---	---	---
VWA3A	146177	broad.mit.edu	37	16	22154163	22154163	+	Intron	DEL	G	-	-	rs143580498	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:22154163delG	uc010vbq.1	+						VWA3A_uc010bxd.2_Intron|VWA3A_uc002dkg.3_5'Flank	NM_173615	NP_775886			von Willebrand factor A domain containing 3A							extracellular region				skin(1)	1				GBM - Glioblastoma multiforme(48;0.0439)														---	---	---	---
VWA3A	146177	broad.mit.edu	37	16	22162873	22162873	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:22162873delT	uc010vbq.1	+						VWA3A_uc010bxd.2_Intron|VWA3A_uc002dkg.3_Intron|VWA3A_uc010bxe.1_Intron	NM_173615	NP_775886			von Willebrand factor A domain containing 3A							extracellular region				skin(1)	1				GBM - Glioblastoma multiforme(48;0.0439)														---	---	---	---
EEF2K	29904	broad.mit.edu	37	16	22260294	22260299	+	Intron	DEL	TTTTTT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:22260294_22260299delTTTTTT	uc002dki.2	+						EEF2K_uc002dkh.2_Intron	NM_013302	NP_037434			elongation factor-2 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)														---	---	---	---
Unknown	0	broad.mit.edu	37	16	22958780	22958780	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:22958780delA								HS3ST2 (31123 upstream) : USP31 (113949 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	23036439	23036444	+	IGR	DEL	AAAAAA	-	-	rs112706632		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:23036439_23036444delAAAAAA								HS3ST2 (108782 upstream) : USP31 (36285 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	23059314	23059314	+	IGR	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:23059314delC								HS3ST2 (131657 upstream) : USP31 (13415 downstream)																																			---	---	---	---
SCNN1G	6340	broad.mit.edu	37	16	23208793	23208793	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:23208793delT	uc002dlm.1	+							NM_001039	NP_001030			sodium channel, nonvoltage-gated 1, gamma						excretion|sensory perception of taste	apical plasma membrane|integral to plasma membrane	ligand-gated sodium channel activity|WW domain binding			ovary(2)|skin(2)|large_intestine(1)|pancreas(1)	6				GBM - Glioblastoma multiforme(48;0.0366)	Amiloride(DB00594)|Triamterene(DB00384)													---	---	---	---
Unknown	0	broad.mit.edu	37	16	23282632	23282632	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:23282632delT								SCNN1G (54432 upstream) : SCNN1B (30959 downstream)																																			---	---	---	---
SCNN1B	6338	broad.mit.edu	37	16	23376454	23376454	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:23376454delA	uc002dln.2	+							NM_000336	NP_000327			sodium channel, nonvoltage-gated 1, beta						excretion|sensory perception of taste	apical plasma membrane	ligand-gated sodium channel activity|WW domain binding			ovary(3)|breast(2)|large_intestine(1)|pancreas(1)	7				GBM - Glioblastoma multiforme(48;0.0465)	Amiloride(DB00594)|Triamterene(DB00384)													---	---	---	---
EARS2	124454	broad.mit.edu	37	16	23542590	23542590	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:23542590delT	uc002dlt.3	-						EARS2_uc002dlr.3_Intron|EARS2_uc002dls.3_Intron|EARS2_uc002dlu.2_Intron	NM_001083614	NP_001077083			glutamyl-tRNA synthetase 2 precursor						glutamyl-tRNA aminoacylation	mitochondrial matrix	ATP binding|glutamate-tRNA ligase activity|RNA binding				0				GBM - Glioblastoma multiforme(48;0.0353)	L-Glutamic Acid(DB00142)													---	---	---	---
PRKCB	5579	broad.mit.edu	37	16	24229970	24229971	+	Intron	INS	-	GA	GA	rs149796731	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:24229970_24229971insGA	uc002dmd.2	+						PRKCB_uc002dme.2_3'UTR	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	24602761	24602762	+	IGR	INS	-	TG	TG	rs139519644	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:24602761_24602762insTG								RBBP6 (18580 upstream) : TNRC6A (138287 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	24625662	24625663	+	IGR	INS	-	TTG	TTG	rs140617555	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:24625662_24625663insTTG								RBBP6 (41481 upstream) : TNRC6A (115386 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	24702766	24702766	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:24702766delA								RBBP6 (118585 upstream) : TNRC6A (38283 downstream)																																			---	---	---	---
ARHGAP17	55114	broad.mit.edu	37	16	25009754	25009754	+	Intron	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:25009754delG	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)														---	---	---	---
Unknown	0	broad.mit.edu	37	16	25620557	25620558	+	IGR	INS	-	TTG	TTG	rs147943037	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:25620557_25620558insTTG								ZKSCAN2 (351702 upstream) : HS3ST4 (82789 downstream)																																			---	---	---	---
HS3ST4	9951	broad.mit.edu	37	16	25959237	25959237	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:25959237delA	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	26156685	26156685	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:26156685delA								HS3ST4 (7677 upstream) : C16orf82 (921534 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	26230021	26230021	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:26230021delA								HS3ST4 (81013 upstream) : C16orf82 (848198 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	26939574	26939577	+	IGR	DEL	GAAG	-	-	rs12934605		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:26939574_26939577delGAAG								HS3ST4 (790566 upstream) : C16orf82 (138642 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	27008281	27008281	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:27008281delA								HS3ST4 (859273 upstream) : C16orf82 (69938 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	27036683	27036683	+	IGR	DEL	A	-	-	rs72234995		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:27036683delA								HS3ST4 (887675 upstream) : C16orf82 (41536 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	27074610	27074610	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:27074610delA								HS3ST4 (925602 upstream) : C16orf82 (3609 downstream)																																			---	---	---	---
KIAA0556	23247	broad.mit.edu	37	16	27748706	27748706	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:27748706delA	uc002dow.2	+							NM_015202	NP_056017			hypothetical protein LOC23247											ovary(4)|large_intestine(2)|upper_aerodigestive_tract(1)|skin(1)	8																		---	---	---	---
SBK1	388228	broad.mit.edu	37	16	28314478	28314478	+	Intron	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:28314478delG	uc002dpd.2	+							NM_001024401	NP_001019572			SH3-binding kinase 1							cytoplasm	ATP binding|protein serine/threonine kinase activity			ovary(1)|kidney(1)	2																		---	---	---	---
SBK1	388228	broad.mit.edu	37	16	28329003	28329003	+	Intron	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:28329003delG	uc002dpd.2	+							NM_001024401	NP_001019572			SH3-binding kinase 1							cytoplasm	ATP binding|protein serine/threonine kinase activity			ovary(1)|kidney(1)	2																OREG0023701	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
Unknown	0	broad.mit.edu	37	16	28521004	28521006	+	Intron	DEL	TTT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:28521004_28521006delTTT	uc010vct.1	-						IL27_uc002dqc.2_5'Flank					RecName: Full=Nuclear pore complex-interacting protein-like 2; Flags: Precursor;																														---	---	---	---
Unknown	0	broad.mit.edu	37	16	28549999	28549999	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:28549999delA	uc010vct.1	-						NUPR1_uc002dqd.1_Intron|NUPR1_uc002dqe.1_Intron					RecName: Full=Nuclear pore complex-interacting protein-like 2; Flags: Precursor;																														---	---	---	---
Unknown	0	broad.mit.edu	37	16	28561086	28561087	+	Intron	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:28561086_28561087delTT	uc010vct.1	-											RecName: Full=Nuclear pore complex-interacting protein-like 2; Flags: Precursor;																														---	---	---	---
Unknown	0	broad.mit.edu	37	16	28606578	28606578	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:28606578delT	uc010vct.1	-						SULT1A2_uc002dqg.1_Intron|SULT1A2_uc002dqh.1_Intron					RecName: Full=Nuclear pore complex-interacting protein-like 2; Flags: Precursor;																														---	---	---	---
Unknown	0	broad.mit.edu	37	16	28967913	28967913	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:28967913delT	uc010vct.1	-						NFATC2IP_uc002drt.2_Intron|NFATC2IP_uc002dru.2_Intron|NFATC2IP_uc002drv.2_Intron|NFATC2IP_uc010vdh.1_5'Flank					RecName: Full=Nuclear pore complex-interacting protein-like 2; Flags: Precursor;																														---	---	---	---
Unknown	0	broad.mit.edu	37	16	29010427	29010427	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:29010427delT	uc010vct.1	-											RecName: Full=Nuclear pore complex-interacting protein-like 2; Flags: Precursor;																														---	---	---	---
BOLA2	552900	broad.mit.edu	37	16	29565637	29565637	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:29565637delA	uc010bzb.1	-						LOC440354_uc002dsp.3_Intron|uc002dtf.2_Intron|LOC440354_uc010bza.1_Intron|LOC440354_uc002dtj.2_Intron|LOC440354_uc010vds.1_Intron					SubName: Full=Putative uncharacterized protein ENSP00000369970; Flags: Fragment;												0																		---	---	---	---
BOLA2	552900	broad.mit.edu	37	16	29600932	29600932	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:29600932delA	uc010bzb.1	-						LOC440354_uc002dsp.3_Intron|uc002dtf.2_Intron|LOC440354_uc010vds.1_Intron|LOC440354_uc010vdt.1_Intron					SubName: Full=Putative uncharacterized protein ENSP00000369970; Flags: Fragment;												0																		---	---	---	---
INO80E	283899	broad.mit.edu	37	16	30016653	30016653	+	Frame_Shift_Del	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:30016653delC	uc002dvg.1	+	7	726	c.625delC	c.(625-627)CCCfs	p.P209fs	uc002dtf.2_Intron|BOLA2_uc010bzb.1_Intron|INO80E_uc002dvh.1_RNA|INO80E_uc002dvi.1_3'UTR|INO80E_uc002dvj.1_RNA|INO80E_uc002dvk.1_Frame_Shift_Del_p.P170fs	NM_173618	NP_775889	Q8NBZ0	IN80E_HUMAN	INO80 complex subunit E	209	Pro-rich.				DNA recombination|DNA repair|regulation of transcription, DNA-dependent|transcription, DNA-dependent	Ino80 complex				skin(1)	1																		---	---	---	---
BOLA2	552900	broad.mit.edu	37	16	30032323	30032323	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:30032323delA	uc010bzb.1	-						uc002dtf.2_Intron|C16orf92_uc002dvr.2_5'Flank|C16orf92_uc002dvs.2_5'Flank					SubName: Full=Putative uncharacterized protein ENSP00000369970; Flags: Fragment;												0																		---	---	---	---
BOLA2	552900	broad.mit.edu	37	16	30033192	30033192	+	Intron	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:30033192delC	uc010bzb.1	-						uc002dtf.2_Intron|C16orf92_uc002dvr.2_5'Flank|C16orf92_uc002dvs.2_5'Flank					SubName: Full=Putative uncharacterized protein ENSP00000369970; Flags: Fragment;												0																		---	---	---	---
BOLA2	552900	broad.mit.edu	37	16	30171987	30171987	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:30171987delA	uc010bzb.1	-						uc002dtf.2_Intron					SubName: Full=Putative uncharacterized protein ENSP00000369970; Flags: Fragment;												0																		---	---	---	---
LOC595101	595101	broad.mit.edu	37	16	30309933	30309934	+	Intron	INS	-	AA	AA			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:30309933_30309934insAA	uc002dxp.1	-							NR_002453				Homo sapiens cDNA FLJ39663 fis, clone SMINT2007187.												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	16	30414717	30414717	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:30414717delT								ZNF48 (4002 upstream) : ZNF771 (4018 downstream)																																			---	---	---	---
ITGAL	3683	broad.mit.edu	37	16	30503577	30503580	+	Intron	DEL	TTTT	-	-	rs113363303		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:30503577_30503580delTTTT	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)													---	---	---	---
ZNF689	115509	broad.mit.edu	37	16	30622813	30622813	+	5'Flank	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:30622813delT	uc002dyx.2	-						ZNF689_uc010bzy.2_5'Flank	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)															---	---	---	---
Unknown	0	broad.mit.edu	37	16	30646484	30646484	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:30646484delA								ZNF689 (24802 upstream) : PRR14 (15757 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	30655154	30655155	+	IGR	INS	-	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:30655154_30655155insA								ZNF689 (33472 upstream) : PRR14 (7086 downstream)																																			---	---	---	---
SRCAP	10847	broad.mit.edu	37	16	30746111	30746111	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:30746111delA	uc002dze.1	+						SRCAP_uc002dzf.2_Intron|SRCAP_uc002dzg.1_Intron	NM_006662	NP_006653			Snf2-related CBP activator protein						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)															---	---	---	---
ZNF646	9726	broad.mit.edu	37	16	31094516	31094518	+	3'UTR	DEL	CTC	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:31094516_31094518delCTC	uc002eap.2	+	3						NM_014699	NP_055514			zinc finger protein 646						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|protein binding|zinc ion binding			breast(2)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	16	31169115	31169115	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:31169115delT								PRSS36 (7700 upstream) : FUS (22338 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	31250748	31250749	+	IGR	DEL	TT	-	-	rs75781461		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:31250748_31250749delTT								TRIM72 (14238 upstream) : ITGAM (20539 downstream)																																			---	---	---	---
ITGAX	3687	broad.mit.edu	37	16	31383487	31383488	+	Intron	DEL	GG	-	-	rs67981265		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:31383487_31383488delGG	uc002ebu.1	+						ITGAX_uc002ebt.2_Intron	NM_000887	NP_000878			integrin alpha X precursor						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																		---	---	---	---
ITGAX	3687	broad.mit.edu	37	16	31390455	31390455	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:31390455delT	uc002ebu.1	+						ITGAX_uc002ebt.2_Intron	NM_000887	NP_000878			integrin alpha X precursor						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																		---	---	---	---
ITGAD	3681	broad.mit.edu	37	16	31419301	31419301	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:31419301delT	uc002ebv.1	+						ITGAD_uc010vfl.1_Intron|ITGAD_uc010cap.1_Intron|ITGAD_uc002ebw.1_Intron	NM_005353	NP_005344			integrin, alpha D precursor						cell-cell adhesion|cell-matrix adhesion|immune response|integrin-mediated signaling pathway	integrin complex	receptor activity			skin(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	16	31442793	31442794	+	IGR	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:31442793_31442794delTT								COX6A2 (3072 upstream) : ZNF843 (4091 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	31465437	31465438	+	IGR	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:31465437_31465438delTT								ZNF843 (11089 upstream) : ARMC5 (4156 downstream)																																			---	---	---	---
SLC5A2	6524	broad.mit.edu	37	16	31492132	31492133	+	5'Flank	DEL	AG	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:31492132_31492133delAG	uc002ecf.3	+						SLC5A2_uc010car.2_5'Flank	NM_003041	NP_003032			solute carrier family 5 (sodium/glucose						carbohydrate metabolic process	integral to membrane	low-affinity glucose:sodium symporter activity			ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	16	31523403	31523403	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:31523403delA								C16orf58 (3697 upstream) : AHSP (15800 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	31556145	31556146	+	IGR	INS	-	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:31556145_31556146insC								AHSP (16022 upstream) : CSDAP1 (22942 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	31586567	31586567	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:31586567delA								CSDAP1 (5722 upstream) : KIAA0664P3 (125367 downstream)																																			---	---	---	---
ZNF720	124411	broad.mit.edu	37	16	31803938	31803938	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:31803938delT	uc002eco.2	+											Homo sapiens cDNA FLJ61641 complete cds, moderately similar to Zinc finger protein 267.						regulation of transcription, DNA-dependent	intracellular	nucleic acid binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	16	31944378	31944378	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:31944378delT								ZNF267 (15752 upstream) : HERC2P4 (218232 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	32034872	32034872	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:32034872delT								ZNF267 (106246 upstream) : HERC2P4 (127738 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	32152597	32152597	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:32152597delA								ZNF267 (223971 upstream) : HERC2P4 (10013 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	32444576	32444576	+	IGR	DEL	A	-	-	rs76291016		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:32444576delA								HERC2P4 (280702 upstream) : TP53TG3B (240265 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	32516350	32516350	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:32516350delA								HERC2P4 (352476 upstream) : TP53TG3B (168491 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	32551255	32551255	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:32551255delT								HERC2P4 (387381 upstream) : TP53TG3B (133586 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	32558889	32558889	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:32558889delT								HERC2P4 (395015 upstream) : TP53TG3B (125952 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	32818642	32818645	+	IGR	DEL	TTCA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:32818642_32818645delTTCA								TP53TG3B (129764 upstream) : SLC6A10P (70152 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	32851409	32851409	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:32851409delA								TP53TG3B (162531 upstream) : SLC6A10P (37388 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	33354280	33354280	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:33354280delA								SLC6A10P (457817 upstream) : MIR1826 (611228 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	33377239	33377240	+	IGR	DEL	TT	-	-	rs112623856		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:33377239_33377240delTT								SLC6A10P (480776 upstream) : MIR1826 (588268 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	33383209	33383236	+	IGR	DEL	GGAGAGACCATGCCCCAATGCTGGGGCT	-	-	rs140056428	by1000genomes;by1000genomes;by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:33383209_33383236delGGAGAGACCATGCCCCAATGCTGGGGCT								SLC6A10P (486746 upstream) : MIR1826 (582272 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	33410317	33410317	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:33410317delT								SLC6A10P (513854 upstream) : MIR1826 (555191 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	33411899	33411900	+	IGR	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:33411899_33411900delTT								SLC6A10P (515436 upstream) : MIR1826 (553608 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	33441507	33441507	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-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	33489495	33489496	+	IGR	INS	-	A	A	rs139089319	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:33489495_33489496insA								SLC6A10P (593032 upstream) : MIR1826 (476012 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	33543022	33543023	+	IGR	INS	-	ATT	ATT	rs138472598	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:33543022_33543023insATT								SLC6A10P (646559 upstream) : MIR1826 (422485 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	33752190	33752190	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:33752190delA								SLC6A10P (855727 upstream) : MIR1826 (213318 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	33920175	33920175	+	IGR	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:33920175delG								None (None upstream) : MIR1826 (45333 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	33920371	33920371	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:33920371delT								None (None upstream) : MIR1826 (45137 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	33985407	33985408	+	IGR	INS	-	AAAG	AAAG	rs112918630		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:33985407_33985408insAAAG								MIR1826 (19815 upstream) : UBE2MP1 (418394 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	34500938	34500938	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:34500938delT								UBE2MP1 (96176 upstream) : LOC283914 (96849 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	34660154	34660154	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:34660154delA								LOC283914 (34070 upstream) : LOC146481 (51631 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	46449840	46449841	+	IGR	INS	-	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:46449840_46449841insT								None (None upstream) : ANKRD26P1 (53408 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	46493871	46493872	+	IGR	DEL	TG	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:46493871_46493872delTG								None (None upstream) : ANKRD26P1 (9377 downstream)																																			---	---	---	---
SHCBP1	79801	broad.mit.edu	37	16	46631320	46631321	+	Intron	INS	-	A	A	rs76889153		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:46631320_46631321insA	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)																---	---	---	---
NETO2	81831	broad.mit.edu	37	16	47166018	47166018	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:47166018delA	uc002eer.1	-						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)			---	---	---	---
Unknown	0	broad.mit.edu	37	16	47850969	47850969	+	IGR	DEL	A	-	-	rs34982504		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:47850969delA								PHKB (115536 upstream) : ABCC12 (265915 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	47921788	47921788	+	5'Flank	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:47921788delA	uc002eex.1	-											Homo sapiens cDNA clone IMAGE:5303550.																														---	---	---	---
ABCC11	85320	broad.mit.edu	37	16	48212885	48212885	+	Intron	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:48212885delC	uc002eff.1	-						ABCC11_uc002efg.1_Intron|ABCC11_uc002efh.1_Intron|ABCC11_uc010cbg.1_Intron	NM_033151	NP_149163			ATP-binding cassette, sub-family C, member 11							integral to membrane	ATP binding|ATPase activity, coupled to transmembrane movement of substances			ovary(3)|skin(2)|central_nervous_system(1)	6		all_cancers(37;0.127)|all_lung(18;0.132)|Breast(268;0.166)												Cerumen_Type				---	---	---	---
Unknown	0	broad.mit.edu	37	16	48393628	48393628	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:48393628delA	uc002efk.1	+						SIAH1_uc002efl.2_Intron					Homo sapiens cDNA FLJ31489 fis, clone NT2NE2003308.																														---	---	---	---
Unknown	0	broad.mit.edu	37	16	49030423	49030423	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:49030423delA								N4BP1 (386303 upstream) : CBLN1 (281788 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	49056530	49056530	+	IGR	DEL	T	-	-	rs34542074		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:49056530delT								N4BP1 (412410 upstream) : CBLN1 (255681 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	49492036	49492036	+	IGR	DEL	A	-	-	rs113239511		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:49492036delA								C16orf78 (58719 upstream) : ZNF423 (32486 downstream)																																			---	---	---	---
ZNF423	23090	broad.mit.edu	37	16	49759312	49759312	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:49759312delA	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)																---	---	---	---
Unknown	0	broad.mit.edu	37	16	49977326	49977327	+	IGR	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:49977326_49977327delAA								ZNF423 (116408 upstream) : TMEM188 (81862 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	50049534	50049534	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:50049534delT								ZNF423 (188616 upstream) : TMEM188 (9655 downstream)																																			---	---	---	---
TMEM188	255919	broad.mit.edu	37	16	50058033	50058033	+	5'Flank	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:50058033delT	uc002efu.2	+						TMEM188_uc002eft.2_5'Flank|TMEM188_uc002efv.2_5'Flank					SubName: Full=TMP125; SubName: Full=Putative uncharacterized protein FLJ38101;							integral to membrane					0																		---	---	---	---
HEATR3	55027	broad.mit.edu	37	16	50119019	50119019	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:50119019delA	uc002efw.2	+						HEATR3_uc002efx.2_Intron	NM_182922	NP_891552			HEAT repeat containing 3								binding			ovary(1)|skin(1)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	16	50174098	50174099	+	IGR	INS	-	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:50174098_50174099insA								HEATR3 (34725 upstream) : PAPD5 (12730 downstream)																																			---	---	---	---
PAPD5	64282	broad.mit.edu	37	16	50198801	50198801	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:50198801delA	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)														---	---	---	---
ADCY7	113	broad.mit.edu	37	16	50345711	50345717	+	Intron	DEL	CCCCCCC	-	-	rs35078746		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:50345711_50345717delCCCCCCC	uc002egd.1	+							NM_001114	NP_001105			adenylate cyclase 7						activation of adenylate cyclase activity by G-protein signaling pathway|activation of phospholipase C activity|activation of protein kinase A activity|cellular response to ethanol|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|positive regulation of cAMP biosynthetic process|synaptic transmission|transmembrane transport|water transport	integral to membrane|plasma membrane	adenylate cyclase activity|ATP binding|metal ion binding			skin(1)	1		all_cancers(37;0.0127)		GBM - Glioblastoma multiforme(240;0.195)	Bromocriptine(DB01200)													---	---	---	---
Unknown	0	broad.mit.edu	37	16	50497090	50497090	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:50497090delA								BRD7 (94261 upstream) : NKD1 (85151 downstream)																																			---	---	---	---
CYLD	1540	broad.mit.edu	37	16	50810292	50810292	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:50810292delT	uc002egp.1	+						CYLD_uc002egn.1_Intron|CYLD_uc002ego.2_Intron|CYLD_uc010cbs.1_Intron|CYLD_uc002egq.1_Intron|CYLD_uc002egr.1_Intron|CYLD_uc002egs.1_Intron	NM_015247	NP_056062			ubiquitin carboxyl-terminal hydrolase CYLD						cell cycle|negative regulation of canonical Wnt receptor signaling pathway|negative regulation of NF-kappaB import into nucleus|negative regulation of NF-kappaB transcription factor activity|negative regulation of type I interferon production|protein K63-linked deubiquitination|regulation of microtubule cytoskeleton organization|regulation of mitotic cell cycle|translation|ubiquitin-dependent protein catabolic process|Wnt receptor signaling pathway	cytosol|extrinsic to internal side of plasma membrane|microtubule|perinuclear region of cytoplasm|ribosome	proline-rich region binding|protein kinase binding|structural constituent of ribosome|ubiquitin thiolesterase activity|ubiquitin-specific protease activity|zinc ion binding			skin(19)|large_intestine(3)|haematopoietic_and_lymphoid_tissue(3)|central_nervous_system(3)	28		all_cancers(37;0.0156)						Mis|N|F|S		cylindroma	cylindroma			Familial_Cylindromatosis|Multiple_Trichoepithelioma_Familial				---	---	---	---
Unknown	0	broad.mit.edu	37	16	51356527	51356528	+	IGR	DEL	AC	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:51356527_51356528delAC								SALL1 (171344 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	51496339	51496339	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:51496339delA								SALL1 (311156 upstream) : TOX3 (975579 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	51933888	51933895	+	IGR	DEL	AAAAAAAA	-	-	rs72358314		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:51933888_51933895delAAAAAAAA								SALL1 (748705 upstream) : TOX3 (538023 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	52308300	52308300	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:52308300delT								None (None upstream) : TOX3 (163618 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	52315747	52315748	+	IGR	INS	-	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:52315747_52315748insA								None (None upstream) : TOX3 (156170 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	52340830	52340830	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:52340830delT								None (None upstream) : TOX3 (131088 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	53075693	53075694	+	IGR	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:53075693_53075694delAA								TOX3 (493979 upstream) : CHD9 (13251 downstream)																																			---	---	---	---
CHD9	80205	broad.mit.edu	37	16	53284732	53284732	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:53284732delT	uc002ehb.2	+						CHD9_uc002egy.2_Intron|CHD9_uc002ehc.2_Intron|CHD9_uc002ehf.2_Intron|CHD9_uc002ehd.2_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)																---	---	---	---
CHD9	80205	broad.mit.edu	37	16	53324545	53324545	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:53324545delA	uc002ehb.2	+						CHD9_uc002egy.2_Intron|CHD9_uc002ehc.2_Intron|CHD9_uc002ehf.2_Intron|CHD9_uc010cbw.2_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)																---	---	---	---
CHD9	80205	broad.mit.edu	37	16	53326631	53326632	+	Intron	INS	-	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:53326631_53326632insT	uc002ehb.2	+						CHD9_uc002egy.2_Intron|CHD9_uc002ehc.2_Intron|CHD9_uc002ehf.2_Intron|CHD9_uc010cbw.2_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)																---	---	---	---
RBL2	5934	broad.mit.edu	37	16	53515565	53515566	+	Intron	DEL	TT	-	-	rs72027669		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-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																		---	---	---	---
Unknown	0	broad.mit.edu	37	16	53550793	53550793	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:53550793delA								AKTIP (13623 upstream) : RPGRIP1L (83030 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	53623362	53623362	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:53623362delT								AKTIP (86192 upstream) : RPGRIP1L (10461 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	53626759	53626759	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:53626759delA								AKTIP (89589 upstream) : RPGRIP1L (7064 downstream)																																			---	---	---	---
FTO	79068	broad.mit.edu	37	16	53967839	53967839	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:53967839delT	uc002ehr.2	+						FTO_uc010vha.1_Intron|FTO_uc010cbz.2_Intron|FTO_uc002ehs.2_5'Flank	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	54381271	54381274	+	IGR	DEL	TTTT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:54381271_54381274delTTTT								IRX3 (60893 upstream) : IRX5 (583837 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	54454835	54454835	+	IGR	DEL	A	-	-	rs78850444		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:54454835delA								IRX3 (134457 upstream) : IRX5 (510276 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	54782424	54782424	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:54782424delT								IRX3 (462046 upstream) : IRX5 (182687 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	54906442	54906443	+	IGR	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:54906442_54906443delAA								IRX3 (586064 upstream) : IRX5 (58668 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	55053530	55053531	+	IGR	INS	-	AC	AC			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:55053530_55053531insAC								IRX5 (85137 upstream) : IRX6 (304940 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	55198503	55198503	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:55198503delA								IRX5 (230110 upstream) : IRX6 (159968 downstream)																																			---	---	---	---
SLC6A2	6530	broad.mit.edu	37	16	55736048	55736048	+	Intron	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:55736048delG	uc002eif.2	+						SLC6A2_uc010ccd.2_Intron|SLC6A2_uc002eig.2_Intron|SLC6A2_uc002eih.2_Intron|SLC6A2_uc002eii.2_Intron|SLC6A2_uc002eij.2_Intron	NM_001043	NP_001034			solute carrier family 6 member 2						synaptic transmission	integral to plasma membrane|membrane fraction	norepinephrine:sodium symporter activity			lung(4)|ovary(2)|pancreas(2)	8				BRCA - Breast invasive adenocarcinoma(181;0.01)|Kidney(780;0.0267)	Amineptine(DB04836)|Amitriptyline(DB00321)|Amoxapine(DB00543)|Atomoxetine(DB00289)|Bethanidine(DB00217)|Bupropion(DB01156)|Clomipramine(DB01242)|Cocaine(DB00907)|Debrisoquin(DB04840)|Desipramine(DB01151)|Diethylpropion(DB00937)|Doxepin(DB01142)|Duloxetine(DB00476)|Ergotamine(DB00696)|Guanadrel Sulfate(DB00226)|Guanethidine(DB01170)|Imipramine(DB00458)|Maprotiline(DB00934)|Mazindol(DB00579)|Methylphenidate(DB00422)|Milnacipran(DB04896)|Nefazodone(DB01149)|Norepinephrine(DB00368)|Nortriptyline(DB00540)|Paroxetine(DB00715)|Phenmetrazine(DB00830)|Phentermine(DB00191)|Protriptyline(DB00344)|Reboxetine(DB00234)|Sibutramine(DB01105)|Tramadol(DB00193)|Trazodone(DB00656)|Trimipramine(DB00726)|Venlafaxine(DB00285)											OREG0023807	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
Unknown	0	broad.mit.edu	37	16	55764231	55764231	+	IGR	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:55764231delC								SLC6A2 (26533 upstream) : CES4 (30280 downstream)																																			---	---	---	---
AMFR	267	broad.mit.edu	37	16	56406926	56406926	+	Intron	DEL	G	-	-	rs2587869	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:56406926delG	uc002eiy.2	-						AMFR_uc002eix.2_Intron	NM_001144	NP_001135			autocrine motility factor receptor						endoplasmic reticulum unfolded protein response|ER-associated protein catabolic process|protein oligomerization|protein polyubiquitination	integral to endoplasmic reticulum membrane|integral to membrane of membrane fraction	protein binding|protein binding|receptor activity|ubiquitin-protein ligase activity|zinc ion binding			breast(2)	2																		---	---	---	---
BBS2	583	broad.mit.edu	37	16	56532619	56532619	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:56532619delA	uc002ejd.2	-						BBS2_uc010ccg.2_3'UTR	NM_031885	NP_114091			Bardet-Biedl syndrome 2 protein						adult behavior|brain morphogenesis|cerebral cortex development|cilium morphogenesis|fat cell differentiation|hippocampus development|melanosome transport|negative regulation of multicellular organism growth|photoreceptor cell maintenance|protein localization to organelle|regulation of cilium beat frequency involved in ciliary motility|sperm axoneme assembly|striatum development	BBSome|cilium membrane|microtubule basal body|motile cilium	protein binding			ovary(1)	1														Bardet-Biedl_syndrome				---	---	---	---
MT1A	4489	broad.mit.edu	37	16	56653155	56653156	+	Intron	INS	-	T	T	rs148863924	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:56653155_56653156insT	uc002eji.2	+						MT1M_uc010vhe.1_Intron					Synthetic construct DNA, clone: pF1KB6498, Homo sapiens MT2A gene for metallothionein 2A, without stop codon, in Flexi system.							cytoplasm	cadmium ion binding|copper ion binding|zinc ion binding				0																		---	---	---	---
MT1F	4494	broad.mit.edu	37	16	56693131	56693131	+	3'UTR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:56693131delT	uc002ejt.2	+	3						NM_005949	NP_005940			metallothionein 1F							cytoplasm	cadmium ion binding|copper ion binding|zinc ion binding				0																		---	---	---	---
NUP93	9688	broad.mit.edu	37	16	56815633	56815633	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:56815633delA	uc002eka.2	+						NUP93_uc002ekb.2_5'Flank|NUP93_uc010vhi.1_5'Flank	NM_014669	NP_055484			nucleoporin 93kDa						carbohydrate metabolic process|glucose transport|mRNA transport|protein transport|regulation of glucose transport|transmembrane transport|viral reproduction	nuclear pore	protein binding			ovary(1)|lung(1)	2																		---	---	---	---
SLC12A3	6559	broad.mit.edu	37	16	56945220	56945223	+	Intron	DEL	TTTG	-	-	rs72001638		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:56945220_56945223delTTTG	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)													---	---	---	---
Unknown	0	broad.mit.edu	37	16	56981501	56981501	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:56981501delA								HERPUD1 (3708 upstream) : CETP (14334 downstream)																																			---	---	---	---
FAM192A	80011	broad.mit.edu	37	16	57206385	57206385	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:57206385delA	uc010vhk.1	-						FAM192A_uc002ekz.3_Intron|FAM192A_uc002ekv.3_Intron|FAM192A_uc002ekw.3_Intron|FAM192A_uc002ekx.3_Intron|FAM192A_uc002eky.3_Intron|FAM192A_uc010ccx.2_Intron	NM_024946	NP_079222			NEFA-interacting nuclear protein NIP30							nucleus					0																		---	---	---	---
Unknown	0	broad.mit.edu	37	16	57540574	57540574	+	IGR	DEL	T	-	-	rs66809713		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:57540574delT								DOK4 (20189 upstream) : CCDC102A (5518 downstream)																																			---	---	---	---
GPR97	222487	broad.mit.edu	37	16	57708992	57708992	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:57708992delA	uc002emh.2	+						GPR97_uc010cdc.2_Intron|GPR97_uc010vhv.1_Intron|GPR97_uc010cdd.2_Intron	NM_170776	NP_740746			G protein-coupled receptor 97 precursor						neuropeptide signaling pathway	integral to membrane|plasma membrane	G-protein coupled receptor activity			ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	16	58096723	58096723	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:58096723delT								MMP15 (15921 upstream) : C16orf80 (50774 downstream)																																			---	---	---	---
CCDC113	29070	broad.mit.edu	37	16	58307011	58307012	+	Intron	INS	-	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:58307011_58307012insT	uc002ene.2	+						CCDC113_uc010vid.1_Intron	NM_014157	NP_054876			coiled-coil domain containing 113 isoform 1							protein complex					0																		---	---	---	---
Unknown	0	broad.mit.edu	37	16	58413222	58413222	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:58413222delA								PRSS54 (84271 upstream) : GINS3 (13076 downstream)																																			---	---	---	---
CNOT1	23019	broad.mit.edu	37	16	58586141	58586141	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:58586141delA	uc002env.2	-						CNOT1_uc002enw.2_Intron|CNOT1_uc002enu.3_Intron|CNOT1_uc002enx.2_Intron|CNOT1_uc002enz.1_Intron|CNOT1_uc010vik.1_5'Flank	NM_016284	NP_057368			CCR4-NOT transcription complex, subunit 1						nuclear-transcribed mRNA poly(A) tail shortening|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasmic mRNA processing body|cytosol				ovary(4)|central_nervous_system(2)	6				Kidney(780;0.0722)|OV - Ovarian serous cystadenocarcinoma(108;0.173)|Epithelial(162;0.239)														---	---	---	---
GOT2	2806	broad.mit.edu	37	16	58745990	58745990	+	Intron	DEL	A	-	-	rs151284672	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:58745990delA	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	58869972	58869973	+	IGR	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:58869972_58869973delTT								GOT2 (101726 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	58940633	58940634	+	IGR	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:58940633_58940634delAA								GOT2 (172387 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	59016517	59016517	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:59016517delT								GOT2 (248271 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	59113576	59113577	+	IGR	DEL	TG	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:59113576_59113577delTG								GOT2 (345330 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	60086721	60086721	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:60086721delT								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	60207854	60207854	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:60207854delT								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	60396498	60396498	+	IGR	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:60396498delC								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	60445101	60445101	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:60445101delA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	60641580	60641581	+	IGR	INS	-	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:60641580_60641581insT								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	61017605	61017605	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:61017605delA								None (None upstream) : CDH8 (669630 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	61574452	61574453	+	IGR	INS	-	T	T	rs141253653	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:61574452_61574453insT								None (None upstream) : CDH8 (112782 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	62652459	62652460	+	IGR	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:62652459_62652460delAA								CDH8 (582423 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	62917828	62917829	+	IGR	INS	-	GT	GT			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:62917828_62917829insGT								CDH8 (847792 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	63801764	63801764	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:63801764delA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	64225494	64225494	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:64225494delT								None (None upstream) : CDH11 (755191 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	65764347	65764347	+	IGR	DEL	T	-	-	rs72172253		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:65764347delT								LOC283867 (154144 upstream) : CDH5 (636178 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	65799889	65799889	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:65799889delT								LOC283867 (189686 upstream) : CDH5 (600636 downstream)																																			---	---	---	---
DYNC1LI2	1783	broad.mit.edu	37	16	66770164	66770164	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:66770164delA	uc002eqb.1	-						DYNC1LI2_uc010vis.1_Intron|DYNC1LI2_uc010vit.1_Intron|DYNC1LI2_uc010viu.1_Intron	NM_006141	NP_006132			dynein, cytoplasmic, light intermediate						transport	centrosome|cytoplasmic dynein complex|microtubule	ATP binding|motor activity			central_nervous_system(3)|skin(1)	4		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.0907)|Epithelial(162;0.212)														---	---	---	---
CCDC79	283847	broad.mit.edu	37	16	66824397	66824397	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:66824397delA	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																		---	---	---	---
RRAD	6236	broad.mit.edu	37	16	66958197	66958197	+	Intron	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:66958197delG	uc002eqn.2	-						RRAD_uc002eqo.2_Intron	NM_001128850	NP_001122322			Ras-related associated with diabetes						small GTPase mediated signal transduction	plasma membrane	calmodulin binding|GTP binding|GTPase activity				0		Ovarian(137;0.192)		OV - Ovarian serous cystadenocarcinoma(108;0.0862)|Epithelial(162;0.198)														---	---	---	---
CES3	23491	broad.mit.edu	37	16	66992886	66992886	+	5'Flank	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:66992886delG	uc002eqt.2	+						CES3_uc010cdz.2_5'Flank|CES3_uc010cea.2_5'Flank	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)														---	---	---	---
CES3	23491	broad.mit.edu	37	16	67000964	67000964	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:67000964delT	uc002eqt.2	+						CES3_uc010cdz.2_Intron|CES3_uc010cea.2_Intron|CES3_uc010viw.1_5'Flank	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)														---	---	---	---
CES8	283848	broad.mit.edu	37	16	67041691	67041692	+	Intron	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:67041691_67041692delTT	uc002eqv.2	+						CES8_uc010vix.1_Intron|CES8_uc002eqw.2_Intron|CES8_uc002eqy.2_Intron|CES8_uc002eqx.2_Intron|CES8_uc010viy.1_Intron|CES8_uc010viz.1_Intron|CES8_uc002eqz.2_Intron	NM_173815	NP_776176			carboxylesterase 8 (putative)							extracellular region	carboxylesterase activity				0																		---	---	---	---
CES8	283848	broad.mit.edu	37	16	67042296	67042297	+	Intron	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:67042296_67042297delTT	uc002eqv.2	+						CES8_uc010vix.1_Intron|CES8_uc002eqw.2_Intron|CES8_uc002eqy.2_Intron|CES8_uc002eqx.2_Intron|CES8_uc010viy.1_Intron|CES8_uc010viz.1_Intron|CES8_uc002eqz.2_Intron	NM_173815	NP_776176			carboxylesterase 8 (putative)							extracellular region	carboxylesterase activity				0																		---	---	---	---
CBFB	865	broad.mit.edu	37	16	67072598	67072600	+	Intron	DEL	GAA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:67072598_67072600delGAA	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								---	---	---	---
C16orf70	80262	broad.mit.edu	37	16	67165179	67165179	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:67165179delT	uc002erc.2	+						C16orf70_uc002erd.2_Intron|C16orf70_uc002ere.1_Intron	NM_025187	NP_079463			lin-10											ovary(2)	2		Ovarian(137;0.192)		OV - Ovarian serous cystadenocarcinoma(108;0.0017)|Epithelial(162;0.00655)|all cancers(182;0.0579)														---	---	---	---
KCTD19	146212	broad.mit.edu	37	16	67333641	67333641	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:67333641delT	uc002esu.2	-						KCTD19_uc002est.2_5'UTR|KCTD19_uc010vjj.1_Intron	NM_001100915	NP_001094385			potassium channel tetramerisation domain							voltage-gated potassium channel complex	voltage-gated potassium channel activity			skin(1)	1		Ovarian(137;0.192)		OV - Ovarian serous cystadenocarcinoma(108;0.0311)|Epithelial(162;0.0906)														---	---	---	---
KCTD19	146212	broad.mit.edu	37	16	67342074	67342077	+	Intron	DEL	TTTT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:67342074_67342077delTTTT	uc002esu.2	-						KCTD19_uc002est.2_Intron|KCTD19_uc010vjj.1_Intron	NM_001100915	NP_001094385			potassium channel tetramerisation domain							voltage-gated potassium channel complex	voltage-gated potassium channel activity			skin(1)	1		Ovarian(137;0.192)		OV - Ovarian serous cystadenocarcinoma(108;0.0311)|Epithelial(162;0.0906)														---	---	---	---
ATP6V0D1	9114	broad.mit.edu	37	16	67502503	67502504	+	Intron	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:67502503_67502504delAA	uc002ete.1	-						ATP6V0D1_uc010vjo.1_Intron	NM_004691	NP_004682			ATPase, H+ transporting, lysosomal, V0 subunit						ATP hydrolysis coupled proton transport|cellular iron ion homeostasis|insulin receptor signaling pathway|transferrin transport	endosome membrane|proton-transporting V-type ATPase, V0 domain|vacuolar proton-transporting V-type ATPase complex					0		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.0439)|Epithelial(162;0.101)														---	---	---	---
CTCF	10664	broad.mit.edu	37	16	67631245	67631245	+	Intron	DEL	T	-	-	rs113177518		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:67631245delT	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	67635158	67635158	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:67635158delT	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)														---	---	---	---
GFOD2	81577	broad.mit.edu	37	16	67713790	67713791	+	Intron	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:67713790_67713791delAA	uc002eub.2	-						GFOD2_uc002eua.1_5'Flank|GFOD2_uc002euc.2_Intron	NM_030819	NP_110446			glucose-fructose oxidoreductase domain							proteinaceous extracellular matrix	binding|oxidoreductase activity			ovary(2)|skin(1)	3		Acute lymphoblastic leukemia(13;3.23e-05)|all_hematologic(13;0.00251)|Ovarian(137;0.192)		OV - Ovarian serous cystadenocarcinoma(108;0.0151)|Epithelial(162;0.0505)|all cancers(182;0.242)														---	---	---	---
CENPT	80152	broad.mit.edu	37	16	67862087	67862087	+	3'UTR	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:67862087delG	uc002eun.3	-	16					CENPT_uc002eum.3_3'UTR|CENPT_uc010vkc.1_3'UTR	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)														---	---	---	---
PSKH1	5681	broad.mit.edu	37	16	67945589	67945590	+	Intron	INS	-	A	A	rs114755401	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:67945589_67945590insA	uc002euv.2	+							NM_006742	NP_006733			protein serine kinase H1							endoplasmic reticulum membrane|Golgi apparatus|microtubule organizing center|nuclear speck|plasma membrane	ATP binding|protein serine/threonine kinase activity				0		Ovarian(137;0.192)		OV - Ovarian serous cystadenocarcinoma(108;0.0044)|Epithelial(162;0.0197)|all cancers(182;0.128)														---	---	---	---
DUS2L	54920	broad.mit.edu	37	16	68073644	68073645	+	Intron	INS	-	AAGG	AAGG	rs146249095	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:68073644_68073645insAAGG	uc002evi.2	+						DUS2L_uc002evj.2_Intron|DUS2L_uc010vkk.1_Intron|DUS2L_uc010cez.2_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)														---	---	---	---
DUS2L	54920	broad.mit.edu	37	16	68094751	68094751	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:68094751delA	uc002evi.2	+						DUS2L_uc002evj.2_Intron|DUS2L_uc010vkk.1_Intron|DUS2L_uc010cez.2_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)														---	---	---	---
ZFP90	146198	broad.mit.edu	37	16	68569304	68569304	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:68569304delA	uc002ewb.2	+											Homo sapiens mRNA for KIAA1954 protein.						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)														---	---	---	---
Unknown	0	broad.mit.edu	37	16	68664189	68664190	+	IGR	DEL	TT	-	-	rs112287693		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:68664189_68664190delTT								ZFP90 (63151 upstream) : CDH3 (13961 downstream)														p.?(1)																					---	---	---	---
CDH3	1001	broad.mit.edu	37	16	68725950	68725950	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:68725950delT	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)														---	---	---	---
CDH1	999	broad.mit.edu	37	16	68830073	68830073	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:68830073delA	uc002ewg.1	+						CDH1_uc010vlj.1_Intron|CDH1_uc010cfg.1_Intron	NM_004360	NP_004351			cadherin 1, type 1 preproprotein						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			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				---	---	---	---
TMCO7	79613	broad.mit.edu	37	16	69059840	69059840	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:69059840delA	uc002ewi.3	+							NM_024562	NP_078838			transmembrane and coiled-coil domains 7							integral to membrane	binding				0		Ovarian(137;0.0568)		OV - Ovarian serous cystadenocarcinoma(108;0.0446)|Epithelial(162;0.198)														---	---	---	---
CIRH1A	84916	broad.mit.edu	37	16	69190058	69190060	+	Intron	DEL	TTT	-	-	rs72463058		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:69190058_69190060delTTT	uc002ews.3	+						CIRH1A_uc002ewr.2_Intron|CIRH1A_uc002ewt.3_Intron|CIRH1A_uc010cfi.2_Intron	NM_032830	NP_116219			cirhin							nucleolus	protein binding				0				OV - Ovarian serous cystadenocarcinoma(108;0.125)														---	---	---	---
NFAT5	10725	broad.mit.edu	37	16	69643905	69643906	+	Intron	DEL	AG	-	-	rs10599522		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:69643905_69643906delAG	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	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																		---	---	---	---
NFAT5	10725	broad.mit.edu	37	16	69707628	69707628	+	Intron	DEL	A	-	-	rs149862885		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:69707628delA	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	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																		---	---	---	---
Unknown	0	broad.mit.edu	37	16	69791975	69791975	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:69791975delT								NOB1 (3146 upstream) : WWP2 (4299 downstream)																																			---	---	---	---
WWP2	11060	broad.mit.edu	37	16	69930035	69930035	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:69930035delT	uc002exu.1	+						WWP2_uc002ext.2_Intron|WWP2_uc002exv.1_Intron|WWP2_uc010vlm.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																		---	---	---	---
WWP2	11060	broad.mit.edu	37	16	69944319	69944320	+	Intron	DEL	TT	-	-	rs74443425		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:69944319_69944320delTT	uc002exu.1	+						WWP2_uc002exv.1_Intron|WWP2_uc010vlm.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	70196861	70196861	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:70196861delT	uc002exy.2	+						uc002eyi.1_Intron	NM_182619	NP_872425			secretory protein LOC348174 precursor							extracellular region	sugar binding				0																		---	---	---	---
AARS	16	broad.mit.edu	37	16	70303887	70303887	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:70303887delT	uc002eyn.1	-						AARS_uc010vlu.1_Intron	NM_001605	NP_001596			alanyl-tRNA synthetase						alanyl-tRNA aminoacylation|tRNA processing	cytosol|soluble fraction	alanine-tRNA ligase activity|ATP binding|metal ion binding|tRNA binding			pancreas(1)	1		Ovarian(137;0.0365)		BRCA - Breast invasive adenocarcinoma(221;0.161)	L-Alanine(DB00160)													---	---	---	---
AARS	16	broad.mit.edu	37	16	70312787	70312787	+	Intron	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:70312787delC	uc002eyn.1	-							NM_001605	NP_001596			alanyl-tRNA synthetase						alanyl-tRNA aminoacylation|tRNA processing	cytosol|soluble fraction	alanine-tRNA ligase activity|ATP binding|metal ion binding|tRNA binding			pancreas(1)	1		Ovarian(137;0.0365)		BRCA - Breast invasive adenocarcinoma(221;0.161)	L-Alanine(DB00160)													---	---	---	---
AARS	16	broad.mit.edu	37	16	70316698	70316698	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:70316698delA	uc002eyn.1	-							NM_001605	NP_001596			alanyl-tRNA synthetase						alanyl-tRNA aminoacylation|tRNA processing	cytosol|soluble fraction	alanine-tRNA ligase activity|ATP binding|metal ion binding|tRNA binding			pancreas(1)	1		Ovarian(137;0.0365)		BRCA - Breast invasive adenocarcinoma(221;0.161)	L-Alanine(DB00160)													---	---	---	---
DDX19B	11269	broad.mit.edu	37	16	70327357	70327359	+	5'Flank	DEL	AAA	-	-	rs74496820		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:70327357_70327359delAAA	uc010vlv.1	+						DDX19B_uc010vlw.1_5'Flank	NM_001014451	NP_001014451			DEAD (Asp-Glu-Ala-As) box polypeptide 19 isoform						mRNA export from nucleus|protein transport|transmembrane transport	cytoplasm|nuclear membrane|nuclear pore	ATP binding|ATP-dependent helicase activity|protein binding|RNA binding			kidney(1)	1		Ovarian(137;0.0694)																---	---	---	---
Unknown	0	broad.mit.edu	37	16	70615304	70615308	+	IGR	DEL	TTTTT	-	-	rs71797250		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:70615304_70615308delTTTTT								SF3B3 (3734 upstream) : IL34 (65160 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	70632509	70632510	+	IGR	DEL	GC	-	-	rs140518309	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:70632509_70632510delGC								SF3B3 (20939 upstream) : IL34 (47958 downstream)																																			---	---	---	---
HYDIN	54768	broad.mit.edu	37	16	71061896	71061897	+	Intron	DEL	TT	-	-	rs142337199		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:71061896_71061897delTT	uc002ezr.2	-						HYDIN_uc010cfz.1_Intron|HYDIN_uc002ezv.2_Intron	NM_032821	NP_116210			hydrocephalus inducing isoform a											ovary(1)|skin(1)	2		Ovarian(137;0.0654)																---	---	---	---
Unknown	0	broad.mit.edu	37	16	71649991	71649991	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:71649991delA								TAT (38993 upstream) : MARVELD3 (10079 downstream)																																			---	---	---	---
PHLPP2	23035	broad.mit.edu	37	16	71742696	71742696	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:71742696delA	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																		---	---	---	---
PHLPP2	23035	broad.mit.edu	37	16	71745235	71745235	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:71745235delA	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																		---	---	---	---
HPR	3250	broad.mit.edu	37	16	72097650	72097650	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:72097650delT	uc002fby.2	+						TXNL4B_uc010cgl.2_Intron	NM_020995	NP_066275			haptoglobin-related protein precursor						proteolysis	spherical high-density lipoprotein particle	hemoglobin binding|serine-type endopeptidase activity			central_nervous_system(1)	1		Ovarian(137;0.125)																---	---	---	---
Unknown	0	broad.mit.edu	37	16	72322380	72322380	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-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	72536266	72536266	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:72536266delA	uc002fci.1	+											Homo sapiens cDNA FLJ38299 fis, clone FCBBF3017255.																														---	---	---	---
Unknown	0	broad.mit.edu	37	16	72775925	72775926	+	Intron	DEL	CT	-	-	rs146439325	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:72775925_72775926delCT	uc002fcj.1	+											Homo sapiens cDNA FLJ11501 fis, clone HEMBA1002100.																														---	---	---	---
Unknown	0	broad.mit.edu	37	16	73214568	73214569	+	IGR	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:73214568_73214569delTT								HTA (86898 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	73221242	73221243	+	IGR	DEL	TT	-	-	rs35275518		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:73221242_73221243delTT								HTA (93572 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	73331619	73331619	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:73331619delA								HTA (203949 upstream) : PSMD7 (999062 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	73400488	73400494	+	IGR	DEL	AAAAAAA	-	-	rs67244051		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:73400488_73400494delAAAAAAA								HTA (272818 upstream) : PSMD7 (930187 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	73607363	73607363	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:73607363delA								HTA (479693 upstream) : PSMD7 (723318 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	73905634	73905634	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:73905634delA								HTA (777964 upstream) : PSMD7 (425047 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	74081740	74081740	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:74081740delA								HTA (954070 upstream) : PSMD7 (248941 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	74154650	74154650	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:74154650delA								None (None upstream) : PSMD7 (176031 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	74164540	74164543	+	IGR	DEL	GGAA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:74164540_74164543delGGAA								None (None upstream) : PSMD7 (166138 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	74261653	74261653	+	IGR	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:74261653delC								None (None upstream) : PSMD7 (69028 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	74267012	74267013	+	IGR	DEL	AC	-	-	rs71944990		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:74267012_74267013delAC								None (None upstream) : PSMD7 (63668 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	75166882	75166882	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:75166882delT								LDHD (16217 upstream) : ZFP1 (15539 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	75216239	75216240	+	IGR	DEL	TA	-	-	rs79574713		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:75216239_75216240delTA								ZFP1 (10108 upstream) : CTRB2 (21755 downstream)																																			---	---	---	---
CFDP1	10428	broad.mit.edu	37	16	75336801	75336801	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:75336801delT	uc002fdy.2	-						CFDP1_uc002fdz.2_Intron	NM_006324	NP_006315			craniofacial development protein 1						multicellular organismal development					upper_aerodigestive_tract(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	16	76105619	76105619	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:76105619delT								TERF2IP (414291 upstream) : CNTNAP4 (205557 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	76911490	76911490	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:76911490delT								CNTNAP4 (318355 upstream) : MON1B (313346 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	77190542	77190543	+	IGR	DEL	AG	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:77190542_77190543delAG								CNTNAP4 (597407 upstream) : MON1B (34293 downstream)																																			---	---	---	---
ADAMTS18	170692	broad.mit.edu	37	16	77450091	77450091	+	Intron	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:77450091delG	uc002ffc.3	-						ADAMTS18_uc002ffe.1_Intron|ADAMTS18_uc010vni.1_Intron	NM_199355	NP_955387			ADAM metallopeptidase with thrombospondin type 1						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																		---	---	---	---
Unknown	0	broad.mit.edu	37	16	77550715	77550716	+	IGR	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:77550715_77550716delAA								ADAMTS18 (81704 upstream) : NUDT7 (205695 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	77577132	77577132	+	IGR	DEL	A	-	-	rs112301346		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:77577132delA								ADAMTS18 (108121 upstream) : NUDT7 (179279 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	77731401	77731401	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:77731401delA								ADAMTS18 (262390 upstream) : NUDT7 (25010 downstream)																																			---	---	---	---
NUDT7	283927	broad.mit.edu	37	16	77775744	77775744	+	Frame_Shift_Del	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:77775744delA	uc010chd.2	+	4	683	c.614delA	c.(613-615)GAAfs	p.E205fs	NUDT7_uc010vnj.1_Frame_Shift_Del_p.E152fs	NM_001105663	NP_001099133	P0C024	NUDT7_HUMAN	nudix motif 7	205					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																		---	---	---	---
WWOX	51741	broad.mit.edu	37	16	78138258	78138259	+	Intron	DEL	AC	-	-	rs112614697		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:78138258_78138259delAC	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	78275184	78275184	+	Intron	DEL	T	-	-	rs72790025	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:78275184delT	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	78690066	78690067	+	Intron	DEL	TG	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:78690066_78690067delTG	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	78693011	78693011	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:78693011delA	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	78743632	78743634	+	Intron	DEL	TTT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:78743632_78743634delTTT	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	78767958	78767959	+	Intron	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:78767958_78767959delAA	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	79749138	79749138	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:79749138delT								MAF (114516 upstream) : DYNLRB2 (825716 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	79893723	79893724	+	IGR	DEL	TG	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:79893723_79893724delTG								MAF (259101 upstream) : DYNLRB2 (681130 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	80988000	80988001	+	IGR	DEL	AA	-	-	rs139484015		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:80988000_80988001delAA								CDYL2 (149825 upstream) : C16orf61 (21700 downstream)																																			---	---	---	---
CENPN	55839	broad.mit.edu	37	16	81045518	81045518	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:81045518delT	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																		---	---	---	---
CENPN	55839	broad.mit.edu	37	16	81066160	81066164	+	Intron	DEL	TTTTT	-	-	rs74416741	byFrequency;by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:81066160_81066164delTTTTT	uc002ffy.3	+							NM_001100625	NP_001094095			centromere protein N isoform 1						CenH3-containing nucleosome assembly at centromere|mitotic prometaphase	condensed chromosome kinetochore|cytosol|nucleoplasm					0																		---	---	---	---
C16orf46	123775	broad.mit.edu	37	16	81105193	81105193	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:81105193delT	uc002fgc.3	-						C16orf46_uc010chf.2_Intron|C16orf46_uc010vno.1_Intron	NM_152337	NP_689550			chromosome 16 open reading frame 46 isoform 2												0																		---	---	---	---
GCSH	2653	broad.mit.edu	37	16	81116351	81116351	+	3'UTR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:81116351delT	uc002fgd.2	-	5					GCSH_uc002fge.2_RNA	NM_004483	NP_004474			glycine cleavage system protein H (aminomethyl							glycine cleavage complex|mitochondrion	aminomethyltransferase activity				0					Glycine(DB00145)													---	---	---	---
GCSH	2653	broad.mit.edu	37	16	81128120	81128120	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:81128120delA	uc002fgd.2	-						GCSH_uc002fge.2_Intron	NM_004483	NP_004474			glycine cleavage system protein H (aminomethyl							glycine cleavage complex|mitochondrion	aminomethyltransferase activity				0					Glycine(DB00145)													---	---	---	---
GAN	8139	broad.mit.edu	37	16	81362785	81362785	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:81362785delT	uc002fgo.2	+							NM_022041	NP_071324			gigaxonin						cell death	cytoplasm|neurofilament	protein binding			ovary(2)	2		Colorectal(91;0.153)																---	---	---	---
Unknown	0	broad.mit.edu	37	16	82209218	82209218	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:82209218delA								MPHOSPH6 (5389 upstream) : CDH13 (451360 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	82583727	82583727	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:82583727delA								MPHOSPH6 (379898 upstream) : CDH13 (76851 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	82640728	82640728	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:82640728delA								MPHOSPH6 (436899 upstream) : CDH13 (19850 downstream)																																			---	---	---	---
CDH13	1012	broad.mit.edu	37	16	82998439	82998439	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:82998439delT	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	83171478	83171478	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:83171478delT	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)														---	---	---	---
LRRC50	123872	broad.mit.edu	37	16	84201624	84201625	+	Intron	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:84201624_84201625delAA	uc002fhl.3	+						LRRC50_uc010vnw.1_Intron	NM_178452	NP_848547			leucine rich repeat containing 50						axonemal dynein complex assembly|cilium morphogenesis	cilium axoneme|cytoplasm|spindle pole	dynein binding				0														Kartagener_syndrome				---	---	---	---
ADAD2	161931	broad.mit.edu	37	16	84226453	84226454	+	Intron	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:84226453_84226454delTT	uc002fhq.2	+						ADAD2_uc002fhr.2_Intron|uc002fhs.1_3'UTR	NM_139174	NP_631913			adenosine deaminase domain containing 2 isoform						RNA processing	intracellular	adenosine deaminase activity|double-stranded RNA binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	16	84250450	84250451	+	IGR	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:84250450_84250451delAA								ADAD2 (19678 upstream) : KCNG4 (5374 downstream)																																			---	---	---	---
ATP2C2	9914	broad.mit.edu	37	16	84456440	84456440	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:84456440delT	uc002fhx.2	+						ATP2C2_uc010chj.2_Intron|ATP2C2_uc002fhy.2_Intron|ATP2C2_uc002fhz.2_Intron	NM_014861	NP_055676			ATPase, Ca++ transporting, type 2C, member 2						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																		---	---	---	---
Unknown	0	broad.mit.edu	37	16	84656989	84656989	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:84656989delA								COTL1 (5320 upstream) : KLHL36 (25142 downstream)																																			---	---	---	---
CRISPLD2	83716	broad.mit.edu	37	16	84886271	84886271	+	Intron	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:84886271delG	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	85252495	85252495	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:85252495delT								FAM92B (106381 upstream) : KIAA0182 (392534 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	85617134	85617135	+	IGR	INS	-	AC	AC	rs144285060	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:85617134_85617135insAC								FAM92B (471020 upstream) : KIAA0182 (27894 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	86057207	86057207	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:86057207delT								IRF8 (100998 upstream) : LOC732275 (308249 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	86348872	86348872	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:86348872delT								IRF8 (392663 upstream) : LOC732275 (16584 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	86385895	86385895	+	IGR	DEL	A	-	-	rs76209091		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:86385895delA								LOC732275 (6610 upstream) : FOXF1 (158238 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	86832845	86832846	+	IGR	INS	-	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:86832845_86832846insT								FOXL1 (217542 upstream) : FBXO31 (530098 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	87055203	87055203	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:87055203delT								FOXL1 (439900 upstream) : FBXO31 (307741 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	87108583	87108583	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:87108583delT								FOXL1 (493280 upstream) : FBXO31 (254361 downstream)																																			---	---	---	---
ZCCHC14	23174	broad.mit.edu	37	16	87501765	87501765	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:87501765delT	uc002fjz.1	-						ZCCHC14_uc002fka.1_Intron	NM_015144	NP_055959			zinc finger, CCHC domain containing 14						cell communication		nucleic acid binding|phosphatidylinositol binding|zinc ion binding			upper_aerodigestive_tract(1)|breast(1)	2				BRCA - Breast invasive adenocarcinoma(80;0.0285)														---	---	---	---
Unknown	0	broad.mit.edu	37	16	87561233	87561234	+	IGR	DEL	TT	-	-	rs75500374		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:87561233_87561234delTT								ZCCHC14 (35773 upstream) : JPH3 (74207 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	88376279	88376280	+	IGR	INS	-	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:88376279_88376280insG								BANP (265356 upstream) : ZNF469 (117599 downstream)																																			---	---	---	---
MGC23284	197187	broad.mit.edu	37	16	88732094	88732095	+	Intron	INS	-	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:88732094_88732095insA	uc010chy.2	+						MGC23284_uc002flh.2_Intron|MGC23284_uc002fli.3_Intron|MVD_uc002flg.1_5'Flank	NR_024402				Homo sapiens cDNA FLJ37518 fis, clone BRCAN2004653.												0																		---	---	---	---
ACSF3	197322	broad.mit.edu	37	16	89162644	89162645	+	Intron	INS	-	TGA	TGA	rs145110748	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:89162644_89162645insTGA	uc002fmp.2	+						ACSF3_uc010cig.1_Intron|ACSF3_uc010cih.1_Intron|ACSF3_uc002fmq.1_5'Flank	NM_174917	NP_777577			acyl-CoA synthetase family member 3 precursor						fatty acid metabolic process	mitochondrion	acid-thiol ligase activity|ATP binding				0				BRCA - Breast invasive adenocarcinoma(80;0.0281)														---	---	---	---
ANKRD11	29123	broad.mit.edu	37	16	89423852	89423853	+	Intron	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:89423852_89423853delAA	uc002fmx.1	-						ANKRD11_uc002fmy.1_Intron|ANKRD11_uc002fnc.1_Intron|ANKRD11_uc002fnd.2_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)														---	---	---	---
C16orf7	9605	broad.mit.edu	37	16	89785128	89785130	+	Intron	DEL	TTT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:89785128_89785130delTTT	uc002fom.1	-						C16orf7_uc002fol.1_Intron|ZNF276_uc010ciq.2_5'Flank|ZNF276_uc002fop.2_5'Flank|ZNF276_uc002foq.3_5'Flank|ZNF276_uc010cir.2_5'Flank|ZNF276_uc002for.3_5'Flank|ZNF276_uc010cis.2_5'Flank|ZNF276_uc002fos.3_5'Flank|ZNF276_uc002fot.3_5'Flank	NM_004913	NP_004904			chromosome 16 open reading frame 7						ATP synthesis coupled proton transport		GTPase activator activity|transporter activity				0		Lung NSC(15;2.19e-05)|all_lung(18;3.07e-05)|all_hematologic(23;0.0256)		BRCA - Breast invasive adenocarcinoma(80;0.0273)														---	---	---	---
FANCA	2175	broad.mit.edu	37	16	89809062	89809074	+	Intron	DEL	AAAAAAAAAAAAA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:89809062_89809074delAAAAAAAAAAAAA	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	89878135	89878135	+	Intron	DEL	T	-	-	rs67424778		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:89878135delT	uc002fou.1	-						FANCA_uc010vpn.1_Intron|FANCA_uc002fov.1_Intron|FANCA_uc002fow.1_Intron|FANCA_uc002fox.1_Intron|FANCA_uc010ciu.1_Intron|FANCA_uc002foy.2_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				---	---	---	---
Unknown	0	broad.mit.edu	37	17	42941	42942	+	IGR	INS	-	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:42941_42942insG								DOC2B (11521 upstream) : RPH3AL (19352 downstream)																																			---	---	---	---
VPS53	55275	broad.mit.edu	37	17	527002	527002	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:527002delA	uc002frn.2	-						VPS53_uc002frk.2_Intron|VPS53_uc010cjo.1_Intron|VPS53_uc002frl.2_Intron|VPS53_uc002frm.2_Intron|VPS53_uc002fro.2_Intron|VPS53_uc010cjp.1_Intron	NM_018289	NP_060759			vacuolar protein sorting 53 isoform 2						protein transport	endosome membrane|Golgi apparatus					0				UCEC - Uterine corpus endometrioid carcinoma (25;0.0265)														---	---	---	---
GLOD4	51031	broad.mit.edu	37	17	663610	663610	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:663610delA	uc002frv.2	-						GLOD4_uc002frt.2_Intron|GLOD4_uc002fru.2_Intron|GLOD4_uc010vqc.1_Intron	NM_016080	NP_057164			glyoxalase domain containing 4							mitochondrion					0				UCEC - Uterine corpus endometrioid carcinoma (25;0.022)														---	---	---	---
NXN	64359	broad.mit.edu	37	17	747826	747826	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:747826delT	uc002fsa.2	-						NXN_uc002fsb.1_Intron|NXN_uc002frz.2_Intron|NXN_uc010vqe.1_Intron	NM_022463	NP_071908			nucleoredoxin						cell differentiation|cell redox homeostasis|multicellular organismal development|Wnt receptor signaling pathway	cytosol|nucleus	protein-disulfide reductase activity			ovary(2)|breast(1)|pancreas(1)	4				UCEC - Uterine corpus endometrioid carcinoma (25;0.0237)														---	---	---	---
NXN	64359	broad.mit.edu	37	17	771136	771140	+	Intron	DEL	AAAAA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:771136_771140delAAAAA	uc002fsa.2	-						NXN_uc002fsb.1_Intron	NM_022463	NP_071908			nucleoredoxin						cell differentiation|cell redox homeostasis|multicellular organismal development|Wnt receptor signaling pathway	cytosol|nucleus	protein-disulfide reductase activity			ovary(2)|breast(1)|pancreas(1)	4				UCEC - Uterine corpus endometrioid carcinoma (25;0.0237)														---	---	---	---
Unknown	0	broad.mit.edu	37	17	1223771	1223771	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:1223771delA								TUSC5 (19490 upstream) : YWHAE (24065 downstream)																																			---	---	---	---
YWHAE	7531	broad.mit.edu	37	17	1298388	1298388	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:1298388delA	uc002fsj.2	-						YWHAE_uc002fsk.2_Intron|YWHAE_uc010vqh.1_Intron|YWHAE_uc010vqi.1_Intron	NM_006761	NP_006752			tyrosine 3/tryptophan 5 -monooxygenase						apoptosis|G2/M transition of mitotic cell cycle|induction of apoptosis by extracellular signals|interspecies interaction between organisms|intracellular signal transduction|nerve growth factor receptor signaling pathway	cytosol|melanosome	histone deacetylase binding|phosphoserine binding			lung(2)|ovary(1)	3			OV - Ovarian serous cystadenocarcinoma(18;0.203)	UCEC - Uterine corpus endometrioid carcinoma (25;0.0887)														---	---	---	---
MYO1C	4641	broad.mit.edu	37	17	1381684	1381684	+	Intron	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:1381684delG	uc002fsp.2	-						MYO1C_uc002fsn.2_Intron|MYO1C_uc002fso.2_Intron|MYO1C_uc010vqj.1_Intron|MYO1C_uc010vqk.1_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)														---	---	---	---
Unknown	0	broad.mit.edu	37	17	1824122	1824122	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:1824122delA								RPA1 (21274 upstream) : RTN4RL1 (13851 downstream)																																			---	---	---	---
SMG6	23293	broad.mit.edu	37	17	1980968	1980968	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:1980968delA	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	1999812	1999812	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:1999812delT	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	2007843	2007844	+	Intron	DEL	AA	-	-	rs113719745		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:2007843_2007844delAA	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	2143777	2143778	+	Intron	DEL	AA	-	-	rs72428762		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:2143777_2143778delAA	uc002fub.1	-							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	2202012	2202019	+	Intron	DEL	AAAAAAAA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:2202012_2202019delAAAAAAAA	uc002fub.1	-							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																		---	---	---	---
MNT	4335	broad.mit.edu	37	17	2298768	2298768	+	Intron	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:2298768delG	uc002fur.2	-							NM_020310	NP_064706			MAX binding protein						multicellular organismal development|negative regulation of cell proliferation|transcription from RNA polymerase II promoter	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|transcription coactivator activity|transcription corepressor activity			skin(1)	1				Colorectal(2;1.37e-05)|READ - Rectum adenocarcinoma(2;8.68e-05)														---	---	---	---
METT10D	79066	broad.mit.edu	37	17	2380251	2380253	+	Intron	DEL	AAA	-	-	rs72496353		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:2380251_2380253delAAA	uc002fut.2	-						METT10D_uc002fuu.3_Intron|METT10D_uc010cka.2_Intron|METT10D_uc002fuv.2_Intron|METT10D_uc010vqx.1_Intron|METT10D_uc010vqy.1_Intron	NM_024086	NP_076991			methyltransferase 10 domain containing								methyltransferase activity				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	17	2436076	2436076	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:2436076delT								METT10D (20876 upstream) : PAFAH1B1 (60847 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	2453153	2453153	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:2453153delT								METT10D (37953 upstream) : PAFAH1B1 (43770 downstream)																																			---	---	---	---
PAFAH1B1	5048	broad.mit.edu	37	17	2568632	2568632	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:2568632delT	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																		---	---	---	---
Unknown	0	broad.mit.edu	37	17	2662305	2662306	+	IGR	INS	-	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:2662305_2662306insT								MIR1253 (10829 upstream) : RAP1GAP2 (37426 downstream)																																			---	---	---	---
RAP1GAP2	23108	broad.mit.edu	37	17	2786878	2786878	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:2786878delT	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																		---	---	---	---
RAP1GAP2	23108	broad.mit.edu	37	17	2820564	2820564	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:2820564delT	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																		---	---	---	---
RAP1GAP2	23108	broad.mit.edu	37	17	2880418	2880420	+	Intron	DEL	AAA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:2880418_2880420delAAA	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	3079715	3079715	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:3079715delA								OR1G1 (48870 upstream) : OR1A2 (21098 downstream)																																			---	---	---	---
TRPV3	162514	broad.mit.edu	37	17	3429777	3429778	+	Intron	DEL	AA	-	-	rs112541565		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:3429777_3429778delAA	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)													---	---	---	---
SHPK	23729	broad.mit.edu	37	17	3523731	3523731	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:3523731delT	uc002fvz.1	-							NM_013276	NP_037408			carbohydrate kinase-like						carbohydrate metabolic process	cytoplasm	ATP binding|sedoheptulokinase activity			ovary(1)	1				COAD - Colon adenocarcinoma(5;0.0828)														---	---	---	---
ITGAE	3682	broad.mit.edu	37	17	3634493	3634493	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:3634493delA	uc002fwo.3	-							NM_002208	NP_002199			integrin, alpha E precursor						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)														---	---	---	---
Unknown	0	broad.mit.edu	37	17	3758504	3758505	+	IGR	DEL	GA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:3758504_3758505delGA								C17orf85 (8964 upstream) : CAMKK1 (5120 downstream)																																			---	---	---	---
ZZEF1	23140	broad.mit.edu	37	17	3968692	3968692	+	Intron	DEL	A	-	-	rs74396828		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:3968692delA	uc002fxe.2	-						ZZEF1_uc002fxh.2_5'Flank|ZZEF1_uc002fxi.2_5'Flank|ZZEF1_uc002fxj.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																		---	---	---	---
ZZEF1	23140	broad.mit.edu	37	17	4009253	4009253	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:4009253delT	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																		---	---	---	---
ANKFY1	51479	broad.mit.edu	37	17	4085525	4085525	+	Frame_Shift_Del	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:4085525delG	uc002fxq.1	-	15	2110	c.2072delC	c.(2071-2073)CCGfs	p.P691fs	ANKFY1_uc002fxn.2_Frame_Shift_Del_p.P733fs|ANKFY1_uc002fxo.2_Frame_Shift_Del_p.P692fs|ANKFY1_uc002fxp.2_Frame_Shift_Del_p.P690fs|ANKFY1_uc010ckp.2_Frame_Shift_Del_p.P633fs	NM_016376	NP_057460	Q9P2R3	ANFY1_HUMAN	ankyrin repeat and FYVE domain containing 1	691	ANK 11.					endosome membrane	metal ion binding|protein binding			ovary(2)|skin(1)	3																		---	---	---	---
ANKFY1	51479	broad.mit.edu	37	17	4131713	4131715	+	Intron	DEL	TTT	-	-	rs71383534		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:4131713_4131715delTTT	uc002fxq.1	-						ANKFY1_uc002fxn.2_Intron|ANKFY1_uc002fxo.2_Intron|ANKFY1_uc002fxp.2_Intron|ANKFY1_uc010ckp.2_Intron|ANKFY1_uc002fxr.2_Intron|ANKFY1_uc010vrz.1_Intron	NM_016376	NP_057460			ankyrin repeat and FYVE domain containing 1							endosome membrane	metal ion binding|protein binding			ovary(2)|skin(1)	3																		---	---	---	---
ANKFY1	51479	broad.mit.edu	37	17	4150410	4150411	+	Intron	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:4150410_4150411delAA	uc002fxq.1	-						ANKFY1_uc002fxn.2_Intron|ANKFY1_uc002fxo.2_Intron|ANKFY1_uc002fxp.2_Intron|ANKFY1_uc010ckp.2_Intron|ANKFY1_uc002fxr.2_Intron|ANKFY1_uc010vrz.1_Intron	NM_016376	NP_057460			ankyrin repeat and FYVE domain containing 1							endosome membrane	metal ion binding|protein binding			ovary(2)|skin(1)	3																		---	---	---	---
Unknown	0	broad.mit.edu	37	17	4306618	4306618	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:4306618delT								UBE2G1 (36649 upstream) : SPNS3 (30601 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	4397002	4397002	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:4397002delT								SPNS3 (5504 upstream) : SPNS2 (5127 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	5096766	5096766	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:5096766delA	uc002gbf.1	+						uc002gbg.1_Intron|ZNF594_uc010cla.1_5'Flank					Homo sapiens cDNA FLJ11816 fis, clone HEMBA1006416.																														---	---	---	---
NUP88	4927	broad.mit.edu	37	17	5296276	5296276	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:5296276delT	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																		---	---	---	---
NLRP1	22861	broad.mit.edu	37	17	5446980	5446983	+	Intron	DEL	AAAA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:5446980_5446983delAAAA	uc002gci.2	-						NLRP1_uc002gcg.1_Intron|NLRP1_uc002gck.2_Intron|NLRP1_uc002gcj.2_Intron|NLRP1_uc002gcl.2_Intron|NLRP1_uc002gch.3_Intron|NLRP1_uc010clh.2_Intron	NM_033004	NP_127497			NLR family, pyrin domain containing 1 isoform 1						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)																---	---	---	---
Unknown	0	broad.mit.edu	37	17	5884177	5884179	+	IGR	DEL	TTT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:5884177_5884179delTTT								NLRP1 (396345 upstream) : WSCD1 (88258 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	6114837	6114838	+	IGR	INS	-	T	T	rs146502549	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:6114837_6114838insT								WSCD1 (87092 upstream) : AIPL1 (212222 downstream)																																			---	---	---	---
FAM64A	54478	broad.mit.edu	37	17	6350599	6350599	+	Intron	DEL	T	-	-	rs113827676		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:6350599delT	uc002gcw.1	+						FAM64A_uc002gct.1_Intron|FAM64A_uc002gcu.1_Intron|FAM64A_uc002gcv.1_Intron|FAM64A_uc002gcx.1_Intron|FAM64A_uc002gcy.1_Intron|FAM64A_uc002gcz.1_Intron|FAM64A_uc002gda.1_Intron|FAM64A_uc002gdb.1_Intron	NM_019013	NP_061886			family with sequence similarity 64, member A							nucleolus	protein binding				0				COAD - Colon adenocarcinoma(228;0.141)														---	---	---	---
MED31	51003	broad.mit.edu	37	17	6547714	6547714	+	3'UTR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-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	6965480	6965480	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:6965480delA								SLC16A11 (18238 upstream) : CLEC10A (12377 downstream)																																			---	---	---	---
ACADVL	37	broad.mit.edu	37	17	7123678	7123679	+	Intron	INS	-	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:7123678_7123679insA	uc002gev.2	+						DLG4_uc010cly.2_5'Flank|DLG4_uc002get.3_5'Flank|DLG4_uc010vto.1_5'Flank|DLG4_uc002geu.2_5'Flank|ACADVL_uc010vtp.1_Intron|ACADVL_uc010vtq.1_Intron|ACADVL_uc002gew.2_Intron|ACADVL_uc002gex.2_Intron	NM_000018	NP_000009			acyl-Coenzyme A dehydrogenase, very long chain						energy derivation by oxidation of organic compounds|fatty acid beta-oxidation using acyl-CoA dehydrogenase|negative regulation of fatty acid biosynthetic process|negative regulation of fatty acid oxidation|regulation of cholesterol metabolic process|temperature homeostasis	mitochondrial inner membrane|mitochondrial nucleoid	long-chain-acyl-CoA dehydrogenase activity			ovary(3)	3																		---	---	---	---
DVL2	1856	broad.mit.edu	37	17	7132243	7132243	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:7132243delA	uc002gez.1	-						DVL2_uc010vtr.1_Intron	NM_004422	NP_004413			dishevelled 2						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																		---	---	---	---
SHBG	6462	broad.mit.edu	37	17	7527575	7527575	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:7527575delT	uc010cmt.2	+						SHBG_uc010cmo.2_Intron|SHBG_uc010cmp.2_Intron|SHBG_uc010cmq.2_Intron|SHBG_uc010cmr.2_Intron|SHBG_uc010cms.2_Intron|SHBG_uc010cmu.2_Intron	NM_001040	NP_001031			sex hormone-binding globulin isoform 1						hormone transport	extracellular region	androgen binding|protein homodimerization activity	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)													---	---	---	---
SHBG	6462	broad.mit.edu	37	17	7534641	7534641	+	Frame_Shift_Del	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:7534641delG	uc002gie.2	+	4	555	c.517delG	c.(517-519)GGGfs	p.G173fs	SHBG_uc010cmo.2_Intron|SHBG_uc010cmp.2_Frame_Shift_Del_p.G115fs|SHBG_uc010cmq.2_Intron|SHBG_uc010cmr.2_Intron|SHBG_uc010cms.2_Intron|SHBG_uc010cmt.2_Frame_Shift_Del_p.G115fs|SHBG_uc010cmu.2_Frame_Shift_Del_p.G115fs|SHBG_uc010cmz.2_Frame_Shift_Del_p.G115fs|SHBG_uc010cmv.2_Intron|SHBG_uc010cmw.2_Intron|SHBG_uc010cmx.2_Intron|SHBG_uc010cmy.2_Frame_Shift_Del_p.G115fs|SHBG_uc002gid.3_Frame_Shift_Del_p.G115fs|SHBG_uc010cnd.2_Intron|SHBG_uc010cna.2_Intron|SHBG_uc010vue.1_Frame_Shift_Del_p.G173fs|SHBG_uc010vuf.1_Frame_Shift_Del_p.G173fs|SHBG_uc010cnb.2_Frame_Shift_Del_p.G173fs|SHBG_uc010cnc.2_Intron	NM_001040	NP_001031	P04278	SHBG_HUMAN	sex hormone-binding globulin isoform 1	173	Laminin G-like 1.				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)													---	---	---	---
TP53	7157	broad.mit.edu	37	17	7572963	7572963	+	Frame_Shift_Del	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:7572963delT	uc002gim.2	-	11	1340	c.1146delA	c.(1144-1146)AAAfs	p.K382fs	TP53_uc002gig.1_Intron|TP53_uc002gih.2_Intron|TP53_uc010cne.1_RNA|TP53_uc010cnf.1_3'UTR|TP53_uc010cng.1_3'UTR|TP53_uc002gii.1_Frame_Shift_Del_p.K250fs|TP53_uc010cnh.1_3'UTR|TP53_uc010cni.1_3'UTR|TP53_uc002gij.2_Frame_Shift_Del_p.K382fs	NM_001126112	NP_001119584	P04637	P53_HUMAN	tumor protein p53 isoform a	382	Basic (repression of DNA-binding).|Interaction with CARM1.			K->R: Abolishes monomethylation by SETD8.|K->A: Abolishes acetylation by CREBBP.	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?(7)|p.K382fs*40(3)|p.K382fs*13(2)|p.?(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)			---	---	---	---
WRAP53	55135	broad.mit.edu	37	17	7598278	7598279	+	Intron	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:7598278_7598279delTT	uc010vuh.1	+						WRAP53_uc010vui.1_Intron|WRAP53_uc002gip.2_Intron|WRAP53_uc002gir.2_Intron|WRAP53_uc002giq.2_Intron|WRAP53_uc010cnl.2_Intron	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	7669104	7669104	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:7669104delT	uc002giu.1	+							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)																---	---	---	---
DNAH2	146754	broad.mit.edu	37	17	7686121	7686121	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:7686121delA	uc002giu.1	+							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)																---	---	---	---
CHD3	1107	broad.mit.edu	37	17	7798765	7798765	+	Frame_Shift_Del	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:7798765delC	uc002gje.2	+	10	1762	c.1612delC	c.(1612-1614)CCCfs	p.P538fs	CHD3_uc002gjd.2_Frame_Shift_Del_p.P597fs|CHD3_uc002gjf.2_Frame_Shift_Del_p.P538fs|CHD3_uc002gjg.1_Frame_Shift_Del_p.P366fs	NM_001005273	NP_001005273	Q12873	CHD3_HUMAN	chromodomain helicase DNA binding protein 3	538	Chromo 1.				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|protein binding|zinc ion binding			breast(1)	1		Prostate(122;0.202)																---	---	---	---
Unknown	0	broad.mit.edu	37	17	8258049	8258049	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:8258049delA								ODF4 (8686 upstream) : LOC100128288 (3682 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	8577233	8577233	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:8577233delA								MYH10 (43197 upstream) : CCDC42 (56014 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	8579300	8579300	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:8579300delT								MYH10 (45264 upstream) : CCDC42 (53947 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	8654029	8654030	+	IGR	INS	-	AAAC	AAAC	rs143989040	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:8654029_8654030insAAAC								CCDC42 (5875 upstream) : SPDYE4 (2394 downstream)																																			---	---	---	---
PIK3R5	23533	broad.mit.edu	37	17	8846394	8846394	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:8846394delT	uc010vuz.1	-						PIK3R5_uc002glu.3_Intron|PIK3R5_uc010coa.1_Intron|PIK3R5_uc010cob.1_Intron	NM_001142633	NP_001136105			phosphoinositide-3-kinase, regulatory subunit 5						platelet activation	cytosol|membrane|nucleus				breast(2)|large_intestine(1)|central_nervous_system(1)|skin(1)	5																		---	---	---	---
NTN1	9423	broad.mit.edu	37	17	8951972	8951973	+	Intron	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:8951972_8951973delTT	uc002glw.3	+							NM_004822	NP_004813			netrin 1 precursor						apoptosis|axon guidance		protein binding				0																		---	---	---	---
STX8	9482	broad.mit.edu	37	17	9253270	9253270	+	Intron	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:9253270delC	uc002glx.2	-							NM_004853	NP_004844			syntaxin 8						transport	endoplasmic reticulum|integral to plasma membrane				central_nervous_system(1)	1																		---	---	---	---
STX8	9482	broad.mit.edu	37	17	9270490	9270491	+	Intron	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:9270490_9270491delTT	uc002glx.2	-							NM_004853	NP_004844			syntaxin 8						transport	endoplasmic reticulum|integral to plasma membrane				central_nervous_system(1)	1																		---	---	---	---
STX8	9482	broad.mit.edu	37	17	9282137	9282137	+	Intron	DEL	A	-	-	rs139246965	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:9282137delA	uc002glx.2	-							NM_004853	NP_004844			syntaxin 8						transport	endoplasmic reticulum|integral to plasma membrane				central_nervous_system(1)	1																		---	---	---	---
GAS7	8522	broad.mit.edu	37	17	9855715	9855715	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:9855715delT	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*								---	---	---	---
GAS7	8522	broad.mit.edu	37	17	9995473	9995474	+	Intron	DEL	TC	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:9995473_9995474delTC	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	10054653	10054653	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:10054653delT	uc002gmg.1	-							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	10104716	10104720	+	5'Flank	DEL	AAAAG	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:10104716_10104720delAAAAG	uc002gmg.1	-							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*								---	---	---	---
Unknown	0	broad.mit.edu	37	17	10121563	10121563	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:10121563delT								GAS7 (19695 upstream) : MYH13 (82620 downstream)																																			---	---	---	---
MYH8	4626	broad.mit.edu	37	17	10302566	10302567	+	Intron	INS	-	TG	TG	rs141203224	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:10302566_10302567insTG	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				---	---	---	---
MYH8	4626	broad.mit.edu	37	17	10304145	10304145	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:10304145delT	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				---	---	---	---
Unknown	0	broad.mit.edu	37	17	10574375	10574375	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:10574375delT								MYH3 (14910 upstream) : SCO1 (9276 downstream)																																			---	---	---	---
TMEM220	388335	broad.mit.edu	37	17	10633933	10633933	+	5'Flank	DEL	A	-	-	rs78141100		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:10633933delA	uc002gmx.2	-						TMEM220_uc002gmy.2_5'Flank	NM_001004313	NP_001004313			transmembrane protein 220							integral to membrane					0																		---	---	---	---
Unknown	0	broad.mit.edu	37	17	10846537	10846537	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:10846537delT								PIRT (105119 upstream) : SHISA6 (298203 downstream)																																			---	---	---	---
SHISA6	388336	broad.mit.edu	37	17	11367231	11367231	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:11367231delT	uc002gna.3	+						SHISA6_uc002gnb.3_Intron|SHISA6_uc010com.2_Intron	NM_207386	NP_997269			shisa homolog 6							integral to membrane				breast(1)	1																		---	---	---	---
SHISA6	388336	broad.mit.edu	37	17	11405014	11405015	+	Intron	INS	-	AG	AG			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:11405014_11405015insAG	uc002gna.3	+						SHISA6_uc002gnb.3_Intron|SHISA6_uc010com.2_Intron	NM_207386	NP_997269			shisa homolog 6							integral to membrane				breast(1)	1																		---	---	---	---
SHISA6	388336	broad.mit.edu	37	17	11440414	11440414	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:11440414delT	uc002gna.3	+						SHISA6_uc002gnb.3_Intron|SHISA6_uc010com.2_Intron	NM_207386	NP_997269			shisa homolog 6							integral to membrane				breast(1)	1																		---	---	---	---
ZNF18	7566	broad.mit.edu	37	17	11892814	11892814	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:11892814delA	uc002gng.1	-						ZNF18_uc002gnh.1_Intron|ZNF18_uc002gni.1_Intron	NM_144680	NP_653281			zinc finger protein 18						viral reproduction	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			central_nervous_system(1)	1				Colorectal(4;3.33e-05)|COAD - Colon adenocarcinoma(4;0.000494)|READ - Rectum adenocarcinoma(10;0.233)														---	---	---	---
Unknown	0	broad.mit.edu	37	17	12424909	12424909	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:12424909delT								MAP2K4 (377859 upstream) : MYOCD (144298 downstream)																																			---	---	---	---
RICH2	9912	broad.mit.edu	37	17	12894042	12894042	+	3'UTR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:12894042delA	uc002gnr.3	+	21					RICH2_uc010vvk.1_3'UTR|RICH2_uc010vvl.1_3'UTR|RICH2_uc002gns.3_3'UTR|RICH2_uc010vvm.1_3'UTR|RICH2_uc010vvn.1_RNA	NM_014859	NP_055674			Rho GTPase-activating protein RICH2						regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol	GTPase activator activity				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	17	13872920	13872921	+	IGR	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:13872920_13872921delTT								HS3ST3A1 (367676 upstream) : CDRT15P (54894 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	13874647	13874647	+	IGR	DEL	G	-	-	rs113323359		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:13874647delG								HS3ST3A1 (369403 upstream) : CDRT15P (53168 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	14729198	14729199	+	IGR	DEL	GT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:14729198_14729199delGT								HS3ST3B1 (479706 upstream) : PMP22 (403898 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	14851004	14851004	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:14851004delT								HS3ST3B1 (601512 upstream) : PMP22 (282093 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	14897415	14897415	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:14897415delT								HS3ST3B1 (647923 upstream) : PMP22 (235682 downstream)																																			---	---	---	---
CDRT4	284040	broad.mit.edu	37	17	15343740	15343740	+	Intron	DEL	T	-	-	rs2954764	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:15343740delT	uc002gop.1	-						CDRT4_uc010vvw.1_Intron|FAM18B2_uc010vvx.1_Intron	NM_173622	NP_775893			CMT1A duplicated region transcript 4												0				UCEC - Uterine corpus endometrioid carcinoma (92;0.0874)														---	---	---	---
ZSWIM7	125150	broad.mit.edu	37	17	15892332	15892332	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:15892332delA	uc002gpe.2	-						ZSWIM7_uc002gpf.2_Intron|ZSWIM7_uc002gpg.2_Intron	NM_001042698	NP_001036163			zinc finger, SWIM-type containing 7						DNA recombination|DNA repair	nucleus	zinc ion binding				0				UCEC - Uterine corpus endometrioid carcinoma (92;0.0827)														---	---	---	---
NCOR1	9611	broad.mit.edu	37	17	15943111	15943111	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:15943111delT	uc002gpo.2	-						NCOR1_uc002gpn.2_Intron|NCOR1_uc002gpl.2_Intron|NCOR1_uc002gpm.2_Intron|NCOR1_uc010vwb.1_Intron|NCOR1_uc010coy.2_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	15961099	15961099	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-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	15974580	15974581	+	Intron	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:15974580_15974581delAA	uc002gpo.2	-						NCOR1_uc002gpn.2_Intron|NCOR1_uc002gpp.1_Intron|NCOR1_uc002gpm.2_5'Flank|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	16076827	16076827	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:16076827delA	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|NCOR1_uc002gpu.2_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	16129502	16129502	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:16129502delT	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)														---	---	---	---
UBB	7314	broad.mit.edu	37	17	16282304	16282304	+	5'Flank	DEL	T	-	-	rs11331934		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:16282304delT	uc002gpx.2	+						UBB_uc010vwe.1_5'Flank	NM_018955	NP_061828			ubiquitin B precursor						activation of MAPK activity|anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|anti-apoptosis|apoptosis|cellular membrane organization|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|DNA repair|endosome transport|epidermal growth factor receptor signaling pathway|G1/S transition of mitotic cell cycle|I-kappaB kinase/NF-kappaB cascade|induction of apoptosis by extracellular signals|innate immune response|JNK cascade|M/G1 transition of mitotic cell cycle|mRNA metabolic process|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|negative regulation of epidermal growth factor receptor signaling pathway|negative regulation of type I interferon production|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|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 ubiquitin-protein ligase activity involved in mitotic cell cycle|S phase of mitotic cell cycle|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|viral reproduction	cytosol|endocytic vesicle membrane|endosome membrane|nucleoplasm|plasma membrane	protein binding			skin(3)	3				UCEC - Uterine corpus endometrioid carcinoma (92;0.0822)														---	---	---	---
ZNF287	57336	broad.mit.edu	37	17	16456901	16456901	+	Intron	DEL	A	-	-	rs35856293		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:16456901delA	uc002gqi.2	-							NM_020653	NP_065704			zinc finger protein 287						viral reproduction	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding				0				UCEC - Uterine corpus endometrioid carcinoma (92;0.083)														---	---	---	---
CCDC144A	9720	broad.mit.edu	37	17	16623498	16623498	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:16623498delT	uc002gqk.1	+						CCDC144A_uc002gql.1_Intron|LOC162632_uc010cpj.1_Intron	NM_014695	NP_055510			coiled-coil domain containing 144A												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	17	16748756	16748757	+	IGR	INS	-	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:16748756_16748757insC								LOC162632 (40937 upstream) : TNFRSF13B (84092 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	16779232	16779232	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:16779232delT								LOC162632 (71413 upstream) : TNFRSF13B (53617 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	16779393	16779393	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:16779393delT								LOC162632 (71574 upstream) : TNFRSF13B (53456 downstream)																																			---	---	---	---
MPRIP	23164	broad.mit.edu	37	17	16997442	16997442	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:16997442delT	uc002gqu.1	+						MPRIP_uc002gqv.1_Intron	NM_201274	NP_958431			myosin phosphatase-Rho interacting protein							cytoplasm|cytoskeleton	actin binding				0																		---	---	---	---
MPRIP	23164	broad.mit.edu	37	17	17041158	17041158	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:17041158delA	uc002gqu.1	+						MPRIP_uc002gqv.1_Intron|MPRIP_uc002gqw.1_Intron	NM_201274	NP_958431			myosin phosphatase-Rho interacting protein							cytoplasm|cytoskeleton	actin binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	17	17100268	17100268	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:17100268delA								MPRIP (11395 upstream) : PLD6 (4043 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	17143623	17143625	+	IGR	DEL	TTT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:17143623_17143625delTTT								PLD6 (3121 upstream) : COPS3 (6516 downstream)																																			---	---	---	---
COPS3	8533	broad.mit.edu	37	17	17155383	17155383	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:17155383delA	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	17195635	17195635	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:17195635delT								COPS3 (11044 upstream) : NT5M (11045 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	17273135	17273136	+	IGR	DEL	TG	-	-	rs58347769		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:17273135_17273136delTG								NT5M (22160 upstream) : MED9 (107164 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	17360190	17360190	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:17360190delA								NT5M (109215 upstream) : MED9 (20110 downstream)																																			---	---	---	---
SREBF1	6720	broad.mit.edu	37	17	17737418	17737418	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:17737418delT	uc002gru.1	-						SREBF1_uc002grt.1_Intron|SREBF1_uc010cpq.1_Intron	NM_004176	NP_004167			sterol regulatory element binding transcription						cellular response to starvation|cholesterol metabolic process|positive regulation of transcription from RNA polymerase II promoter|regulation of transcription from RNA polymerase II promoter	endoplasmic reticulum|endoplasmic reticulum membrane|ER to Golgi transport vesicle membrane|Golgi membrane|integral to membrane|nuclear envelope|nucleus	protein binding|protein binding|sequence-specific DNA binding transcription factor activity|sterol response element binding			skin(1)	1																		---	---	---	---
MYO15A	51168	broad.mit.edu	37	17	18034381	18034381	+	Intron	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:18034381delG	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)																	---	---	---	---
TOP3A	7156	broad.mit.edu	37	17	18213749	18213749	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:18213749delA	uc002gsx.1	-						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																		---	---	---	---
Unknown	0	broad.mit.edu	37	17	18293315	18293316	+	IGR	INS	-	TC	TC	rs140161091		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:18293315_18293316insTC								EVPLL (357 upstream) : LOC339240 (29966 downstream)																																			---	---	---	---
PRPSAP2	5636	broad.mit.edu	37	17	18776163	18776163	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:18776163delT	uc002gup.1	+						PRPSAP2_uc002guo.1_Intron|PRPSAP2_uc010vyi.1_Intron|PRPSAP2_uc010vyj.1_Intron|PRPSAP2_uc010vyk.1_Intron	NM_002767	NP_002758			phosphoribosyl pyrophosphate						nucleotide biosynthetic process		enzyme inhibitor activity|magnesium ion binding|ribose phosphate diphosphokinase activity			skin(1)	1																		---	---	---	---
PRPSAP2	5636	broad.mit.edu	37	17	18821388	18821388	+	Intron	DEL	A	-	-	rs28454756	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:18821388delA	uc002gup.1	+						PRPSAP2_uc002guo.1_Intron|PRPSAP2_uc010vyi.1_Intron|PRPSAP2_uc010vyj.1_Intron|PRPSAP2_uc010vyk.1_Intron	NM_002767	NP_002758			phosphoribosyl pyrophosphate						nucleotide biosynthetic process		enzyme inhibitor activity|magnesium ion binding|ribose phosphate diphosphokinase activity			skin(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	17	18850598	18850599	+	IGR	DEL	AA	-	-	rs112037535		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:18850598_18850599delAA								PRPSAP2 (16018 upstream) : SLC5A10 (3390 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	19333871	19333874	+	IGR	DEL	ACAC	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:19333871_19333874delACAC								RNF112 (13284 upstream) : SLC47A1 (103293 downstream)																																			---	---	---	---
ULK2	9706	broad.mit.edu	37	17	19718560	19718560	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:19718560delT	uc002gwm.3	-						ULK2_uc002gwn.2_Intron	NM_001142610	NP_001136082			unc-51-like kinase 2						signal transduction		ATP binding|protein binding|protein serine/threonine kinase activity			skin(2)|large_intestine(1)|stomach(1)	4	all_cancers(12;4.97e-05)|all_epithelial(12;0.00362)|Breast(13;0.186)																	---	---	---	---
CYTSB	92521	broad.mit.edu	37	17	20011976	20011976	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:20011976delT	uc002gwq.2	+						CYTSB_uc010cqx.2_Intron|CYTSB_uc002gwr.2_Intron|CYTSB_uc002gws.2_Intron	NM_001033553	NP_001028725			spectrin domain with coiled-coils 1 NSP5b3b							nucleus					0																		---	---	---	---
CYTSB	92521	broad.mit.edu	37	17	20181415	20181415	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:20181415delT	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	20552717	20552717	+	IGR	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:20552717delC								LGALS9B (181869 upstream) : CCDC144NL (213993 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	20562528	20562528	+	IGR	DEL	G	-	-	rs4985920		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:20562528delG								LGALS9B (191680 upstream) : CCDC144NL (204182 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	20580350	20580350	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:20580350delT								LGALS9B (209502 upstream) : CCDC144NL (186360 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	20641331	20641331	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:20641331delA								LGALS9B (270483 upstream) : CCDC144NL (125379 downstream)																																			---	---	---	---
USP22	23326	broad.mit.edu	37	17	20945742	20945742	+	Intron	DEL	G	-	-	rs111712869		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:20945742delG	uc002gym.3	-						USP22_uc002gyn.3_Intron|USP22_uc002gyl.3_Intron	NM_015276	NP_056091			ubiquitin thiolesterase 22						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																		---	---	---	---
USP22	23326	broad.mit.edu	37	17	20949314	20949314	+	5'Flank	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:20949314delA	uc002gym.3	-						USP22_uc002gyn.3_5'Flank|USP22_uc002gyl.3_5'Flank	NM_015276	NP_056091			ubiquitin thiolesterase 22						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																		---	---	---	---
DHRS7B	25979	broad.mit.edu	37	17	21052466	21052466	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-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																		---	---	---	---
Unknown	0	broad.mit.edu	37	17	21218864	21218865	+	IGR	INS	-	G	G	rs148092055	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:21218864_21218865insG								MAP2K3 (315 upstream) : KCNJ12 (60834 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	21227696	21227697	+	IGR	DEL	AG	-	-	rs149665353		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:21227696_21227697delAG								MAP2K3 (9147 upstream) : KCNJ12 (52002 downstream)																																			---	---	---	---
KCNJ12	3768	broad.mit.edu	37	17	21301404	21301405	+	Intron	DEL	TG	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:21301404_21301405delTG	uc002gyv.1	+							NM_021012	NP_066292			potassium inwardly-rectifying channel, subfamily						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	21304101	21304109	+	Intron	DEL	ACCAGAAAT	-	-	rs144693746		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:21304101_21304109delACCAGAAAT	uc002gyv.1	+							NM_021012	NP_066292			potassium inwardly-rectifying channel, subfamily						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)			---	---	---	---
Unknown	0	broad.mit.edu	37	17	21333938	21333938	+	IGR	DEL	G	-	-	rs63355163		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:21333938delG								KCNJ12 (10759 upstream) : C17orf51 (97634 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	21339292	21339292	+	IGR	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:21339292delG								KCNJ12 (16113 upstream) : C17orf51 (92280 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	21353107	21353107	+	IGR	DEL	A	-	-	rs5819778		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:21353107delA								KCNJ12 (29928 upstream) : C17orf51 (78465 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	21480958	21480958	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:21480958delA								C17orf51 (3227 upstream) : FAM27L (344412 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	21517266	21517267	+	IGR	DEL	GG	-	-	rs112302358		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:21517266_21517267delGG								C17orf51 (39535 upstream) : FAM27L (308103 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	21537625	21537626	+	IGR	DEL	CT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:21537625_21537626delCT								C17orf51 (59894 upstream) : FAM27L (287744 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	21541432	21541433	+	IGR	INS	-	AT	AT	rs139523404	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:21541432_21541433insAT								C17orf51 (63701 upstream) : FAM27L (283937 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	21548062	21548062	+	IGR	DEL	G	-	-	rs148427516		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:21548062delG								C17orf51 (70331 upstream) : FAM27L (277308 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	21775749	21775749	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:21775749delA								C17orf51 (298018 upstream) : FAM27L (49621 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	21834701	21834701	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:21834701delA								FAM27L (8198 upstream) : FLJ36000 (69361 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	25268619	25268620	+	IGR	INS	-	G	G	rs140313576		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:25268619_25268620insG								None (None upstream) : WSB1 (352486 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	25273475	25273475	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:25273475delT								None (None upstream) : WSB1 (347631 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	25770725	25770726	+	IGR	DEL	AG	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:25770725_25770726delAG								WSB1 (130080 upstream) : KSR1 (28310 downstream)																																			---	---	---	---
KSR1	8844	broad.mit.edu	37	17	25831445	25831445	+	Intron	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:25831445delG	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)														---	---	---	---
KSR1	8844	broad.mit.edu	37	17	25842929	25842929	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:25842929delT	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)														---	---	---	---
KSR1	8844	broad.mit.edu	37	17	25872713	25872714	+	Intron	INS	-	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:25872713_25872714insG	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)														---	---	---	---
KSR1	8844	broad.mit.edu	37	17	25932884	25932884	+	Intron	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:25932884delC	uc010crg.2	+						KSR1_uc002gzm.2_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)														---	---	---	---
NOS2	4843	broad.mit.edu	37	17	26177373	26177373	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:26177373delA	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)													---	---	---	---
NLK	51701	broad.mit.edu	37	17	26479592	26479592	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:26479592delA	uc010crj.2	+						NLK_uc010cri.1_Intron	NM_016231	NP_057315			nemo like kinase						intracellular protein kinase cascade|negative regulation of Wnt receptor signaling pathway|peptidyl-threonine phosphorylation|regulation of transcription, DNA-dependent|serine phosphorylation of STAT3 protein|transcription, DNA-dependent|transforming growth factor beta receptor signaling pathway|Wnt receptor signaling pathway	cytoplasm|nucleus	ATP binding|magnesium ion binding|MAP kinase activity|SH2 domain binding|transcription factor binding|ubiquitin protein ligase binding			ovary(1)|lung(1)|central_nervous_system(1)	3	all_lung(13;0.000343)|Lung NSC(42;0.00184)			UCEC - Uterine corpus endometrioid carcinoma (53;0.168)														---	---	---	---
NLK	51701	broad.mit.edu	37	17	26523191	26523191	+	3'UTR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:26523191delT	uc010crj.2	+	11					NLK_uc010cri.1_Intron	NM_016231	NP_057315			nemo like kinase						intracellular protein kinase cascade|negative regulation of Wnt receptor signaling pathway|peptidyl-threonine phosphorylation|regulation of transcription, DNA-dependent|serine phosphorylation of STAT3 protein|transcription, DNA-dependent|transforming growth factor beta receptor signaling pathway|Wnt receptor signaling pathway	cytoplasm|nucleus	ATP binding|magnesium ion binding|MAP kinase activity|SH2 domain binding|transcription factor binding|ubiquitin protein ligase binding			ovary(1)|lung(1)|central_nervous_system(1)	3	all_lung(13;0.000343)|Lung NSC(42;0.00184)			UCEC - Uterine corpus endometrioid carcinoma (53;0.168)														---	---	---	---
Unknown	0	broad.mit.edu	37	17	26537750	26537750	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:26537750delT								NLK (14348 upstream) : PYY2 (15839 downstream)																																			---	---	---	---
FLJ40504	284085	broad.mit.edu	37	17	26609219	26609219	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:26609219delA	uc002has.3	-							NM_173624	NP_775895			SubName: Full=Putative uncharacterized protein FLJ40504; SubName: Full=cDNA FLJ40504 fis, clone TESTI2045509, highly similar to KERATIN, TYPE I CYTOSKELETAL 18;												0	all_lung(13;0.000238)|Lung NSC(42;0.000789)			UCEC - Uterine corpus endometrioid carcinoma (53;0.155)														---	---	---	---
TNFAIP1	7126	broad.mit.edu	37	17	26664088	26664088	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:26664088delT	uc002hax.1	+						IFT20_uc002hau.1_5'Flank|IFT20_uc002hav.1_5'Flank|IFT20_uc002haw.1_5'Flank|IFT20_uc010wae.1_5'Flank|TNFAIP1_uc002hay.2_Intron|TNFAIP1_uc010waf.1_Intron	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)														---	---	---	---
SLC13A2	9058	broad.mit.edu	37	17	26817308	26817308	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:26817308delT	uc002hbh.2	+						SLC13A2_uc010wal.1_Intron|SLC13A2_uc010wam.1_Intron|SLC13A2_uc010wan.1_Intron|SLC13A2_uc010wao.1_Intron|SLC13A2_uc002hbi.2_Intron	NM_003984	NP_003975			solute carrier family 13, member 2 isoform b							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)													---	---	---	---
KIAA0100	9703	broad.mit.edu	37	17	26946487	26946488	+	Intron	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:26946487_26946488delAA	uc002hbu.2	-						KIAA0100_uc002hbt.2_Intron	NM_014680	NP_055495			hypothetical protein LOC9703 precursor							extracellular region				ovary(2)|breast(1)|skin(1)	4	Lung NSC(42;0.00431)																	---	---	---	---
KIAA0100	9703	broad.mit.edu	37	17	26959820	26959820	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:26959820delA	uc002hbu.2	-							NM_014680	NP_055495			hypothetical protein LOC9703 precursor							extracellular region				ovary(2)|breast(1)|skin(1)	4	Lung NSC(42;0.00431)																	---	---	---	---
KIAA0100	9703	broad.mit.edu	37	17	26962813	26962814	+	Intron	DEL	AT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:26962813_26962814delAT	uc002hbu.2	-							NM_014680	NP_055495			hypothetical protein LOC9703 precursor							extracellular region				ovary(2)|breast(1)|skin(1)	4	Lung NSC(42;0.00431)																	---	---	---	---
SDF2	6388	broad.mit.edu	37	17	26977401	26977401	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:26977401delA	uc002hbw.2	-						SDF2_uc002hbx.2_Intron	NM_006923	NP_008854			stromal cell-derived factor 2 precursor						protein glycosylation	extracellular space|membrane	dolichyl-phosphate-mannose-protein mannosyltransferase activity				0	Lung NSC(42;0.00431)																	---	---	---	---
SUPT6H	6830	broad.mit.edu	37	17	27000968	27000968	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:27000968delA	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)																	---	---	---	---
C17orf63	55731	broad.mit.edu	37	17	27153543	27153543	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:27153543delA	uc010wax.1	-						C17orf63_uc010way.1_Intron|C17orf63_uc002hcw.2_Intron	NM_018182	NP_060652			hypothetical protein LOC55731											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)															---	---	---	---
ERAL1	26284	broad.mit.edu	37	17	27186400	27186400	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:27186400delT	uc002hcy.1	+						ERAL1_uc002hcz.1_Intron|ERAL1_uc002hda.1_Intron|ERAL1_uc002hdb.1_Intron	NM_005702	NP_005693			Era-like 1						ribosomal small subunit assembly	mitochondrial inner membrane|mitochondrial matrix	GTP binding|ribosomal small subunit binding|rRNA binding			skin(1)	1	all_cancers(5;2.12e-15)|all_epithelial(6;3.44e-19)|Lung NSC(42;0.01)		Epithelial(11;1.12e-05)|all cancers(11;5.32e-05)|BRCA - Breast invasive adenocarcinoma(11;0.000272)|OV - Ovarian serous cystadenocarcinoma(11;0.105)															---	---	---	---
Unknown	0	broad.mit.edu	37	17	27710561	27710564	+	IGR	DEL	AAAA	-	-	rs78590471		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:27710561_27710564delAAAA								NUFIP2 (89395 upstream) : TAOK1 (7379 downstream)																																			---	---	---	---
TAOK1	57551	broad.mit.edu	37	17	27778450	27778450	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:27778450delT	uc002hdz.1	+						TAOK1_uc010wbe.1_Intron|TAOK1_uc010wbf.1_Intron	NM_020791	NP_065842			TAO kinase 1						mitotic prometaphase	cytosol|intracellular membrane-bounded organelle	ATP binding|protein serine/threonine kinase activity			upper_aerodigestive_tract(1)|lung(1)|central_nervous_system(1)|skin(1)	4			Colorectal(6;0.198)															---	---	---	---
TAOK1	57551	broad.mit.edu	37	17	27794299	27794299	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:27794299delT	uc002hdz.1	+						TAOK1_uc010wbe.1_Intron|TAOK1_uc010wbf.1_Intron	NM_020791	NP_065842			TAO kinase 1						mitotic prometaphase	cytosol|intracellular membrane-bounded organelle	ATP binding|protein serine/threonine kinase activity			upper_aerodigestive_tract(1)|lung(1)|central_nervous_system(1)|skin(1)	4			Colorectal(6;0.198)															---	---	---	---
TAOK1	57551	broad.mit.edu	37	17	27807408	27807410	+	In_Frame_Del	DEL	CTT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:27807408_27807410delCTT	uc002hdz.1	+	7	666_668	c.472_474delCTT	c.(472-474)CTTdel	p.L159del	TAOK1_uc010wbe.1_In_Frame_Del_p.L159del|TAOK1_uc010wbf.1_In_Frame_Del_p.L159del|TAOK1_uc002heb.1_5'UTR	NM_020791	NP_065842	Q7L7X3	TAOK1_HUMAN	TAO kinase 1	159	Protein kinase.				mitotic prometaphase	cytosol|intracellular membrane-bounded organelle	ATP binding|protein serine/threonine kinase activity			upper_aerodigestive_tract(1)|lung(1)|central_nervous_system(1)|skin(1)	4			Colorectal(6;0.198)															---	---	---	---
TAOK1	57551	broad.mit.edu	37	17	27871476	27871476	+	3'UTR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:27871476delA	uc002hdz.1	+	20					TAOK1_uc010wbe.1_3'UTR|TAOK1_uc010wbf.1_3'UTR	NM_020791	NP_065842			TAO kinase 1						mitotic prometaphase	cytosol|intracellular membrane-bounded organelle	ATP binding|protein serine/threonine kinase activity			upper_aerodigestive_tract(1)|lung(1)|central_nervous_system(1)|skin(1)	4			Colorectal(6;0.198)															---	---	---	---
SSH2	85464	broad.mit.edu	37	17	28047745	28047745	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-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	28348155	28348155	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:28348155delT	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																		---	---	---	---
BLMH	642	broad.mit.edu	37	17	28621007	28621007	+	5'Flank	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:28621007delG	uc002hez.1	-						BLMH_uc010wbn.1_5'Flank	NM_000386	NP_000377			bleomycin hydrolase						proteolysis	cytoplasm|nucleus	aminopeptidase activity|carboxypeptidase activity|cysteine-type endopeptidase activity|protein binding			ovary(1)	1																		---	---	---	---
SUZ12P	440423	broad.mit.edu	37	17	29096087	29096087	+	RNA	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:29096087delT	uc002hfn.1	+	6		c.1599delT			SUZ12P_uc002hfo.2_Intron|SUZ12P_uc002hfq.2_Intron					Homo sapiens cDNA clone IMAGE:5299523, containing frame-shift errors.												0																		---	---	---	---
ATAD5	79915	broad.mit.edu	37	17	29157795	29157798	+	5'Flank	DEL	CAAA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:29157795_29157798delCAAA	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)																---	---	---	---
ADAP2	55803	broad.mit.edu	37	17	29284439	29284439	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:29284439delT	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	29606104	29606105	+	Intron	INS	-	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:29606104_29606105insA	uc002hgg.2	+						NF1_uc002hgh.2_Intron|NF1_uc002hgi.1_Intron|NF1_uc010cso.2_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.?(3)		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	30287237	30287237	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:30287237delT	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								---	---	---	---
RHOT1	55288	broad.mit.edu	37	17	30550097	30550098	+	Intron	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:30550097_30550098delTT	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	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)																---	---	---	---
C17orf75	64149	broad.mit.edu	37	17	30666110	30666110	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:30666110delA	uc002hhg.2	-							NM_022344	NP_071739			hypothetical protein LOC64149						spermatogenesis					ovary(1)	1		Breast(31;0.116)|Ovarian(249;0.182)	BRCA - Breast invasive adenocarcinoma(9;0.239)															---	---	---	---
C17orf75	64149	broad.mit.edu	37	17	30667981	30667981	+	Intron	DEL	A	-	-	rs7501832		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:30667981delA	uc002hhg.2	-							NM_022344	NP_071739			hypothetical protein LOC64149						spermatogenesis					ovary(1)	1		Breast(31;0.116)|Ovarian(249;0.182)	BRCA - Breast invasive adenocarcinoma(9;0.239)															---	---	---	---
PSMD11	5717	broad.mit.edu	37	17	30773801	30773801	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:30773801delT	uc010cta.1	+						PSMD11_uc010wbz.1_Intron|PSMD11_uc002hhm.2_Intron	NM_002815	NP_002806			proteasome 26S non-ATPase subunit 11						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 complex	protein binding			ovary(1)	1		Breast(31;0.159)|Ovarian(249;0.182)	BRCA - Breast invasive adenocarcinoma(9;0.109)															---	---	---	---
MYO1D	4642	broad.mit.edu	37	17	30898024	30898025	+	Intron	INS	-	G	G	rs142636127	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:30898024_30898025insG	uc002hho.1	-							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)															---	---	---	---
MYO1D	4642	broad.mit.edu	37	17	31038671	31038671	+	Intron	DEL	A	-	-	rs112201977		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:31038671delA	uc002hho.1	-						MYO1D_uc002hhp.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)															---	---	---	---
MYO1D	4642	broad.mit.edu	37	17	31103177	31103177	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-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)															---	---	---	---
MYO1D	4642	broad.mit.edu	37	17	31196237	31196237	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:31196237delA	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)															---	---	---	---
Unknown	0	broad.mit.edu	37	17	31275023	31275024	+	IGR	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:31275023_31275024delTT								TMEM98 (6358 upstream) : SPACA3 (43858 downstream)																																			---	---	---	---
UNC45B	146862	broad.mit.edu	37	17	33501869	33501870	+	Intron	DEL	AG	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:33501869_33501870delAG	uc002hja.2	+						UNC45B_uc002hjb.2_Intron|UNC45B_uc002hjc.2_Intron|UNC45B_uc010cto.2_Intron	NM_173167	NP_775259			cardiomyopathy associated 4 isoform 1						cell differentiation|muscle organ development	cytosol	binding			ovary(3)|central_nervous_system(2)|breast(1)	6		Ovarian(249;0.17)																---	---	---	---
AMAC1	146861	broad.mit.edu	37	17	33523116	33523116	+	5'Flank	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:33523116delT	uc002hjd.2	-							NM_152462	NP_689675			acyl-malonyl condensing enzyme 1							integral to membrane					0				BRCA - Breast invasive adenocarcinoma(366;0.0917)														---	---	---	---
Unknown	0	broad.mit.edu	37	17	34291560	34291560	+	IGR	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:34291560delG								LYZL6 (20889 upstream) : CCL16 (11976 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	34818776	34818777	+	IGR	DEL	AA	-	-	rs71157602		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:34818776_34818777delAA								TBC1D3G (10673 upstream) : ZNHIT3 (23696 downstream)																																			---	---	---	---
MRM1	79922	broad.mit.edu	37	17	34964978	34964978	+	3'UTR	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:34964978delG	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	35081788	35081788	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:35081788delT								MRM1 (116382 upstream) : LHX1 (212711 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	35081797	35081799	+	IGR	DEL	TTA	-	-	rs7220157	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:35081797_35081799delTTA								MRM1 (116391 upstream) : LHX1 (212700 downstream)																																			---	---	---	---
AATF	26574	broad.mit.edu	37	17	35346372	35346372	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-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	35523880	35523880	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:35523880delT	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	35574827	35574827	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:35574827delA	uc002hnm.2	-						ACACA_uc002hnk.2_Intron|ACACA_uc002hnl.2_Intron|ACACA_uc002hnn.2_Intron|ACACA_uc002hno.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	35642051	35642051	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:35642051delA	uc002hnm.2	-						ACACA_uc002hnk.2_Intron|ACACA_uc002hnl.2_Intron|ACACA_uc002hnn.2_Intron|ACACA_uc002hno.2_Intron|ACACA_uc010cuz.2_Intron|ACACA_uc002hnq.2_Intron|ACACA_uc002hnp.1_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	35686900	35686900	+	Intron	DEL	A	-	-	rs112617527		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:35686900delA	uc002hnm.2	-						ACACA_uc002hnn.2_Intron|ACACA_uc002hno.2_Intron|ACACA_uc010cuz.2_Intron|ACACA_uc002hnq.2_Intron|ACACA_uc002hnp.1_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)													---	---	---	---
DUSP14	11072	broad.mit.edu	37	17	35862296	35862296	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:35862296delT	uc002hnx.2	+						DUSP14_uc002hny.2_Intron	NM_007026	NP_008957			dual specificity phosphatase 14								MAP kinase tyrosine/serine/threonine phosphatase activity|protein tyrosine phosphatase activity				0		Breast(25;0.00637)|Ovarian(249;0.15)																---	---	---	---
DUSP14	11072	broad.mit.edu	37	17	35872185	35872185	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:35872185delA	uc002hnx.2	+						DUSP14_uc002hny.2_Intron|DUSP14_uc002hnz.2_Intron	NM_007026	NP_008957			dual specificity phosphatase 14								MAP kinase tyrosine/serine/threonine phosphatase activity|protein tyrosine phosphatase activity				0		Breast(25;0.00637)|Ovarian(249;0.15)																---	---	---	---
DDX52	11056	broad.mit.edu	37	17	35985898	35985899	+	Intron	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:35985898_35985899delAA	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	36403151	36403151	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:36403151delT	uc002hpx.2	-											Homo sapiens cDNA FLJ43844 fis, clone TESTI4006308, highly  similar to Puromycin-sensitive aminopeptidase (EC 3.4.11.-).																														---	---	---	---
MRPL45	84311	broad.mit.edu	37	17	36462377	36462380	+	Intron	DEL	AAAA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:36462377_36462380delAAAA	uc002hpy.2	+							NM_032351	NP_115727			mitochondrial ribosomal protein L45 precursor						intracellular protein transport|translation	mitochondrial inner membrane presequence translocase complex|ribosome	P-P-bond-hydrolysis-driven protein transmembrane transporter activity|structural constituent of ribosome				0	Breast(7;2.97e-12)	Breast(25;0.0101)|Ovarian(249;0.15)																---	---	---	---
SRCIN1	80725	broad.mit.edu	37	17	36700783	36700783	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:36700783delA	uc002hqd.2	-						SRCIN1_uc002hqf.1_Intron|SRCIN1_uc002hqe.2_Intron	NM_025248	NP_079524			SNAP25-interacting protein						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																		---	---	---	---
CWC25	54883	broad.mit.edu	37	17	36964634	36964635	+	Intron	INS	-	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:36964634_36964635insA	uc002hqu.2	-						CWC25_uc010wdv.1_Intron|CWC25_uc010wdw.1_Intron|CWC25_uc010wdx.1_Intron	NM_017748	NP_060218			coiled-coil domain containing 49												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	17	37004147	37004147	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:37004147delA								C17orf98 (6505 upstream) : RPL23 (2174 downstream)																																			---	---	---	---
FBXO47	494188	broad.mit.edu	37	17	37113661	37113662	+	Intron	INS	-	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:37113661_37113662insA	uc002hrc.2	-							NM_001008777	NP_001008777			F-box protein 47												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	17	37211082	37211082	+	5'Flank	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:37211082delA	uc002hre.1	+											Homo sapiens cDNA FLJ37796 fis, clone BRSSN1000092.																														---	---	---	---
PLXDC1	57125	broad.mit.edu	37	17	37222844	37222846	+	3'UTR	DEL	TTT	-	-	rs74701941		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:37222844_37222846delTTT	uc002hrg.2	-	14					uc002hre.1_Intron|uc002hrf.1_Intron|PLXDC1_uc010cvr.1_3'UTR|PLXDC1_uc002hrh.2_RNA|PLXDC1_uc002hri.2_RNA|PLXDC1_uc002hrj.1_RNA|PLXDC1_uc002hrk.1_RNA	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																		---	---	---	---
LOC90110	90110	broad.mit.edu	37	17	37413249	37413249	+	5'Flank	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:37413249delT	uc010wec.1	-							NR_026953				Homo sapiens mRNA; cDNA DKFZp564O2364 (from clone DKFZp564O2364).												0																		---	---	---	---
MED1	5469	broad.mit.edu	37	17	37597110	37597110	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-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)			---	---	---	---
STARD3	10948	broad.mit.edu	37	17	37818600	37818600	+	Intron	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:37818600delG	uc002hsd.2	+						STARD3_uc010weh.1_Intron|STARD3_uc002hse.2_Intron|STARD3_uc010wei.1_Intron|STARD3_uc002hsf.2_Intron|STARD3_uc002hsg.2_Intron|TCAP_uc002hsh.2_5'Flank	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)															---	---	---	---
C17orf37	84299	broad.mit.edu	37	17	37889403	37889403	+	5'Flank	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:37889403delT	uc002hsq.2	-							NM_032339	NP_115715			hypothetical protein LOC84299						cell redox homeostasis	cytosol|membrane	selenium binding				0	all_cancers(6;1.06e-93)|all_epithelial(6;2.33e-113)|Breast(7;9.37e-100)|Lung NSC(9;9.76e-10)|all_lung(9;5.34e-09)|Colorectal(19;0.000442)|Esophageal squamous(10;0.052)		UCEC - Uterine corpus endometrioid carcinoma (11;0.000126)|Epithelial(3;3.72e-63)|all cancers(3;1.87e-56)|BRCA - Breast invasive adenocarcinoma(8;6.8e-45)|STAD - Stomach adenocarcinoma(3;1.43e-12)|Colorectal(5;6.23e-08)|COAD - Colon adenocarcinoma(5;8.58e-06)|Lung(15;0.00193)|LUAD - Lung adenocarcinoma(14;0.0664)|OV - Ovarian serous cystadenocarcinoma(8;0.0917)|LUSC - Lung squamous cell carcinoma(15;0.171)															---	---	---	---
THRA	7067	broad.mit.edu	37	17	38243562	38243563	+	Intron	DEL	AC	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:38243562_38243563delAC	uc002htw.2	+						THRA_uc010cwp.1_Intron|THRA_uc002htv.2_Intron|THRA_uc002htx.2_Intron	NM_003250	NP_003241			thyroid hormone receptor, alpha isoform 2						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)													---	---	---	---
MSL1	339287	broad.mit.edu	37	17	38276192	38276192	+	5'Flank	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:38276192delA	uc002hua.3	+							NM_001012241	NP_001012241			hampin						histone H4-K16 acetylation	MSL complex					0																		---	---	---	---
CASC3	22794	broad.mit.edu	37	17	38319330	38319330	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:38319330delA	uc010cwt.1	+						CASC3_uc010cws.1_Intron|CASC3_uc002hue.2_Intron	NM_007359	NP_031385			metastatic lymph node 51						mRNA processing|mRNA transport|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay|regulation of translation|response to stress|RNA splicing	exon-exon junction complex|nuclear speck|perinuclear region of cytoplasm	identical protein binding|RNA binding|ubiquitin protein ligase binding			ovary(1)	1																		---	---	---	---
WIPF2	147179	broad.mit.edu	37	17	38373062	38373064	+	5'Flank	DEL	AAA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:38373062_38373064delAAA	uc002hug.1	+						WIPF2_uc010cwv.1_5'Flank|WIPF2_uc002huh.1_5'Flank|WIPF2_uc010cww.1_5'Flank|WIPF2_uc002hui.1_5'Flank|WIPF2_uc010cwx.1_5'Flank|WIPF2_uc010cwy.1_5'Flank	NM_133264	NP_573571			WIRE protein							cytoplasm|cytoskeleton	actin binding			upper_aerodigestive_tract(1)|ovary(1)|pancreas(1)	3															HNSCC(43;0.11)			---	---	---	---
KRT28	162605	broad.mit.edu	37	17	38958592	38958593	+	5'Flank	INS	-	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:38958592_38958593insG	uc002hvh.1	-							NM_181535	NP_853513			keratin 25D							cytoplasm|intermediate filament	structural molecule activity			ovary(1)	1		Breast(137;0.000301)																---	---	---	---
Unknown	0	broad.mit.edu	37	17	39102882	39102882	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:39102882delT								KRT23 (9046 upstream) : KRT39 (11787 downstream)																																			---	---	---	---
KRTAP3-2	83897	broad.mit.edu	37	17	39155659	39155659	+	3'UTR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:39155659delT	uc002hvs.2	-	1						NM_031959	NP_114165			keratin associated protein 3.2							keratin filament	structural molecule activity				0		Breast(137;0.00043)																---	---	---	---
HAP1	9001	broad.mit.edu	37	17	39884413	39884414	+	Intron	INS	-	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:39884413_39884414insG	uc002hxm.1	-						JUP_uc010wfs.1_Intron|HAP1_uc002hxn.1_Intron|HAP1_uc002hxo.1_Intron|HAP1_uc002hxp.1_Intron	NM_177977	NP_817084			huntingtin-associated protein 1 isoform 2						brain development|protein localization|synaptic transmission	actin cytoskeleton	protein binding			ovary(2)	2		Breast(137;0.000162)	BRCA - Breast invasive adenocarcinoma(4;0.0677)															---	---	---	---
KLHL10	317719	broad.mit.edu	37	17	39994908	39994908	+	Intron	DEL	T	-	-	rs67825523		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:39994908delT	uc010cxr.2	+						NT5C3L_uc002hyb.3_5'Flank|NT5C3L_uc002hyc.3_5'Flank|NT5C3L_uc002hyd.3_5'Flank|NT5C3L_uc002hxy.3_5'Flank|NT5C3L_uc002hxz.3_5'Flank|NT5C3L_uc002hya.3_5'Flank|KLHL10_uc010wfv.1_Intron|KLHL10_uc010wfw.1_Intron	NM_152467	NP_689680			kelch-like 10							cytoplasm				ovary(1)|lung(1)|breast(1)|central_nervous_system(1)	4		Breast(137;0.000162)																---	---	---	---
KLHL11	55175	broad.mit.edu	37	17	40011270	40011271	+	Frame_Shift_Del	DEL	TC	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:40011270_40011271delTC	uc002hyf.1	-	2	854_855	c.848_849delGA	c.(847-849)AGAfs	p.R283fs		NM_018143	NP_060613	Q9NVR0	KLH11_HUMAN	kelch-like 11 precursor	283	BACK.					extracellular region					0		Breast(137;0.00156)																---	---	---	---
ACLY	47	broad.mit.edu	37	17	40024854	40024855	+	Intron	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:40024854_40024855delAA	uc002hyg.2	-						ACLY_uc002hyh.2_Intron|ACLY_uc002hyi.2_Intron|ACLY_uc010wfx.1_Intron|ACLY_uc010wfy.1_Intron	NM_001096	NP_001087			ATP citrate lyase isoform 1						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)																---	---	---	---
ACLY	47	broad.mit.edu	37	17	40057216	40057216	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:40057216delT	uc002hyg.2	-						ACLY_uc002hyh.2_Intron|ACLY_uc002hyi.2_Intron|ACLY_uc010wfx.1_Intron|ACLY_uc010wfy.1_Intron	NM_001096	NP_001087			ATP citrate lyase isoform 1						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)																---	---	---	---
TTC25	83538	broad.mit.edu	37	17	40104924	40104924	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:40104924delT	uc002hyj.3	+						TTC25_uc010cxt.2_Intron	NM_031421	NP_113609			tetratricopeptide repeat domain 25							cytoplasm	protein binding			ovary(1)	1		all_cancers(22;8.16e-06)|Breast(137;0.000143)|all_epithelial(22;0.000236)																---	---	---	---
Unknown	0	broad.mit.edu	37	17	40236808	40236808	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:40236808delT								NKIRAS2 (59154 upstream) : DHX58 (16614 downstream)																																			---	---	---	---
STAT5B	6777	broad.mit.edu	37	17	40419977	40419980	+	Intron	DEL	AAAA	-	-	rs74539890		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:40419977_40419980delAAAA	uc002hzh.2	-						STAT5B_uc002hzi.3_Intron	NM_012448	NP_036580			signal transducer and activator of transcription						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)													---	---	---	---
STAT5A	6776	broad.mit.edu	37	17	40457521	40457521	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:40457521delA	uc002hzj.1	+						STAT5A_uc010cya.1_Intron|STAT5A_uc010cyb.1_Intron|STAT5A_uc010cyc.1_Intron|STAT5A_uc010cyd.1_5'Flank|STAT5A_uc010cye.1_5'Flank	NM_003152	NP_003143			signal transducer and activator of transcription						2-oxoglutarate metabolic process|allantoin metabolic process|citrate metabolic process|creatine metabolic process|creatinine metabolic process|fatty acid metabolic process|isoleucine metabolic process|oxaloacetate metabolic process|succinate metabolic process|taurine metabolic process|valine metabolic process	cytosol|nucleoplasm	calcium ion binding|DNA binding|protein binding|sequence-specific DNA binding transcription factor activity			lung(1)	1		all_cancers(22;1.56e-06)|all_epithelial(22;3.17e-05)|Breast(137;0.000143)		BRCA - Breast invasive adenocarcinoma(366;0.128)														---	---	---	---
Unknown	0	broad.mit.edu	37	17	40905438	40905438	+	IGR	DEL	A	-	-	rs150921188	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:40905438delA								EZH1 (8367 upstream) : LOC100190938 (86 downstream)																																			---	---	---	---
LOC388387	388387	broad.mit.edu	37	17	41034618	41034619	+	Intron	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:41034618_41034619delAA	uc010whe.1	-						LOC388387_uc002ibz.2_Intron|LOC388387_uc002iby.2_Intron|LOC388387_uc002ica.2_Intron					SubName: Full=cDNA FLJ57415;												0																		---	---	---	---
DHX8	1659	broad.mit.edu	37	17	41565341	41565341	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:41565341delA	uc002idu.1	+						DHX8_uc010wif.1_Intron|DHX8_uc010wig.1_Intron	NM_004941	NP_004932			DEAH (Asp-Glu-Ala-His) box polypeptide 8							catalytic step 2 spliceosome	ATP binding|ATP-dependent RNA helicase activity|protein binding|RNA binding			ovary(2)|kidney(1)|pancreas(1)	4		Breast(137;0.00908)		BRCA - Breast invasive adenocarcinoma(366;0.08)														---	---	---	---
ETV4	2118	broad.mit.edu	37	17	41609865	41609865	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:41609865delA	uc002idw.2	-						ETV4_uc002idv.2_5'Flank|ETV4_uc010wih.1_Intron|ETV4_uc010czh.2_Intron|ETV4_uc010wii.1_Intron|ETV4_uc002idx.2_Intron|ETV4_uc010wij.1_Intron	NM_001986	NP_001977			ets variant gene 4 (E1A enhancer binding						positive regulation of transcription, DNA-dependent	nucleolus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity		EWSR1/ETV4(6)	bone(4)|soft_tissue(2)|ovary(1)	7		Breast(137;0.00908)		BRCA - Breast invasive adenocarcinoma(366;0.0798)				T	EWSR1|TMPRSS2|DDX5|KLK2|CANT1	Ewing sarcoma|Prostate carcinoma								---	---	---	---
Unknown	0	broad.mit.edu	37	17	41703568	41703568	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:41703568delT								ETV4 (79806 upstream) : MEOX1 (14199 downstream)																																			---	---	---	---
MEOX1	4222	broad.mit.edu	37	17	41739508	41739508	+	5'Flank	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:41739508delT	uc002idz.2	-						MEOX1_uc002iea.2_5'Flank|MEOX1_uc002ieb.2_5'Flank	NM_004527	NP_004518			mesenchyme homeobox 1 isoform 1							nucleus	sequence-specific DNA binding				0		Breast(137;0.00908)		BRCA - Breast invasive adenocarcinoma(366;0.0753)														---	---	---	---
PYY	5697	broad.mit.edu	37	17	42075274	42075274	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:42075274delA	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)														---	---	---	---
LSM12	124801	broad.mit.edu	37	17	42136919	42136920	+	Intron	INS	-	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:42136919_42136920insA	uc002iev.2	-						LSM12_uc010wit.1_Intron|LSM12_uc002iew.1_Intron	NM_152344	NP_689557			LSM12 homolog								protein binding				0		Breast(137;0.0313)|Prostate(33;0.0861)		BRCA - Breast invasive adenocarcinoma(366;0.115)														---	---	---	---
RUNDC3A	10900	broad.mit.edu	37	17	42392043	42392047	+	Intron	DEL	GGGGG	-	-	rs67278675		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:42392043_42392047delGGGGG	uc002igl.3	+						RUNDC3A_uc002igi.2_Intron|RUNDC3A_uc002igj.2_Intron|RUNDC3A_uc002igk.2_Intron	NM_001144825	NP_001138297			RUN domain containing 3A isoform 1						small GTPase mediated signal transduction		small GTPase regulator activity				0		Prostate(33;0.0233)		BRCA - Breast invasive adenocarcinoma(366;0.189)														---	---	---	---
ITGA2B	3674	broad.mit.edu	37	17	42459669	42459669	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:42459669delT	uc002igt.1	-						ITGA2B_uc002igu.1_5'Flank	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)													---	---	---	---
GPATCH8	23131	broad.mit.edu	37	17	42529659	42529659	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:42529659delA	uc002igw.1	-						GPATCH8_uc002igv.1_Intron|GPATCH8_uc010wiz.1_Intron	NM_001002909	NP_001002909			G patch domain containing 8							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)														---	---	---	---
GPATCH8	23131	broad.mit.edu	37	17	42553531	42553531	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:42553531delT	uc002igw.1	-						GPATCH8_uc010wiz.1_Intron	NM_001002909	NP_001002909			G patch domain containing 8							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)														---	---	---	---
Unknown	0	broad.mit.edu	37	17	42599249	42599251	+	IGR	DEL	TTG	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:42599249_42599251delTTG								GPATCH8 (18447 upstream) : FZD2 (35674 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	42630297	42630298	+	IGR	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:42630297_42630298delTT								GPATCH8 (49495 upstream) : FZD2 (4627 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	42678089	42678089	+	IGR	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:42678089delC								FZD2 (41182 upstream) : C17orf104 (55893 downstream)																																			---	---	---	---
CCDC43	124808	broad.mit.edu	37	17	42756253	42756253	+	Frame_Shift_Del	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-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)																---	---	---	---
DBF4B	80174	broad.mit.edu	37	17	42818501	42818501	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:42818501delA	uc002ihf.2	+						DBF4B_uc010wjb.1_Intron|DBF4B_uc002ihe.2_Intron|DBF4B_uc010wjc.1_Intron	NM_145663	NP_663696			DBF4 homolog B isoform 1						cell cycle	nucleus	nucleic acid binding|zinc ion binding				0		Prostate(33;0.0322)																---	---	---	---
GFAP	2670	broad.mit.edu	37	17	42994176	42994176	+	5'Flank	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:42994176delC	uc002ihq.2	-						GFAP_uc002ihr.2_5'Flank|GFAP_uc010wjg.1_5'Flank	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)																---	---	---	---
Unknown	0	broad.mit.edu	37	17	43297126	43297126	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:43297126delA	uc002iil.3	-						uc002iim.2_Intron|FMNL1_uc002iin.2_5'Flank					Homo sapiens hypothetical protein LOC339192, mRNA (cDNA clone IMAGE:4638737), partial cds.																														---	---	---	---
KIAA1267	284058	broad.mit.edu	37	17	44226115	44226115	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:44226115delT	uc002ikb.2	-						KIAA1267_uc002ikc.2_Intron|KIAA1267_uc002ikd.2_Intron|KIAA1267_uc010dav.2_Intron	NM_015443	NP_056258			hypothetical protein LOC284058							MLL1 complex	protein binding			skin(2)	2		Melanoma(429;0.211)																---	---	---	---
KIAA1267	284058	broad.mit.edu	37	17	44243580	44243582	+	Intron	DEL	AAA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:44243580_44243582delAAA	uc002ikb.2	-						KIAA1267_uc002ikc.2_Intron|KIAA1267_uc002ikd.2_Intron|KIAA1267_uc010dav.2_Intron	NM_015443	NP_056258			hypothetical protein LOC284058							MLL1 complex	protein binding			skin(2)	2		Melanoma(429;0.211)																---	---	---	---
KIAA1267	284058	broad.mit.edu	37	17	44244422	44244423	+	Intron	DEL	AA	-	-	rs66866969		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:44244422_44244423delAA	uc002ikb.2	-						KIAA1267_uc002ikc.2_Intron|KIAA1267_uc002ikd.2_Intron|KIAA1267_uc010dav.2_Intron	NM_015443	NP_056258			hypothetical protein LOC284058							MLL1 complex	protein binding			skin(2)	2		Melanoma(429;0.211)																---	---	---	---
KIAA1267	284058	broad.mit.edu	37	17	44264270	44264271	+	Intron	DEL	TT	-	-	rs68051473		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:44264270_44264271delTT	uc002ikc.2	-						KIAA1267_uc002ikd.2_Intron|KIAA1267_uc010dav.2_Intron	NM_015443	NP_056258			hypothetical protein LOC284058							MLL1 complex	protein binding			skin(2)	2		Melanoma(429;0.211)																---	---	---	---
Unknown	0	broad.mit.edu	37	17	44333777	44333777	+	IGR	DEL	A	-	-	rs72176661		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:44333777delA								KIAA1267 (31060 upstream) : ARL17B (30086 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	44448142	44448144	+	IGR	DEL	AAA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:44448142_44448144delAAA								ARL17A (8979 upstream) : LRRC37A2 (141932 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	44569115	44569115	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:44569115delT								ARL17A (129952 upstream) : LRRC37A2 (20961 downstream)																																			---	---	---	---
NSF	4905	broad.mit.edu	37	17	44821988	44821988	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:44821988delA	uc002iku.2	+						NSF_uc010wke.1_Intron|NSF_uc010wkf.1_Intron|NSF_uc010wkg.1_Intron	NM_006178	NP_006169			vesicle-fusing ATPase						protein transport|synaptic transmission	cytosol	ATP binding|metal ion binding			ovary(1)	1		Melanoma(429;0.203)	BRCA - Breast invasive adenocarcinoma(9;0.0257)	BRCA - Breast invasive adenocarcinoma(366;0.241)														---	---	---	---
WNT9B	7484	broad.mit.edu	37	17	44933855	44933855	+	Intron	DEL	T	-	-	rs67667407		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:44933855delT	uc002ikw.1	+						WNT9B_uc002ikx.1_Intron	NM_003396	NP_003387			wingless-type MMTV integration site family,						anterior/posterior pattern formation|axis specification|branching involved in ureteric bud morphogenesis|canonical Wnt receptor signaling pathway|cell-cell signaling|cellular response to retinoic acid|collecting duct development|cornea development in camera-type eye|endoderm development|establishment of planar polarity involved in nephron morphogenesis|kidney rudiment formation|male genitalia development|mesonephric duct formation|metanephric tubule development|neuron differentiation|palate development|regulation of mesenchymal to epithelial transition involved in metanephros morphogenesis|uterus morphogenesis|Wnt receptor signaling pathway, calcium modulating pathway|Wnt receptor signaling pathway, planar cell polarity pathway	extracellular space|plasma membrane|proteinaceous extracellular matrix	extracellular matrix structural constituent|G-protein-coupled receptor binding			lung(2)	2			BRCA - Breast invasive adenocarcinoma(9;0.0257)															---	---	---	---
Unknown	0	broad.mit.edu	37	17	45701746	45701747	+	IGR	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:45701746_45701747delAA								NPEPPS (1105 upstream) : KPNB1 (25528 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	45708979	45708979	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:45708979delA								NPEPPS (8338 upstream) : KPNB1 (18296 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	45846340	45846340	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:45846340delA								TBX21 (22855 upstream) : OSBPL7 (38393 downstream)																																			---	---	---	---
CBX1	10951	broad.mit.edu	37	17	46155562	46155562	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:46155562delT	uc002ind.3	-						CBX1_uc002ine.3_Intron	NM_006807	NP_006798			heterochromatin protein 1-beta							nuclear heterochromatin|nucleoplasm|spindle	chromatin binding|enzyme binding				0																		---	---	---	---
SKAP1	8631	broad.mit.edu	37	17	46438216	46438216	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:46438216delT	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																		---	---	---	---
Unknown	0	broad.mit.edu	37	17	46718726	46718727	+	IGR	DEL	AC	-	-	rs140588521		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:46718726_46718727delAC								MIR196A1 (8805 upstream) : PRAC (80365 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	46761000	46761000	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:46761000delA								MIR196A1 (51079 upstream) : PRAC (38092 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	46783370	46783370	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:46783370delT								MIR196A1 (73449 upstream) : PRAC (15722 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	46952062	46952062	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:46952062delA								CALCOCO2 (9834 upstream) : ATP5G1 (18086 downstream)																																			---	---	---	---
UBE2Z	65264	broad.mit.edu	37	17	47000129	47000130	+	Intron	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:47000129_47000130delAA	uc002ioi.2	+							NM_023079	NP_075567			ubiquitin-conjugating enzyme E2Z						apoptosis	cytoplasm|nucleus	ATP binding|ubiquitin-protein ligase activity				0																		---	---	---	---
IGF2BP1	10642	broad.mit.edu	37	17	47109820	47109820	+	Intron	DEL	T	-	-	rs11334150		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:47109820delT	uc002iom.2	+						IGF2BP1_uc010dbj.2_Intron	NM_006546	NP_006537			insulin-like growth factor 2 mRNA binding						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																OREG0024529	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
SPOP	8405	broad.mit.edu	37	17	47696765	47696765	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:47696765delA	uc010dbk.2	-						SPOP_uc002ipb.2_Intron|SPOP_uc002ipc.2_Intron|SPOP_uc002ipd.2_Intron|SPOP_uc002ipe.2_Intron|SPOP_uc002ipf.2_Intron|SPOP_uc002ipg.2_Intron	NM_003563	NP_003554			speckle-type POZ protein						mRNA processing	nucleus	protein binding			prostate(2)|ovary(2)|lung(2)	6															Prostate(2;0.17)			---	---	---	---
SPOP	8405	broad.mit.edu	37	17	47753382	47753382	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:47753382delA	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)			---	---	---	---
Unknown	0	broad.mit.edu	37	17	47966867	47966868	+	IGR	DEL	GT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:47966867_47966868delGT								TAC4 (41488 upstream) : DLX4 (79694 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	48026282	48026282	+	IGR	DEL	G	-	-	rs147308847	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:48026282delG								TAC4 (100903 upstream) : DLX4 (20280 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	48041167	48041168	+	IGR	DEL	GC	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:48041167_48041168delGC								TAC4 (115788 upstream) : DLX4 (5394 downstream)																																			---	---	---	---
ITGA3	3675	broad.mit.edu	37	17	48141455	48141455	+	Frame_Shift_Del	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:48141455delC	uc010dbl.2	+	2	685	c.221delC	c.(220-222)GCCfs	p.A74fs	ITGA3_uc010dbm.2_Frame_Shift_Del_p.A74fs	NM_002204	NP_002195	P26006	ITA3_HUMAN	integrin alpha 3 isoform a precursor	74	FG-GAP 1.|Extracellular (Potential).				blood coagulation|cell-matrix adhesion|integrin-mediated signaling pathway|leukocyte migration	cell surface|integrin complex	protein binding|receptor activity			ovary(2)|pancreas(1)	3																		---	---	---	---
COL1A1	1277	broad.mit.edu	37	17	48281773	48281773	+	5'Flank	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:48281773delA	uc002iqm.2	-							NM_000088	NP_000079			alpha 1 type I collagen preproprotein						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						---	---	---	---
EME1	146956	broad.mit.edu	37	17	48455122	48455122	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:48455122delT	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					---	---	---	---
ACSF2	80221	broad.mit.edu	37	17	48500993	48500994	+	5'Flank	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:48500993_48500994delTT	uc002iqu.2	+						ACSF2_uc010wml.1_5'Flank|ACSF2_uc010wmm.1_5'Flank|ACSF2_uc010wmn.1_5'Flank|ACSF2_uc010wmo.1_5'Flank	NM_025149	NP_079425			acyl-CoA synthetase family member 2 precursor						fatty acid metabolic process	mitochondrion	ATP binding|ligase activity				0	Breast(11;1.93e-18)		BRCA - Breast invasive adenocarcinoma(22;1.55e-09)															---	---	---	---
ACSF2	80221	broad.mit.edu	37	17	48520276	48520276	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:48520276delT	uc002iqu.2	+						ACSF2_uc010wml.1_Intron|ACSF2_uc010wmm.1_Intron|ACSF2_uc010wmn.1_Intron|ACSF2_uc010wmo.1_Intron	NM_025149	NP_079425			acyl-CoA synthetase family member 2 precursor						fatty acid metabolic process	mitochondrion	ATP binding|ligase activity				0	Breast(11;1.93e-18)		BRCA - Breast invasive adenocarcinoma(22;1.55e-09)															---	---	---	---
ABCC3	8714	broad.mit.edu	37	17	48721208	48721208	+	Intron	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:48721208delG	uc002isl.2	+						ABCC3_uc002isk.3_Intron	NM_003786	NP_003777			ATP-binding cassette, sub-family C, member 3						bile acid metabolic process	integral to plasma membrane|membrane fraction	ATP binding|bile acid-exporting ATPase activity|organic anion transmembrane transporter activity			skin(3)|central_nervous_system(1)	4			BRCA - Breast invasive adenocarcinoma(22;3.05e-09)		Glibenclamide(DB01016)													---	---	---	---
ANKRD40	91369	broad.mit.edu	37	17	48770712	48770712	+	3'UTR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:48770712delA	uc002iso.2	-	5						NM_052855	NP_443087			ankyrin repeat domain 40												0			BRCA - Breast invasive adenocarcinoma(22;2.03e-09)															---	---	---	---
LUC7L3	51747	broad.mit.edu	37	17	48817654	48817654	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:48817654delT	uc002isr.2	+						LUC7L3_uc002isp.1_Intron|LUC7L3_uc010wmw.1_Intron|LUC7L3_uc002isq.2_Intron|LUC7L3_uc002iss.2_Intron	NM_006107	NP_006098			LUC7-like 3						apoptosis|mRNA processing|response to stress|RNA splicing	focal adhesion|nuclear speck	DNA binding|mRNA binding|protein binding				0																		---	---	---	---
SPAG9	9043	broad.mit.edu	37	17	49042424	49042424	+	3'UTR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:49042424delT	uc002itc.2	-	30					SPAG9_uc002itb.2_3'UTR|SPAG9_uc002itd.2_3'UTR|SPAG9_uc002ita.2_3'UTR	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)															---	---	---	---
UTP18	51096	broad.mit.edu	37	17	49350960	49350961	+	Intron	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:49350960_49350961delTT	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	49745677	49745678	+	Intron	DEL	AG	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:49745677_49745678delAG	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	49991617	49991617	+	Intron	DEL	A	-	-	rs11298090		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:49991617delA	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	50190762	50190762	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:50190762delA	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	51187047	51187047	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:51187047delA								CA10 (949670 upstream) : KIF2B (713192 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	51201366	51201366	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:51201366delA								CA10 (963989 upstream) : KIF2B (698873 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	51238548	51238548	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:51238548delT								None (None upstream) : KIF2B (661691 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	51668868	51668868	+	IGR	DEL	A	-	-	rs11868261		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:51668868delA								None (None upstream) : KIF2B (231371 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	51682782	51682783	+	IGR	DEL	TG	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:51682782_51682783delTG								None (None upstream) : KIF2B (217456 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	52559788	52559789	+	IGR	INS	-	A	A	rs74943775		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:52559788_52559789insA								KIF2B (657215 upstream) : TOM1L1 (418263 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	52936517	52936517	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:52936517delA								None (None upstream) : TOM1L1 (41535 downstream)																																			---	---	---	---
TOM1L1	10040	broad.mit.edu	37	17	52986656	52986656	+	Intron	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:52986656delC	uc002iud.2	+						TOM1L1_uc002iub.2_Intron|TOM1L1_uc002iuc.2_Intron|TOM1L1_uc010dca.1_Intron|TOM1L1_uc010wnb.1_Intron|TOM1L1_uc010wnc.1_Intron|TOM1L1_uc010dbz.2_Intron|TOM1L1_uc010wnd.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																		---	---	---	---
STXBP4	252983	broad.mit.edu	37	17	53076905	53076905	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:53076905delT	uc002iuf.1	+						STXBP4_uc010dcc.1_Intron|STXBP4_uc010dcd.1_Intron	NM_178509	NP_848604			syntaxin binding protein 4							cytoplasm	calcium ion binding			ovary(1)	1																		---	---	---	---
STXBP4	252983	broad.mit.edu	37	17	53219998	53219998	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:53219998delA	uc002iuf.1	+						STXBP4_uc010dcd.1_Intron	NM_178509	NP_848604			syntaxin binding protein 4							cytoplasm	calcium ion binding			ovary(1)	1																		---	---	---	---
MMD	23531	broad.mit.edu	37	17	53485194	53485194	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:53485194delA	uc002iui.2	-							NM_012329	NP_036461			monocyte to macrophage						cytolysis	integral to plasma membrane|late endosome membrane|lysosomal membrane|membrane fraction	receptor activity				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	17	53708909	53708909	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:53708909delT								MMD (209568 upstream) : TMEM100 (88081 downstream)																																			---	---	---	---
TMEM100	55273	broad.mit.edu	37	17	53800288	53800288	+	5'Flank	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:53800288delT	uc002iuj.3	-						TMEM100_uc002iuk.3_Intron	NM_018286	NP_060756			transmembrane protein 100							integral to membrane					0																		---	---	---	---
Unknown	0	broad.mit.edu	37	17	54031990	54031990	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:54031990delT								PCTP (177243 upstream) : ANKFN1 (198846 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	54068944	54068944	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:54068944delT								PCTP (214197 upstream) : ANKFN1 (161892 downstream)																																			---	---	---	---
ANKFN1	162282	broad.mit.edu	37	17	54391349	54391349	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:54391349delT	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	54578841	54578841	+	IGR	DEL	A	-	-	rs113560880		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:54578841delA								ANKFN1 (18834 upstream) : NOG (92219 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	54593619	54593620	+	IGR	DEL	GT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:54593619_54593620delGT								ANKFN1 (33612 upstream) : NOG (77440 downstream)																																			---	---	---	---
DGKE	8526	broad.mit.edu	37	17	54918151	54918152	+	Intron	INS	-	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:54918151_54918152insG	uc002iur.2	+						DGKE_uc002ius.1_Intron	NM_003647	NP_003638			diacylglycerol kinase epsilon						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)																	---	---	---	---
MSI2	124540	broad.mit.edu	37	17	55334794	55334794	+	Intron	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:55334794delC	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	55395550	55395557	+	Intron	DEL	GAAGGTGG	-	-	rs28508393	by1000genomes;by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:55395550_55395557delGAAGGTGG	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								---	---	---	---
Unknown	0	broad.mit.edu	37	17	55870877	55870879	+	IGR	DEL	AAA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:55870877_55870879delAAA								MSI2 (113578 upstream) : MRPS23 (45965 downstream)																																			---	---	---	---
LPO	4025	broad.mit.edu	37	17	56341099	56341099	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:56341099delA	uc002ivt.2	+						LPO_uc010wns.1_Intron|LPO_uc010dcp.2_Intron|LPO_uc010dcq.2_Intron|LPO_uc010dcr.2_Intron	NM_006151	NP_006142			lactoperoxidase isoform 1 preproprotein						hydrogen peroxide catabolic process	extracellular space	heme binding|peroxidase activity			ovary(1)|breast(1)	2																		---	---	---	---
RNF43	54894	broad.mit.edu	37	17	56435161	56435161	+	Frame_Shift_Del	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-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)																	---	---	---	---
HSF5	124535	broad.mit.edu	37	17	56554230	56554231	+	Intron	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:56554230_56554231delTT	uc002iwi.1	-							NM_001080439	NP_001073908			heat shock transcription factor family member 5							nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			ovary(2)|skin(1)	3	Medulloblastoma(34;0.127)|all_neural(34;0.237)																	---	---	---	---
HSF5	124535	broad.mit.edu	37	17	56561953	56561954	+	Intron	DEL	AA	-	-	rs71365894		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:56561953_56561954delAA	uc002iwi.1	-							NM_001080439	NP_001073908			heat shock transcription factor family member 5							nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			ovary(2)|skin(1)	3	Medulloblastoma(34;0.127)|all_neural(34;0.237)																	---	---	---	---
RAD51C	5889	broad.mit.edu	37	17	56787147	56787148	+	Intron	DEL	GA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:56787147_56787148delGA	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	57133568	57133568	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:57133568delT	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				---	---	---	---
PRR11	55771	broad.mit.edu	37	17	57247171	57247172	+	Frame_Shift_Del	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:57247171_57247172delAA	uc002ixf.1	+	2	137_138	c.58_59delAA	c.(58-60)AAAfs	p.K20fs	PRR11_uc002ixg.1_RNA	NM_018304	NP_060774	Q96HE9	PRR11_HUMAN	proline rich 11	20										ovary(2)	2	Medulloblastoma(34;0.0922)|all_neural(34;0.101)																	---	---	---	---
GDPD1	284161	broad.mit.edu	37	17	57351110	57351110	+	Frame_Shift_Del	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:57351110delT	uc002ixk.1	+	10	1058	c.921delT	c.(919-921)GATfs	p.D307fs		NM_182569	NP_872375	Q8N9F7	GDPD1_HUMAN	glycerophosphodiester phosphodiesterase domain	307	Extracellular (Potential).				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)																	---	---	---	---
YPEL2	388403	broad.mit.edu	37	17	57463691	57463692	+	Intron	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:57463691_57463692delAA	uc002ixm.1	+							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	57501588	57501588	+	IGR	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:57501588delC								YPEL2 (22493 upstream) : DHX40 (141298 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	57604965	57604968	+	IGR	DEL	TTTT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:57604965_57604968delTTTT								YPEL2 (125870 upstream) : DHX40 (37918 downstream)																																			---	---	---	---
CLTC	1213	broad.mit.edu	37	17	57725154	57725154	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:57725154delT	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 								---	---	---	---
RPS6KB1	6198	broad.mit.edu	37	17	58024323	58024323	+	3'UTR	DEL	A	-	-	rs71685029		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:58024323delA	uc002ixy.2	+	15					RPS6KB1_uc010ddj.1_Intron|RPS6KB1_uc010wom.1_3'UTR|RPS6KB1_uc010won.1_3'UTR|RPS6KB1_uc010woo.1_3'UTR|RPS6KB1_uc002ixz.2_RNA	NM_003161	NP_003152			ribosomal protein S6 kinase, 70kDa, polypeptide						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)															---	---	---	---
HEATR6	63897	broad.mit.edu	37	17	58125494	58125494	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:58125494delA	uc002iyk.1	-						HEATR6_uc010ddk.1_Intron|HEATR6_uc010wos.1_Intron	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)															---	---	---	---
APPBP2	10513	broad.mit.edu	37	17	58524282	58524283	+	3'UTR	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:58524282_58524283delAA	uc002iys.1	-	13					APPBP2_uc010ddl.1_3'UTR	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)															---	---	---	---
APPBP2	10513	broad.mit.edu	37	17	58595865	58595866	+	Intron	DEL	GT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:58595865_58595866delGT	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)															---	---	---	---
APPBP2	10513	broad.mit.edu	37	17	58602692	58602692	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:58602692delA	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)															---	---	---	---
BCAS3	54828	broad.mit.edu	37	17	59295141	59295141	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:59295141delT	uc002iyv.3	+						BCAS3_uc002iyu.3_Intron|BCAS3_uc002iyw.3_Intron|BCAS3_uc002iyy.3_Intron|BCAS3_uc002iyz.3_Intron|BCAS3_uc002iza.3_Intron|BCAS3_uc002izb.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)															---	---	---	---
TBX4	9496	broad.mit.edu	37	17	59560345	59560345	+	Frame_Shift_Del	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:59560345delC	uc002izi.2	+	8	1151	c.1106delC	c.(1105-1107)TCCfs	p.S369fs	TBX4_uc010ddo.2_Frame_Shift_Del_p.S370fs|TBX4_uc010woy.1_Frame_Shift_Del_p.S370fs	NM_018488	NP_060958	P57082	TBX4_HUMAN	T-box 4	369					leg morphogenesis|skeletal system morphogenesis	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity			skin(2)	2																		---	---	---	---
BRIP1	83990	broad.mit.edu	37	17	59880460	59880460	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:59880460delT	uc002izk.1	-							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				---	---	---	---
INTS2	57508	broad.mit.edu	37	17	59980071	59980071	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:59980071delA	uc002izn.2	-						INTS2_uc002izm.2_Intron	NM_020748	NP_065799			integrator complex subunit 2						snRNA processing	integral to membrane|integrator complex|nuclear membrane	protein binding			ovary(1)|lung(1)|pancreas(1)	3																		---	---	---	---
MRC2	9902	broad.mit.edu	37	17	60701855	60701856	+	5'Flank	DEL	AA	-	-	rs112412275		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:60701855_60701856delAA	uc002jad.2	+						MRC2_uc002jac.2_5'Flank	NM_006039	NP_006030			mannose receptor, C type 2						endocytosis	integral to membrane	receptor activity|sugar binding			ovary(1)|central_nervous_system(1)|skin(1)	3																		---	---	---	---
TANC2	26115	broad.mit.edu	37	17	61355160	61355160	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:61355160delA	uc002jal.3	+						TANC2_uc010wpe.1_Intron	NM_025185	NP_079461			tetratricopeptide repeat, ankyrin repeat and								binding			ovary(2)	2																		---	---	---	---
DCAF7	10238	broad.mit.edu	37	17	61664453	61664453	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:61664453delT	uc002jbc.2	+						DCAF7_uc002jbb.2_Intron|DCAF7_uc010wpn.1_Intron	NM_005828	NP_005819			WD-repeat protein						multicellular organismal development	CUL4 RING ubiquitin ligase complex|cytoplasm|nucleus	protein binding			ovary(1)	1																		---	---	---	---
STRADA	92335	broad.mit.edu	37	17	61790069	61790069	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:61790069delA	uc002jbm.2	-						STRADA_uc002jbn.2_Intron|STRADA_uc002jbo.2_Intron|STRADA_uc002jbp.2_Intron|STRADA_uc002jbq.2_Intron|STRADA_uc010wpq.1_Intron|STRADA_uc010wpr.1_Intron|STRADA_uc010ddw.2_Intron|STRADA_uc002jbr.2_Intron	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																		---	---	---	---
CCDC47	57003	broad.mit.edu	37	17	61829637	61829637	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:61829637delA	uc002jbs.3	-						CCDC47_uc010ddx.2_Intron|CCDC47_uc002jbt.2_Intron	NM_020198	NP_064583			coiled-coil domain containing 47 precursor							integral to membrane	protein binding				0																		---	---	---	---
CCDC45	90799	broad.mit.edu	37	17	62532623	62532624	+	Intron	DEL	AA	-	-	rs77058166		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:62532623_62532624delAA	uc002jem.2	+						CCDC45_uc002jen.2_Intron|CCDC45_uc010wqb.1_Intron|CCDC45_uc002jeo.1_3'UTR	NM_138363	NP_612372			coiled-coil domain containing 45							centrosome|spindle pole	protein binding				0	Breast(5;1.32e-14)		BRCA - Breast invasive adenocarcinoma(8;8.6e-12)															---	---	---	---
Unknown	0	broad.mit.edu	37	17	62701155	62701155	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:62701155delT								SMURF2 (42769 upstream) : LOC146880 (44626 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	62730865	62730865	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:62730865delT								SMURF2 (72479 upstream) : LOC146880 (14916 downstream)																																			---	---	---	---
LRRC37A3	374819	broad.mit.edu	37	17	62875785	62875785	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:62875785delT	uc002jey.2	-						LRRC37A3_uc010wqg.1_Intron|LRRC37A3_uc010wqf.1_Intron|LRRC37A3_uc010dek.1_Intron	NM_199340	NP_955372			leucine rich repeat containing 37, member A3							integral to membrane					0																		---	---	---	---
Unknown	0	broad.mit.edu	37	17	62953965	62953965	+	IGR	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:62953965delG								LRRC37A3 (38379 upstream) : AMZ2P1 (8703 downstream)																																			---	---	---	---
RGS9	8787	broad.mit.edu	37	17	63186049	63186049	+	Intron	DEL	T	-	-	rs112552969		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:63186049delT	uc002jfe.2	+						RGS9_uc010dem.2_Intron|RGS9_uc002jfd.2_Intron|RGS9_uc002jff.2_Intron|RGS9_uc002jfg.2_Intron	NM_003835	NP_003826			regulator of G-protein signaling 9 isoform 1						intracellular signal transduction|negative regulation of signal transduction|regulation of G-protein coupled receptor protein signaling pathway|visual perception	cytoplasm|heterotrimeric G-protein complex	GTPase activator activity|signal transducer activity			ovary(2)|skin(2)	4																		---	---	---	---
Unknown	0	broad.mit.edu	37	17	63244540	63244541	+	IGR	DEL	AA	-	-	rs34916183		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:63244540_63244541delAA								RGS9 (20721 upstream) : AXIN2 (280144 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	63381450	63381450	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:63381450delT								RGS9 (157631 upstream) : AXIN2 (143235 downstream)																																			---	---	---	---
AXIN2	8313	broad.mit.edu	37	17	63527998	63527998	+	Intron	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:63527998delC	uc002jfi.2	-						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		OREG0024670	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
AXIN2	8313	broad.mit.edu	37	17	63532780	63532780	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:63532780delA	uc002jfi.2	-						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	64125854	64125854	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:64125854delT	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)															---	---	---	---
APOH	350	broad.mit.edu	37	17	64216930	64216930	+	Intron	DEL	A	-	-	rs78195703		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:64216930delA	uc002jfn.3	-							NM_000042	NP_000033			apolipoprotein H precursor						blood coagulation, intrinsic pathway|negative regulation of angiogenesis|negative regulation of blood coagulation|negative regulation of endothelial cell migration|negative regulation of endothelial cell proliferation|negative regulation of fibrinolysis|negative regulation of myeloid cell apoptosis|negative regulation of smooth muscle cell apoptosis|plasminogen activation|positive regulation of lipoprotein lipase activity|triglyceride metabolic process|triglyceride transport	cell surface|chylomicron|high-density lipoprotein particle|very-low-density lipoprotein particle	eukaryotic cell surface binding|glycoprotein binding|heparin binding|lipoprotein lipase activator activity|phospholipid binding				0			BRCA - Breast invasive adenocarcinoma(6;9.74e-08)															---	---	---	---
PRKCA	5578	broad.mit.edu	37	17	64314973	64314973	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:64314973delA	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)													---	---	---	---
PRKCA	5578	broad.mit.edu	37	17	64333674	64333675	+	Intron	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:64333674_64333675delTT	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)													---	---	---	---
PRKCA	5578	broad.mit.edu	37	17	64540168	64540168	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:64540168delA	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)													---	---	---	---
PRKCA	5578	broad.mit.edu	37	17	64680790	64680790	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:64680790delT	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)													---	---	---	---
PRKCA	5578	broad.mit.edu	37	17	64719753	64719754	+	Intron	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:64719753_64719754delAA	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)													---	---	---	---
CACNG1	786	broad.mit.edu	37	17	65049724	65049724	+	Intron	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:65049724delG	uc002jfu.2	+							NM_000727	NP_000718			voltage-dependent calcium channel gamma-1						muscle contraction	voltage-gated calcium channel complex	voltage-gated calcium channel activity				0	all_cancers(12;1.04e-10)|Breast(2;1.45e-16)|all_epithelial(3;4.81e-12)				Amlodipine(DB00381)|Diltiazem(DB00343)|Ibutilide(DB00308)|Lercanidipine(DB00528)|Magnesium Sulfate(DB00653)|Nimodipine(DB00393)|Nitrendipine(DB01054)|Verapamil(DB00661)													---	---	---	---
HELZ	9931	broad.mit.edu	37	17	65096787	65096787	+	Intron	DEL	A	-	-	rs72848840	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:65096787delA	uc010wqk.1	-						HELZ_uc002jfv.3_Intron|HELZ_uc002jfx.3_Intron	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	65156546	65156547	+	Intron	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:65156546_65156547delAA	uc010wqk.1	-						HELZ_uc002jfv.3_Intron|HELZ_uc002jfx.3_Intron	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	65207031	65207031	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:65207031delA	uc010wqk.1	-						HELZ_uc002jfv.3_Intron|HELZ_uc002jfx.3_Intron|HELZ_uc010des.1_Intron	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	65211269	65211270	+	Intron	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:65211269_65211270delAA	uc010wqk.1	-						HELZ_uc002jfv.3_Intron|HELZ_uc002jfx.3_Intron|HELZ_uc010des.1_Intron	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)																	---	---	---	---
Unknown	0	broad.mit.edu	37	17	65268453	65268453	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:65268453delA								HELZ (27134 upstream) : PSMD12 (68167 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	65318571	65318571	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:65318571delT								HELZ (77252 upstream) : PSMD12 (18049 downstream)																																			---	---	---	---
PSMD12	5718	broad.mit.edu	37	17	65358803	65358803	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:65358803delA	uc002jfy.2	-						PSMD12_uc002jga.2_Intron|PSMD12_uc002jfz.2_Intron|PSMD12_uc010det.1_Intron	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	65411830	65411830	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:65411830delT	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	65458300	65458300	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:65458300delT	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	65670618	65670621	+	Intron	DEL	AAAA	-	-	rs66932178		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:65670618_65670621delAAAA	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)															---	---	---	---
NOL11	25926	broad.mit.edu	37	17	65737187	65737187	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:65737187delT	uc002jgd.1	+						NOL11_uc010wql.1_Intron|NOL11_uc010deu.1_Intron	NM_015462	NP_056277			nucleolar protein 11							nucleolus					0	all_cancers(12;1.54e-10)		BRCA - Breast invasive adenocarcinoma(8;7.48e-08)|Colorectal(3;0.0518)|COAD - Colon adenocarcinoma(4;0.0977)|LUSC - Lung squamous cell carcinoma(166;0.24)															---	---	---	---
Unknown	0	broad.mit.edu	37	17	66026981	66026982	+	IGR	DEL	GA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:66026981_66026982delGA								C17orf58 (37216 upstream) : KPNA2 (4866 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	66240439	66240439	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:66240439delT								LOC440461 (44003 upstream) : AMZ2 (3706 downstream)																																			---	---	---	---
ARSG	22901	broad.mit.edu	37	17	66359608	66359609	+	Intron	INS	-	T	T	rs150938633	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:66359608_66359609insT	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)															---	---	---	---
PRKAR1A	5573	broad.mit.edu	37	17	66527167	66527167	+	3'UTR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:66527167delT	uc002jhg.2	+	11					PRKAR1A_uc002jhh.2_3'UTR|PRKAR1A_uc002jhi.2_3'UTR|PRKAR1A_uc002jhj.2_3'UTR|PRKAR1A_uc002jhk.2_3'UTR|PRKAR1A_uc002jhl.2_3'UTR|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				---	---	---	---
ABCA5	23461	broad.mit.edu	37	17	67281850	67281850	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-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)																	---	---	---	---
Unknown	0	broad.mit.edu	37	17	67397924	67397924	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:67397924delA								ABCA5 (74601 upstream) : MAP2K6 (12914 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	67703569	67703569	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:67703569delA								MAP2K6 (165107 upstream) : KCNJ16 (367857 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	68010203	68010204	+	IGR	INS	-	A	A	rs142710061	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:68010203_68010204insA								MAP2K6 (471741 upstream) : KCNJ16 (61222 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	68225241	68225241	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:68225241delT								KCNJ2 (49060 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	68341296	68341296	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:68341296delA								KCNJ2 (165115 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	68940071	68940071	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:68940071delA								KCNJ2 (763890 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	68974725	68974726	+	IGR	INS	-	GGGA	GGGA			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:68974725_68974726insGGGA								KCNJ2 (798544 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	69099624	69099624	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:69099624delA	uc002jis.3	-											Homo sapiens cDNA clone IMAGE:5267277.																														---	---	---	---
Unknown	0	broad.mit.edu	37	17	69668324	69668324	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:69668324delA								None (None upstream) : SOX9 (448837 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	70017649	70017649	+	IGR	DEL	A	-	-	rs34880056		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:70017649delA								None (None upstream) : SOX9 (99512 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	70421167	70421167	+	Intron	DEL	T	-	-	rs66894945		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:70421167delT	uc002jix.2	-						uc002jiz.1_Intron|uc002jiy.1_5'Flank					Homo sapiens cDNA FLJ20470 fis, clone KAT06815.																														---	---	---	---
Unknown	0	broad.mit.edu	37	17	70435293	70435293	+	Intron	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:70435293delC	uc002jix.2	-						uc002jiz.1_Intron					Homo sapiens cDNA FLJ20470 fis, clone KAT06815.																														---	---	---	---
SLC39A11	201266	broad.mit.edu	37	17	70697936	70697937	+	Intron	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:70697936_70697937delAA	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	70886424	70886424	+	Intron	DEL	A	-	-	rs11335169		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:70886424delA	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	71168615	71168617	+	IGR	DEL	CTT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:71168615_71168617delCTT								SSTR2 (555 upstream) : COG1 (20556 downstream)																																			---	---	---	---
SDK2	54549	broad.mit.edu	37	17	71377554	71377555	+	Intron	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:71377554_71377555delAA	uc010dfm.2	-						SDK2_uc002jjt.3_Intron|SDK2_uc010dfn.2_Intron	NM_001144952	NP_001138424			sidekick 2						cell adhesion	integral to membrane				ovary(2)	2																		---	---	---	---
SDK2	54549	broad.mit.edu	37	17	71607324	71607324	+	Intron	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:71607324delG	uc010dfm.2	-							NM_001144952	NP_001138424			sidekick 2						cell adhesion	integral to membrane				ovary(2)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	17	71732314	71732317	+	IGR	DEL	CTCT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:71732314_71732317delCTCT								SDK2 (92087 upstream) : C17orf54 (13092 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	71898175	71898175	+	IGR	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:71898175delC								C17orf54 (73499 upstream) : RPL38 (301620 downstream)																																			---	---	---	---
DNAI2	64446	broad.mit.edu	37	17	72288974	72288977	+	Intron	DEL	TTTT	-	-	rs77002632		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:72288974_72288977delTTTT	uc002jkf.2	+						DNAI2_uc002jkg.2_Intron|DNAI2_uc010dfp.2_Intron	NM_023036	NP_075462			dynein, axonemal, intermediate polypeptide 2						cilium assembly	axonemal dynein complex|cilium axoneme|cytoplasm|microtubule	microtubule motor activity			ovary(2)|central_nervous_system(1)	3														Kartagener_syndrome				---	---	---	---
BTBD17	388419	broad.mit.edu	37	17	72360854	72360854	+	5'Flank	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:72360854delT	uc002jkn.2	-						GPR142_uc010wqx.1_5'Flank|GPR142_uc010wqy.1_5'Flank	NM_001080466	NP_001073935			BTB (POZ) domain containing 17 precursor							extracellular region					0																		---	---	---	---
Unknown	0	broad.mit.edu	37	17	72550251	72550252	+	IGR	DEL	TC	-	-	rs71892195		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:72550251_72550252delTC								CD300C (7969 upstream) : CD300LD (25859 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	72596351	72596352	+	IGR	INS	-	GAT	GAT	rs138167381	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:72596351_72596352insGAT								C17orf77 (6003 upstream) : CD300E (12360 downstream)																																			---	---	---	---
CD300E	342510	broad.mit.edu	37	17	72615747	72615748	+	Intron	INS	-	CA	CA	rs143498126	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:72615747_72615748insCA	uc002jlb.1	-							NM_181449	NP_852114			CD300e molecule precursor							integral to membrane|plasma membrane	receptor activity			skin(2)|large_intestine(1)|ovary(1)	4																		---	---	---	---
SLC9A3R1	9368	broad.mit.edu	37	17	72746911	72746911	+	Intron	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:72746911delC	uc002jlo.2	+						SLC9A3R1_uc002jln.1_Intron	NM_004252	NP_004243			sodium/hydrogen exchanger regulatory factor 1						apoptosis|bile acid secretion|glutathione transport|microvillus assembly|negative regulation of cell proliferation|negative regulation of ERK1 and ERK2 cascade|negative regulation of phosphatidylinositol 3-kinase cascade|negative regulation of platelet-derived growth factor receptor signaling pathway|negative regulation of protein kinase B signaling cascade|protein complex assembly|regulation of protein kinase activity|regulation of sodium:hydrogen antiporter activity|renal absorption|Wnt receptor signaling pathway	actin cytoskeleton|apical plasma membrane|centrosome|endomembrane system|filopodium|intracellular membrane-bounded organelle|microvillus membrane|ruffle	beta-2 adrenergic receptor binding|beta-catenin binding|chloride channel regulator activity|growth factor receptor binding|PDZ domain binding|phosphatase binding|protein self-association				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	17	72873139	72873139	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:72873139delT								FDXR (3983 upstream) : FADS6 (334 downstream)																																			---	---	---	---
OTOP2	92736	broad.mit.edu	37	17	72922351	72922352	+	Intron	INS	-	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:72922351_72922352insC	uc010wrp.1	+						USH1G_uc002jme.1_5'Flank|USH1G_uc010wro.1_5'Flank|OTOP2_uc002jmf.1_Intron	NM_178160	NP_835454			otopetrin 2							integral to membrane				ovary(3)|large_intestine(1)	4	all_lung(278;0.172)|Lung NSC(278;0.207)																	---	---	---	---
NUP85	79902	broad.mit.edu	37	17	73220765	73220765	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:73220765delA	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)															---	---	---	---
Unknown	0	broad.mit.edu	37	17	73302863	73302863	+	IGR	DEL	A	-	-	rs71971096		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:73302863delA								SLC25A19 (17333 upstream) : GRB2 (11295 downstream)																																			---	---	---	---
ITGB4	3691	broad.mit.edu	37	17	73722650	73722650	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:73722650delA	uc002jpg.2	+						ITGB4_uc002jph.2_Intron|ITGB4_uc010dgo.2_Intron|ITGB4_uc002jpi.3_Intron|ITGB4_uc010dgp.1_Intron|ITGB4_uc002jpj.2_Intron	NM_000213	NP_000204			integrin beta 4 isoform 1 precursor						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)															---	---	---	---
UNC13D	201294	broad.mit.edu	37	17	73835181	73835182	+	Intron	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:73835181_73835182delAA	uc002jpp.2	-						UNC13D_uc010wsk.1_Intron|UNC13D_uc002jpq.1_Intron|UNC13D_uc010dgq.1_Intron	NM_199242	NP_954712			unc-13 homolog D						positive regulation of exocytosis|regulation of mast cell degranulation	exocytic vesicle|late endosome|lysosome|membrane|recycling endosome	protein binding			upper_aerodigestive_tract(1)|skin(1)	2			all cancers(21;2.11e-06)|Epithelial(20;2.32e-06)|BRCA - Breast invasive adenocarcinoma(9;0.000618)|LUSC - Lung squamous cell carcinoma(166;0.154)											Familial_Hemophagocytic_Lymphohistiocytosis				---	---	---	---
FBF1	85302	broad.mit.edu	37	17	73904792	73904792	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:73904792delT	uc002jqa.1	-						MRPL38_uc002jpz.1_Intron					Homo sapiens mRNA for KIAA1863 protein, partial cds.												0																		---	---	---	---
RNF157	114804	broad.mit.edu	37	17	74160693	74160693	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:74160693delA	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)															---	---	---	---
RNF157	114804	broad.mit.edu	37	17	74161765	74161765	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:74161765delT	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)															---	---	---	---
UBE2O	63893	broad.mit.edu	37	17	74385877	74385877	+	3'UTR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:74385877delT	uc002jrm.3	-	18					uc010wtd.1_5'Flank|UBE2O_uc002jrl.3_3'UTR	NM_022066	NP_071349			ubiquitin-conjugating enzyme E2O								ATP binding|ubiquitin-protein ligase activity			breast(2)|skin(2)|lung(1)	5																		---	---	---	---
MXRA7	439921	broad.mit.edu	37	17	74702769	74702776	+	Intron	DEL	AGACAGAC	-	-	rs142352153		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:74702769_74702776delAGACAGAC	uc002jsk.1	-						MXRA7_uc002jsl.2_Intron|MXRA7_uc002jsm.2_Intron	NM_001008528	NP_001008528			transmembrane anchor protein 1 isoform 1							integral to membrane					0																		---	---	---	---
MGAT5B	146664	broad.mit.edu	37	17	74878237	74878237	+	Frame_Shift_Del	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:74878237delG	uc002jtg.3	+	3	500	c.186delG	c.(184-186)ATGfs	p.M62fs	MGAT5B_uc002jth.2_Frame_Shift_Del_p.M62fs|MGAT5B_uc002jti.2_Frame_Shift_Del_p.M73fs			Q3V5L5	MGT5B_HUMAN	Homo sapiens GnT-IX mRNA for N-Acetylglucosaminyltransferase IX, complete cds.	62	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																		---	---	---	---
MGAT5B	146664	broad.mit.edu	37	17	74930873	74930873	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:74930873delA	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																		---	---	---	---
SEPT9	10801	broad.mit.edu	37	17	75278383	75278383	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:75278383delT	uc002jts.3	+						SEPT9_uc010wtk.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	75340267	75340267	+	Intron	DEL	A	-	-	rs66779838		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:75340267delA	uc002jts.3	+						SEPT9_uc010wtk.1_Intron|SEPT9_uc002jtt.3_Intron|SEPT9_uc002jtu.3_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)															---	---	---	---
FLJ45079	400624	broad.mit.edu	37	17	75882151	75882151	+	5'Flank	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:75882151delA	uc002jub.2	-							NM_001001685	NP_001001685			SubName: Full=FLJ45079 protein; SubName: Full=cDNA FLJ45079 fis, clone BRAWH3027675; SubName: Full=cDNA FLJ46474 fis, clone THYMU3024164;												0			BRCA - Breast invasive adenocarcinoma(99;0.00524)|Lung(188;0.154)															---	---	---	---
TNRC6C	57690	broad.mit.edu	37	17	76000699	76000699	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:76000699delT	uc002jud.2	+						TNRC6C_uc002juc.2_Intron|TNRC6C_uc002juf.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)															---	---	---	---
Unknown	0	broad.mit.edu	37	17	76303638	76303638	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:76303638delA								LOC283999 (66571 upstream) : SOCS3 (49221 downstream)																																			---	---	---	---
PGS1	9489	broad.mit.edu	37	17	76375600	76375600	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:76375600delA	uc002jvm.2	+						PGS1_uc010wtt.1_Intron	NM_024419	NP_077733			phosphatidylglycerophosphate synthase 1						phospholipid biosynthetic process	endoplasmic reticulum|mitochondrion	ATP binding|CDP-diacylglycerol-glycerol-3-phosphate 3-phosphatidyltransferase activity				0			BRCA - Breast invasive adenocarcinoma(99;0.00144)|OV - Ovarian serous cystadenocarcinoma(97;0.031)															---	---	---	---
DNAH17	8632	broad.mit.edu	37	17	76450997	76450998	+	Intron	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:76450997_76450998delTT	uc010dhp.1	-						DNAH17_uc002jvs.2_Intron					SubName: Full=DNAH17 variant protein; Flags: Fragment;											ovary(6)|breast(2)|skin(1)	9			BRCA - Breast invasive adenocarcinoma(99;0.00294)|OV - Ovarian serous cystadenocarcinoma(97;0.0656)															---	---	---	---
DNAH17	8632	broad.mit.edu	37	17	76557351	76557351	+	Intron	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:76557351delC	uc002jvv.1	-											RecName: Full=Dynein heavy chain 17, axonemal; AltName: Full=Axonemal beta dynein heavy chain 17; AltName: Full=Ciliary dynein heavy chain 17; AltName: Full=Ciliary dynein heavy chain-like protein 1; AltName: Full=Axonemal dynein heavy chain-like protein 1; AltName: Full=Dynein light chain 2, axonemal;											ovary(6)|breast(2)|skin(1)	9			BRCA - Breast invasive adenocarcinoma(99;0.00294)|OV - Ovarian serous cystadenocarcinoma(97;0.0656)															---	---	---	---
CYTH1	9267	broad.mit.edu	37	17	76684784	76684784	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:76684784delT	uc002jvw.2	-						CYTH1_uc010wtv.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																		---	---	---	---
Unknown	0	broad.mit.edu	37	17	76791694	76791695	+	IGR	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:76791694_76791695delAA								CYTH1 (13318 upstream) : USP36 (40 downstream)																																			---	---	---	---
USP36	57602	broad.mit.edu	37	17	76825834	76825835	+	Intron	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:76825834_76825835delTT	uc002jvz.1	-						USP36_uc002jwa.1_Intron|USP36_uc002jwd.1_Intron	NM_025090	NP_079366			ubiquitin specific peptidase 36						ubiquitin-dependent protein catabolic process	nucleolus	cysteine-type peptidase activity|ubiquitin thiolesterase activity			lung(2)|ovary(1)|breast(1)|kidney(1)	5			BRCA - Breast invasive adenocarcinoma(99;0.000842)|OV - Ovarian serous cystadenocarcinoma(97;0.151)															---	---	---	---
TIMP2	7077	broad.mit.edu	37	17	76868567	76868567	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:76868567delT	uc002jwf.2	-						TIMP2_uc002jwe.2_Intron|TIMP2_uc010wty.1_Intron	NM_003255	NP_003246			TIMP metallopeptidase inhibitor 2 precursor								metal ion binding|metalloendopeptidase inhibitor activity			central_nervous_system(2)	2			BRCA - Breast invasive adenocarcinoma(99;0.0101)|OV - Ovarian serous cystadenocarcinoma(97;0.194)															---	---	---	---
HRNBP3	146713	broad.mit.edu	37	17	77395563	77395563	+	Intron	DEL	T	-	-	rs35720544		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:77395563delT	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	77761442	77761442	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:77761442delT								CBX2 (64 upstream) : CBX8 (6734 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	77902337	77902337	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:77902337delA								CBX4 (89124 upstream) : TBC1D16 (11484 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	77908729	77908729	+	RNA	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:77908729delC	uc002jxg.1	-	1		c.3549delG								Homo sapiens cDNA FLJ20748 fis, clone HEP05772.																														---	---	---	---
EIF4A3	9775	broad.mit.edu	37	17	78114113	78114118	+	Intron	DEL	TTTTTT	-	-	rs34004549		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:78114113_78114118delTTTTTT	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)															---	---	---	---
EIF4A3	9775	broad.mit.edu	37	17	78116010	78116011	+	Intron	INS	-	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:78116010_78116011insT	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)															---	---	---	---
Unknown	0	broad.mit.edu	37	17	78243169	78243170	+	Intron	INS	-	CTAT	CTAT	rs147394603	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:78243169_78243170insCTAT	uc002jye.1	+						uc002jyf.2_Intron					Homo sapiens mRNA for KIAA1618 protein, partial cds.																														---	---	---	---
RPTOR	57521	broad.mit.edu	37	17	78871048	78871048	+	Intron	DEL	A	-	-	rs5822374		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:78871048delA	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																		---	---	---	---
Unknown	0	broad.mit.edu	37	17	78982223	78982223	+	IGR	DEL	T	-	-	rs74004829	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:78982223delT								CHMP6 (8291 upstream) : FLJ90757 (20710 downstream)																																			---	---	---	---
SLC38A10	124565	broad.mit.edu	37	17	79267279	79267279	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:79267279delT	uc002jzz.1	-						SLC38A10_uc002kab.2_Intron	NM_001037984	NP_001033073			solute carrier family 38, member 10 isoform a						amino acid transport|sodium ion transport	integral to membrane				pancreas(1)|skin(1)	2	all_neural(118;0.0804)|Melanoma(429;0.242)		BRCA - Breast invasive adenocarcinoma(99;0.0272)|OV - Ovarian serous cystadenocarcinoma(97;0.117)															---	---	---	---
Unknown	0	broad.mit.edu	37	17	79474039	79474039	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:79474039delA								BAHCC1 (40681 upstream) : ACTG1 (2960 downstream)																																			---	---	---	---
FSCN2	25794	broad.mit.edu	37	17	79502542	79502544	+	Intron	DEL	CCA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:79502542_79502544delCCA	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)															---	---	---	---
CCDC137	339230	broad.mit.edu	37	17	79639371	79639371	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:79639371delA	uc002kbc.3	+						CCDC137_uc002kbd.2_Intron	NM_199287	NP_954981			coiled-coil domain containing 137											central_nervous_system(1)	1	all_neural(118;0.0878)|all_lung(278;0.23)|Melanoma(429;0.242)		BRCA - Breast invasive adenocarcinoma(99;0.0101)|OV - Ovarian serous cystadenocarcinoma(97;0.0739)															---	---	---	---
DUS1L	64118	broad.mit.edu	37	17	80017222	80017222	+	Intron	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:80017222delG	uc002kdq.2	-						DUS1L_uc002kdp.2_Intron|DUS1L_uc002kdr.2_Intron|DUS1L_uc002kds.2_Intron|DUS1L_uc002kdt.2_Intron	NM_022156	NP_071439			PP3111 protein						tRNA processing		flavin adenine dinucleotide binding|tRNA dihydrouridine synthase activity			skin(1)	1	all_neural(118;0.0878)|Ovarian(332;0.227)|all_lung(278;0.246)		BRCA - Breast invasive adenocarcinoma(99;0.0114)|OV - Ovarian serous cystadenocarcinoma(97;0.0211)															---	---	---	---
CCDC57	284001	broad.mit.edu	37	17	80120941	80120941	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:80120941delA	uc002kdz.1	-						CCDC57_uc002kdx.1_Intron|CCDC57_uc010dik.1_Intron	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)															---	---	---	---
FOXK2	3607	broad.mit.edu	37	17	80501962	80501962	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:80501962delT	uc002kfn.2	+						FOXK2_uc002kfm.1_Intron|FOXK2_uc010diu.2_Intron	NM_004514	NP_004505			forkhead box K2						embryo development|pattern specification process|regulation of sequence-specific DNA binding transcription factor activity|regulation of transcription from RNA polymerase II promoter|tissue development	transcription factor complex	DNA bending activity|double-stranded DNA binding|magnesium ion 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	Breast(20;0.00106)|all_neural(118;0.0952)		OV - Ovarian serous cystadenocarcinoma(97;0.0371)|BRCA - Breast invasive adenocarcinoma(99;0.0415)															---	---	---	---
FN3KRP	79672	broad.mit.edu	37	17	80677641	80677641	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:80677641delA	uc002kfu.2	+						FN3KRP_uc010wvr.1_Intron	NM_024619	NP_078895			fructosamine 3 kinase related protein								kinase activity				0	Breast(20;0.000523)|all_neural(118;0.0952)		BRCA - Breast invasive adenocarcinoma(99;0.0344)|OV - Ovarian serous cystadenocarcinoma(97;0.061)															---	---	---	---
TBCD	6904	broad.mit.edu	37	17	80896388	80896388	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:80896388delA	uc002kfz.2	+						TBCD_uc002kfy.1_Intron|TBCD_uc002kgc.2_Intron|TBCD_uc002kgd.2_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)															---	---	---	---
USP14	9097	broad.mit.edu	37	18	172664	172664	+	Intron	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:172664delC	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)																---	---	---	---
ENOSF1	55556	broad.mit.edu	37	18	694117	694117	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:694117delA	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|ENOSF1_uc010wyt.1_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																		---	---	---	---
C18orf2	56651	broad.mit.edu	37	18	1387671	1387672	+	Intron	DEL	AC	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:1387671_1387672delAC	uc002kld.1	-											Homo sapiens C18orf2 isoform 1 mRNA, complete sequence, alternatively spliced.												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	18	1576161	1576162	+	IGR	DEL	TT	-	-	rs5822628		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:1576161_1576162delTT								C18orf2 (168980 upstream) : METTL4 (961363 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	2238996	2238998	+	IGR	DEL	AAA	-	-	rs71365158		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:2238996_2238998delAAA								C18orf2 (831815 upstream) : METTL4 (298527 downstream)																																			---	---	---	---
SMCHD1	23347	broad.mit.edu	37	18	2654077	2654077	+	5'Flank	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:2654077delA	uc002klm.3	+							NM_015295	NP_056110			structural maintenance of chromosomes flexible						chromosome organization		ATP binding				0																		---	---	---	---
SMCHD1	23347	broad.mit.edu	37	18	2724883	2724884	+	Intron	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:2724883_2724884delTT	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	2772110	2772110	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-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																		---	---	---	---
MYOM1	8736	broad.mit.edu	37	18	3120038	3120038	+	Intron	DEL	T	-	-	rs77973657		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:3120038delT	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																		---	---	---	---
Unknown	0	broad.mit.edu	37	18	3324905	3324905	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:3324905delA								MYL12B (46625 upstream) : TGIF1 (87167 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	3485374	3485375	+	IGR	DEL	TT	-	-	rs11431491		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:3485374_3485375delTT								TGIF1 (26970 upstream) : DLGAP1 (13462 downstream)																																			---	---	---	---
DLGAP1	9229	broad.mit.edu	37	18	3810539	3810539	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-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	4085262	4085262	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:4085262delA	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)																---	---	---	---
Unknown	0	broad.mit.edu	37	18	4614029	4614029	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:4614029delT								DLGAP1 (158763 upstream) : LOC642597 (529643 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	4645918	4645918	+	IGR	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:4645918delG								DLGAP1 (190652 upstream) : LOC642597 (497754 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	5077382	5077383	+	IGR	INS	-	A	A	rs138473670	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:5077382_5077383insA								DLGAP1 (622116 upstream) : LOC642597 (66289 downstream)																																			---	---	---	---
EPB41L3	23136	broad.mit.edu	37	18	5455620	5455623	+	Intron	DEL	TTTT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:5455620_5455623delTTTT	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																		---	---	---	---
EPB41L3	23136	broad.mit.edu	37	18	5625427	5625427	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:5625427delA	uc010dkq.1	-						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																		---	---	---	---
EPB41L3	23136	broad.mit.edu	37	18	5630451	5630451	+	5'UTR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:5630451delA	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																		---	---	---	---
EPB41L3	23136	broad.mit.edu	37	18	5632295	5632295	+	5'Flank	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:5632295delA	uc002kmv.1	-											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																		---	---	---	---
Unknown	0	broad.mit.edu	37	18	7369838	7369838	+	IGR	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:7369838delG								LRRC30 (137797 upstream) : PTPRM (197476 downstream)																																			---	---	---	---
PTPRM	5797	broad.mit.edu	37	18	7724074	7724074	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:7724074delT	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	8263114	8263114	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:8263114delT	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	8372944	8372945	+	Intron	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:8372944_8372945delTT	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	8683234	8683235	+	IGR	INS	-	TC	TC			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:8683234_8683235insTC								RAB12 (43855 upstream) : KIAA0802 (24174 downstream)																																			---	---	---	---
KIAA0802	23255	broad.mit.edu	37	18	8710325	8710328	+	Intron	DEL	ACAG	-	-	rs66484056		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:8710325_8710328delACAG	uc002knq.2	+							NM_015210	NP_056025			hypothetical protein LOC23255												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	18	8915059	8915060	+	IGR	DEL	AG	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:8915059_8915060delAG								KIAA0802 (82284 upstream) : NDUFV2 (187615 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	9320365	9320367	+	IGR	DEL	TTG	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:9320365_9320367delTTG								ANKRD12 (35159 upstream) : TWSG1 (14398 downstream)																																			---	---	---	---
RALBP1	10928	broad.mit.edu	37	18	9535851	9535851	+	Frame_Shift_Del	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:9535851delA	uc002kob.2	+	10	2107	c.1884delA	c.(1882-1884)CCAfs	p.P628fs	RALBP1_uc002koc.2_Frame_Shift_Del_p.P628fs	NM_006788	NP_006779	Q15311	RBP1_HUMAN	ralA binding protein 1	628					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	9694808	9694809	+	IGR	DEL	AG	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:9694808_9694809delAG								PPP4R1 (80208 upstream) : RAB31 (13419 downstream)																																			---	---	---	---
APCDD1	147495	broad.mit.edu	37	18	10462990	10462990	+	Intron	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:10462990delC	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)														---	---	---	---
FAM38B	63895	broad.mit.edu	37	18	10804668	10804668	+	Intron	DEL	G	-	-	rs74811226	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:10804668delG	uc002kow.1	-											RecName: Full=Uncharacterized protein C18orf58;							integral to membrane	ion channel activity			ovary(1)	1																		---	---	---	---
FAM38B	63895	broad.mit.edu	37	18	10874306	10874306	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:10874306delA	uc002kow.1	-											RecName: Full=Uncharacterized protein C18orf58;							integral to membrane	ion channel activity			ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	18	10922360	10922361	+	IGR	INS	-	A	A	rs55899542		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:10922360_10922361insA								FAM38B (220381 upstream) : GNAL (766775 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	10993310	10993310	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:10993310delT								FAM38B (291331 upstream) : GNAL (695826 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	11013042	11013043	+	IGR	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:11013042_11013043delAA								FAM38B (311063 upstream) : GNAL (676093 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	11289997	11290000	+	IGR	DEL	AGCA	-	-	rs111813020		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:11289997_11290000delAGCA								FAM38B (588018 upstream) : GNAL (399136 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	11616236	11616237	+	IGR	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:11616236_11616237delTT								FAM38B (914257 upstream) : GNAL (72899 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	11639513	11639513	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:11639513delA								FAM38B (937534 upstream) : GNAL (49623 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	12069273	12069274	+	IGR	DEL	TG	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:12069273_12069274delTG								IMPA2 (38397 upstream) : CIDEA (185044 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	12115075	12115075	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:12115075delT	uc002kqs.2	+											RecName: Full=UPF0634 protein E;																														---	---	---	---
Unknown	0	broad.mit.edu	37	18	12729128	12729129	+	IGR	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:12729128_12729129delAA								PSMG2 (3391 upstream) : PTPN2 (56352 downstream)																																			---	---	---	---
PTPN2	5771	broad.mit.edu	37	18	12811896	12811896	+	Intron	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:12811896delC	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)																---	---	---	---
Unknown	0	broad.mit.edu	37	18	12922373	12922373	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:12922373delA								PTPN2 (38039 upstream) : SEH1L (25610 downstream)																																			---	---	---	---
SEH1L	81929	broad.mit.edu	37	18	12954079	12954079	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-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	13055657	13055658	+	Intron	INS	-	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:13055657_13055658insT	uc010xac.1	+						CEP192_uc010dlf.1_Intron|CEP192_uc010xad.1_Intron|CEP192_uc002kru.2_Intron|CEP192_uc002krv.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	13318267	13318268	+	Intron	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:13318267_13318268delTT	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	13644961	13644961	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:13644961delT	uc002ksa.2	+						C18orf1_uc002ksb.2_Intron|C18orf1_uc002kse.2_Intron|C18orf1_uc002ksf.2_Intron|C18orf1_uc002ksg.1_Intron|C18orf1_uc002ksh.1_Intron|C18orf1_uc002ksi.1_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)														---	---	---	---
Unknown	0	broad.mit.edu	37	18	13848275	13848275	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:13848275delA								MC5R (21535 upstream) : MC2R (33768 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	13948684	13948684	+	IGR	DEL	G	-	-	rs10163711	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:13948684delG								MC2R (33149 upstream) : ZNF519 (127305 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	14927973	14927974	+	IGR	DEL	TT	-	-	rs78222666		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:14927973_14927974delTT								ANKRD30B (75236 upstream) : LOC644669 (385581 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	15091376	15091377	+	IGR	DEL	CT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:15091376_15091377delCT								ANKRD30B (238639 upstream) : LOC644669 (222178 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	15299281	15299282	+	IGR	DEL	CA	-	-	rs113248324		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:15299281_15299282delCA								ANKRD30B (446544 upstream) : LOC644669 (14273 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	15379584	15379584	+	IGR	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:15379584delC								LOC644669 (53666 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	15391617	15391624	+	IGR	DEL	GCTCATGG	-	-	rs9973166	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:15391617_15391624delGCTCATGG								LOC644669 (65699 upstream) : None (None downstream)																																			---	---	---	---
ROCK1	6093	broad.mit.edu	37	18	18641042	18641043	+	Intron	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:18641042_18641043delTT	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)																	---	---	---	---
Unknown	0	broad.mit.edu	37	18	18738945	18738945	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:18738945delA								ROCK1 (47133 upstream) : GREB1L (83258 downstream)																																			---	---	---	---
GREB1L	80000	broad.mit.edu	37	18	18955032	18955032	+	Intron	DEL	T	-	-	rs72006338		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:18955032delT	uc010xam.1	+						GREB1L_uc002ktf.1_Intron|GREB1L_uc010dlp.1_Intron	NM_001142966	NP_001136438			growth regulation by estrogen in breast							integral to membrane					0																		---	---	---	---
ESCO1	114799	broad.mit.edu	37	18	19144359	19144359	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:19144359delT	uc002kth.1	-						ESCO1_uc002kti.1_Intron	NM_052911	NP_443143			establishment of cohesion 1 homolog 1						cell cycle|post-translational protein acetylation|regulation of DNA replication	chromatin|nucleus	acyltransferase activity|metal ion binding				0																		---	---	---	---
MIB1	57534	broad.mit.edu	37	18	19345657	19345657	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:19345657delT	uc002ktq.2	+						MIB1_uc002ktp.2_Intron	NM_020774	NP_065825			mindbomb homolog 1						Notch signaling pathway	centrosome|nuclear membrane|plasma membrane	ubiquitin-protein ligase activity|zinc ion binding			ovary(4)	4			STAD - Stomach adenocarcinoma(5;0.212)															---	---	---	---
Unknown	0	broad.mit.edu	37	18	19792893	19792893	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:19792893delT								GATA6 (10666 upstream) : CTAGE1 (200671 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	20108307	20108307	+	IGR	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:20108307delC								CTAGE1 (110429 upstream) : RBBP8 (404988 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	20708062	20708062	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:20708062delA								RBBP8 (101617 upstream) : CABLES1 (6466 downstream)																																			---	---	---	---
CABLES1	91768	broad.mit.edu	37	18	20755906	20755906	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:20755906delA	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)																	---	---	---	---
CABLES1	91768	broad.mit.edu	37	18	20837406	20837406	+	3'UTR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:20837406delA	uc002kuc.2	+	10					C18orf45_uc010xaq.1_Intron|CABLES1_uc002kub.2_3'UTR|CABLES1_uc002kud.2_3'UTR	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)																	---	---	---	---
RIOK3	8780	broad.mit.edu	37	18	21038223	21038223	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:21038223delA	uc002kui.3	+						RIOK3_uc010dls.2_Intron|RIOK3_uc010xas.1_Intron	NM_003831	NP_003822			sudD suppressor of bimD6 homolog						chromosome segregation		ATP binding|protein binding|protein serine/threonine kinase activity			ovary(2)|central_nervous_system(1)	3	all_cancers(21;0.000106)|all_epithelial(16;6.74e-07)|Lung NSC(20;0.00171)|all_lung(20;0.0055)|Colorectal(14;0.0202)|Ovarian(20;0.127)																	---	---	---	---
RIOK3	8780	broad.mit.edu	37	18	21052197	21052197	+	Intron	DEL	A	-	-	rs34781307		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:21052197delA	uc002kui.3	+						RIOK3_uc010dls.2_Intron|RIOK3_uc010xas.1_Intron|RIOK3_uc010xat.1_Intron	NM_003831	NP_003822			sudD suppressor of bimD6 homolog						chromosome segregation		ATP binding|protein binding|protein serine/threonine kinase activity			ovary(2)|central_nervous_system(1)	3	all_cancers(21;0.000106)|all_epithelial(16;6.74e-07)|Lung NSC(20;0.00171)|all_lung(20;0.0055)|Colorectal(14;0.0202)|Ovarian(20;0.127)																	---	---	---	---
NPC1	4864	broad.mit.edu	37	18	21120909	21120909	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:21120909delT	uc002kum.3	-						NPC1_uc010xaz.1_Intron|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)																	---	---	---	---
NPC1	4864	broad.mit.edu	37	18	21125211	21125211	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:21125211delT	uc002kum.3	-						NPC1_uc010xaz.1_Intron|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)																	---	---	---	---
LAMA3	3909	broad.mit.edu	37	18	21479058	21479058	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:21479058delT	uc002kuq.2	+						LAMA3_uc002kur.2_Intron|LAMA3_uc002kus.3_Intron|LAMA3_uc002kut.3_Intron	NM_198129	NP_937762			laminin alpha 3 subunit isoform 1						cell adhesion|epidermis development|hemidesmosome assembly|regulation of cell adhesion|regulation of cell migration|regulation of embryonic development	laminin-1 complex	receptor binding|structural molecule activity			ovary(8)|skin(2)|central_nervous_system(1)	11	all_cancers(21;7.81e-05)|all_epithelial(16;4.45e-07)|Lung NSC(20;0.00156)|all_lung(20;0.00508)|Colorectal(14;0.0202)|Ovarian(20;0.17)				Alteplase(DB00009)|Anistreplase(DB00029)|Reteplase(DB00015)|Tenecteplase(DB00031)													---	---	---	---
Unknown	0	broad.mit.edu	37	18	22447233	22447236	+	IGR	DEL	TGAG	-	-	rs66740973		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:22447233_22447236delTGAG								HRH4 (387313 upstream) : ZNF521 (194652 downstream)																																			---	---	---	---
ZNF521	25925	broad.mit.edu	37	18	22818510	22818510	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:22818510delA	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	23537463	23537463	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:23537463delT								ZNF521 (605249 upstream) : SS18 (58756 downstream)																																			---	---	---	---
CHST9	83539	broad.mit.edu	37	18	24744995	24744995	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:24744995delA	uc002kwe.2	-						C18orf16_uc010xbm.1_Intron	NM_031422	NP_113610			GalNAc-4-sulfotransferase 2						carbohydrate biosynthetic process|glycosaminoglycan metabolic process|hormone biosynthetic process|proteoglycan biosynthetic process|sulfur compound metabolic process	extracellular region|Golgi membrane|integral to membrane	N-acetylgalactosamine 4-O-sulfotransferase activity			ovary(2)|skin(1)	3	all_lung(6;0.0145)|Ovarian(20;0.124)																	---	---	---	---
Unknown	0	broad.mit.edu	37	18	24844037	24844037	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:24844037delA								C18orf16 (73387 upstream) : CDH2 (686893 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	24848958	24848958	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:24848958delT								C18orf16 (78308 upstream) : CDH2 (681972 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	24930203	24930203	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:24930203delA	uc002kwf.1	-											Homo sapiens cDNA FLJ45994 fis, clone SKMUS2009557.																														---	---	---	---
CDH2	1000	broad.mit.edu	37	18	25572481	25572482	+	Intron	INS	-	AT	AT			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:25572481_25572482insAT	uc002kwg.2	-						CDH2_uc010xbn.1_Intron	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	26073741	26073741	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:26073741delT								CDH2 (316296 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	26219392	26219392	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:26219392delT								CDH2 (461947 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	26383077	26383078	+	IGR	INS	-	AC	AC			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:26383077_26383078insAC								CDH2 (625632 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	27007542	27007543	+	IGR	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:27007542_27007543delTT								None (None upstream) : MIR302F (871333 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	27451238	27451238	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-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	27546388	27546388	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:27546388delA								None (None upstream) : MIR302F (332488 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	28373063	28373064	+	IGR	INS	-	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:28373063_28373064insA								MIR302F (494137 upstream) : DSC3 (196989 downstream)																																			---	---	---	---
DSC3	1825	broad.mit.edu	37	18	28588133	28588133	+	Intron	DEL	A	-	-	rs34151598		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:28588133delA	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)															---	---	---	---
DSC3	1825	broad.mit.edu	37	18	28600549	28600549	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:28600549delT	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	28901072	28901072	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:28901072delA	uc002kwp.2	+							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)															---	---	---	---
DSG1	1828	broad.mit.edu	37	18	28923779	28923779	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-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)															---	---	---	---
TTR	7276	broad.mit.edu	37	18	29174107	29174107	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:29174107delA	uc002kwx.3	+							NM_000371	NP_000362			transthyretin precursor						transport	cytoplasm	hormone activity			ovary(1)	1			OV - Ovarian serous cystadenocarcinoma(10;0.00523)		Diclofenac(DB00586)|Diethylstilbestrol(DB00255)|Diflunisal(DB00861)|Dimethyl sulfoxide(DB01093)|Levothyroxine(DB00451)|Liothyronine(DB00279)													---	---	---	---
Unknown	0	broad.mit.edu	37	18	29362633	29362634	+	IGR	INS	-	CA	CA			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:29362633_29362634insCA								MCART2 (21790 upstream) : KIAA1012 (46503 downstream)																																			---	---	---	---
KIAA1012	22878	broad.mit.edu	37	18	29429382	29429382	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:29429382delA	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	29471172	29471173	+	Intron	INS	-	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:29471172_29471173insA	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	29607568	29607568	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:29607568delA	uc002kxf.1	+							NM_017831	NP_060301			ring finger protein 125						negative regulation of type I interferon production	intracellular	ligase activity|zinc ion binding				0																		---	---	---	---
RNF125	54941	broad.mit.edu	37	18	29615790	29615790	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:29615790delA	uc002kxf.1	+							NM_017831	NP_060301			ring finger protein 125						negative regulation of type I interferon production	intracellular	ligase activity|zinc ion binding				0																		---	---	---	---
RNF138	51444	broad.mit.edu	37	18	29670944	29670944	+	5'Flank	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:29670944delT	uc002kxg.2	+						RNF138_uc002kxh.2_5'Flank	NM_016271	NP_057355			ring finger protein 138 isoform 1						Wnt receptor signaling pathway	intracellular	ligase activity|protein kinase binding|zinc ion binding				0																		---	---	---	---
KLHL14	57565	broad.mit.edu	37	18	30291118	30291118	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:30291118delA	uc002kxm.1	-						KLHL14_uc010dmd.1_Intron	NM_020805	NP_065856			kelch-like 14							cytosol|endoplasmic reticulum membrane				ovary(1)	1																		---	---	---	---
C18orf34	374864	broad.mit.edu	37	18	30634387	30634387	+	Intron	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:30634387delC	uc002kxn.2	-						C18orf34_uc010xbq.1_Intron|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																		---	---	---	---
C18orf34	374864	broad.mit.edu	37	18	30813548	30813549	+	Intron	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:30813548_30813549delTT	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																		---	---	---	---
NOL4	8715	broad.mit.edu	37	18	31639408	31639408	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:31639408delT	uc010dmi.2	-						NOL4_uc002kxr.3_Intron|NOL4_uc010xbt.1_Intron|NOL4_uc010dmh.2_Intron|NOL4_uc010xbu.1_Intron|NOL4_uc002kxt.3_Intron|NOL4_uc010xbw.1_Intron	NM_003787	NP_003778			nucleolar protein 4							nucleolus	RNA binding			ovary(3)	3																		---	---	---	---
NOL4	8715	broad.mit.edu	37	18	31795821	31795821	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:31795821delA	uc010dmi.2	-						NOL4_uc002kxr.3_Intron|NOL4_uc010xbt.1_Intron|NOL4_uc010dmh.2_Intron|NOL4_uc010xbu.1_Intron|NOL4_uc002kxt.3_Intron	NM_003787	NP_003778			nucleolar protein 4							nucleolus	RNA binding			ovary(3)	3																		---	---	---	---
Unknown	0	broad.mit.edu	37	18	31994309	31994310	+	IGR	DEL	AC	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:31994309_31994310delAC								NOL4 (190863 upstream) : DTNA (78944 downstream)																																			---	---	---	---
DTNA	1837	broad.mit.edu	37	18	32158367	32158367	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:32158367delT	uc002kxw.2	+						DTNA_uc002kxu.2_Intron|DTNA_uc010xbx.1_Intron|DTNA_uc002kxv.3_Intron	NM_032975	NP_116757			dystrobrevin alpha isoform 2						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	32257323	32257323	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:32257323delA	uc010dmj.2	+						DTNA_uc002kxu.2_Intron|DTNA_uc010xbx.1_Intron|DTNA_uc002kxv.3_Intron|DTNA_uc002kxw.2_Intron|DTNA_uc002kxx.2_Intron|DTNA_uc002kxz.2_Intron|DTNA_uc002kxy.2_Intron|DTNA_uc010dmk.1_5'Flank	NM_032975	NP_116757			dystrobrevin alpha isoform 2						neuromuscular synaptic transmission|signal transduction|striated muscle contraction	cell junction|cytoplasm|synapse	calcium ion binding|protein binding|zinc ion binding				0																		---	---	---	---
MAPRE2	10982	broad.mit.edu	37	18	32694983	32694983	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:32694983delT	uc002kyg.2	+						MAPRE2_uc010xcb.1_Intron|MAPRE2_uc010xcc.1_Intron|MAPRE2_uc002kyf.2_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	33022763	33022763	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:33022763delA								ZNF396 (65462 upstream) : INO80C (10527 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	33364947	33364948	+	IGR	DEL	TG	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:33364947_33364948delTG								GALNT1 (73150 upstream) : MIR187 (119833 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	33469097	33469097	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:33469097delA								GALNT1 (177300 upstream) : MIR187 (15684 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	33534257	33534258	+	IGR	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:33534257_33534258delAA								MIR187 (49368 upstream) : C18orf21 (18330 downstream)																																			---	---	---	---
RPRD1A	55197	broad.mit.edu	37	18	33620831	33620831	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:33620831delA	uc002kzf.1	-						RPRD1A_uc002kze.1_Intron|RPRD1A_uc002kzg.2_Intron|RPRD1A_uc010dmw.2_Intron|RPRD1A_uc010dmx.2_Intron	NM_018170	NP_060640			regulation of nuclear pre-mRNA domain containing											ovary(1)|breast(1)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	18	33686425	33686426	+	IGR	INS	-	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:33686425_33686426insT								RPRD1A (39052 upstream) : SLC39A6 (2069 downstream)																																			---	---	---	---
ELP2	55250	broad.mit.edu	37	18	33738964	33738964	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:33738964delT	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	33781973	33781973	+	Intron	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:33781973delG	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)													---	---	---	---
MOCOS	55034	broad.mit.edu	37	18	33790652	33790652	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:33790652delA	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	34308556	34308557	+	Intron	DEL	TT	-	-	rs113530739		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:34308556_34308557delTT	uc002kzt.1	+						FHOD3_uc002kzs.1_Intron|FHOD3_uc010dmz.1_Intron|FHOD3_uc010dnb.1_5'Flank	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)																---	---	---	---
KIAA1328	57536	broad.mit.edu	37	18	34592877	34592877	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:34592877delT	uc002kzz.2	+						KIAA1328_uc002lab.2_Intron|KIAA1328_uc002lac.1_Intron|KIAA1328_uc010dnc.1_Intron	NM_020776	NP_065827			hypothetical protein LOC57536											central_nervous_system(1)	1				COAD - Colon adenocarcinoma(74;0.195)														---	---	---	---
KIAA1328	57536	broad.mit.edu	37	18	34692723	34692723	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:34692723delA	uc002kzz.2	+						KIAA1328_uc002lab.2_Intron|KIAA1328_uc002lac.1_Intron|KIAA1328_uc010dnc.1_Intron	NM_020776	NP_065827			hypothetical protein LOC57536											central_nervous_system(1)	1				COAD - Colon adenocarcinoma(74;0.195)														---	---	---	---
KIAA1328	57536	broad.mit.edu	37	18	34789719	34789720	+	Intron	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:34789719_34789720delAA	uc002kzz.2	+						KIAA1328_uc002lab.2_Intron|KIAA1328_uc002lac.1_Intron|KIAA1328_uc010dnc.1_Intron	NM_020776	NP_065827			hypothetical protein LOC57536											central_nervous_system(1)	1				COAD - Colon adenocarcinoma(74;0.195)														---	---	---	---
KIAA1328	57536	broad.mit.edu	37	18	34806244	34806245	+	Intron	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:34806244_34806245delTT	uc010dnc.1	+							NM_020776				hypothetical protein LOC57536											central_nervous_system(1)	1				COAD - Colon adenocarcinoma(74;0.195)														---	---	---	---
CELF4	56853	broad.mit.edu	37	18	35139480	35139480	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:35139480delT	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																		---	---	---	---
Unknown	0	broad.mit.edu	37	18	35254318	35254318	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:35254318delT								CELF4 (108318 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	35487442	35487442	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:35487442delT								CELF4 (341442 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	36463526	36463527	+	IGR	DEL	AA	-	-	rs142358803		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:36463526_36463527delAA								None (None upstream) : LOC647946 (323361 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	36540218	36540218	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:36540218delA								None (None upstream) : LOC647946 (246670 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	36592821	36592821	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:36592821delA								None (None upstream) : LOC647946 (194067 downstream)																																			---	---	---	---
LOC647946	647946	broad.mit.edu	37	18	37337385	37337385	+	Intron	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:37337385delC	uc002lal.1	-											Homo sapiens cDNA FLJ33284 fis, clone ASTRO2009458.												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	18	37915790	37915790	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:37915790delT								LOC647946 (535508 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	38617142	38617144	+	IGR	DEL	TTT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:38617142_38617144delTTT								None (None upstream) : KC6 (443094 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	39059276	39059277	+	IGR	INS	-	AC	AC	rs34239471		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:39059276_39059277insAC								None (None upstream) : KC6 (961 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	39305015	39305015	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:39305015delT								KC6 (204454 upstream) : PIK3C3 (230184 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	39470551	39470551	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:39470551delA								KC6 (369990 upstream) : PIK3C3 (64648 downstream)																																			---	---	---	---
PIK3C3	5289	broad.mit.edu	37	18	39570410	39570410	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:39570410delT	uc002lap.2	+						PIK3C3_uc010xcl.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	39993900	39993900	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:39993900delT	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	40880719	40880719	+	IGR	DEL	T	-	-	rs113713587		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:40880719delT								SYT4 (23104 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	40889231	40889231	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:40889231delT								SYT4 (31616 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	41491247	41491247	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:41491247delT								SYT4 (633632 upstream) : SETBP1 (768891 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	41661939	41661939	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:41661939delA								SYT4 (804324 upstream) : SETBP1 (598199 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	41988039	41988040	+	Intron	INS	-	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:41988039_41988040insA	uc002lax.3	-											Homo sapiens cDNA clone IMAGE:5265929.																														---	---	---	---
Unknown	0	broad.mit.edu	37	18	42161029	42161029	+	IGR	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:42161029delC								None (None upstream) : SETBP1 (99109 downstream)																																			---	---	---	---
SETBP1	26040	broad.mit.edu	37	18	42618293	42618293	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:42618293delT	uc010dni.2	+							NM_015559	NP_056374			SET binding protein 1 isoform a							nucleus	DNA binding			upper_aerodigestive_tract(2)|large_intestine(1)	3				Colorectal(1;0.0622)|COAD - Colon adenocarcinoma(74;0.201)										Schinzel-Giedion_syndrome				---	---	---	---
SETBP1	26040	broad.mit.edu	37	18	42620288	42620289	+	Intron	INS	-	TAG	TAG	rs150044374	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:42620288_42620289insTAG	uc010dni.2	+							NM_015559	NP_056374			SET binding protein 1 isoform a							nucleus	DNA binding			upper_aerodigestive_tract(2)|large_intestine(1)	3				Colorectal(1;0.0622)|COAD - Colon adenocarcinoma(74;0.201)										Schinzel-Giedion_syndrome				---	---	---	---
SLC14A2	8170	broad.mit.edu	37	18	42776269	42776269	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:42776269delT	uc002lbb.2	+							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	42985915	42985915	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:42985915delT	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																		---	---	---	---
KIAA1632	57724	broad.mit.edu	37	18	43518273	43518273	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:43518273delA	uc002lbm.2	-						KIAA1632_uc002lbo.1_Intron	NM_020964	NP_066015			hypothetical protein LOC57724						autophagy						0																		---	---	---	---
C18orf25	147339	broad.mit.edu	37	18	43778571	43778571	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:43778571delT	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	43793353	43793353	+	Intron	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:43793353delC	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	43816797	43816797	+	Intron	DEL	T	-	-	rs67013385		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:43816797delT	uc002lbw.2	+						C18orf25_uc002lbx.2_Intron	NM_145055	NP_659492			ARKadia-like 1 isoform a											central_nervous_system(2)	2																		---	---	---	---
LOXHD1	125336	broad.mit.edu	37	18	44225735	44225736	+	Intron	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:44225735_44225736delAA	uc010xcw.1	-							NM_144612	NP_653213			lipoxygenase homology domains 1 isoform 1						sensory perception of sound	stereocilium	protein binding				0																		---	---	---	---
PIAS2	9063	broad.mit.edu	37	18	44449203	44449203	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:44449203delA	uc002lck.2	-						PIAS2_uc010dnp.2_Intron|PIAS2_uc002lcl.2_Intron|PIAS2_uc010xda.1_Intron|PIAS2_uc002lcm.2_Intron|PIAS2_uc002lcn.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	44573315	44573315	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:44573315delT	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																		---	---	---	---
KATNAL2	83473	broad.mit.edu	37	18	44626462	44626469	+	Intron	DEL	TCTCTTCC	-	-	rs3217429		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:44626462_44626469delTCTCTTCC	uc002lco.2	+						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																OREG0024959	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	44633292	44633293	+	IGR	DEL	CT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:44633292_44633293delCT								KATNAL2 (4679 upstream) : HDHD2 (489 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	45095248	45095249	+	Intron	DEL	AG	-	-	rs4061714		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:45095248_45095249delAG	uc002lcx.2	+											Homo sapiens, clone IMAGE:5538207, mRNA.																														---	---	---	---
Unknown	0	broad.mit.edu	37	18	45105580	45105580	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:45105580delA	uc002lcx.2	+											Homo sapiens, clone IMAGE:5538207, mRNA.																														---	---	---	---
ZBTB7C	201501	broad.mit.edu	37	18	45684405	45684406	+	Intron	DEL	CT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:45684405_45684406delCT	uc010dnv.2	-						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																		---	---	---	---
ZBTB7C	201501	broad.mit.edu	37	18	45701605	45701605	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:45701605delT	uc010dnw.2	-						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																		---	---	---	---
ZBTB7C	201501	broad.mit.edu	37	18	45821928	45821929	+	Intron	INS	-	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:45821928_45821929insT	uc010dnw.2	-						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																OREG0024966	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
ZBTB7C	201501	broad.mit.edu	37	18	45829348	45829348	+	Intron	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:45829348delG	uc010dnw.2	-						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																		---	---	---	---
Unknown	0	broad.mit.edu	37	18	46005696	46005697	+	IGR	INS	-	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:46005696_46005697insT								ZBTB7C (70033 upstream) : KIAA0427 (59730 downstream)																																			---	---	---	---
KIAA0427	9811	broad.mit.edu	37	18	46186150	46186150	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:46186150delT	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	46323866	46323868	+	Intron	DEL	GGT	-	-	rs62103272	by1000genomes;by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:46323866_46323868delGGT	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																		---	---	---	---
DYM	54808	broad.mit.edu	37	18	46858390	46858390	+	Intron	DEL	A	-	-	rs148345006		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:46858390delA	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	47039740	47039740	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:47039740delA								RPL17 (20834 upstream) : LIPG (48687 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	47142544	47142544	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:47142544delA								LIPG (23268 upstream) : ACAA2 (167331 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	47147669	47147669	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-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	47176236	47176237	+	IGR	DEL	AA	-	-	rs79766747		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:47176236_47176237delAA								LIPG (56960 upstream) : ACAA2 (133638 downstream)																																			---	---	---	---
MYO5B	4645	broad.mit.edu	37	18	47484301	47484301	+	Intron	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:47484301delC	uc002leb.2	-						MYO5B_uc002lec.1_Intron	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)														---	---	---	---
MYO5B	4645	broad.mit.edu	37	18	47629291	47629291	+	Intron	DEL	T	-	-	rs111661597		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:47629291delT	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	47740256	47740256	+	IGR	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:47740256delG								MYO5B (18805 upstream) : CCDC11 (13307 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	48284619	48284619	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:48284619delA								MAPK4 (26424 upstream) : MRO (36872 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	48485546	48485547	+	IGR	DEL	CC	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:48485546_48485547delCC								ME2 (11288 upstream) : ELAC1 (8840 downstream)																																			---	---	---	---
SMAD4	4089	broad.mit.edu	37	18	48573269	48573270	+	Intron	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:48573269_48573270delTT	uc010xdp.1	+						SMAD4_uc010xdo.1_Intron	NM_005359	NP_005350			mothers against decapentaplegic homolog 4						BMP signaling pathway|negative regulation of cell growth|negative regulation of protein catabolic process|negative regulation of transcription, DNA-dependent|palate development|positive regulation of epithelial to mesenchymal transition|positive regulation of pathway-restricted SMAD protein phosphorylation|positive regulation of SMAD protein import into nucleus|positive regulation of transforming growth factor beta receptor signaling pathway|regulation of transforming growth factor-beta2 production|response to hypoxia|response to transforming growth factor beta stimulus|SMAD protein complex assembly|SMAD protein signal transduction|transforming growth factor beta receptor signaling pathway	activin responsive factor complex|centrosome|cytosol	I-SMAD binding|protein homodimerization activity|R-SMAD binding|transcription regulatory region DNA binding|transforming growth factor beta receptor, common-partner cytoplasmic mediator activity			pancreas(170)|large_intestine(108)|thyroid(19)|lung(11)|small_intestine(9)|upper_aerodigestive_tract(8)|biliary_tract(8)|ovary(7)|breast(6)|stomach(5)|oesophagus(3)|testis(2)|central_nervous_system(2)|haematopoietic_and_lymphoid_tissue(2)|gastrointestinal_tract_(site_indeterminate)(2)|liver(2)|kidney(1)|urinary_tract(1)|vulva(1)|skin(1)|NS(1)	369		all_cancers(7;0.203)|Colorectal(6;0.003)|all_epithelial(6;0.00336)		Colorectal(16;0.0032)|COAD - Colon adenocarcinoma(17;0.0708)|READ - Rectum adenocarcinoma(32;0.155)										Juvenile_Polyposis|Hereditary_Hemorrhagic_Telangiectasia				---	---	---	---
SMAD4	4089	broad.mit.edu	37	18	48608589	48608589	+	3'UTR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:48608589delT	uc010xdp.1	+	12					SMAD4_uc002lfb.3_3'UTR	NM_005359	NP_005350			mothers against decapentaplegic homolog 4						BMP signaling pathway|negative regulation of cell growth|negative regulation of protein catabolic process|negative regulation of transcription, DNA-dependent|palate development|positive regulation of epithelial to mesenchymal transition|positive regulation of pathway-restricted SMAD protein phosphorylation|positive regulation of SMAD protein import into nucleus|positive regulation of transforming growth factor beta receptor signaling pathway|regulation of transforming growth factor-beta2 production|response to hypoxia|response to transforming growth factor beta stimulus|SMAD protein complex assembly|SMAD protein signal transduction|transforming growth factor beta receptor signaling pathway	activin responsive factor complex|centrosome|cytosol	I-SMAD binding|protein homodimerization activity|R-SMAD binding|transcription regulatory region DNA binding|transforming growth factor beta receptor, common-partner cytoplasmic mediator activity			pancreas(170)|large_intestine(108)|thyroid(19)|lung(11)|small_intestine(9)|upper_aerodigestive_tract(8)|biliary_tract(8)|ovary(7)|breast(6)|stomach(5)|oesophagus(3)|testis(2)|central_nervous_system(2)|haematopoietic_and_lymphoid_tissue(2)|gastrointestinal_tract_(site_indeterminate)(2)|liver(2)|kidney(1)|urinary_tract(1)|vulva(1)|skin(1)|NS(1)	369		all_cancers(7;0.203)|Colorectal(6;0.003)|all_epithelial(6;0.00336)		Colorectal(16;0.0032)|COAD - Colon adenocarcinoma(17;0.0708)|READ - Rectum adenocarcinoma(32;0.155)										Juvenile_Polyposis|Hereditary_Hemorrhagic_Telangiectasia				---	---	---	---
Unknown	0	broad.mit.edu	37	18	48619223	48619223	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:48619223delT								SMAD4 (7814 upstream) : MEX3C (81699 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	48656438	48656438	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:48656438delT								SMAD4 (45029 upstream) : MEX3C (44484 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	49484087	49484088	+	IGR	INS	-	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:49484087_49484088insA								MEX3C (760397 upstream) : DCC (382483 downstream)																																			---	---	---	---
DCC	1630	broad.mit.edu	37	18	50951476	50951476	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:50951476delT	uc002lfe.1	+						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	51012694	51012695	+	Intron	DEL	TC	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:51012694_51012695delTC	uc002lfe.1	+						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	51668878	51668878	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:51668878delA								DCC (611096 upstream) : MBD2 (11697 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	52453343	52453343	+	IGR	DEL	T	-	-	rs75271107		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:52453343delT								C18orf26 (186619 upstream) : RAB27B (42497 downstream)																																			---	---	---	---
TCF4	6925	broad.mit.edu	37	18	53070794	53070794	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:53070794delA	uc002lfz.2	-						TCF4_uc010xdu.1_5'Flank|TCF4_uc010xdv.1_5'Flank|TCF4_uc002lfx.2_Intron|TCF4_uc010xdw.1_Intron|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_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)														---	---	---	---
TCF4	6925	broad.mit.edu	37	18	53224660	53224660	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:53224660delA	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	53377484	53377485	+	IGR	DEL	TG	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:53377484_53377485delTG								TCF4 (74299 upstream) : TXNL1 (892570 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	53455338	53455338	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:53455338delA								TCF4 (152153 upstream) : TXNL1 (814717 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	53995602	53995602	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:53995602delA								TCF4 (692417 upstream) : TXNL1 (274453 downstream)																																			---	---	---	---
WDR7	23335	broad.mit.edu	37	18	54591392	54591392	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:54591392delT	uc002lgk.1	+						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	55098126	55098126	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:55098126delA								ST8SIA3 (61967 upstream) : ONECUT2 (4791 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	55526741	55526742	+	IGR	INS	-	AG	AG	rs148288517	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:55526741_55526742insAG								ATP8B1 (127702 upstream) : NEDD4L (184877 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	55559410	55559411	+	IGR	DEL	TC	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:55559410_55559411delTC								ATP8B1 (160371 upstream) : NEDD4L (152208 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	55610954	55610956	+	IGR	DEL	TCT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:55610954_55610956delTCT								ATP8B1 (211915 upstream) : NEDD4L (100663 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	55618823	55618823	+	IGR	DEL	T	-	-	rs35100190		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:55618823delT								ATP8B1 (219784 upstream) : NEDD4L (92796 downstream)																																			---	---	---	---
NEDD4L	23327	broad.mit.edu	37	18	55727830	55727830	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:55727830delA	uc002lgy.2	+						NEDD4L_uc002lgz.2_Intron|NEDD4L_uc002lgx.2_Intron|NEDD4L_uc010xee.1_Intron|NEDD4L_uc002lha.1_Intron	NM_001144967	NP_001138439			neural precursor cell expressed, developmentally						cellular sodium ion homeostasis|excretion|interspecies interaction between organisms|positive regulation of endocytosis|protein ubiquitination involved in ubiquitin-dependent protein catabolic process|regulation of protein catabolic process|response to metal ion|sodium ion transport|water homeostasis	cytoplasm	protein binding|sodium channel regulator activity|ubiquitin-protein ligase activity			lung(4)	4																		---	---	---	---
NEDD4L	23327	broad.mit.edu	37	18	55990672	55990672	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:55990672delA	uc002lgy.2	+						NEDD4L_uc002lgz.2_Intron|NEDD4L_uc002lgx.2_Intron|NEDD4L_uc010xee.1_Intron|NEDD4L_uc002lhc.2_Intron|NEDD4L_uc002lhd.2_Intron|NEDD4L_uc002lhb.2_Intron|NEDD4L_uc002lhe.2_Intron|NEDD4L_uc002lhf.2_Intron|NEDD4L_uc002lhg.2_Intron|NEDD4L_uc002lhh.2_Intron|NEDD4L_uc010dpm.1_Intron	NM_001144967	NP_001138439			neural precursor cell expressed, developmentally						cellular sodium ion homeostasis|excretion|interspecies interaction between organisms|positive regulation of endocytosis|protein ubiquitination involved in ubiquitin-dependent protein catabolic process|regulation of protein catabolic process|response to metal ion|sodium ion transport|water homeostasis	cytoplasm	protein binding|sodium channel regulator activity|ubiquitin-protein ligase activity			lung(4)	4																		---	---	---	---
NEDD4L	23327	broad.mit.edu	37	18	56053590	56053590	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:56053590delT	uc002lgy.2	+						NEDD4L_uc002lgz.2_Intron|NEDD4L_uc002lgx.2_Intron|NEDD4L_uc010xee.1_Intron|NEDD4L_uc002lhc.2_Intron|NEDD4L_uc002lhd.2_Intron|NEDD4L_uc002lhb.2_Intron|NEDD4L_uc002lhe.2_Intron|NEDD4L_uc002lhf.2_Intron|NEDD4L_uc002lhg.2_Intron|NEDD4L_uc002lhh.2_Intron|NEDD4L_uc010dpn.2_Intron	NM_001144967	NP_001138439			neural precursor cell expressed, developmentally						cellular sodium ion homeostasis|excretion|interspecies interaction between organisms|positive regulation of endocytosis|protein ubiquitination involved in ubiquitin-dependent protein catabolic process|regulation of protein catabolic process|response to metal ion|sodium ion transport|water homeostasis	cytoplasm	protein binding|sodium channel regulator activity|ubiquitin-protein ligase activity			lung(4)	4																		---	---	---	---
ALPK2	115701	broad.mit.edu	37	18	56184954	56184954	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:56184954delT	uc002lhj.3	-							NM_052947	NP_443179			heart alpha-kinase								ATP binding|protein serine/threonine kinase activity			ovary(7)|skin(5)|lung(1)|central_nervous_system(1)	14																		---	---	---	---
ALPK2	115701	broad.mit.edu	37	18	56271044	56271044	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:56271044delA	uc002lhj.3	-							NM_052947	NP_443179			heart alpha-kinase								ATP binding|protein serine/threonine kinase activity			ovary(7)|skin(5)|lung(1)|central_nervous_system(1)	14																		---	---	---	---
Unknown	0	broad.mit.edu	37	18	56915943	56915943	+	IGR	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:56915943delG								GRP (17943 upstream) : RAX (18326 downstream)																																			---	---	---	---
CPLX4	339302	broad.mit.edu	37	18	56985740	56985740	+	5'UTR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:56985740delA	uc002lhy.2	-	1						NM_181654	NP_857637			complexin 4 precursor						exocytosis|neurotransmitter transport	cell junction|synapse	syntaxin binding			ovary(1)	1		Colorectal(73;0.175)																---	---	---	---
CCBE1	147372	broad.mit.edu	37	18	57273388	57273389	+	Intron	INS	-	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:57273388_57273389insA	uc002lib.2	-							NM_133459	NP_597716			collagen and calcium binding EGF domains 1						lymphangiogenesis|sprouting angiogenesis|venous blood vessel morphogenesis	collagen	calcium ion binding			skin(2)|ovary(1)	3		Colorectal(73;0.175)																---	---	---	---
Unknown	0	broad.mit.edu	37	18	58166823	58166823	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:58166823delA								MC4R (126822 upstream) : CDH20 (834165 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	58861557	58861558	+	IGR	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:58861557_58861558delAA								MC4R (821556 upstream) : CDH20 (139430 downstream)																																			---	---	---	---
CDH20	28316	broad.mit.edu	37	18	59024630	59024630	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:59024630delT	uc002lif.2	+							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)																---	---	---	---
Unknown	0	broad.mit.edu	37	18	59400984	59400984	+	IGR	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:59400984delG								CDH20 (178619 upstream) : RNF152 (81320 downstream)																																			---	---	---	---
RNF152	220441	broad.mit.edu	37	18	59496759	59496760	+	Intron	DEL	GA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:59496759_59496760delGA	uc002lih.1	-							NM_173557	NP_775828			ring finger protein 152						apoptosis|protein K48-linked ubiquitination	integral to membrane|lysosomal membrane	ubiquitin-protein ligase activity|zinc ion binding			breast(1)	1		Colorectal(73;0.186)																---	---	---	---
Unknown	0	broad.mit.edu	37	18	59592644	59592644	+	IGR	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:59592644delC								RNF152 (32340 upstream) : PIGN (118816 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	59621035	59621035	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:59621035delA								RNF152 (60731 upstream) : PIGN (90425 downstream)																																			---	---	---	---
KIAA1468	57614	broad.mit.edu	37	18	59888438	59888438	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:59888438delT	uc002lil.2	+						KIAA1468_uc002lik.1_Intron|KIAA1468_uc010xel.1_Intron|KIAA1468_uc002lim.2_5'Flank	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	60101716	60101716	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:60101716delT								TNFRSF11A (48214 upstream) : ZCCHC2 (88942 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	60141073	60141073	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:60141073delT								TNFRSF11A (87571 upstream) : ZCCHC2 (49585 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	60272044	60272045	+	IGR	INS	-	AGGAGGAGA	AGGAGGAGA	rs55893096	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:60272044_60272045insAGGAGGAGA								ZCCHC2 (18082 upstream) : PHLPP1 (110689 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	60347161	60347161	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:60347161delA								ZCCHC2 (93199 upstream) : PHLPP1 (35573 downstream)																																			---	---	---	---
KDSR	2531	broad.mit.edu	37	18	61015077	61015077	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:61015077delA	uc010dpw.2	-						KDSR_uc010xem.1_Intron	NM_002035	NP_002026			3-ketodihydrosphingosine reductase precursor						3-keto-sphinganine metabolic process	endoplasmic reticulum membrane|extracellular space|integral to membrane	3-dehydrosphinganine reductase activity|binding			skin(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	18	61188848	61188848	+	IGR	DEL	A	-	-	rs115946894	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:61188848delA								SERPINB5 (16531 upstream) : SERPINB12 (34545 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	61268562	61268562	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:61268562delT								SERPINB13 (2130 upstream) : SERPINB4 (35933 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	61396962	61396963	+	IGR	INS	-	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:61396962_61396963insA								SERPINB11 (3298 upstream) : SERPINB7 (23314 downstream)																																			---	---	---	---
SERPINB2	5055	broad.mit.edu	37	18	61554876	61554876	+	5'Flank	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:61554876delA	uc010xeu.1	+						SERPINB2_uc002ljo.2_5'Flank|SERPINB2_uc010dqh.2_5'Flank	NM_001143818	NP_001137290			serine (or cysteine) proteinase inhibitor, clade						anti-apoptosis|blood coagulation|fibrinolysis|regulation of proteolysis	extracellular space|Golgi apparatus|plasma membrane	serine-type endopeptidase inhibitor activity			lung(1)|skin(1)	2		Esophageal squamous(42;0.131)			Alteplase(DB00009)|Anistreplase(DB00029)|Reteplase(DB00015)|Tenecteplase(DB00031)|Urokinase(DB00013)													---	---	---	---
Unknown	0	broad.mit.edu	37	18	61977090	61977090	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:61977090delA	uc002ljx.2	+											Homo sapiens hypothetical protein LOC284294, mRNA (cDNA clone IMAGE:4823205).																														---	---	---	---
Unknown	0	broad.mit.edu	37	18	62337708	62337708	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:62337708delA								C18orf20 (521448 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	62873352	62873352	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:62873352delA								None (None upstream) : CDH7 (544136 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	63142649	63142662	+	IGR	DEL	AAAAAAAAAAAAAA	-	-	rs74171765		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:63142649_63142662delAAAAAAAAAAAAAA								None (None upstream) : CDH7 (274826 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	63204107	63204107	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:63204107delA								None (None upstream) : CDH7 (213381 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	63255565	63255566	+	IGR	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:63255565_63255566delTT								None (None upstream) : CDH7 (161922 downstream)																																			---	---	---	---
CDH7	1005	broad.mit.edu	37	18	63481586	63481586	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:63481586delT	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	63947308	63947308	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:63947308delA								CDH7 (399134 upstream) : CDH19 (224013 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	64142234	64142234	+	IGR	DEL	A	-	-	rs113573703		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:64142234delA								CDH7 (594060 upstream) : CDH19 (29087 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	64397034	64397034	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:64397034delT								CDH19 (125818 upstream) : DSEL (776785 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	65042307	65042308	+	IGR	DEL	TT	-	-	rs75002100		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:65042307_65042308delTT								CDH19 (771091 upstream) : DSEL (131511 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	66176669	66176670	+	IGR	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:66176669_66176670delTT								DSEL (992702 upstream) : TMX3 (164257 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	66209531	66209532	+	IGR	DEL	AA	-	-	rs139458955	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:66209531_66209532delAA								None (None upstream) : TMX3 (131395 downstream)																																			---	---	---	---
CCDC102B	79839	broad.mit.edu	37	18	66630668	66630668	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:66630668delA	uc002lkk.2	+						CCDC102B_uc002lki.2_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)																---	---	---	---
Unknown	0	broad.mit.edu	37	18	67661929	67661929	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:67661929delA								CD226 (37697 upstream) : RTTN (9114 downstream)																																			---	---	---	---
RTTN	25914	broad.mit.edu	37	18	67835048	67835048	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:67835048delA	uc002lkp.2	-						RTTN_uc002lko.2_Intron|RTTN_uc010xfb.1_Intron|RTTN_uc002lkq.1_Intron	NM_173630	NP_775901			rotatin								binding			ovary(3)|pancreas(2)|skin(1)|breast(1)|central_nervous_system(1)	8		Esophageal squamous(42;0.129)																---	---	---	---
Unknown	0	broad.mit.edu	37	18	67936254	67936254	+	IGR	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:67936254delC								RTTN (63292 upstream) : SOCS6 (19883 downstream)																																			---	---	---	---
SOCS6	9306	broad.mit.edu	37	18	67987236	67987236	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:67987236delT	uc002lkr.1	+						SOCS6_uc010dqq.2_Intron	NM_004232	NP_004223			suppressor of cytokine signaling 6						defense response|JAK-STAT cascade|negative regulation of signal transduction|regulation of growth	cytoplasm				large_intestine(1)|lung(1)	2		Esophageal squamous(42;0.129)|Colorectal(73;0.152)																---	---	---	---
Unknown	0	broad.mit.edu	37	18	68902882	68902882	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:68902882delA								SOCS6 (905448 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	68939513	68939516	+	IGR	DEL	AAAA	-	-	rs34909434		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:68939513_68939516delAAAA								SOCS6 (942079 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	69402773	69402774	+	IGR	DEL	AC	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:69402773_69402774delAC								None (None upstream) : CBLN2 (801141 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	69676819	69676819	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:69676819delA								None (None upstream) : CBLN2 (527096 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	69779055	69779055	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:69779055delT								None (None upstream) : CBLN2 (424860 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	70126490	70126491	+	IGR	DEL	AC	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:70126490_70126491delAC								None (None upstream) : CBLN2 (77424 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	70405796	70405797	+	IGR	DEL	GA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:70405796_70405797delGA								CBLN2 (194073 upstream) : NETO1 (3754 downstream)																																			---	---	---	---
NETO1	81832	broad.mit.edu	37	18	70526116	70526116	+	Frame_Shift_Del	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:70526116delA	uc002lkw.2	-	4	698	c.414delT	c.(412-414)TTTfs	p.F138fs	NETO1_uc002lkx.1_Frame_Shift_Del_p.F137fs|NETO1_uc002lky.1_Frame_Shift_Del_p.F138fs|NETO1_uc002lkz.2_Frame_Shift_Del_p.F137fs	NM_138966	NP_620416	Q8TDF5	NETO1_HUMAN	neuropilin- and tolloid-like protein 1 isoform 3	138	CUB 1.|Extracellular (Potential).				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	70605650	70605651	+	IGR	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:70605650_70605651delTT								NETO1 (70840 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	70884181	70884181	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:70884181delA	uc002lla.1	-						uc002llb.2_Intron					Homo sapiens cDNA clone IMAGE:3842655.																														---	---	---	---
FAM69C	125704	broad.mit.edu	37	18	72117233	72117233	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:72117233delA	uc002llk.2	-							NM_001044369	NP_001037834			hypothetical protein LOC125704							endoplasmic reticulum membrane|integral to membrane					0																		---	---	---	---
ZNF407	55628	broad.mit.edu	37	18	72441462	72441462	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:72441462delT	uc002llw.2	+						ZNF407_uc010xfc.1_Intron|ZNF407_uc010dqu.1_Intron	NM_017757	NP_060227			zinc finger protein 407 isoform 1						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(2)	2		Esophageal squamous(42;0.131)|Prostate(75;0.173)		BRCA - Breast invasive adenocarcinoma(31;0.184)														---	---	---	---
ZADH2	284273	broad.mit.edu	37	18	72913368	72913368	+	3'UTR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:72913368delT	uc002llx.2	-	2					ZADH2_uc010dqv.2_3'UTR	NM_175907	NP_787103			zinc binding alcohol dehydrogenase domain							peroxisome	oxidoreductase activity|zinc ion binding				0		Esophageal squamous(42;0.131)|Prostate(75;0.155)		READ - Rectum adenocarcinoma(2;0.0276)|BRCA - Breast invasive adenocarcinoma(31;0.216)														---	---	---	---
Unknown	0	broad.mit.edu	37	18	73264404	73264404	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:73264404delT								C18orf62 (124815 upstream) : ZNF516 (807215 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	73631678	73631678	+	IGR	DEL	C	-	-	rs11873707	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:73631678delC								C18orf62 (492089 upstream) : ZNF516 (439941 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	74281015	74281015	+	IGR	DEL	T	-	-	rs145563979	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:74281015delT								LOC284276 (9232 upstream) : ZNF236 (255101 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	74504541	74504541	+	IGR	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:74504541delG								LOC284276 (232758 upstream) : ZNF236 (31575 downstream)																																			---	---	---	---
MBP	4155	broad.mit.edu	37	18	74738413	74738413	+	Intron	DEL	C	-	-	rs138662159		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:74738413delC	uc010xfd.1	-						MBP_uc002lmr.2_Intron	NM_001025101	NP_001020272			Golli-mbp isoform 1						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	74760785	74760785	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:74760785delA	uc010xfd.1	-						MBP_uc002lmr.2_Intron	NM_001025101	NP_001020272			Golli-mbp isoform 1						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)														---	---	---	---
Unknown	0	broad.mit.edu	37	18	75280185	75280186	+	IGR	INS	-	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:75280185_75280186insA								GALR1 (298091 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	75380848	75380849	+	IGR	INS	-	GAGA	GAGA	rs140822329	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:75380848_75380849insGAGA								GALR1 (398754 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	75518638	75518638	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:75518638delT								GALR1 (536544 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	75530659	75530660	+	IGR	INS	-	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:75530659_75530660insT								GALR1 (548565 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	75640195	75640195	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:75640195delT								GALR1 (658101 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	75656882	75656882	+	IGR	DEL	A	-	-	rs78277550	byFrequency;by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:75656882delA								GALR1 (674788 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	75891419	75891419	+	IGR	DEL	A	-	-	rs67947426		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:75891419delA								GALR1 (909325 upstream) : SALL3 (848856 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	75966643	75966644	+	IGR	INS	-	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:75966643_75966644insG								GALR1 (984549 upstream) : SALL3 (773631 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	76459419	76459420	+	IGR	INS	-	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:76459419_76459420insA								None (None upstream) : SALL3 (280855 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	76600355	76600356	+	IGR	DEL	TG	-	-	rs72225895		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:76600355_76600356delTG								None (None upstream) : SALL3 (139919 downstream)																																			---	---	---	---
ATP9B	374868	broad.mit.edu	37	18	76872745	76872745	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:76872745delA	uc002lmx.2	+						ATP9B_uc002lmv.1_Intron|ATP9B_uc002lmw.1_Intron|ATP9B_uc002lmy.1_Intron|ATP9B_uc002lmz.1_5'Flank|ATP9B_uc002lmu.2_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)														---	---	---	---
Unknown	0	broad.mit.edu	37	18	77146176	77146176	+	IGR	DEL	T	-	-	rs71816848		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:77146176delT								ATP9B (7896 upstream) : NFATC1 (9596 downstream)																																			---	---	---	---
NFATC1	4772	broad.mit.edu	37	18	77187123	77187123	+	Intron	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:77187123delG	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)														---	---	---	---
PPAP2C	8612	broad.mit.edu	37	19	283833	283833	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:283833delT	uc002loi.2	-						PPAP2C_uc002loh.2_Intron|PPAP2C_uc002loj.2_Intron	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)														---	---	---	---
SHC2	25759	broad.mit.edu	37	19	437668	437668	+	Intron	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:437668delC	uc002loq.3	-						SHC2_uc002lop.3_Intron	NM_012435	NP_036567			SHC (Src homology 2 domain containing)						insulin receptor signaling pathway|nerve growth factor receptor signaling pathway|Ras protein signal transduction	cytosol					0		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)														---	---	---	---
CDC34	997	broad.mit.edu	37	19	537358	537358	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:537358delT	uc002lov.2	+							NM_004359	NP_004350			ubiquitin-conjugating enzyme Cdc34						DNA-dependent DNA replication initiation|G1/S transition of mitotic cell cycle|negative regulation of cAMP-mediated signaling|proteasomal ubiquitin-dependent protein catabolic process|protein K48-linked ubiquitination	cytoplasm|nucleus	ATP binding|protein binding|ubiquitin-protein ligase activity				0		all_cancers(10;1.94e-35)|all_epithelial(18;5.94e-23)|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)														---	---	---	---
Unknown	0	broad.mit.edu	37	19	780017	780018	+	IGR	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:780017_780018delAA								C19orf21 (15699 upstream) : PTBP1 (17374 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	19	836455	836456	+	IGR	INS	-	GAGACA	GAGACA	rs147339752	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:836455_836456insGAGACA								AZU1 (4438 upstream) : PRTN3 (4529 downstream)																																			---	---	---	---
C19orf22	91300	broad.mit.edu	37	19	910626	910626	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:910626delA	uc002lqg.2	-						C19orf22_uc002lqh.2_Intron|C19orf22_uc002lqi.2_Intron|C19orf22_uc002lqj.2_Intron	NM_138774	NP_620129			hypothetical protein LOC91300							nucleus	nucleic acid binding			pancreas(1)	1		Acute lymphoblastic leukemia(61;4.36e-14)|all_hematologic(61;4.84e-09)|Lung NSC(49;0.000226)|all_lung(49;0.000353)|Breast(49;0.00066)		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)														---	---	---	---
WDR18	57418	broad.mit.edu	37	19	986523	986523	+	Intron	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:986523delC	uc002lqm.1	+						WDR18_uc002lqn.1_Intron|WDR18_uc010drx.1_Intron|WDR18_uc010dry.1_Intron	NM_024100	NP_077005			WD repeat domain 18											skin(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)														---	---	---	---
HMHA1	23526	broad.mit.edu	37	19	1066729	1066729	+	5'Flank	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:1066729delC	uc002lqz.1	+						HMHA1_uc010xgd.1_Intron|HMHA1_uc010xge.1_5'Flank|HMHA1_uc002lra.1_5'Flank	NM_012292	NP_036424			minor histocompatibility antigen HA-1						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)														---	---	---	---
HMHA1	23526	broad.mit.edu	37	19	1072058	1072061	+	Intron	DEL	TTTT	-	-	rs139265073		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:1072058_1072061delTTTT	uc002lqz.1	+						HMHA1_uc010xgd.1_Intron|HMHA1_uc010xge.1_Intron|HMHA1_uc002lra.1_Intron|HMHA1_uc002lrb.1_Intron	NM_012292	NP_036424			minor histocompatibility antigen HA-1						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)														---	---	---	---
SBNO2	22904	broad.mit.edu	37	19	1164488	1164488	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:1164488delA	uc002lrk.3	-						SBNO2_uc010dse.2_Intron	NM_014963	NP_055778			strawberry notch homolog 2 isoform 1						macrophage activation involved in immune response|negative regulation of transcription, DNA-dependent|regulation of inflammatory response|transcription, DNA-dependent						0		Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;7.93e-06)|all_lung(49;1.25e-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)														---	---	---	---
DAZAP1	26528	broad.mit.edu	37	19	1427578	1427578	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:1427578delT	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)														---	---	---	---
MEX3D	399664	broad.mit.edu	37	19	1570308	1570310	+	5'Flank	DEL	TTT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:1570308_1570310delTTT	uc010dsn.2	-							NM_203304	NP_976049			ring finger and KH domain containing 1						mRNA destabilization|posttranscriptional regulation of gene expression by mRNA localization|regulation of anti-apoptosis	nucleus|perinuclear region of cytoplasm	AU-rich element binding|zinc ion binding			lung(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)														---	---	---	---
ATP8B3	148229	broad.mit.edu	37	19	1805851	1805851	+	Intron	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:1805851delC	uc002ltw.2	-						ATP8B3_uc002ltv.2_Intron|ATP8B3_uc002ltx.2_Intron|ATP8B3_uc002lty.1_Intron|ATP8B3_uc002ltz.1_Intron	NM_138813	NP_620168			ATPase, class I, type 8B, member 3						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)														---	---	---	---
REXO1	57455	broad.mit.edu	37	19	1824576	1824576	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:1824576delA	uc002lua.3	-						REXO1_uc010dsq.2_5'Flank|REXO1_uc010xgs.1_5'Flank	NM_020695	NP_065746			transcription elongation factor B polypeptide 3							nucleus	exonuclease activity|nucleic acid 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)														---	---	---	---
Unknown	0	broad.mit.edu	37	19	1984715	1984716	+	IGR	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:1984715_1984716delTT								CSNK1G2 (3381 upstream) : BTBD2 (731 downstream)																																			---	---	---	---
BTBD2	55643	broad.mit.edu	37	19	1997185	1997185	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-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)														---	---	---	---
Unknown	0	broad.mit.edu	37	19	2022453	2022460	+	IGR	DEL	TTCTTTCC	-	-	rs112312383		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:2022453_2022460delTTCTTTCC								BTBD2 (6751 upstream) : MKNK2 (15010 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	19	2025576	2025577	+	IGR	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:2025576_2025577delTT								BTBD2 (9874 upstream) : MKNK2 (11893 downstream)																																			---	---	---	---
MKNK2	2872	broad.mit.edu	37	19	2048040	2048041	+	Intron	INS	-	A	A	rs143612431	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:2048040_2048041insA	uc002lus.2	-						MKNK2_uc010xgu.1_5'Flank|MKNK2_uc010xgv.1_Intron|MKNK2_uc002lur.2_Intron	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	2077788	2077788	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:2077788delT	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)														---	---	---	---
Unknown	0	broad.mit.edu	37	19	2157005	2157006	+	IGR	INS	-	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:2157005_2157006insA								AP3D1 (5449 upstream) : DOT1L (7142 downstream)																																			---	---	---	---
DOT1L	84444	broad.mit.edu	37	19	2209229	2209230	+	Intron	DEL	TC	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:2209229_2209230delTC	uc002lvb.3	+						DOT1L_uc002lvc.1_5'Flank	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)														---	---	---	---
LINGO3	645191	broad.mit.edu	37	19	2294054	2294054	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:2294054delA	uc010dsx.1	-						SPPL2B_uc010dsw.1_Intron	NM_001101391	NP_001094861			leucine rich repeat and Ig domain containing 3							integral to membrane					0																		---	---	---	---
GNG7	2788	broad.mit.edu	37	19	2590484	2590487	+	Intron	DEL	CATC	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:2590484_2590487delCATC	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	2632073	2632073	+	Intron	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:2632073delC	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	2648871	2648872	+	Intron	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:2648871_2648872delTT	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	2707322	2707323	+	IGR	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:2707322_2707323delTT								GNG7 (4576 upstream) : DIRAS1 (7242 downstream)																																			---	---	---	---
GNA15	2769	broad.mit.edu	37	19	3154013	3154016	+	Intron	DEL	GATG	-	-	rs114826966	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:3154013_3154016delGATG	uc002lxf.2	+							NM_002068	NP_002059			guanine nucleotide binding protein (G protein),						activation of phospholipase C activity by dopamine receptor signaling pathway|activation of phospholipase C activity by muscarinic acetylcholine receptor signaling pathway|elevation of cytosolic calcium ion concentration|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			skin(2)	2		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;7.04e-05)|OV - Ovarian serous cystadenocarcinoma(105;5.08e-113)|Epithelial(107;6.19e-111)|all cancers(105;6.19e-103)|BRCA - Breast invasive adenocarcinoma(158;0.00145)|STAD - Stomach adenocarcinoma(1328;0.184)														---	---	---	---
GIPC3	126326	broad.mit.edu	37	19	3586444	3586444	+	Intron	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:3586444delG	uc002lyd.3	+							NM_133261	NP_573568			GIPC PDZ domain containing family, member 3											breast(1)	1				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0025)|STAD - Stomach adenocarcinoma(1328;0.18)												OREG0025154	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
PIP5K1C	23396	broad.mit.edu	37	19	3633460	3633460	+	Frame_Shift_Del	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:3633460delG	uc002lyj.1	-	17	2036	c.1979delC	c.(1978-1980)CCGfs	p.P660fs	PIP5K1C_uc010xhq.1_Intron	NM_012398	NP_036530	O60331	PI51C_HUMAN	phosphatidylinositol-4-phosphate 5-kinase, type	660	Mediates interaction with TLN2.				axon guidance	cytosol|plasma membrane	1-phosphatidylinositol-4-phosphate 5-kinase activity|ATP binding			stomach(2)|skin(2)	4		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.95e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0026)|STAD - Stomach adenocarcinoma(1328;0.183)														---	---	---	---
ATCAY	85300	broad.mit.edu	37	19	3887294	3887294	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:3887294delA	uc002lyy.3	+						ATCAY_uc010xhz.1_Intron	NM_033064	NP_149053			caytaxin						transport		protein binding			breast(1)	1		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.00485)|STAD - Stomach adenocarcinoma(1328;0.183)														---	---	---	---
TICAM1	148022	broad.mit.edu	37	19	4816465	4816465	+	Frame_Shift_Del	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:4816465delG	uc002mbi.2	-	2	2176	c.1925delC	c.(1924-1926)CCAfs	p.P642fs		NM_182919	NP_891549	Q8IUC6	TCAM1_HUMAN	toll-like receptor adaptor molecule 1	642	Sufficient to induce apoptosis.|Pro-rich.			Missing (in Ref. 6; AAO85488).	apoptosis|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|positive regulation of I-kappaB kinase/NF-kappaB 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|endosome membrane|plasma membrane	protein kinase binding|signal transducer activity			breast(1)	1				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0139)														---	---	---	---
Unknown	0	broad.mit.edu	37	19	4835257	4835257	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:4835257delT								TICAM1 (3520 upstream) : PLIN3 (3089 downstream)																																			---	---	---	---
UHRF1	29128	broad.mit.edu	37	19	4946592	4946593	+	Intron	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:4946592_4946593delTT	uc002mbo.2	+						UHRF1_uc010xik.1_Intron|UHRF1_uc010duf.2_Intron|UHRF1_uc002mbp.2_Intron	NM_001048201	NP_001041666			ubiquitin-like with PHD and ring finger domains						cell cycle|cell proliferation|DNA repair|regulation of transcription from RNA polymerase II promoter	nucleus	acid-amino acid ligase activity|methyl-CpG binding|methylated histone residue binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			lung(2)	2				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0276)														---	---	---	---
Unknown	0	broad.mit.edu	37	19	4965613	4965616	+	IGR	DEL	TTTT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:4965613_4965616delTTTT								UHRF1 (3449 upstream) : KDM4B (3508 downstream)																																			---	---	---	---
PTPRS	5802	broad.mit.edu	37	19	5309143	5309143	+	Intron	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:5309143delG	uc002mbv.2	-						PTPRS_uc002mbu.1_Intron|PTPRS_uc002mbw.2_Intron|PTPRS_uc002mbx.2_Intron|PTPRS_uc002mby.2_Intron	NM_002850	NP_002841			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	5483339	5483339	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:5483339delT								ZNRF4 (26473 upstream) : PLAC2 (74841 downstream)																																			---	---	---	---
TMEM146	257062	broad.mit.edu	37	19	5769499	5769499	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:5769499delT	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																		---	---	---	---
Unknown	0	broad.mit.edu	37	19	5809494	5809494	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:5809494delT								DUS3L (18245 upstream) : NRTN (14324 downstream)																																			---	---	---	---
RFX2	5990	broad.mit.edu	37	19	6058997	6058998	+	Intron	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:6058997_6058998delTT	uc002meb.2	-						RFX2_uc002mec.2_Intron|RFX2_uc010xiy.1_Intron	NM_000635	NP_000626			regulatory factor X2 isoform a						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding			breast(4)|ovary(1)|skin(1)	6																		---	---	---	---
KHSRP	8570	broad.mit.edu	37	19	6414076	6414076	+	3'UTR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:6414076delA	uc002mer.3	-	20						NM_003685	NP_003676			KH-type splicing regulatory protein						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																		---	---	---	---
Unknown	0	broad.mit.edu	37	19	6523684	6523684	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:6523684delT								TUBB4 (21354 upstream) : TNFSF9 (7326 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	19	6562770	6562770	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:6562770delT								TNFSF9 (26831 upstream) : CD70 (20365 downstream)																																			---	---	---	---
VAV1	7409	broad.mit.edu	37	19	6792383	6792383	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:6792383delA	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																		---	---	---	---
VAV1	7409	broad.mit.edu	37	19	6852736	6852737	+	Intron	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:6852736_6852737delAA	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																		---	---	---	---
Unknown	0	broad.mit.edu	37	19	7095675	7095676	+	IGR	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:7095675_7095676delAA								ZNF557 (7699 upstream) : INSR (16590 downstream)																																			---	---	---	---
ZNF358	140467	broad.mit.edu	37	19	7579514	7579514	+	5'Flank	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:7579514delT	uc002mgn.2	+							NM_018083	NP_060553			zinc finger protein 358						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																		---	---	---	---
FCER2	2208	broad.mit.edu	37	19	7767509	7767509	+	5'Flank	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:7767509delA	uc002mhn.2	-						FCER2_uc010xjs.1_5'Flank|FCER2_uc010xjt.1_5'Flank|FCER2_uc002mhm.2_5'Flank|FCER2_uc010dvo.2_5'Flank	NM_002002	NP_001993			Fc fragment of IgE, low affinity II, receptor						positive regulation of killing of cells of other organism|positive regulation of nitric-oxide synthase 2 biosynthetic process|positive regulation of nitric-oxide synthase activity	extracellular region|integral to plasma membrane	IgE binding|integrin binding|receptor activity|sugar binding				0																		---	---	---	---
EVI5L	115704	broad.mit.edu	37	19	7904192	7904193	+	Intron	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:7904192_7904193delAA	uc002min.2	+							NM_145245	NP_660288			ecotropic viral integration site 5-like isoform							intracellular	protein binding|Rab GTPase activator activity			ovary(1)	1																		---	---	---	---
FBN3	84467	broad.mit.edu	37	19	8158678	8158680	+	Intron	DEL	AAC	-	-	rs113798564		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:8158678_8158680delAAC	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																		---	---	---	---
LASS4	79603	broad.mit.edu	37	19	8313906	8313909	+	Intron	DEL	TGGA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:8313906_8313909delTGGA	uc002mjg.2	+						LASS4_uc002mjh.2_Intron|LASS4_uc002mji.2_Intron|LASS4_uc010dvz.2_Intron	NM_024552	NP_078828			LAG1 homolog, ceramide synthase 4							endoplasmic reticulum membrane|integral to membrane|nuclear membrane	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|sphingosine N-acyltransferase activity			ovary(1)	1																		---	---	---	---
MARCH2	51257	broad.mit.edu	37	19	8502571	8502571	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:8502571delT	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																		---	---	---	---
MYO1F	4542	broad.mit.edu	37	19	8635257	8635257	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:8635257delT	uc002mkg.2	-						MYO1F_uc002mkh.2_Intron|MYO1F_uc010xkf.1_Intron	NM_012335	NP_036467			myosin IF							unconventional myosin complex	actin binding|ATP binding|calmodulin binding|motor activity			ovary(2)|skin(1)	3																		---	---	---	---
Unknown	0	broad.mit.edu	37	19	9165852	9165852	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:9165852delT								MUC16 (73834 upstream) : OR1M1 (38069 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	19	9555412	9555412	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:9555412delA								ZNF266 (9178 upstream) : ZNF560 (21619 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	19	9555417	9555418	+	IGR	INS	-	AAG	AAG	rs4804439		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:9555417_9555418insAAG								ZNF266 (9183 upstream) : ZNF560 (21613 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	19	9577019	9577019	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:9577019delA								ZNF266 (30785 upstream) : ZNF560 (12 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	19	9673272	9673274	+	5'Flank	DEL	TCT	-	-	rs147918159		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:9673272_9673274delTCT	uc010xko.1	-											Homo sapiens cDNA FLJ34771 fis, clone NT2NE2003150.																														---	---	---	---
Unknown	0	broad.mit.edu	37	19	9713365	9713366	+	IGR	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:9713365_9713366delTT								ZNF121 (18156 upstream) : ZNF561 (4637 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	19	9804225	9804226	+	Intron	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:9804225_9804226delTT	uc010xkx.1	-											RecName: Full=Zinc finger protein 562;																														---	---	---	---
PIN1	5300	broad.mit.edu	37	19	9956184	9956184	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:9956184delA	uc002mml.1	+						PIN1_uc002mmk.1_Intron|PIN1_uc002mmm.1_Intron|PIN1_uc002mmn.1_Intron	NM_006221	NP_006212			protein (peptidyl-prolyl cis/trans isomerase)						cell cycle|negative regulation of cell motility|negative regulation of ERK1 and ERK2 cascade|negative regulation of transforming growth factor beta receptor signaling pathway|negative regulation of type I interferon production|positive regulation of Rho GTPase activity|positive regulation of ubiquitin-protein ligase activity|protein folding|regulation of mitosis|regulation of pathway-restricted SMAD protein phosphorylation	nucleoplasm	GTPase activating protein binding|mitogen-activated protein kinase kinase binding|peptidyl-prolyl cis-trans isomerase activity|phosphoserine binding|phosphothreonine binding			skin(1)	1																		---	---	---	---
OLFM2	93145	broad.mit.edu	37	19	10039480	10039480	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:10039480delA	uc002mmp.2	-							NM_058164	NP_477512			olfactomedin 2 precursor							extracellular region				large_intestine(1)|skin(1)	2																		---	---	---	---
OLFM2	93145	broad.mit.edu	37	19	10040716	10040716	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:10040716delA	uc002mmp.2	-							NM_058164	NP_477512			olfactomedin 2 precursor							extracellular region				large_intestine(1)|skin(1)	2																		---	---	---	---
DNMT1	1786	broad.mit.edu	37	19	10288073	10288073	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-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)													---	---	---	---
MRPL4	51073	broad.mit.edu	37	19	10364701	10364701	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-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-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:10377498delT								MRPL4 (6764 upstream) : ICAM1 (4019 downstream)																																			---	---	---	---
PDE4A	5141	broad.mit.edu	37	19	10544890	10544892	+	Intron	DEL	TTT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:10544890_10544892delTTT	uc002moj.2	+						PDE4A_uc002mok.2_Intron|PDE4A_uc002mol.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)													---	---	---	---
PDE4A	5141	broad.mit.edu	37	19	10557259	10557263	+	Intron	DEL	TTTTT	-	-	rs77762191		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:10557259_10557263delTTTTT	uc002moj.2	+						PDE4A_uc002mok.2_Intron|PDE4A_uc002mol.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)													---	---	---	---
PDE4A	5141	broad.mit.edu	37	19	10570030	10570030	+	Intron	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:10570030delC	uc002moj.2	+						PDE4A_uc002mok.2_Intron|PDE4A_uc002mol.2_Intron|PDE4A_uc002mom.2_Intron|PDE4A_uc002mon.2_Intron|PDE4A_uc002moo.2_Frame_Shift_Del_p.G18fs	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)													---	---	---	---
PDE4A	5141	broad.mit.edu	37	19	10575900	10575902	+	Intron	DEL	TTT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:10575900_10575902delTTT	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)													---	---	---	---
Unknown	0	broad.mit.edu	37	19	10621985	10621985	+	IGR	DEL	A	-	-	rs74178268		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:10621985delA								KEAP1 (7931 upstream) : S1PR5 (1638 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	19	10633221	10633221	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:10633221delA								S1PR5 (4614 upstream) : ATG4D (21372 downstream)																																			---	---	---	---
ATG4D	84971	broad.mit.edu	37	19	10659805	10659805	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:10659805delT	uc002mov.2	+						ATG4D_uc010xlh.1_Intron|ATG4D_uc010dxh.2_Intron|ATG4D_uc010dxi.2_Intron|ATG4D_uc010dxj.2_Intron|MIR1238_hsa-mir-1238|MI0006328_5'Flank	NM_032885	NP_116274			APG4 autophagy 4 homolog D						autophagy|protein transport	cytoplasm	cysteine-type endopeptidase activity				0			Epithelial(33;9.2e-06)|all cancers(31;3.9e-05)															---	---	---	---
AP1M2	10053	broad.mit.edu	37	19	10690721	10690731	+	Intron	DEL	TTTTTTTTTTT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:10690721_10690731delTTTTTTTTTTT	uc002mpc.2	-						AP1M2_uc002mpd.2_Intron	NM_005498	NP_005489			adaptor-related protein complex 1, mu 2 subunit						cellular membrane organization|post-Golgi vesicle-mediated transport|protein targeting|regulation of defense response to virus by virus|vesicle targeting|viral reproduction	clathrin adaptor complex|clathrin coated vesicle membrane|cytosol|Golgi membrane|lysosomal membrane	protein binding			ovary(2)	2			Epithelial(33;1.58e-05)|all cancers(31;6.36e-05)															---	---	---	---
SLC44A2	57153	broad.mit.edu	37	19	10730106	10730106	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:10730106delA	uc002mpe.3	+							NM_001145056	NP_001138528			solute carrier family 44, member 2 isoform 2						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)													---	---	---	---
CARM1	10498	broad.mit.edu	37	19	10992950	10992950	+	Intron	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:10992950delG	uc002mpz.2	+						CARM1_uc010dxn.2_Intron	NM_199141	NP_954592			coactivator-associated arginine						cellular lipid metabolic process|histone H3-R2 methylation|interspecies interaction between organisms|pathogenesis|positive regulation of fat cell differentiation|regulation of estrogen receptor signaling pathway|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytosol|nucleoplasm	beta-catenin binding|histone acetyl-lysine binding|histone methyltransferase activity (H3-R17 specific)|ligand-dependent nuclear receptor transcription coactivator activity|protein-arginine omega-N asymmetric methyltransferase activity|transcription regulatory region DNA binding				0																		---	---	---	---
CARM1	10498	broad.mit.edu	37	19	11008791	11008793	+	Intron	DEL	AAA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:11008791_11008793delAAA	uc002mpz.2	+						CARM1_uc010dxn.2_Intron	NM_199141	NP_954592			coactivator-associated arginine						cellular lipid metabolic process|histone H3-R2 methylation|interspecies interaction between organisms|pathogenesis|positive regulation of fat cell differentiation|regulation of estrogen receptor signaling pathway|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytosol|nucleoplasm	beta-catenin binding|histone acetyl-lysine binding|histone methyltransferase activity (H3-R17 specific)|ligand-dependent nuclear receptor transcription coactivator activity|protein-arginine omega-N asymmetric methyltransferase activity|transcription regulatory region DNA binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	19	11186995	11186996	+	IGR	INS	-	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:11186995_11186996insT								SMARCA4 (14036 upstream) : LDLR (13061 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	19	11188545	11188545	+	IGR	DEL	T	-	-	rs78505081		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:11188545delT								SMARCA4 (15586 upstream) : LDLR (11512 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	19	11250350	11250350	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:11250350delT								LDLR (5847 upstream) : SPC24 (7481 downstream)																																			---	---	---	---
SPC24	147841	broad.mit.edu	37	19	11261162	11261162	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:11261162delA	uc002mql.2	-						SPC24_uc010xlp.1_Intron	NM_182513	NP_872319			spindle pole body component 24 homolog						cell division|mitotic prometaphase	condensed chromosome kinetochore|cytosol|Ndc80 complex|nucleus	protein binding				0																		---	---	---	---
DOCK6	57572	broad.mit.edu	37	19	11326767	11326768	+	Intron	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:11326767_11326768delTT	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																		---	---	---	---
CCDC159	126075	broad.mit.edu	37	19	11465067	11465067	+	Intron	DEL	A	-	-	rs113087457		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:11465067delA	uc010xlw.1	+						CCDC159_uc010xlt.1_Intron|LPPR2_uc002mre.1_5'Flank|LPPR2_uc002mrf.1_5'Flank	NM_001080503	NP_001073972			coiled-coil domain-containing-like											ovary(1)	1																		---	---	---	---
RGL3	57139	broad.mit.edu	37	19	11527821	11527821	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:11527821delT	uc002mrp.2	-						RGL3_uc002mrn.2_Intron|RGL3_uc002mrm.2_Intron|RGL3_uc002mro.2_Intron|RGL3_uc002mrq.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																		---	---	---	---
ZNF653	115950	broad.mit.edu	37	19	11612613	11612613	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:11612613delT	uc002mrz.1	-							NM_138783	NP_620138			zinc finger protein 653						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0																		---	---	---	---
ELOF1	84337	broad.mit.edu	37	19	11667123	11667123	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:11667123delT	uc002mse.1	-						ELOF1_uc002msd.1_5'Flank	NM_032377	NP_115753			elongation factor 1 homolog (ELF1, S.						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	metal ion binding				0																		---	---	---	---
ELOF1	84337	broad.mit.edu	37	19	11667822	11667822	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:11667822delA	uc002mse.1	-						ELOF1_uc002msd.1_5'Flank|uc002msf.2_5'Flank	NM_032377	NP_115753			elongation factor 1 homolog (ELF1, S.						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	metal ion binding				0																		---	---	---	---
ZNF440	126070	broad.mit.edu	37	19	11937136	11937137	+	Intron	DEL	TT	-	-	rs34745315		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:11937136_11937137delTT	uc002msp.1	+							NM_152357	NP_689570			zinc finger protein 440						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0																		---	---	---	---
ZNF439	90594	broad.mit.edu	37	19	11973561	11973561	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:11973561delT	uc002msr.2	+							NM_152262	NP_689475			zinc finger protein 439						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			skin(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	19	12097139	12097140	+	5'Flank	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:12097139_12097140delTT	uc002msx.1	+											Homo sapiens cDNA FLJ34878 fis, clone NT2NE2015565, weakly similar to RETROVIRUS-RELATED ENV POLYPROTEIN.																														---	---	---	---
ZNF136	7695	broad.mit.edu	37	19	12279497	12279497	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:12279497delT	uc002mti.2	+						ZNF136_uc010xmh.1_Intron	NM_003437	NP_003428			zinc finger protein 136						negative regulation of transcription from RNA polymerase II promoter|transcription from RNA polymerase II promoter	nucleus	DNA binding|protein binding|transcription corepressor activity|zinc ion binding			ovary(1)|pancreas(1)	2																		---	---	---	---
ZNF136	7695	broad.mit.edu	37	19	12286012	12286014	+	Intron	DEL	TTT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:12286012_12286014delTTT	uc002mti.2	+						ZNF136_uc010xmh.1_Intron	NM_003437	NP_003428			zinc finger protein 136						negative regulation of transcription from RNA polymerase II promoter|transcription from RNA polymerase II promoter	nucleus	DNA binding|protein binding|transcription corepressor activity|zinc ion binding			ovary(1)|pancreas(1)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	19	12307105	12307105	+	Intron	DEL	T	-	-	rs80224150		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:12307105delT	uc002mtk.1	+						uc010dyq.1_Intron|uc002mtj.1_Intron					Homo sapiens cDNA FLJ13242 fis, clone OVARC1000578.																														---	---	---	---
TNPO2	30000	broad.mit.edu	37	19	12828804	12828804	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:12828804delT	uc002muo.2	-						TNPO2_uc002mup.2_Intron|TNPO2_uc002muq.2_Intron|TNPO2_uc002mur.2_Intron	NM_001136196	NP_001129668			transportin 2 (importin 3, karyopherin beta 2b)						intracellular protein transport	cytoplasm|nucleus	nuclear localization sequence binding|protein binding|protein transporter activity			ovary(1)	1																		---	---	---	---
RTBDN	83546	broad.mit.edu	37	19	12941653	12941654	+	5'Flank	DEL	GT	-	-	rs35204642		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:12941653_12941654delGT	uc002mvi.2	-						RTBDN_uc002mvh.1_Intron|RTBDN_uc002mvj.2_Intron	NM_001080997	NP_001074466			retbindin isoform 1							extracellular region					0																		---	---	---	---
SYCE2	256126	broad.mit.edu	37	19	13024652	13024652	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:13024652delT	uc002mvr.2	-							NM_001105578	NP_001099048			synaptonemal complex central element protein 2						cell division	central element					0																		---	---	---	---
Unknown	0	broad.mit.edu	37	19	13086037	13086037	+	IGR	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:13086037delG								DAND5 (470 upstream) : NFIX (20547 downstream)																																			---	---	---	---
NFIX	4784	broad.mit.edu	37	19	13139754	13139754	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:13139754delA	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)															---	---	---	---
NACC1	112939	broad.mit.edu	37	19	13240980	13240980	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:13240980delT	uc002mwm.2	+							NM_052876	NP_443108			transcriptional repressor NAC1						negative regulation of transcription, DNA-dependent|positive regulation of cell proliferation|protein homooligomerization|transcription, DNA-dependent	cytoplasm|nuclear body					0																		---	---	---	---
Unknown	0	broad.mit.edu	37	19	13252120	13252121	+	IGR	INS	-	AC	AC	rs148055495	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:13252120_13252121insAC								NACC1 (162 upstream) : STX10 (3104 downstream)																																			---	---	---	---
CACNA1A	773	broad.mit.edu	37	19	13366978	13366979	+	Intron	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:13366978_13366979delTT	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	13387838	13387838	+	Intron	DEL	A	-	-	rs34471308		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:13387838delA	uc010dze.2	-						CACNA1A_uc010xnd.1_5'Flank|CACNA1A_uc002mwx.3_5'Flank|CACNA1A_uc010dzc.2_Intron|CACNA1A_uc002mwy.3_Intron|CACNA1A_uc010xne.1_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)											OREG0025295	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
CACNA1A	773	broad.mit.edu	37	19	13403430	13403430	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:13403430delA	uc010dze.2	-						CACNA1A_uc010dzc.2_Intron|CACNA1A_uc002mwy.3_Intron|CACNA1A_uc010xne.1_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	13411132	13411133	+	Intron	DEL	TT	-	-	rs138629534		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:13411132_13411133delTT	uc010dze.2	-						CACNA1A_uc010dzc.2_Intron|CACNA1A_uc002mwy.3_Intron|CACNA1A_uc010xne.1_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	13445408	13445411	+	Intron	DEL	TGTG	-	-	rs138143360		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:13445408_13445411delTGTG	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)													---	---	---	---
Unknown	0	broad.mit.edu	37	19	13699287	13699289	+	IGR	DEL	TTT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:13699287_13699289delTTT								CACNA1A (82013 upstream) : CCDC130 (143285 downstream)																																			---	---	---	---
ZSWIM4	65249	broad.mit.edu	37	19	13903740	13903741	+	5'Flank	INS	-	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:13903740_13903741insT	uc002mxh.1	+							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	13964480	13964480	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:13964480delT								MIR23A (17007 upstream) : MIR181C (21033 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	19	13980589	13980590	+	IGR	DEL	CA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:13980589_13980590delCA								MIR23A (33116 upstream) : MIR181C (4923 downstream)																																			---	---	---	---
CC2D1A	54862	broad.mit.edu	37	19	14036388	14036388	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:14036388delA	uc002mxo.2	+						CC2D1A_uc002mxp.2_Intron|CC2D1A_uc010dzh.2_Intron|CC2D1A_uc002mxq.1_Intron	NM_017721	NP_060191			coiled-coil and C2 domain containing 1A						positive regulation of I-kappaB kinase/NF-kappaB cascade|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleolus|plasma membrane	DNA binding|signal transducer activity				0			OV - Ovarian serous cystadenocarcinoma(19;3.49e-23)															---	---	---	---
IL27RA	9466	broad.mit.edu	37	19	14158171	14158172	+	Intron	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:14158171_14158172delTT	uc002mxx.2	+							NM_004843	NP_004834			class I cytokine receptor precursor						cell surface receptor linked signaling pathway|immune response	integral to plasma membrane	transmembrane receptor activity				0																		---	---	---	---
LPHN1	22859	broad.mit.edu	37	19	14277909	14277909	+	Intron	DEL	A	-	-	rs79500350		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:14277909delA	uc010xnn.1	-						LPHN1_uc010xno.1_Intron|uc002myf.2_Intron	NM_001008701	NP_001008701			latrophilin 1 isoform 1 precursor						neuropeptide signaling pathway	integral to membrane|plasma membrane	G-protein coupled receptor activity|sugar binding			ovary(2)|lung(2)|central_nervous_system(1)	5																		---	---	---	---
Unknown	0	broad.mit.edu	37	19	14368736	14368740	+	IGR	DEL	TTTTT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:14368736_14368740delTTTTT								LPHN1 (51739 upstream) : CD97 (123473 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	19	14392181	14392182	+	IGR	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:14392181_14392182delTT								LPHN1 (75184 upstream) : CD97 (100031 downstream)																																			---	---	---	---
CD97	976	broad.mit.edu	37	19	14516481	14516481	+	Intron	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:14516481delG	uc002myl.2	+						CD97_uc002mym.2_Intron|CD97_uc002myn.2_Intron	NM_078481	NP_510966			CD97 antigen isoform 1 precursor						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																		---	---	---	---
PKN1	5585	broad.mit.edu	37	19	14562088	14562088	+	Intron	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:14562088delC	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	14655389	14655389	+	Intron	DEL	G	-	-	rs35751479		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:14655389delG	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																		---	---	---	---
CLEC17A	388512	broad.mit.edu	37	19	14692971	14692971	+	5'Flank	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:14692971delT	uc010dzn.1	+						CLEC17A_uc002mzh.1_5'Flank|CLEC17A_uc010xnt.1_5'Flank|CLEC17A_uc010xnu.1_5'Flank|CLEC17A_uc010dzo.1_5'Flank					SubName: Full=CLEC17A protein;							cell surface|integral to membrane	fucose binding|mannose binding|metal ion binding|receptor activity				0																		---	---	---	---
OR7A5	26659	broad.mit.edu	37	19	14944291	14944291	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:14944291delA	uc010xoa.1	-							NM_017506	NP_059976			olfactory receptor, family 7, subfamily A,						sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			central_nervous_system(2)	2																		---	---	---	---
NOTCH3	4854	broad.mit.edu	37	19	15274654	15274654	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:15274654delA	uc002nan.2	-							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	15280884	15280884	+	Intron	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:15280884delG	uc002nan.2	-							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)															---	---	---	---
AKAP8	10270	broad.mit.edu	37	19	15482303	15482304	+	Intron	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:15482303_15482304delTT	uc002nav.2	-						AKAP8_uc010dzy.2_Intron|AKAP8_uc010dzz.1_Intron|AKAP8_uc010xog.1_Intron	NM_005858	NP_005849			A-kinase anchor protein 8						signal transduction	nuclear matrix				ovary(1)|breast(1)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	19	15741106	15741106	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:15741106delT								CYP4F8 (661 upstream) : CYP4F3 (10601 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	19	16109990	16109993	+	IGR	DEL	AAAA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:16109990_16109993delAAAA								OR10H4 (49223 upstream) : LOC126536 (16451 downstream)																																			---	---	---	---
TPM4	7171	broad.mit.edu	37	19	16212005	16212005	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:16212005delT	uc002ndj.2	+						TPM4_uc002ndi.2_Intron|TPM4_uc002ndl.1_RNA	NM_003290	NP_003281			tropomyosin 4 isoform 2						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								---	---	---	---
HSH2D	84941	broad.mit.edu	37	19	16261350	16261350	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:16261350delA	uc002ndp.3	+						HSH2D_uc002ndr.2_Intron|HSH2D_uc010ead.2_Intron	NM_032855	NP_116244			hematopoietic SH2 domain containing							cytoplasm|nucleus					0																		---	---	---	---
Unknown	0	broad.mit.edu	37	19	16444819	16444820	+	IGR	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:16444819_16444820delTT								KLF2 (6482 upstream) : EPS15L1 (21241 downstream)																																			---	---	---	---
CALR3	125972	broad.mit.edu	37	19	16606795	16606795	+	Intron	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:16606795delG	uc002ned.2	-						MED26_uc002nee.2_Intron|C19orf44_uc002nef.1_5'Flank|C19orf44_uc002neg.2_5'Flank|C19orf44_uc002neh.1_5'Flank|C19orf44_uc010eai.1_5'Flank	NM_145046	NP_659483			calreticulin 3 precursor						protein folding	endoplasmic reticulum lumen	calcium ion binding|sugar binding|unfolded protein binding				0																		---	---	---	---
C19orf44	84167	broad.mit.edu	37	19	16625243	16625243	+	Intron	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:16625243delG	uc002neh.1	+						MED26_uc002nee.2_Intron|C19orf44_uc002neg.2_Intron|C19orf44_uc010eai.1_Intron	NM_032207	NP_115583			hypothetical protein LOC84167												0																		---	---	---	---
SLC35E1	79939	broad.mit.edu	37	19	16677999	16678000	+	Intron	DEL	TT	-	-	rs77424971		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:16677999_16678000delTT	uc010xph.1	-						MED26_uc002nee.2_Intron|SLC35E1_uc002nem.1_Intron	NM_024881	NP_079157			solute carrier family 35, member E1						transport	integral to membrane				ovary(1)|central_nervous_system(1)	2																		---	---	---	---
TMEM38A	79041	broad.mit.edu	37	19	16795130	16795131	+	Intron	DEL	AG	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:16795130_16795131delAG	uc002nes.2	+							NM_024074	NP_076979			transmembrane protein 38A							integral to membrane|nuclear membrane|sarcoplasmic reticulum membrane	potassium channel activity			central_nervous_system(2)|ovary(1)	3																		---	---	---	---
NWD1	284434	broad.mit.edu	37	19	16828336	16828336	+	5'Flank	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:16828336delT	uc002neu.3	+						NWD1_uc002net.3_5'Flank					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	16841903	16841903	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:16841903delA	uc002neu.3	+						NWD1_uc002net.3_Intron|NWD1_uc002nev.3_5'Flank					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	16857505	16857505	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:16857505delA	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	16969772	16969772	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:16969772delA	uc002ney.1	+						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																		---	---	---	---
SIN3B	23309	broad.mit.edu	37	19	16975302	16975303	+	Intron	INS	-	GTT	GTT	rs138638788	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:16975302_16975303insGTT	uc002ney.1	+						SIN3B_uc002nez.1_Intron|SIN3B_uc010xpi.1_Intron	NM_015260	NP_056075			SIN3 homolog B, transcription regulator						cellular lipid metabolic process|transcription, DNA-dependent	nucleoplasm	protein binding			ovary(2)	2																		---	---	---	---
CPAMD8	27151	broad.mit.edu	37	19	17101063	17101063	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:17101063delA	uc002nfb.2	-							NM_015692	NP_056507			C3 and PZP-like, alpha-2-macroglobulin domain							extracellular space|plasma membrane	serine-type endopeptidase inhibitor activity			ovary(4)|breast(4)|large_intestine(3)|pancreas(1)|skin(1)	13																		---	---	---	---
HAUS8	93323	broad.mit.edu	37	19	17170524	17170524	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-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																		---	---	---	---
MYO9B	4650	broad.mit.edu	37	19	17226839	17226840	+	Intron	INS	-	ACAG	ACAG	rs146779874	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:17226839_17226840insACAG	uc010eak.2	+						MYO9B_uc002nfi.2_Intron|MYO9B_uc002nfj.1_Intron	NM_004145	NP_004136			myosin IXB isoform 1						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																		---	---	---	---
MYO9B	4650	broad.mit.edu	37	19	17294803	17294803	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:17294803delA	uc010eak.2	+						MYO9B_uc002nfi.2_Intron|MYO9B_uc002nfj.1_Intron	NM_004145	NP_004136			myosin IXB isoform 1						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																		---	---	---	---
USE1	55850	broad.mit.edu	37	19	17329936	17329936	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:17329936delA	uc002nfo.2	+						USE1_uc010eal.1_Intron	NM_018467	NP_060937			unconventional SNARE in the ER 1 homolog						lysosomal transport|protein catabolic process|protein transport|secretion by cell|vesicle-mediated transport	endoplasmic reticulum membrane|integral to membrane	protein binding				0																		---	---	---	---
PLVAP	83483	broad.mit.edu	37	19	17485441	17485441	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:17485441delT	uc002ngk.1	-							NM_031310	NP_112600			plasmalemma vesicle associated protein							caveola|integral to membrane|perinuclear region of cytoplasm					0																		---	---	---	---
FAM129C	199786	broad.mit.edu	37	19	17636388	17636388	+	Intron	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:17636388delC	uc010xpr.1	+						FAM129C_uc010xpq.1_Intron|FAM129C_uc010xps.1_5'Flank|FAM129C_uc010xpt.1_5'Flank	NM_173544	NP_775815			B-cell novel protein 1 isoform a												0																		---	---	---	---
GLT25D1	79709	broad.mit.edu	37	19	17669969	17669969	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:17669969delA	uc002nhc.1	+							NM_024656	NP_078932			glycosyltransferase 25 domain containing 1						lipopolysaccharide biosynthetic process	endoplasmic reticulum lumen	procollagen galactosyltransferase activity				0																		---	---	---	---
GLT25D1	79709	broad.mit.edu	37	19	17682650	17682650	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:17682650delT	uc002nhc.1	+						GLT25D1_uc010eax.1_Intron	NM_024656	NP_078932			glycosyltransferase 25 domain containing 1						lipopolysaccharide biosynthetic process	endoplasmic reticulum lumen	procollagen galactosyltransferase activity				0																		---	---	---	---
UNC13A	23025	broad.mit.edu	37	19	17736960	17736963	+	Intron	DEL	ATCC	-	-	rs35036813		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:17736960_17736963delATCC	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																		---	---	---	---
UNC13A	23025	broad.mit.edu	37	19	17737206	17737207	+	Intron	DEL	AT	-	-	rs56133357		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:17737206_17737207delAT	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																		---	---	---	---
UNC13A	23025	broad.mit.edu	37	19	17741883	17741886	+	Intron	DEL	TCCT	-	-	rs145348480		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:17741883_17741886delTCCT	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																		---	---	---	---
MAP1S	55201	broad.mit.edu	37	19	17832965	17832965	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:17832965delA	uc002nhe.1	+						MAP1S_uc010eaz.1_Intron|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																		---	---	---	---
FCHO1	23149	broad.mit.edu	37	19	17873103	17873104	+	Intron	DEL	TT	-	-	rs72333343		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:17873103_17873104delTT	uc010ebb.2	+						FCHO1_uc002nhg.3_Intron|FCHO1_uc002nhh.2_Intron|FCHO1_uc010xpw.1_Intron|FCHO1_uc010ebc.1_5'Flank	NM_001161358	NP_001154830			FCH domain only 1 isoform b											breast(1)	1																		---	---	---	---
PDE4C	5143	broad.mit.edu	37	19	18338324	18338325	+	Intron	INS	-	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:18338324_18338325insG	uc010xqc.1	-						PDE4C_uc002nik.3_Intron|PDE4C_uc002nil.3_Intron|PDE4C_uc002nii.3_5'Flank|PDE4C_uc010ebl.2_Intron|PDE4C_uc010xqd.1_5'Flank|PDE4C_uc002nim.1_Intron	NM_001098819	NP_001092289			phosphodiesterase 4C isoform PDE4C-2						signal transduction	cytosol	3',5'-cyclic-AMP phosphodiesterase activity|metal ion binding			ovary(2)|skin(2)|central_nervous_system(1)	5					Dyphylline(DB00651)													---	---	---	---
PGPEP1	54858	broad.mit.edu	37	19	18451914	18451914	+	Intron	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:18451914delC	uc002nis.1	+						PGPEP1_uc002nir.1_Intron|PGPEP1_uc002nit.1_Intron|PGPEP1_uc010xqg.1_Intron	NM_017712	NP_060182			pyroglutamyl-peptidase I								cysteine-type peptidase activity				0																		---	---	---	---
PGPEP1	54858	broad.mit.edu	37	19	18458864	18458864	+	Intron	DEL	C	-	-	rs67431792		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:18458864delC	uc002nis.1	+						PGPEP1_uc002nir.1_Intron|PGPEP1_uc002nit.1_Intron|PGPEP1_uc010xqg.1_Intron	NM_017712	NP_060182			pyroglutamyl-peptidase I								cysteine-type peptidase activity				0																		---	---	---	---
CRLF1	9244	broad.mit.edu	37	19	18707343	18707343	+	Intron	DEL	A	-	-	rs78616489		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:18707343delA	uc010ebt.1	-							NM_004750	NP_004741			cytokine receptor-like factor 1 precursor						negative regulation of neuron apoptosis|positive regulation of cell proliferation|positive regulation of tyrosine phosphorylation of Stat3 protein	extracellular space	cytokine binding|protein heterodimerization activity|receptor activity			central_nervous_system(1)	1																		---	---	---	---
CRTC1	23373	broad.mit.edu	37	19	18813765	18813765	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:18813765delT	uc002nkb.3	+						CRTC1_uc010ebv.2_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																		---	---	---	---
CRTC1	23373	broad.mit.edu	37	19	18823064	18823065	+	Intron	INS	-	GTTT	GTTT	rs141632789	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:18823064_18823065insGTTT	uc002nkb.3	+						CRTC1_uc010ebv.2_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																		---	---	---	---
CRTC1	23373	broad.mit.edu	37	19	18826043	18826043	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:18826043delT	uc002nkb.3	+						CRTC1_uc010ebv.2_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																		---	---	---	---
CRTC1	23373	broad.mit.edu	37	19	18841770	18841777	+	Intron	DEL	TCCCTCCT	-	-	rs71876806		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:18841770_18841777delTCCCTCCT	uc002nkb.3	+						CRTC1_uc010ebv.2_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																		---	---	---	---
Unknown	0	broad.mit.edu	37	19	19067575	19067577	+	IGR	DEL	TTT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:19067575_19067577delTTT								HOMER3 (15534 upstream) : SFRS14 (34120 downstream)																																			---	---	---	---
ZNF486	90649	broad.mit.edu	37	19	20293715	20293715	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:20293715delA	uc002nou.2	+							NM_052852	NP_443084			zinc finger protein 486						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	19	20385790	20385790	+	IGR	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:20385790delG								LOC284441 (15287 upstream) : ZNF826 (65288 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	19	21184305	21184305	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:21184305delT								ZNF85 (50804 upstream) : ZNF430 (19192 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	19	21448308	21448308	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:21448308delA								ZNF431 (79503 upstream) : ZNF708 (25655 downstream)																																			---	---	---	---
ZNF676	163223	broad.mit.edu	37	19	22367272	22367272	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:22367272delT	uc002nqs.1	-							NM_001001411	NP_001001411			zinc finger protein 676						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)																---	---	---	---
Unknown	0	broad.mit.edu	37	19	22454960	22454961	+	IGR	DEL	TC	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:22454960_22454961delTC								ZNF676 (75207 upstream) : ZNF98 (118938 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	19	22983577	22983577	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:22983577delT								ZNF99 (30793 upstream) : ZNF91 (537842 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	19	23089707	23089707	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:23089707delT								ZNF99 (136923 upstream) : ZNF91 (431712 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	19	23095457	23095457	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:23095457delA								ZNF99 (142673 upstream) : ZNF91 (425962 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	19	23255000	23255000	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:23255000delA								ZNF99 (302216 upstream) : ZNF91 (266419 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	19	23280179	23280179	+	IGR	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:23280179delG								ZNF99 (327395 upstream) : ZNF91 (241240 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	19	23738556	23738556	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:23738556delT								ZNF91 (160287 upstream) : ZNF675 (97153 downstream)																																			---	---	---	---
ZNF681	148213	broad.mit.edu	37	19	23934277	23934279	+	Intron	DEL	AAA	-	-	rs79539572		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:23934277_23934279delAAA	uc002nrk.3	-						ZNF681_uc002nrl.3_Intron|ZNF681_uc002nrj.3_Intron|ZNF681_uc002nrm.1_Intron	NM_138286	NP_612143			zinc finger protein 681						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0		all_lung(12;0.11)|Lung NSC(12;0.163)|all_epithelial(12;0.206)																---	---	---	---
ZNF681	148213	broad.mit.edu	37	19	23938518	23938518	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:23938518delT	uc002nrk.3	-						ZNF681_uc002nrl.3_Intron|ZNF681_uc002nrj.3_Intron|ZNF681_uc002nrm.1_5'Flank	NM_138286	NP_612143			zinc finger protein 681						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0		all_lung(12;0.11)|Lung NSC(12;0.163)|all_epithelial(12;0.206)																---	---	---	---
Unknown	0	broad.mit.edu	37	19	24536773	24536773	+	IGR	DEL	T	-	-	rs74723622		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:24536773delT								LOC100101266 (190524 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	19	24566099	24566099	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:24566099delT								LOC100101266 (219850 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	19	27858357	27858357	+	IGR	DEL	C	-	-	rs143331608		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:27858357delC								None (None upstream) : LOC148189 (423045 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	19	27870563	27870563	+	IGR	DEL	T	-	-	rs111794544		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:27870563delT								None (None upstream) : LOC148189 (410839 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	19	28172585	28172585	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:28172585delA								None (None upstream) : LOC148189 (108817 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	19	28297113	28297113	+	RNA	DEL	T	-	-	rs77586400		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:28297113delT	uc002nry.1	+	2		c.758delT								Homo sapiens cDNA clone IMAGE:3867353.																														---	---	---	---
Unknown	0	broad.mit.edu	37	19	29647225	29647226	+	IGR	INS	-	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:29647225_29647226insT								LOC148145 (187170 upstream) : UQCRFS1 (50941 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	19	30005650	30005651	+	Intron	INS	-	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:30005650_30005651insG	uc002nse.1	-											Homo sapiens cDNA FLJ37474 fis, clone BRAWH2012619.																														---	---	---	---
Unknown	0	broad.mit.edu	37	19	30116032	30116032	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:30116032delT								POP4 (7870 upstream) : PLEKHF1 (40295 downstream)																																			---	---	---	---
C19orf2	8725	broad.mit.edu	37	19	30459831	30459831	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:30459831delA	uc002nsr.2	+						C19orf2_uc002nsq.2_Intron|C19orf2_uc002nss.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	30695064	30695064	+	IGR	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:30695064delG								C19orf2 (188453 upstream) : ZNF536 (168264 downstream)																																			---	---	---	---
ZNF536	9745	broad.mit.edu	37	19	31030026	31030026	+	Intron	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:31030026delC	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	31338025	31338028	+	IGR	DEL	ACAT	-	-	rs143727083	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:31338025_31338028delACAT								ZNF536 (289060 upstream) : DKFZp566F0947 (302755 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	19	31605838	31605839	+	IGR	DEL	AA	-	-	rs71335109		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:31605838_31605839delAA								ZNF536 (556873 upstream) : DKFZp566F0947 (34944 downstream)																																			---	---	---	---
TSHZ3	57616	broad.mit.edu	37	19	31792003	31792003	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:31792003delT	uc002nsy.3	-							NM_020856	NP_065907			zinc finger protein 537						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	31826060	31826060	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:31826060delT	uc002nsy.3	-							NM_020856	NP_065907			zinc finger protein 537						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	31830132	31830132	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:31830132delA	uc002nsy.3	-							NM_020856	NP_065907			zinc finger protein 537						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)																	---	---	---	---
Unknown	0	broad.mit.edu	37	19	31949910	31949910	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:31949910delA								TSHZ3 (109720 upstream) : ZNF507 (886604 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	19	32176962	32176963	+	IGR	INS	-	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:32176962_32176963insA								TSHZ3 (336772 upstream) : ZNF507 (659551 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	19	32406996	32406996	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:32406996delA								TSHZ3 (566806 upstream) : ZNF507 (429518 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	19	32573627	32573627	+	IGR	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:32573627delG								TSHZ3 (733437 upstream) : ZNF507 (262887 downstream)																																			---	---	---	---
ANKRD27	84079	broad.mit.edu	37	19	33153658	33153658	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:33153658delA	uc002ntn.1	-						ANKRD27_uc002nto.1_Intron	NM_032139	NP_115515			ankyrin repeat domain 27 (VPS9 domain)						early endosome to late endosome transport	early endosome|lysosome	GTPase activator activity|guanyl-nucleotide exchange factor activity			ovary(2)|skin(2)|pancreas(1)	5	Esophageal squamous(110;0.137)																	---	---	---	---
NUDT19	390916	broad.mit.edu	37	19	33200934	33200934	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:33200934delT	uc010edf.2	+							NM_001105570	NP_001099040			nudix (nucleoside diphosphate linked moiety							mitochondrion|peroxisome	hydrolase activity|metal ion binding				0	Esophageal squamous(110;0.137)																	---	---	---	---
RHPN2	85415	broad.mit.edu	37	19	33499157	33499162	+	Intron	DEL	TTTTTT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:33499157_33499162delTTTTTT	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)																	---	---	---	---
RHPN2	85415	broad.mit.edu	37	19	33558398	33558398	+	5'Flank	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:33558398delA	uc002nuf.2	-						RHPN2_uc010xro.1_5'Flank	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	33587442	33587442	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-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)																	---	---	---	---
Unknown	0	broad.mit.edu	37	19	34045609	34045612	+	IGR	DEL	ACAC	-	-	rs71825877		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:34045609_34045612delACAC								PEPD (32808 upstream) : CHST8 (67249 downstream)																																			---	---	---	---
CHST8	64377	broad.mit.edu	37	19	34189302	34189308	+	Intron	DEL	AAAAAAG	-	-	rs68012158		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:34189302_34189308delAAAAAAG	uc002nus.3	+						CHST8_uc002nut.3_Intron|CHST8_uc002nuu.2_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	34357708	34357708	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:34357708delA								KCTD15 (51043 upstream) : LSM14A (305644 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	19	34491255	34491255	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:34491255delT								KCTD15 (184590 upstream) : LSM14A (172097 downstream)																																			---	---	---	---
KIAA0355	9710	broad.mit.edu	37	19	34742927	34742927	+	5'Flank	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:34742927delT	uc002nvd.3	+							NM_014686	NP_055501			hypothetical protein LOC9710											ovary(1)	1	Esophageal squamous(110;0.162)																	---	---	---	---
KIAA0355	9710	broad.mit.edu	37	19	34812367	34812367	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:34812367delT	uc002nvd.3	+							NM_014686	NP_055501			hypothetical protein LOC9710											ovary(1)	1	Esophageal squamous(110;0.162)																	---	---	---	---
UBA2	10054	broad.mit.edu	37	19	34925890	34925890	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:34925890delT	uc002nvk.2	+						UBA2_uc010xrx.1_Intron|UBA2_uc002nvl.2_Intron	NM_005499	NP_005490			SUMO-1 activating enzyme subunit 2						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)															---	---	---	---
Unknown	0	broad.mit.edu	37	19	34995309	34995310	+	IGR	DEL	TG	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:34995309_34995310delTG								WTIP (3225 upstream) : LOC643719 (72329 downstream)																																			---	---	---	---
HPN	3249	broad.mit.edu	37	19	35556034	35556034	+	Intron	DEL	T	-	-	rs113406953		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-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)													---	---	---	---
USF2	7392	broad.mit.edu	37	19	35761964	35761964	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:35761964delT	uc002nyq.1	+						USF2_uc010xss.1_Intron|USF2_uc002nyr.1_Intron|USF2_uc002nys.1_Intron|USF2_uc002nyt.1_Intron|USF2_uc002nyu.1_Intron|USF2_uc002nyv.1_Intron	NM_003367	NP_003358			upstream stimulatory factor 2 isoform 1						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)															---	---	---	---
Unknown	0	broad.mit.edu	37	19	35930996	35930996	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:35930996delA								FFAR3 (79609 upstream) : FFAR2 (8207 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	19	36087013	36087013	+	IGR	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:36087013delG								ATP4A (32453 upstream) : HAUS5 (16633 downstream)																																			---	---	---	---
MLL4	9757	broad.mit.edu	37	19	36228856	36228856	+	Intron	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:36228856delG	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)															---	---	---	---
C19orf55	148137	broad.mit.edu	37	19	36254407	36254409	+	Intron	DEL	TTT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:36254407_36254409delTTT	uc002obq.1	+							NM_001039887	NP_001034976			hypothetical protein LOC148137											ovary(1)	1	all_lung(56;2.87e-07)|Lung NSC(56;4.32e-07)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0515)															---	---	---	---
ARHGAP33	115703	broad.mit.edu	37	19	36269329	36269329	+	Intron	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:36269329delG	uc002obr.1	+						ARHGAP33_uc002obs.1_Intron|ARHGAP33_uc002obt.1_Intron|ARHGAP33_uc010eek.1_Intron	NM_052948	NP_443180			sorting nexin 26						cell communication|protein transport|signal transduction	intracellular	GTPase activator activity|phosphatidylinositol binding|protein binding			skin(2)|ovary(1)|pancreas(1)	4																		---	---	---	---
APLP1	333	broad.mit.edu	37	19	36363749	36363750	+	Intron	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:36363749_36363750delTT	uc002oce.2	+						APLP1_uc010xsz.1_Intron|APLP1_uc002ocf.2_Intron|APLP1_uc002ocg.2_Intron|APLP1_uc010xta.1_Intron	NM_005166	NP_005157			amyloid precursor-like protein 1 isoform 2						apoptosis|cell adhesion|cellular response to norepinephrine stimulus|endocytosis|negative regulation of cAMP biosynthetic process|nervous system development|organ morphogenesis	basement membrane|integral to membrane|perinuclear region of cytoplasm|plasma membrane	alpha-2A adrenergic receptor binding|alpha-2B adrenergic receptor binding|alpha-2C adrenergic receptor binding|heparin binding|identical protein binding|metal ion binding			ovary(2)	2	all_lung(56;7.14e-07)|Lung NSC(56;1.12e-06)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0515)															---	---	---	---
Unknown	0	broad.mit.edu	37	19	36458177	36458184	+	IGR	DEL	TTTCTTTT	-	-	rs67206936		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:36458177_36458184delTTTCTTTT								LRFN3 (22082 upstream) : SDHAF1 (27917 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	19	36493448	36493448	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:36493448delT								SDHAF1 (6235 upstream) : C19orf46 (554 downstream)																																			---	---	---	---
CAPNS1	826	broad.mit.edu	37	19	36627936	36627936	+	5'Flank	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:36627936delA	uc002odj.2	+						CAPNS1_uc002odi.1_5'Flank|CAPNS1_uc002odk.2_5'Flank	NM_001749	NP_001740			calpain, small subunit 1						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)															---	---	---	---
ZNF146	7705	broad.mit.edu	37	19	36706562	36706562	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:36706562delT	uc002odq.3	+						ZNF565_uc002odn.2_5'Flank|ZNF565_uc010ees.2_5'Flank|ZNF565_uc002odo.2_5'Flank|ZNF565_uc002odp.1_5'Flank|ZNF146_uc010eet.2_Intron|ZNF146_uc010eeu.2_Intron	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	36859756	36859756	+	5'Flank	DEL	T	-	-	rs79137544		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:36859756delT	uc002odx.1	-						ZFP14_uc010xtd.1_5'Flank|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)																	---	---	---	---
Unknown	0	broad.mit.edu	37	19	36882146	36882146	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:36882146delA								ZFP14 (12048 upstream) : ZFP82 (715 downstream)																																			---	---	---	---
ZNF461	92283	broad.mit.edu	37	19	37137008	37137022	+	Intron	DEL	TTGTTGTTGTTGTTA	-	-	rs141622020		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:37137008_37137022delTTGTTGTTGTTGTTA	uc002oem.2	-						ZNF461_uc002oen.2_Intron|ZNF461_uc010xtj.1_Intron	NM_153257	NP_694989			gonadotropin inducible transcription repressor						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)															---	---	---	---
ZNF461	92283	broad.mit.edu	37	19	37155707	37155707	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:37155707delA	uc002oem.2	-						ZNF461_uc002oen.2_Intron|ZNF461_uc010xtj.1_Intron	NM_153257	NP_694989			gonadotropin inducible transcription repressor						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)															---	---	---	---
ZNF567	163081	broad.mit.edu	37	19	37204354	37204355	+	Intron	DEL	AA	-	-	rs77092060		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:37204354_37204355delAA	uc010xtl.1	+						ZNF567_uc002oeo.1_Intron|ZNF567_uc010xtk.1_Intron|ZNF567_uc002oep.3_Intron|ZNF567_uc002oeq.1_Intron	NM_152603	NP_689816			zinc finger protein 567						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)															---	---	---	---
Unknown	0	broad.mit.edu	37	19	37254467	37254467	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:37254467delA	uc010efc.2	-						uc010xtm.1_Intron					Homo sapiens zinc finger protein 850 pseudogene, mRNA (cDNA clone IMAGE:6082150).																														---	---	---	---
ZNF585B	92285	broad.mit.edu	37	19	37681158	37681158	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:37681158delT	uc002ofq.2	-						ZNF585B_uc002ofr.1_Intron	NM_152279	NP_689492			zinc finger protein 585B						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)															---	---	---	---
ZNF527	84503	broad.mit.edu	37	19	37877043	37877046	+	Intron	DEL	TTTT	-	-	rs71765649		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:37877043_37877046delTTTT	uc010efk.1	+						ZNF527_uc002ogf.3_Intron|ZNF527_uc010xtq.1_Intron	NM_032453	NP_115829			zinc finger protein 527						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)															---	---	---	---
ZNF569	148266	broad.mit.edu	37	19	37916539	37916539	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:37916539delT	uc002ogi.2	-						ZNF569_uc002ogh.2_Intron|ZNF569_uc002ogj.2_Intron	NM_152484	NP_689697			zinc finger protein 569						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			breast(2)|skin(1)	3			COAD - Colon adenocarcinoma(19;0.114)|Colorectal(19;0.177)															---	---	---	---
ZNF569	148266	broad.mit.edu	37	19	37951438	37951440	+	Intron	DEL	AAA	-	-	rs78775959		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:37951438_37951440delAAA	uc002ogi.2	-						ZNF569_uc002ogj.2_Intron	NM_152484	NP_689697			zinc finger protein 569						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			breast(2)|skin(1)	3			COAD - Colon adenocarcinoma(19;0.114)|Colorectal(19;0.177)															---	---	---	---
ZNF540	163255	broad.mit.edu	37	19	38052875	38052875	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:38052875delT	uc002ogq.2	+						uc002ogm.2_Intron|uc002ogn.2_Intron|ZNF540_uc002ogo.2_Intron|ZNF540_uc002ogp.2_Intron|ZNF571_uc002ogr.1_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	38583011	38583014	+	Intron	DEL	AAAA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:38583011_38583014delAAAA	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)															---	---	---	---
CATSPERG	57828	broad.mit.edu	37	19	38833805	38833806	+	Intron	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:38833805_38833806delTT	uc002oih.3	+						CATSPERG_uc002oig.3_Intron|CATSPERG_uc002oif.3_Intron|CATSPERG_uc010efw.2_5'Flank	NM_021185	NP_067008			cation channel, sperm-associated, gamma						cell differentiation|multicellular organismal development|spermatogenesis	integral to membrane				ovary(1)|skin(1)	2																		---	---	---	---
MAP4K1	11184	broad.mit.edu	37	19	39098897	39098898	+	Intron	INS	-	G	G	rs149270812	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:39098897_39098898insG	uc002oix.1	-						MAP4K1_uc002oiw.1_5'Flank|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)															---	---	---	---
Unknown	0	broad.mit.edu	37	19	39127966	39127966	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:39127966delT								EIF3K (371 upstream) : ACTN4 (10361 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	19	39723680	39723680	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:39723680delT								SYCN (28774 upstream) : IL28B (10593 downstream)																																			---	---	---	---
SUPT5H	6829	broad.mit.edu	37	19	39935357	39935358	+	5'Flank	INS	-	A	A	rs139172068	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:39935357_39935358insA	uc002olo.3	+						SUPT5H_uc010xvb.1_5'Flank|SUPT5H_uc002olp.3_5'Flank|SUPT5H_uc002olq.3_5'Flank|SUPT5H_uc002oln.3_5'Flank|SUPT5H_uc002olr.3_5'Flank	NM_001111020	NP_001104490			suppressor of Ty 5 homolog isoform a						cell cycle|chromatin remodeling|mRNA capping|negative regulation of transcription elongation, DNA-dependent|negative regulation of transcription from RNA polymerase II promoter|positive regulation of transcription elongation from RNA polymerase II promoter|positive regulation of transcription from RNA polymerase II promoter|positive regulation of viral transcription|response to organic substance|retroviral genome replication|transcription elongation from RNA polymerase II promoter	nucleoplasm	enzyme binding|protein heterodimerization activity			ovary(3)|pancreas(1)	4	all_cancers(60;6.69e-07)|all_lung(34;2.66e-08)|Lung NSC(34;3e-08)|all_epithelial(25;1.57e-06)|Ovarian(47;0.159)		Epithelial(26;3.9e-26)|all cancers(26;1.35e-23)|LUSC - Lung squamous cell carcinoma(53;0.000657)															---	---	---	---
Unknown	0	broad.mit.edu	37	19	39982295	39982295	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:39982295delA								TIMM50 (767 upstream) : DLL3 (7262 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	19	40014852	40014852	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:40014852delT								SELV (3526 upstream) : EID2B (6778 downstream)																																			---	---	---	---
EID2B	126272	broad.mit.edu	37	19	40021719	40021719	+	3'UTR	DEL	A	-	-	rs34833151		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:40021719delA	uc002olz.1	-	1						NM_152361	NP_689574			EP300 interacting inhibitor of differentiation						cell differentiation|muscle organ development|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus					0	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;8.61e-26)|all cancers(26;2.76e-23)|LUSC - Lung squamous cell carcinoma(53;0.000657)															---	---	---	---
LGALS14	56891	broad.mit.edu	37	19	40192792	40192793	+	5'Flank	INS	-	C	C	rs147256960	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:40192792_40192793insC	uc002omg.2	+						LGALS14_uc002omf.2_5'Flank	NM_020129	NP_064514			lectin, galactoside-binding, soluble, 14 isoform							nucleus	sugar binding			ovary(1)|skin(1)	2	all_cancers(60;4.39e-06)|all_lung(34;6.76e-08)|Lung NSC(34;7.98e-08)|Ovarian(47;0.06)	Myeloproliferative disorder(2;0.0741)	Epithelial(26;1.08e-24)|OV - Ovarian serous cystadenocarcinoma(5;1.92e-24)|all cancers(26;4.12e-22)															---	---	---	---
FCGBP	8857	broad.mit.edu	37	19	40369566	40369566	+	Intron	DEL	A	-	-	rs67861877		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:40369566delA	uc002omp.3	-							NM_003890	NP_003881			Fc fragment of IgG binding protein precursor							extracellular region	protein binding			ovary(4)|skin(4)|central_nervous_system(1)	9	all_cancers(60;6.03e-06)|all_lung(34;5.58e-08)|Lung NSC(34;6.62e-08)|Ovarian(47;0.06)		Epithelial(26;6.25e-23)|all cancers(26;1.13e-20)															---	---	---	---
AKT2	208	broad.mit.edu	37	19	40787404	40787404	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:40787404delA	uc002onf.2	-						AKT2_uc010egt.2_Intron|AKT2_uc010xvj.1_Intron|AKT2_uc010egu.1_Intron|AKT2_uc010xvk.1_5'Flank	NM_001626	NP_001617			AKT2 kinase						insulin receptor signaling pathway|negative regulation of plasma membrane long-chain fatty acid transport|positive regulation of fatty acid beta-oxidation|positive regulation of glucose import|positive regulation of glycogen biosynthetic process	cytosol|nucleus	ATP binding|protein binding|protein serine/threonine kinase activity			lung(2)	2			Lung(22;0.000499)					A		ovarian|pancreatic 								---	---	---	---
Unknown	0	broad.mit.edu	37	19	40817287	40817287	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:40817287delA								AKT2 (26022 upstream) : C19orf47 (9686 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	19	40826728	40826728	+	IGR	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:40826728delG								AKT2 (35463 upstream) : C19orf47 (245 downstream)																																			---	---	---	---
HIPK4	147746	broad.mit.edu	37	19	40889492	40889492	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:40889492delT	uc002onp.2	-							NM_144685	NP_653286			homeodomain interacting protein kinase 4							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)															---	---	---	---
SPTBN4	57731	broad.mit.edu	37	19	41010047	41010047	+	Intron	DEL	C	-	-	rs843779	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:41010047delC	uc002ony.2	+						SPTBN4_uc002onx.2_Intron|SPTBN4_uc002onz.2_Intron	NM_020971	NP_066022			spectrin, beta, non-erythrocytic 4 isoform						actin filament capping|axon guidance|cytoskeletal anchoring at plasma membrane|vesicle-mediated transport	cytosol|nuclear matrix|PML body|spectrin	actin binding|ankyrin binding|structural constituent of cytoskeleton			ovary(3)|central_nervous_system(1)|skin(1)	5			Lung(22;0.000114)|LUSC - Lung squamous cell carcinoma(20;0.000384)															---	---	---	---
SPTBN4	57731	broad.mit.edu	37	19	41054240	41054240	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:41054240delA	uc002ony.2	+						SPTBN4_uc002onx.2_Intron|SPTBN4_uc002onz.2_Intron|SPTBN4_uc010egx.2_Intron|SPTBN4_uc010egy.1_Intron|SPTBN4_uc002ooa.2_Intron	NM_020971	NP_066022			spectrin, beta, non-erythrocytic 4 isoform						actin filament capping|axon guidance|cytoskeletal anchoring at plasma membrane|vesicle-mediated transport	cytosol|nuclear matrix|PML body|spectrin	actin binding|ankyrin binding|structural constituent of cytoskeleton			ovary(3)|central_nervous_system(1)|skin(1)	5			Lung(22;0.000114)|LUSC - Lung squamous cell carcinoma(20;0.000384)															---	---	---	---
EGLN2	112398	broad.mit.edu	37	19	41287544	41287545	+	Intron	DEL	GA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:41287544_41287545delGA	uc010ehd.2	+						MIA_uc010xvt.1_Intron|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)													---	---	---	---
Unknown	0	broad.mit.edu	37	19	41319835	41319836	+	IGR	DEL	TC	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:41319835_41319836delTC								EGLN2 (5499 upstream) : CYP2A6 (29608 downstream)																																			---	---	---	---
CYP2A7	1549	broad.mit.edu	37	19	41411462	41411464	+	Intron	DEL	TTT	-	-	rs10547319		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:41411462_41411464delTTT	uc002opo.2	-							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)															---	---	---	---
CYP2F1	1572	broad.mit.edu	37	19	41674998	41674998	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:41674998delA	uc010xvw.1	+											SubName: Full=cDNA FLJ51986, highly similar to Homo sapiens cytochrome P450, family 2, subfamily F, polypeptide 1 (CYP2F1), mRNA;						naphthalene metabolic process|xenobiotic metabolic process	endoplasmic reticulum membrane|microsome	aromatase activity|electron carrier activity|heme binding|oxygen binding				0																		---	---	---	---
BCKDHA	593	broad.mit.edu	37	19	41883369	41883369	+	Intron	DEL	G	-	-	rs144486085	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:41883369delG	uc002oqm.3	+						CYP2F1_uc010xvw.1_Intron|TMEM91_uc002oqi.2_Intron|TMEM91_uc010ehq.2_Intron|TMEM91_uc002oql.2_Intron|TMEM91_uc010ehr.2_Intron|TMEM91_uc010ehs.2_Intron|TMEM91_uc010eht.2_Intron|TMEM91_uc002oqk.3_Intron|TMEM91_uc002oqn.2_Intron	NM_000709	NP_000700			branched chain keto acid dehydrogenase E1, alpha						branched chain family amino acid catabolic process	mitochondrial alpha-ketoglutarate dehydrogenase complex	3-methyl-2-oxobutanoate dehydrogenase (2-methylpropanoyl-transferring) activity|alpha-ketoacid dehydrogenase activity|carboxy-lyase activity|metal ion binding|protein binding				0																		---	---	---	---
DMRTC2	63946	broad.mit.edu	37	19	42352414	42352416	+	Intron	DEL	AAA	-	-	rs79959130		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:42352414_42352416delAAA	uc002ors.2	+						DMRTC2_uc002orr.1_Intron|DMRTC2_uc010xwe.1_Intron	NM_001040283	NP_001035373			DMRT-like family C2						cell differentiation|sex differentiation	nucleus	DNA binding|metal ion binding|sequence-specific DNA binding transcription factor activity				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	19	42357440	42357442	+	IGR	DEL	CTC	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:42357440_42357442delCTC								DMRTC2 (1045 upstream) : RPS19 (6546 downstream)																																			---	---	---	---
MEGF8	1954	broad.mit.edu	37	19	42836179	42836179	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:42836179delT	uc002otl.3	+							NM_001410	NP_001401			multiple EGF-like-domains 8							integral to membrane	calcium ion binding|structural molecule activity			ovary(1)	1		Prostate(69;0.00682)																---	---	---	---
MEGF8	1954	broad.mit.edu	37	19	42858271	42858273	+	Intron	DEL	TTT	-	-	rs36065839		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:42858271_42858273delTTT	uc002otl.3	+						MEGF8_uc002otm.3_Intron	NM_001410	NP_001401			multiple EGF-like-domains 8							integral to membrane	calcium ion binding|structural molecule activity			ovary(1)	1		Prostate(69;0.00682)																---	---	---	---
PSG1	5669	broad.mit.edu	37	19	43358577	43358578	+	Intron	DEL	AC	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:43358577_43358578delAC	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_uc002oul.3_Intron|PSG8_uc002oum.3_Intron|PSG1_uc002oun.2_Intron|PSG8_uc002oup.3_Intron|PSG10_uc010eip.2_Intron|PSG1_uc002our.1_Intron|PSG1_uc002oux.1_Intron|PSG1_uc002ouy.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	43460948	43460948	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-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)																---	---	---	---
Unknown	0	broad.mit.edu	37	19	43816494	43816495	+	IGR	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:43816494_43816495delTT								PSG9 (42812 upstream) : PRG1 (36713 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	19	43935697	43935698	+	IGR	DEL	AG	-	-	rs9749089	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:43935697_43935698delAG								TEX101 (12931 upstream) : LYPD3 (29248 downstream)																																			---	---	---	---
LYPD3	27076	broad.mit.edu	37	19	43966189	43966189	+	Intron	DEL	A	-	-	rs35056869		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:43966189delA	uc002owl.1	-						LYPD3_uc002owm.2_3'UTR	NM_014400	NP_055215			GPI-anchored metastasis-associated protein							anchored to plasma membrane				pancreas(1)	1		Prostate(69;0.0153)																---	---	---	---
SRRM5	100170229	broad.mit.edu	37	19	44112265	44112265	+	Intron	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:44112265delG	uc002oxb.2	+						ZNF428_uc002oxa.2_Intron	NM_001145641	NP_001139113			serine/arginine repetitive matrix 5												0																		---	---	---	---
KCNN4	3783	broad.mit.edu	37	19	44280870	44280870	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:44280870delT	uc002oxl.2	-						KCNN4_uc010eiz.2_5'Flank|KCNN4_uc010eja.1_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)													---	---	---	---
Unknown	0	broad.mit.edu	37	19	44392673	44392675	+	IGR	DEL	AAA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:44392673_44392675delAAA								ZNF404 (8385 upstream) : ZNF45 (24106 downstream)																																			---	---	---	---
ZNF223	7766	broad.mit.edu	37	19	44566682	44566682	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:44566682delT	uc002oyf.1	+						ZNF284_uc010ejd.2_Intron	NM_013361	NP_037493			zinc finger protein 223						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1		Prostate(69;0.0352)																---	---	---	---
ZNF235	9310	broad.mit.edu	37	19	44750252	44750252	+	Intron	DEL	C	-	-	rs1233470	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:44750252delC	uc010eji.2	-						ZNF235_uc002oyx.1_Intron					SubName: Full=Kruppel-associated box; Flags: Fragment;						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(2)|large_intestine(1)	3		Prostate(69;0.0352)|all_neural(266;0.116)																---	---	---	---
ZNF180	7733	broad.mit.edu	37	19	44982020	44982020	+	Frame_Shift_Del	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:44982020delT	uc002ozf.3	-	5	960	c.678delA	c.(676-678)AAAfs	p.K226fs	ZNF180_uc002ozh.3_Translation_Start_Site|ZNF180_uc002ozi.3_Frame_Shift_Del_p.K199fs|ZNF180_uc002ozg.3_Frame_Shift_Del_p.K225fs|ZNF180_uc010ejm.2_Frame_Shift_Del_p.K201fs	NM_013256	NP_037388	Q9UJW8	ZN180_HUMAN	zinc finger protein 180	226					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(2)	2		Prostate(69;0.0435)																---	---	---	---
Unknown	0	broad.mit.edu	37	19	45036669	45036669	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:45036669delA								CEACAM20 (3121 upstream) : CEACAM22P (4376 downstream)																																			---	---	---	---
BCL3	602	broad.mit.edu	37	19	45259690	45259690	+	Intron	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:45259690delG	uc010xxe.1	+							NM_005178	NP_005169			B-cell CLL/lymphoma 3						DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|I-kappaB kinase/NF-kappaB cascade|maintenance of protein location in nucleus|negative regulation of apoptosis|negative regulation of interleukin-8 biosynthetic process|negative regulation of transcription, DNA-dependent|positive regulation of translation|protein import into nucleus, translocation|regulation of DNA binding|regulation of NF-kappaB import into nucleus|response to UV-C|response to virus	Bcl3-Bcl10 complex|Bcl3/NF-kappaB2 complex|nucleus|perinuclear region of cytoplasm	protein binding, bridging|transcription factor binding			ovary(1)|lung(1)	2	Lung NSC(12;0.000698)|all_lung(12;0.002)	Ovarian(192;0.0728)						T	IGH@	CLL 								---	---	---	---
BCAM	4059	broad.mit.edu	37	19	45316331	45316333	+	Intron	DEL	GGA	-	-	rs28399609		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:45316331_45316333delGGA	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)																---	---	---	---
BCAM	4059	broad.mit.edu	37	19	45320492	45320492	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:45320492delA	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)																---	---	---	---
EXOC3L2	90332	broad.mit.edu	37	19	45716496	45716496	+	Frame_Shift_Del	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:45716496delG	uc002pay.1	-	10	1102	c.1061delC	c.(1060-1062)CCTfs	p.P354fs		NM_138568	NP_612635	Q2M3D2	EX3L2_HUMAN	exocyst complex component 3-like 2	354										ovary(1)	1		all_neural(266;0.224)|Ovarian(192;0.231)		OV - Ovarian serous cystadenocarcinoma(262;0.00883)														---	---	---	---
EXOC3L2	90332	broad.mit.edu	37	19	45731576	45731576	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:45731576delT	uc002pay.1	-							NM_138568	NP_612635			exocyst complex component 3-like 2											ovary(1)	1		all_neural(266;0.224)|Ovarian(192;0.231)		OV - Ovarian serous cystadenocarcinoma(262;0.00883)														---	---	---	---
MARK4	57787	broad.mit.edu	37	19	45783560	45783560	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:45783560delA	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	45798617	45798617	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:45798617delA	uc002pbb.1	+						MARK4_uc002pba.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)														---	---	---	---
CKM	1158	broad.mit.edu	37	19	45817616	45817616	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:45817616delT	uc002pbd.2	-							NM_001824	NP_001815			muscle creatine kinase						creatine metabolic process	cytosol	ATP binding|creatine kinase activity			skin(1)	1		Ovarian(192;0.0336)|all_neural(266;0.112)		OV - Ovarian serous cystadenocarcinoma(262;2.29e-44)|Epithelial(262;1.05e-38)|GBM - Glioblastoma multiforme(486;3.56e-07)	Creatine(DB00148)													---	---	---	---
CKM	1158	broad.mit.edu	37	19	45822685	45822685	+	Intron	DEL	C	-	-	rs68016783		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:45822685delC	uc002pbd.2	-							NM_001824	NP_001815			muscle creatine kinase						creatine metabolic process	cytosol	ATP binding|creatine kinase activity			skin(1)	1		Ovarian(192;0.0336)|all_neural(266;0.112)		OV - Ovarian serous cystadenocarcinoma(262;2.29e-44)|Epithelial(262;1.05e-38)|GBM - Glioblastoma multiforme(486;3.56e-07)	Creatine(DB00148)													---	---	---	---
Unknown	0	broad.mit.edu	37	19	45833506	45833506	+	IGR	DEL	T	-	-	rs71338768		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:45833506delT								CKM (7372 upstream) : KLC3 (10492 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	19	45875768	45875769	+	IGR	DEL	AA	-	-	rs112212484		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:45875768_45875769delAA								ERCC2 (1923 upstream) : PPP1R13L (7124 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	19	46384901	46384901	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:46384901delT								FOXA3 (7847 upstream) : IRF2BP1 (1965 downstream)																																			---	---	---	---
HIF3A	64344	broad.mit.edu	37	19	46845661	46845661	+	3'UTR	DEL	A	-	-	rs112522642		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:46845661delA	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	46921742	46921742	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:46921742delT								CCDC8 (4823 upstream) : PNMAL1 (48007 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	19	47308085	47308086	+	IGR	DEL	AA	-	-	rs80011142		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:47308085_47308086delAA								SLC1A5 (16243 upstream) : SNAR-E (25756 downstream)																																			---	---	---	---
GRLF1	2909	broad.mit.edu	37	19	47426802	47426802	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:47426802delT	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)														---	---	---	---
SAE1	10055	broad.mit.edu	37	19	47671077	47671077	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:47671077delT	uc002pgc.2	+						SAE1_uc002pgd.2_Intron|SAE1_uc010ekx.2_Intron|SAE1_uc010ekw.2_Intron|SAE1_uc010xyk.1_Intron|SAE1_uc002pge.2_Intron	NM_016402	NP_057486			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;						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)														---	---	---	---
Unknown	0	broad.mit.edu	37	19	47805798	47805799	+	IGR	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:47805798_47805799delTT								PRR24 (26819 upstream) : C5AR1 (7305 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	19	47809572	47809572	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:47809572delA								PRR24 (30593 upstream) : C5AR1 (3532 downstream)																																			---	---	---	---
DHX34	9704	broad.mit.edu	37	19	47853987	47853987	+	Intron	DEL	T	-	-	rs78170153		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:47853987delT	uc010xyn.1	+						DHX34_uc010elc.1_5'Flank	NM_014681	NP_055496			DEAH (Asp-Glu-Ala-His) box polypeptide 34							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)														---	---	---	---
DHX34	9704	broad.mit.edu	37	19	47870424	47870424	+	Intron	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:47870424delC	uc010xyn.1	+						DHX34_uc010elc.1_Intron	NM_014681	NP_055496			DEAH (Asp-Glu-Ala-His) box polypeptide 34							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	47950110	47950111	+	Intron	INS	-	T	T	rs141720064	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:47950110_47950111insT	uc002pgx.2	-						SLC8A2_uc010xyq.1_Intron|SLC8A2_uc010xyr.1_Intron|SLC8A2_uc010ele.2_Intron	NM_015063	NP_055878			solute carrier family 8 member 2 precursor						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	48007349	48007349	+	Intron	DEL	A	-	-	rs8110717	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:48007349delA	uc002pha.1	-						NAPA_uc002phb.1_Intron|NAPA_uc002phc.1_Intron|NAPA_uc002phd.1_Intron|NAPA_uc010elf.1_Intron|NAPA_uc010elg.1_Intron|NAPA_uc002phe.2_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)														---	---	---	---
GLTSCR1	29998	broad.mit.edu	37	19	48160127	48160127	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:48160127delT	uc002phh.3	+							NM_015711	NP_056526			glioma tumor suppressor candidate region gene 1								protein binding			pancreas(3)	3		all_cancers(25;1.8e-07)|all_lung(116;5.73e-06)|Lung NSC(112;9.69e-06)|all_epithelial(76;2.42e-05)|all_neural(266;0.0332)|Ovarian(192;0.086)		all cancers(93;0.000358)|OV - Ovarian serous cystadenocarcinoma(262;0.000576)|Epithelial(262;0.0212)|GBM - Glioblastoma multiforme(486;0.0355)														---	---	---	---
GLTSCR1	29998	broad.mit.edu	37	19	48201844	48201844	+	Intron	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:48201844delC	uc002phh.3	+						GLTSCR1_uc002phi.3_Intron	NM_015711	NP_056526			glioma tumor suppressor candidate region gene 1								protein binding			pancreas(3)	3		all_cancers(25;1.8e-07)|all_lung(116;5.73e-06)|Lung NSC(112;9.69e-06)|all_epithelial(76;2.42e-05)|all_neural(266;0.0332)|Ovarian(192;0.086)		all cancers(93;0.000358)|OV - Ovarian serous cystadenocarcinoma(262;0.000576)|Epithelial(262;0.0212)|GBM - Glioblastoma multiforme(486;0.0355)												OREG0025594	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
SEPW1	6415	broad.mit.edu	37	19	48284247	48284248	+	Intron	INS	-	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:48284247_48284248insG	uc010xyw.1	+						SEPW1_uc002pho.1_5'Flank	NM_003009	NP_003000			selenoprotein W, 1						cell redox homeostasis	cytoplasm	selenium binding				0		all_cancers(25;3.02e-09)|all_epithelial(76;7e-07)|all_lung(116;2.48e-06)|Lung NSC(112;5.15e-06)|Ovarian(192;0.0139)|all_neural(266;0.0146)|Breast(70;0.133)		all cancers(93;0.000291)|OV - Ovarian serous cystadenocarcinoma(262;0.000305)|Epithelial(262;0.0146)|GBM - Glioblastoma multiforme(486;0.0273)														---	---	---	---
PLA2G4C	8605	broad.mit.edu	37	19	48578790	48578791	+	Intron	DEL	CT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:48578790_48578791delCT	uc002phx.2	-						PLA2G4C_uc002phw.2_Intron|PLA2G4C_uc010elr.2_Intron|PLA2G4C_uc010xzd.1_Intron	NM_003706	NP_003697			phospholipase A2, group IVC isoform 1 precursor						arachidonic acid metabolic process|glycerophospholipid catabolic process|inflammatory response|intracellular signal transduction|parturition	cytosol|membrane	calcium-independent phospholipase A2 activity|phospholipid binding			ovary(1)|skin(1)	2		all_cancers(25;2.84e-05)|all_lung(116;4.62e-05)|Lung NSC(112;7.61e-05)|all_epithelial(76;0.000192)|all_neural(266;0.0506)|Ovarian(192;0.113)		OV - Ovarian serous cystadenocarcinoma(262;8.09e-05)|all cancers(93;0.000517)|Epithelial(262;0.0135)|GBM - Glioblastoma multiforme(486;0.0717)														---	---	---	---
LIG1	3978	broad.mit.edu	37	19	48638084	48638084	+	Intron	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:48638084delG	uc002pia.1	-						LIG1_uc010xze.1_Intron|LIG1_uc002phz.1_Intron|LIG1_uc002pib.1_Intron|LIG1_uc010xzf.1_Intron|LIG1_uc010xzg.1_Intron	NM_000234	NP_000225			DNA ligase I						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					---	---	---	---
LMTK3	114783	broad.mit.edu	37	19	48998273	48998273	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:48998273delT	uc002pjk.2	-							NM_001080434	NP_001073903			lemur tyrosine kinase 3											lung(5)|central_nervous_system(1)	6		all_lung(116;0.000147)|Lung NSC(112;0.000251)|all_epithelial(76;0.000326)|all_neural(266;0.0506)|Ovarian(192;0.113)		OV - Ovarian serous cystadenocarcinoma(262;0.000114)|all cancers(93;0.000141)|Epithelial(262;0.00854)|GBM - Glioblastoma multiforme(486;0.0231)														---	---	---	---
SULT2B1	6820	broad.mit.edu	37	19	49101325	49101325	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:49101325delT	uc002pjl.2	+						SULT2B1_uc002pjm.2_Intron	NM_177973	NP_814444			sulfotransferase family, cytosolic, 2B, member 1						3'-phosphoadenosine 5'-phosphosulfate metabolic process|steroid metabolic process|xenobiotic metabolic process	cytosol	alcohol sulfotransferase activity|protein binding|steroid sulfotransferase 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;0.000115)|all cancers(93;0.000147)|GBM - Glioblastoma multiforme(486;0.00707)|Epithelial(262;0.0178)														---	---	---	---
SEC1	653677	broad.mit.edu	37	19	49141790	49141790	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:49141790delA	uc010xzv.1	+						SEC1_uc002pka.2_Intron|SEC1_uc010xzw.1_Intron|SEC1_uc010ema.2_Intron|DBP_uc002pjx.3_5'Flank|DBP_uc002pjy.2_5'Flank|DBP_uc010elz.1_5'Flank|CA11_uc002pjz.1_Intron	NR_004401				SubName: Full=cDNA FLJ58287, highly similar to Galactoside 2-alpha-L-fucosyltransferase 2 (EC 2.4.1.69);												0																		---	---	---	---
SEC1	653677	broad.mit.edu	37	19	49161328	49161328	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:49161328delT	uc010xzv.1	+						SEC1_uc002pka.2_Intron|SEC1_uc010xzw.1_Intron|SEC1_uc010ema.2_Intron	NR_004401				SubName: Full=cDNA FLJ58287, highly similar to Galactoside 2-alpha-L-fucosyltransferase 2 (EC 2.4.1.69);												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	19	49187441	49187445	+	IGR	DEL	AAAAA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:49187441_49187445delAAAAA								SEC1 (1940 upstream) : FUT2 (11783 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	19	49277183	49277184	+	IGR	INS	-	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:49277183_49277184insT								FGF21 (15601 upstream) : BCAT2 (21136 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	19	49282329	49282329	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:49282329delA								FGF21 (20747 upstream) : BCAT2 (15991 downstream)																																			---	---	---	---
CGB5	93659	broad.mit.edu	37	19	49547325	49547325	+	5'UTR	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:49547325delC	uc002ply.2	+	1					CGB_uc010yad.1_Intron|CGB5_uc002plz.2_5'Flank	NM_033043	NP_149032			chorionic gonadotropin, beta polypeptide 5						apoptosis|cell-cell signaling|cellular nitrogen compound metabolic process|female gamete generation|hormone biosynthetic process|peptide hormone processing|signal transduction	extracellular region|soluble fraction	hormone activity				0		all_epithelial(76;9.62e-07)|all_lung(116;1.7e-06)|Lung NSC(112;3.55e-06)|all_neural(266;0.0189)|Ovarian(192;0.0261)		all cancers(93;0.000371)|OV - Ovarian serous cystadenocarcinoma(262;0.000503)|GBM - Glioblastoma multiforme(486;0.00518)|Epithelial(262;0.0427)	Choriogonadotropin alfa(DB00097)													---	---	---	---
TEAD2	8463	broad.mit.edu	37	19	49855802	49855802	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:49855802delT	uc002pnj.2	-						TEAD2_uc002png.2_Intron|TEAD2_uc002pnh.2_Intron|TEAD2_uc002pni.2_Intron|TEAD2_uc010yao.1_Intron|TEAD2_uc010emw.2_Intron	NM_003598	NP_003589			TEA domain family member 2						hippo signaling cascade		DNA binding|protein binding|sequence-specific DNA binding transcription factor activity			central_nervous_system(2)|ovary(1)	3		all_lung(116;7.65e-05)|Lung NSC(112;0.000132)|all_neural(266;0.0506)|Ovarian(192;0.15)		OV - Ovarian serous cystadenocarcinoma(262;0.00093)|GBM - Glioblastoma multiforme(486;0.0467)														---	---	---	---
SLC17A7	57030	broad.mit.edu	37	19	49937768	49937768	+	Intron	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-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)														---	---	---	---
Unknown	0	broad.mit.edu	37	19	50009033	50009033	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:50009033delA								MIR150 (4908 upstream) : FCGRT (6503 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	19	50056896	50056896	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:50056896delA								RCN3 (10007 upstream) : NOSIP (2074 downstream)																																			---	---	---	---
PRR12	57479	broad.mit.edu	37	19	50118386	50118387	+	Intron	INS	-	AG	AG			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:50118386_50118387insAG	uc002poo.3	+							NM_020719	NP_065770			proline rich 12								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)														---	---	---	---
BCL2L12	83596	broad.mit.edu	37	19	50171350	50171355	+	Intron	DEL	TTTTTT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:50171350_50171355delTTTTTT	uc002ppa.2	+						IRF3_uc010end.1_5'Flank|IRF3_uc002pox.1_5'Flank|IRF3_uc002poy.1_5'Flank|IRF3_uc002pou.2_5'Flank|IRF3_uc002pov.2_5'Flank|IRF3_uc002pow.2_5'Flank|IRF3_uc002poz.1_5'Flank|BCL2L12_uc002ppb.2_Intron	NM_138639	NP_619580			BCL2-like 12 isoform 1						apoptosis					central_nervous_system(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;0.000681)|GBM - Glioblastoma multiforme(134;0.0214)														---	---	---	---
Unknown	0	broad.mit.edu	37	19	50222670	50222670	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:50222670delT								CPT1C (5682 upstream) : TSKS (20342 downstream)																																			---	---	---	---
TSKS	60385	broad.mit.edu	37	19	50265062	50265062	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:50265062delA	uc002ppm.2	-							NM_021733	NP_068379			testis-specific kinase substrate								protein binding			large_intestine(1)|skin(1)	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;0.00153)|GBM - Glioblastoma multiforme(134;0.0145)														---	---	---	---
IL4I1	259307	broad.mit.edu	37	19	50399704	50399704	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:50399704delT	uc002pqt.1	-						IL4I1_uc002pqv.1_Intron|IL4I1_uc010eno.1_Intron|IL4I1_uc002pqw.1_Intron|IL4I1_uc002pqu.1_Intron	NM_152899	NP_690863			interleukin 4 induced 1 isoform 1 precursor							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)														---	---	---	---
Unknown	0	broad.mit.edu	37	19	50469795	50469796	+	IGR	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:50469795_50469796delTT								SIGLEC11 (5366 upstream) : SIGLEC16 (3116 downstream)																																			---	---	---	---
SIGLEC16	400709	broad.mit.edu	37	19	50475206	50475206	+	Intron	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:50475206delC	uc002prf.2	+						uc010ybk.1_Frame_Shift_Del_p.T44fs	NR_002825				Homo sapiens cDNA FLJ50062 complete cds, highly similar to Sialic acid-binding Ig-like lectin 11 precursor.												0																		---	---	---	---
VRK3	51231	broad.mit.edu	37	19	50496642	50496643	+	Intron	INS	-	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:50496642_50496643insT	uc002prg.2	-						VRK3_uc002prh.1_Intron|VRK3_uc002pri.1_Intron|VRK3_uc010ens.2_Intron|VRK3_uc010ybl.1_Intron|VRK3_uc010ybm.1_Intron|VRK3_uc002prj.1_Intron|VRK3_uc002prk.1_Intron|VRK3_uc010ent.1_Intron|VRK3_uc002prl.2_Intron|VRK3_uc010ybn.1_Intron	NM_016440	NP_057524			vaccinia related kinase 3 isoform 1							nucleus	ATP binding|protein kinase activity			stomach(1)|skin(1)	2		all_neural(266;0.0459)|Ovarian(192;0.0481)		GBM - Glioblastoma multiforme(134;0.00166)|OV - Ovarian serous cystadenocarcinoma(262;0.00652)														---	---	---	---
ZNF473	25888	broad.mit.edu	37	19	50547362	50547363	+	Intron	DEL	AG	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:50547362_50547363delAG	uc002prn.2	+						ZNF473_uc002prm.2_Intron|ZNF473_uc010ybo.1_Intron	NM_001006656	NP_001006657			zinc finger protein 473						histone mRNA 3'-end processing|regulation of transcription, DNA-dependent|termination of RNA polymerase II transcription	Cajal body	DNA binding|protein binding|zinc ion binding			ovary(1)|central_nervous_system(1)	2		all_neural(266;0.0459)|Ovarian(192;0.0728)		GBM - Glioblastoma multiforme(134;0.00111)|OV - Ovarian serous cystadenocarcinoma(262;0.0058)														---	---	---	---
MYH14	79784	broad.mit.edu	37	19	50774330	50774330	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:50774330delT	uc002prr.1	+						MYH14_uc010enu.1_Intron|MYH14_uc002prq.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	50973771	50973772	+	Intron	DEL	AA	-	-	rs111469119		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:50973771_50973772delAA	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	50998227	50998227	+	IGR	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:50998227delG								C19orf63 (11620 upstream) : JOSD2 (11032 downstream)																																			---	---	---	---
KLK15	55554	broad.mit.edu	37	19	51335569	51335569	+	5'Flank	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:51335569delT	uc002ptl.2	-						KLK15_uc002ptm.2_5'Flank|KLK15_uc002ptn.2_5'Flank|KLK15_uc002pto.2_5'Flank|KLK15_uc010ych.1_5'Flank|KLK15_uc010yci.1_5'Flank|KLK15_uc010eod.2_5'Flank	NM_017509	NP_059979			kallikrein-related peptidase 15 isoform 4						proteolysis	extracellular region	serine-type endopeptidase activity			lung(1)|breast(1)	2		all_neural(266;0.057)		OV - Ovarian serous cystadenocarcinoma(262;0.00758)|GBM - Glioblastoma multiforme(134;0.0143)														---	---	---	---
Unknown	0	broad.mit.edu	37	19	51476254	51476254	+	IGR	DEL	G	-	-	rs76933831	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:51476254delG								KLK6 (3325 upstream) : KLK7 (3476 downstream)																																			---	---	---	---
SIGLEC10	89790	broad.mit.edu	37	19	51922611	51922611	+	5'Flank	DEL	T	-	-	rs34057387		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:51922611delT	uc002pwo.2	-						SIGLEC10_uc002pwp.2_5'Flank|SIGLEC10_uc002pwq.2_5'Flank|SIGLEC10_uc002pwr.2_5'Flank|SIGLEC10_uc010ycy.1_5'Flank|SIGLEC10_uc010ycz.1_5'Flank|SIGLEC10_uc010eow.2_5'Flank|SIGLEC10_uc002pws.1_5'Flank	NM_033130	NP_149121			sialic acid binding Ig-like lectin 10 precursor						cell adhesion	extracellular region|integral to membrane|plasma membrane	sugar binding			skin(1)	1		all_neural(266;0.0199)		GBM - Glioblastoma multiforme(134;0.000668)|OV - Ovarian serous cystadenocarcinoma(262;0.0101)														---	---	---	---
Unknown	0	broad.mit.edu	37	19	52210484	52210489	+	IGR	DEL	TTTTTT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:52210484_52210489delTTTTTT								NCRNA00085 (2042 upstream) : HAS1 (5876 downstream)																																			---	---	---	---
ZNF616	90317	broad.mit.edu	37	19	52620301	52620301	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:52620301delT	uc002pym.2	-						ZNF616_uc002pyn.2_Intron	NM_178523	NP_848618			zinc finger protein 616						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0				GBM - Glioblastoma multiforme(134;0.00392)|OV - Ovarian serous cystadenocarcinoma(262;0.0189)														---	---	---	---
ZNF480	147657	broad.mit.edu	37	19	52822112	52822112	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:52822112delT	uc010ydl.1	+						ZNF480_uc002pyv.2_Intron|ZNF480_uc010ydm.1_Intron|ZNF480_uc010epn.2_Intron|uc002pyw.1_Intron	NM_144684	NP_653285			zinc finger protein 480						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	nucleic acid binding|zinc ion binding			large_intestine(1)	1				GBM - Glioblastoma multiforme(134;0.00212)|OV - Ovarian serous cystadenocarcinoma(262;0.00369)														---	---	---	---
ZNF83	55769	broad.mit.edu	37	19	53188049	53188050	+	Intron	DEL	AA	-	-	rs7250433	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:53188049_53188050delAA	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)														---	---	---	---
ZNF845	91664	broad.mit.edu	37	19	53849109	53849112	+	Intron	DEL	TTTT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:53849109_53849112delTTTT	uc010ydv.1	+						ZNF845_uc010ydw.1_Intron	NM_138374	NP_612383			zinc finger protein 845						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	19	54120451	54120451	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:54120451delT								LOC284379 (13700 upstream) : DPRX (14859 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	19	54143181	54143181	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:54143181delT								DPRX (2918 upstream) : MIR512-1 (26752 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	19	54146108	54146109	+	IGR	DEL	TC	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:54146108_54146109delTC								DPRX (5845 upstream) : MIR512-1 (23824 downstream)																																			---	---	---	---
MIR517B	574483	broad.mit.edu	37	19	54223531	54223531	+	5'Flank	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:54223531delT	hsa-mir-517b|MI0003165	+						MIR520G_hsa-mir-520g|MI0003166_5'Flank																	0																		---	---	---	---
NLRP12	91662	broad.mit.edu	37	19	54304348	54304348	+	Intron	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:54304348delC	uc002qch.3	-						NLRP12_uc010eqw.2_Intron|NLRP12_uc002qci.3_Intron|NLRP12_uc002qcj.3_Intron|NLRP12_uc002qck.3_Intron|NLRP12_uc010eqx.2_Intron	NM_144687	NP_653288			NLR family, pyrin domain containing 12 isoform						negative regulation of I-kappaB kinase/NF-kappaB cascade|negative regulation of interleukin-1 secretion|negative regulation of interleukin-6 biosynthetic process|negative regulation of protein autophosphorylation|negative regulation of Toll signaling pathway|positive regulation of inflammatory response|positive regulation of interleukin-1 beta secretion|regulation of interleukin-18 biosynthetic process|release of cytoplasmic sequestered NF-kappaB	cytoplasm	ATP binding|caspase activator activity|protein binding			ovary(4)|upper_aerodigestive_tract(2)|lung(1)	7	Ovarian(34;0.19)			GBM - Glioblastoma multiforme(134;0.026)														---	---	---	---
NLRP12	91662	broad.mit.edu	37	19	54317613	54317614	+	Intron	INS	-	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:54317613_54317614insT	uc002qch.3	-						NLRP12_uc002qci.3_Intron|NLRP12_uc002qcj.3_Intron|NLRP12_uc002qck.3_Intron|NLRP12_uc010eqx.2_Intron	NM_144687	NP_653288			NLR family, pyrin domain containing 12 isoform						negative regulation of I-kappaB kinase/NF-kappaB cascade|negative regulation of interleukin-1 secretion|negative regulation of interleukin-6 biosynthetic process|negative regulation of protein autophosphorylation|negative regulation of Toll signaling pathway|positive regulation of inflammatory response|positive regulation of interleukin-1 beta secretion|regulation of interleukin-18 biosynthetic process|release of cytoplasmic sequestered NF-kappaB	cytoplasm	ATP binding|caspase activator activity|protein binding			ovary(4)|upper_aerodigestive_tract(2)|lung(1)	7	Ovarian(34;0.19)			GBM - Glioblastoma multiforme(134;0.026)														---	---	---	---
PRKCG	5582	broad.mit.edu	37	19	54406145	54406155	+	Intron	DEL	AAAAAAAAAAA	-	-	rs72513707		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:54406145_54406155delAAAAAAAAAAA	uc002qcq.1	+						PRKCG_uc010yeg.1_Intron|PRKCG_uc010yeh.1_Intron	NM_002739	NP_002730			protein kinase C, gamma						activation of phospholipase C activity|cell death|intracellular signal transduction|negative regulation of protein catabolic process|negative regulation of protein ubiquitination|nerve growth factor receptor signaling pathway|platelet activation|positive regulation of mismatch repair|synaptic transmission	cytosol	ATP binding|protein kinase C activity|zinc ion binding			lung(4)|ovary(2)|pancreas(2)|large_intestine(1)	9	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;0.0521)														---	---	---	---
CACNG6	59285	broad.mit.edu	37	19	54505344	54505344	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:54505344delT	uc002qct.2	+						CACNG6_uc002qcu.2_Intron|CACNG6_uc002qcv.2_Intron	NM_145814	NP_665813			voltage-dependent calcium channel gamma-6							voltage-gated calcium channel complex	voltage-gated calcium channel activity			ovary(2)	2	all_cancers(19;0.0128)|all_epithelial(19;0.00564)|all_lung(19;0.031)|Lung NSC(19;0.0358)|Ovarian(34;0.19)			GBM - Glioblastoma multiforme(134;0.168)														---	---	---	---
Unknown	0	broad.mit.edu	37	19	54856515	54856517	+	IGR	DEL	TTT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:54856515_54856517delTTT								LILRA4 (6094 upstream) : LAIR1 (8718 downstream)																																			---	---	---	---
LENG8	114823	broad.mit.edu	37	19	54972802	54972802	+	3'UTR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:54972802delT	uc002qfw.2	+	16						NM_052925	NP_443157			leukocyte receptor cluster member 8								protein binding			central_nervous_system(1)|pancreas(1)	2	Ovarian(34;0.19)			GBM - Glioblastoma multiforme(193;0.139)														---	---	---	---
LILRB1	10859	broad.mit.edu	37	19	55132993	55132993	+	Intron	DEL	T	-	-	rs150702404		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:55132993delT	uc002qgj.2	+						LILRB1_uc010erp.1_Intron	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)			---	---	---	---
LILRB1	10859	broad.mit.edu	37	19	55148385	55148385	+	3'UTR	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-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)			---	---	---	---
NLRP2	55655	broad.mit.edu	37	19	55479012	55479012	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:55479012delA	uc002qij.2	+						NLRP7_uc010esl.2_5'Flank|NLRP2_uc010yfp.1_Intron|NLRP2_uc010esn.2_Intron|NLRP2_uc010eso.2_Intron|NLRP2_uc010esp.2_Intron	NM_017852	NP_060322			NLR family, pyrin domain containing 2						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)														---	---	---	---
C19orf51	352909	broad.mit.edu	37	19	55673003	55673003	+	Intron	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:55673003delC	uc002qji.1	-						C19orf51_uc002qjh.1_Intron|C19orf51_uc002qjj.1_Intron|C19orf51_uc002qjk.1_Intron|C19orf51_uc002qjl.1_Intron					RecName: Full=UPF0470 protein C19orf51;												0			BRCA - Breast invasive adenocarcinoma(297;0.209)	GBM - Glioblastoma multiforme(193;0.044)														---	---	---	---
SYT5	6861	broad.mit.edu	37	19	55690306	55690306	+	Intron	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:55690306delC	uc002qjm.1	-						SYT5_uc002qjp.2_Intron|SYT5_uc002qjn.1_Intron|SYT5_uc002qjo.1_Intron	NM_003180	NP_003171			synaptotagmin V						energy reserve metabolic process|regulation of insulin secretion|synaptic transmission	cell junction|integral to membrane|recycling endosome membrane|synaptic vesicle membrane	metal ion binding|transporter activity				0			BRCA - Breast invasive adenocarcinoma(297;0.209)	GBM - Glioblastoma multiforme(193;0.0452)														---	---	---	---
SUV420H2	84787	broad.mit.edu	37	19	55854755	55854755	+	Intron	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:55854755delG	uc002qkj.3	+						SUV420H2_uc002qkl.2_Intron	NM_032701	NP_116090			suppressor of variegation 4-20 homolog 2						regulation of transcription, DNA-dependent|transcription, DNA-dependent		protein binding				0	Breast(117;0.191)		BRCA - Breast invasive adenocarcinoma(297;0.209)	GBM - Glioblastoma multiforme(193;0.044)														---	---	---	---
IL11	3589	broad.mit.edu	37	19	55883790	55883790	+	5'Flank	DEL	G	-	-	rs138507936	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:55883790delG	uc002qks.1	-						IL11_uc010yfx.1_5'Flank	NM_000641	NP_000632			interleukin 11 precursor						B cell differentiation|fat cell differentiation|megakaryocyte differentiation|negative regulation of hormone secretion|platelet activation|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	extracellular space	cytokine activity|growth factor activity|interleukin-11 receptor binding				0	Breast(117;0.191)	Renal(1328;0.245)	BRCA - Breast invasive adenocarcinoma(297;0.209)	GBM - Glioblastoma multiforme(193;0.044)	Oprelvekin(DB00038)													---	---	---	---
U2AF2	11338	broad.mit.edu	37	19	56181832	56181832	+	Intron	DEL	C	-	-	rs66835098		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:56181832delC	uc002qlu.2	+						U2AF2_uc002qlt.2_Intron	NM_007279	NP_009210			U2 (RNU2) small nuclear RNA auxiliary factor 2						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)														---	---	---	---
Unknown	0	broad.mit.edu	37	19	56217650	56217651	+	IGR	DEL	TT	-	-	rs79506554		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:56217650_56217651delTT								EPN1 (10518 upstream) : NLRP9 (2148 downstream)																																			---	---	---	---
NLRP9	338321	broad.mit.edu	37	19	56235161	56235163	+	Intron	DEL	CTT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:56235161_56235163delCTT	uc002qly.2	-							NM_176820	NP_789790			NLR family, pyrin domain containing 9							cytoplasm	ATP binding			skin(4)|ovary(2)|breast(1)	7		Colorectal(82;0.000133)|Ovarian(87;0.133)		GBM - Glioblastoma multiforme(193;0.123)														---	---	---	---
Unknown	0	broad.mit.edu	37	19	57155383	57155383	+	Intron	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:57155383delC	uc002qnn.1	+											Homo sapiens cDNA FLJ37880 fis, clone BRSTN2000220.																														---	---	---	---
ZIM2	23619	broad.mit.edu	37	19	57287026	57287027	+	Intron	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:57287026_57287027delAA	uc002qnr.2	-						uc010ygp.1_Intron|uc002qnp.1_Intron|ZIM2_uc010ygq.1_Intron|ZIM2_uc010ygr.1_Intron|ZIM2_uc002qnq.2_Intron|ZIM2_uc010etp.2_Intron|ZIM2_uc010ygs.1_Intron	NM_015363	NP_056178			zinc finger, imprinted 2						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(3)	3		Colorectal(82;0.000256)|all_neural(62;0.103)|Ovarian(87;0.243)		GBM - Glioblastoma multiforme(193;0.0314)														---	---	---	---
ZIM3	114026	broad.mit.edu	37	19	57646264	57646264	+	3'UTR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:57646264delT	uc002qnz.1	-	5						NM_052882	NP_443114			zinc finger, imprinted 3						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			pancreas(1)|skin(1)	2		Colorectal(82;0.000256)|all_neural(62;0.0577)|Ovarian(87;0.243)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.026)														---	---	---	---
Unknown	0	broad.mit.edu	37	19	57783114	57783114	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:57783114delA								ZNF805 (9009 upstream) : ZNF460 (8305 downstream)																																			---	---	---	---
ZNF549	256051	broad.mit.edu	37	19	58049571	58049574	+	Frame_Shift_Del	DEL	ACAA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:58049571_58049574delACAA	uc002qpb.1	+	4	1448_1451	c.1199_1202delACAA	c.(1198-1203)TACAAAfs	p.Y400fs	ZNF547_uc002qpm.3_Intron|ZNF549_uc010eud.1_Intron|ZNF549_uc002qpa.1_Frame_Shift_Del_p.Y387fs	NM_153263	NP_694995	Q6P9A3	ZN549_HUMAN	zinc finger protein 549	400_401	C2H2-type 7.				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)|Ovarian(87;0.221)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.026)														---	---	---	---
ZNF547	284306	broad.mit.edu	37	19	58109471	58109472	+	Intron	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:58109471_58109472delTT	uc002qpm.3	+						ZNF530_uc002qpk.2_5'Flank|ZNF530_uc002qpl.2_5'Flank					RecName: Full=Zinc finger protein 547;						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)|central_nervous_system(1)	2		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)														---	---	---	---
ZNF587	84914	broad.mit.edu	37	19	58374333	58374334	+	3'UTR	INS	-	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:58374333_58374334insT	uc002qql.2	+	3					ZNF587_uc002qqj.1_RNA|ZNF814_uc002qqk.2_Intron	NM_032828	NP_116217			zinc finger protein 587						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0		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;0.0264)														---	---	---	---
C19orf18	147685	broad.mit.edu	37	19	58485258	58485259	+	Intron	INS	-	AAAG	AAAG	rs139629844	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:58485258_58485259insAAAG	uc002qqv.2	-							NM_152474	NP_689687			hypothetical protein LOC147685 precursor							integral to membrane				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;0.017)														---	---	---	---
ZNF135	7694	broad.mit.edu	37	19	58576258	58576258	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:58576258delA	uc010yhq.1	+						ZNF135_uc002qre.2_Intron|ZNF135_uc002qrd.1_Intron|ZNF135_uc002qrf.2_Intron|ZNF135_uc002qrg.2_Intron|ZNF135_uc010yhr.1_Intron	NM_003436	NP_003427			zinc finger protein 135 isoform 2						regulation of transcription, DNA-dependent	intracellular	nucleic acid binding|zinc ion binding			ovary(1)	1		Colorectal(82;0.000256)|all_neural(62;0.0412)|Breast(46;0.147)|Ovarian(87;0.156)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0161)														---	---	---	---
ZNF544	27300	broad.mit.edu	37	19	58765590	58765590	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:58765590delA	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	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)														---	---	---	---
RPS5	6193	broad.mit.edu	37	19	58905831	58905831	+	Intron	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:58905831delG	uc002qsn.2	+						RPS5_uc002qso.2_Intron	NM_001009	NP_001000			ribosomal protein S5						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)														---	---	---	---
Unknown	0	broad.mit.edu	37	19	58934169	58934169	+	IGR	DEL	A	-	-	rs72435236		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:58934169delA								ZNF584 (4479 upstream) : ZNF132 (10013 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	316978	316980	+	IGR	DEL	CTC	-	-	rs71191938		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:316978_316980delCTC								SOX12 (6113 upstream) : NRSN2 (10390 downstream)																																			---	---	---	---
TBC1D20	128637	broad.mit.edu	37	20	440851	440851	+	Intron	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:440851delG	uc002wds.2	-						TBC1D20_uc002wdv.2_Intron|TBC1D20_uc002wdt.2_Intron|TBC1D20_uc002wdu.2_Intron	NM_144628	NP_653229			TBC1 domain family, member 20						interspecies interaction between organisms	integral to membrane|intracellular	Rab GTPase activator activity			central_nervous_system(1)	1		all_epithelial(17;0.228)|Breast(17;0.231)																---	---	---	---
Unknown	0	broad.mit.edu	37	20	564540	564540	+	IGR	DEL	T	-	-	rs61036156		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:564540delT								CSNK2A1 (40058 upstream) : TCF15 (20099 downstream)																																			---	---	---	---
TCF15	6939	broad.mit.edu	37	20	591617	591617	+	5'Flank	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:591617delA	uc002wdz.2	-							NM_004609	NP_004600			basic helix-loop-helix transcription factor 15						regulation of transcription from RNA polymerase II promoter	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity				0		Breast(17;0.231)																---	---	---	---
Unknown	0	broad.mit.edu	37	20	798515	798515	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:798515delA								C20orf54 (49287 upstream) : FAM110A (15841 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	839458	839458	+	IGR	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:839458delC								FAM110A (1355 upstream) : ANGPT4 (13841 downstream)																																			---	---	---	---
ANGPT4	51378	broad.mit.edu	37	20	854647	854647	+	Intron	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:854647delC	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																		---	---	---	---
TMC2	117532	broad.mit.edu	37	20	2522293	2522294	+	Intron	DEL	AA	-	-	rs79968197		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:2522293_2522294delAA	uc002wgf.1	+						TMC2_uc002wgg.1_Intron	NM_080751	NP_542789			transmembrane cochlear-expressed protein 2							integral to membrane				ovary(3)	3																		---	---	---	---
Unknown	0	broad.mit.edu	37	20	2771622	2771623	+	IGR	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:2771622_2771623delTT								EBF4 (30869 upstream) : CPXM1 (3093 downstream)																																			---	---	---	---
C20orf194	25943	broad.mit.edu	37	20	3240371	3240372	+	Intron	INS	-	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:3240371_3240372insG	uc002wii.2	-						C20orf194_uc002wij.3_Intron|C20orf194_uc002wik.2_Intron	NM_001009984	NP_001009984			hypothetical protein LOC25943												0																		---	---	---	---
C20orf194	25943	broad.mit.edu	37	20	3259365	3259365	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:3259365delA	uc002wii.2	-						C20orf194_uc002wij.3_Intron|C20orf194_uc002wik.2_Intron	NM_001009984	NP_001009984			hypothetical protein LOC25943												0																		---	---	---	---
ATRN	8455	broad.mit.edu	37	20	3509014	3509015	+	Intron	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:3509014_3509015delAA	uc002wim.2	+						ATRN_uc002wil.2_Intron	NM_139321	NP_647537			attractin isoform 1						inflammatory response	extracellular space|integral to plasma membrane	receptor activity|sugar binding			ovary(1)|breast(1)	2																		---	---	---	---
ATRN	8455	broad.mit.edu	37	20	3525143	3525144	+	Intron	INS	-	GTG	GTG			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:3525143_3525144insGTG	uc002wim.2	+						ATRN_uc002wil.2_Intron	NM_139321	NP_647537			attractin isoform 1						inflammatory response	extracellular space|integral to plasma membrane	receptor activity|sugar binding			ovary(1)|breast(1)	2																		---	---	---	---
ATRN	8455	broad.mit.edu	37	20	3577009	3577009	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:3577009delT	uc002wim.2	+						ATRN_uc002wil.2_Intron	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	3858178	3858179	+	IGR	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:3858178_3858179delAA								MAVS (1417 upstream) : PANK2 (11307 downstream)																																			---	---	---	---
PANK2	80025	broad.mit.edu	37	20	3874572	3874587	+	Intron	DEL	TTTTTTGTTTTTTTTT	-	-	rs28399007		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:3874572_3874587delTTTTTTGTTTTTTTTT	uc002wkc.2	+						PANK2_uc002wkb.2_Intron|PANK2_uc010gbd.1_Intron|PANK2_uc002wkd.2_Intron|PANK2_uc002wke.2_Intron|PANK2_uc002wkf.2_Intron	NM_153638	NP_705902			pantothenate kinase 2 isoform 1 preproprotein						cell death|coenzyme A biosynthetic process|pantothenate metabolic process	mitochondrial intermembrane space|nucleus	ATP binding|pantothenate kinase activity|protein binding				0																		---	---	---	---
RNF24	11237	broad.mit.edu	37	20	3915839	3915839	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:3915839delA	uc002wkh.2	-						RNF24_uc002wki.2_Intron|RNF24_uc002wkj.2_Intron	NM_007219	NP_009150			ring finger protein 24 isoform 1							Golgi membrane|integral to membrane	zinc ion binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	20	4194905	4194906	+	IGR	INS	-	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:4194905_4194906insT								SMOX (26536 upstream) : ADRA1D (6372 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	4999482	4999482	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:4999482delA								SLC23A2 (8543 upstream) : C20orf30 (49648 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	5016432	5016432	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:5016432delT								SLC23A2 (25493 upstream) : C20orf30 (32698 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	5033089	5033089	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:5033089delA								SLC23A2 (42150 upstream) : C20orf30 (16041 downstream)																																			---	---	---	---
CDS2	8760	broad.mit.edu	37	20	5165756	5165758	+	Intron	DEL	AAA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:5165756_5165758delAAA	uc002wls.2	+						CDS2_uc002wlr.1_Intron|CDS2_uc010zqt.1_Intron|CDS2_uc002wlu.2_Intron|CDS2_uc010zqu.1_Intron|CDS2_uc002wlv.2_Intron|CDS2_uc010zqv.1_Intron	NM_003818	NP_003809			phosphatidate cytidylyltransferase 2						phospholipid biosynthetic process	integral to membrane|mitochondrial inner membrane	phosphatidate cytidylyltransferase activity				0																		---	---	---	---
GPCPD1	56261	broad.mit.edu	37	20	5561524	5561528	+	Intron	DEL	TTTTT	-	-	rs11476572		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:5561524_5561528delTTTTT	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	5617054	5617054	+	IGR	DEL	A	-	-	rs76232786		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:5617054delA								GPCPD1 (25382 upstream) : C20orf196 (113989 downstream)																																			---	---	---	---
CRLS1	54675	broad.mit.edu	37	20	5997100	5997101	+	Intron	INS	-	GT	GT	rs28436095		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:5997100_5997101insGT	uc002wmn.3	+						CRLS1_uc010gbq.2_Intron|CRLS1_uc010gbr.2_Intron	NM_019095	NP_061968			cardiolipin synthase 1 isoform 1						phospholipid biosynthetic process	integral to membrane|mitochondrial inner membrane	phosphotransferase activity, for other substituted phosphate groups				0																		---	---	---	---
CRLS1	54675	broad.mit.edu	37	20	5997614	5997614	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:5997614delT	uc002wmn.3	+						CRLS1_uc010gbq.2_Intron|CRLS1_uc010gbr.2_Intron	NM_019095	NP_061968			cardiolipin synthase 1 isoform 1						phospholipid biosynthetic process	integral to membrane|mitochondrial inner membrane	phosphotransferase activity, for other substituted phosphate groups				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	20	6201921	6201921	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:6201921delA								FERMT1 (97730 upstream) : BMP2 (546824 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	6778825	6778825	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:6778825delT								BMP2 (17915 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	7560988	7560988	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:7560988delT								BMP2 (800078 upstream) : HAO1 (302643 downstream)																																			---	---	---	---
PLCB1	23236	broad.mit.edu	37	20	8731631	8731632	+	Intron	INS	-	GAGTGCA	GAGTGCA			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:8731631_8731632insGAGTGCA	uc002wnb.2	+						PLCB1_uc010zrb.1_Intron|PLCB1_uc002wna.2_Intron|PLCB1_uc002wnc.1_Intron|PLCB1_uc002wnd.1_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	8738041	8738041	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:8738041delA	uc002wnb.2	+						PLCB1_uc010zrb.1_Intron|PLCB1_uc002wna.2_Intron|PLCB1_uc002wnc.1_Intron|PLCB1_uc002wnd.1_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																		---	---	---	---
PLCB4	5332	broad.mit.edu	37	20	9174999	9174999	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:9174999delT	uc002wnf.2	+						PLCB4_uc010gbw.1_Intron|PLCB4_uc010gbx.2_Intron|PLCB4_uc002wne.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	9261113	9261113	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:9261113delA	uc002wnf.2	+						PLCB4_uc010gbw.1_Intron|PLCB4_uc010gbx.2_Intron|PLCB4_uc002wne.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																		---	---	---	---
Unknown	0	broad.mit.edu	37	20	9929170	9929170	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:9929170delT								PAK7 (109483 upstream) : ANKRD5 (86527 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	10303857	10303857	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:10303857delT								SNAP25 (15792 upstream) : MKKS (81976 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	11205582	11205582	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:11205582delA								JAG1 (550888 upstream) : BTBD3 (665895 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	12075352	12075352	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:12075352delA								BTBD3 (168110 upstream) : SPTLC3 (914275 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	12532914	12532915	+	IGR	INS	-	AA	AA			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:12532914_12532915insAA								BTBD3 (625672 upstream) : SPTLC3 (456712 downstream)																																			---	---	---	---
SPTLC3	55304	broad.mit.edu	37	20	13008888	13008888	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:13008888delT	uc002wod.1	+						SPTLC3_uc002wob.1_Intron|SPTLC3_uc002woc.2_Intron	NM_018327	NP_060797			serine palmitoyltransferase, long chain base						sphingoid biosynthetic process	integral to membrane|serine C-palmitoyltransferase complex	pyridoxal phosphate binding|serine C-palmitoyltransferase activity|transferase activity, transferring nitrogenous groups				0					Pyridoxal Phosphate(DB00114)													---	---	---	---
TASP1	55617	broad.mit.edu	37	20	13305011	13305011	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:13305011delT	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	13526911	13526912	+	Intron	DEL	AA	-	-	rs34313740		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:13526911_13526912delAA	uc002woi.2	-						TASP1_uc010zri.1_Intron|TASP1_uc002woh.2_Intron|TASP1_uc010zrj.1_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																		---	---	---	---
Unknown	0	broad.mit.edu	37	20	13683054	13683054	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:13683054delA								TASP1 (63471 upstream) : ESF1 (11916 downstream)																																			---	---	---	---
ESF1	51575	broad.mit.edu	37	20	13698201	13698201	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:13698201delT	uc002woj.2	-							NM_016649	NP_057733			ABT1-associated protein						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleolus|nucleoplasm				ovary(1)	1																		---	---	---	---
C20orf7	79133	broad.mit.edu	37	20	13786574	13786574	+	Intron	DEL	A	-	-	rs112796431		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:13786574delA	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)																---	---	---	---
Unknown	0	broad.mit.edu	37	20	13823646	13823647	+	IGR	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:13823646_13823647delTT								C20orf7 (25774 upstream) : SEL1L2 (6405 downstream)																																			---	---	---	---
SEL1L2	80343	broad.mit.edu	37	20	13946940	13946942	+	Intron	DEL	TCT	-	-	rs11468038		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:13946940_13946942delTCT	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	14225033	14225034	+	Intron	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:14225033_14225034delAA	uc002wou.2	+						MACROD2_uc002wot.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	14228558	14228558	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:14228558delA	uc002wou.2	+						MACROD2_uc002wot.2_Intron	NM_080676	NP_542407			MACRO domain containing 2 isoform 1												0		all_neural(2;0.0381)|Acute lymphoblastic leukemia(2;0.175)																---	---	---	---
FLRT3	23767	broad.mit.edu	37	20	14308221	14308221	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:14308221delA	uc002wov.1	-						MACROD2_uc002wot.2_Intron|MACROD2_uc002wou.2_Intron|FLRT3_uc002wow.1_Intron	NM_198391	NP_938205			fibronectin leucine rich transmembrane protein 3						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)														---	---	---	---
MACROD2	140733	broad.mit.edu	37	20	14428145	14428146	+	Intron	DEL	GT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:14428145_14428146delGT	uc002wou.2	+						MACROD2_uc002wot.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	14659599	14659599	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:14659599delA	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	14700304	14700304	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:14700304delA	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	14708190	14708191	+	Intron	DEL	AG	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:14708190_14708191delAG	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	15240400	15240400	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:15240400delT	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	15440462	15440462	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:15440462delT	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	16022094	16022095	+	Intron	INS	-	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:16022094_16022095insT	uc002wou.2	+						MACROD2_uc002wot.2_Intron|MACROD2_uc002woz.2_Intron|MACROD2_uc002wpb.2_Intron|MACROD2_uc002wpd.2_Intron	NM_080676	NP_542407			MACRO domain containing 2 isoform 1												0		all_neural(2;0.0381)|Acute lymphoblastic leukemia(2;0.175)																---	---	---	---
KIF16B	55614	broad.mit.edu	37	20	16398608	16398608	+	Intron	DEL	A	-	-	rs6111106	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:16398608delA	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	16589194	16589194	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:16589194delA								KIF16B (35116 upstream) : SNRPB2 (121435 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	16705147	16705147	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:16705147delT								KIF16B (151069 upstream) : SNRPB2 (5482 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	17032179	17032181	+	IGR	DEL	TTG	-	-	rs11698561	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:17032179_17032181delTTG								OTOR (299371 upstream) : PCSK2 (174571 downstream)																																			---	---	---	---
PCSK2	5126	broad.mit.edu	37	20	17350043	17350044	+	Intron	INS	-	CA	CA	rs147119089	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:17350043_17350044insCA	uc002wpm.2	+						PCSK2_uc002wpl.2_Intron|PCSK2_uc010zrm.1_Intron	NM_002594	NP_002585			proprotein convertase subtilisin/kexin type 2						enkephalin processing|insulin processing|islet amyloid polypeptide processing	extracellular space|membrane|soluble fraction|transport vesicle	serine-type endopeptidase activity			ovary(3)|central_nervous_system(2)|large_intestine(1)|pancreas(1)	7					Insulin Glargine recombinant(DB00047)|Insulin Lyspro recombinant(DB00046)|Insulin recombinant(DB00030)|Insulin, porcine(DB00071)													---	---	---	---
DSTN	11034	broad.mit.edu	37	20	17569865	17569865	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:17569865delT	uc002wpr.2	+						DSTN_uc002wpq.2_Intron	NM_006870	NP_006861			destrin isoform a						actin filament severing|actin polymerization or depolymerization		actin binding			large_intestine(1)|skin(1)	2																		---	---	---	---
RRBP1	6238	broad.mit.edu	37	20	17625438	17625439	+	Intron	INS	-	A	A	rs113471045		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:17625438_17625439insA	uc002wpv.1	-						RRBP1_uc002wpu.2_Intron|RRBP1_uc002wpw.1_Intron|RRBP1_uc010gcl.1_Intron	NM_001042576	NP_001036041			ribosome binding protein 1						protein transport|translation|transmembrane transport	integral to endoplasmic reticulum membrane|ribosome	receptor activity			ovary(1)	1																		---	---	---	---
BANF2	140836	broad.mit.edu	37	20	17701625	17701625	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:17701625delA	uc002wpz.2	+						BANF2_uc010zrs.1_Intron|BANF2_uc002wqa.2_Intron	NM_178477	NP_848572			barrier to autointegration factor 2 isoform 1							cytoplasm|nucleus	DNA binding			skin(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	20	17806374	17806374	+	IGR	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:17806374delG								BANF2 (89857 upstream) : SNX5 (115872 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	17872504	17872504	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:17872504delA								BANF2 (155987 upstream) : SNX5 (49742 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	17913572	17913572	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:17913572delA								BANF2 (197055 upstream) : SNX5 (8674 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	18354800	18354800	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:18354800delA								ZNF133 (57162 upstream) : C20orf12 (9212 downstream)																																			---	---	---	---
POLR3F	10621	broad.mit.edu	37	20	18459790	18459791	+	Intron	INS	-	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:18459790_18459791insA	uc002wqv.2	+						POLR3F_uc002wqw.2_Intron|POLR3F_uc002wqx.2_Intron	NM_006466	NP_006457			DNA-directed RNA polymerase III 39 kDa						innate immune response|positive regulation of innate immune response|positive regulation of interferon-beta production|regulation of transcription from RNA polymerase III promoter|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|protein binding				0																		---	---	---	---
SEC23B	10483	broad.mit.edu	37	20	18501053	18501054	+	Intron	INS	-	AG	AG	rs143807674	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:18501053_18501054insAG	uc002wqz.1	+						SEC23B_uc002wra.1_Intron|SEC23B_uc002wrb.1_Intron|SEC23B_uc010zsb.1_Intron|SEC23B_uc002wrc.1_Intron	NM_006363	NP_006354			Sec23 homolog B						ER to Golgi vesicle-mediated transport|intracellular protein transport	COPII vesicle coat|endoplasmic reticulum membrane|ER-Golgi intermediate compartment membrane|Golgi membrane	zinc ion binding			ovary(1)	1																		---	---	---	---
DTD1	92675	broad.mit.edu	37	20	18571049	18571049	+	Intron	DEL	T	-	-	rs5840818		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:18571049delT	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																		---	---	---	---
SLC24A3	57419	broad.mit.edu	37	20	19363652	19363652	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:19363652delA	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	19386825	19386826	+	Intron	INS	-	GTGTGT	GTGTGT	rs11467580		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:19386825_19386826insGTGTGT	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																		---	---	---	---
RIN2	54453	broad.mit.edu	37	20	19910762	19910762	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:19910762delA	uc002wro.1	+						RIN2_uc010gcu.1_Intron	NM_018993	NP_061866			Ras and Rab interactor 2						endocytosis|small GTPase mediated signal transduction	cytoplasm	GTPase activator activity|Rab guanyl-nucleotide exchange factor activity			lung(4)|ovary(1)	5																		---	---	---	---
RIN2	54453	broad.mit.edu	37	20	19950022	19950022	+	Intron	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:19950022delC	uc002wro.1	+						RIN2_uc010gcu.1_Intron|RIN2_uc010gcv.1_Intron	NM_018993	NP_061866			Ras and Rab interactor 2						endocytosis|small GTPase mediated signal transduction	cytoplasm	GTPase activator activity|Rab guanyl-nucleotide exchange factor activity			lung(4)|ovary(1)	5																		---	---	---	---
Unknown	0	broad.mit.edu	37	20	19989436	19989437	+	IGR	DEL	CT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:19989436_19989437delCT								RIN2 (6336 upstream) : NAA20 (8500 downstream)																																			---	---	---	---
C20orf26	26074	broad.mit.edu	37	20	20205139	20205139	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:20205139delT	uc002wru.2	+						C20orf26_uc010zse.1_Intron|C20orf26_uc002wrw.2_5'Flank|C20orf26_uc002wrv.2_Intron	NM_015585	NP_056400			hypothetical protein LOC26074											ovary(3)|pancreas(1)	4				READ - Rectum adenocarcinoma(2;0.171)														---	---	---	---
RALGAPA2	57186	broad.mit.edu	37	20	20501478	20501478	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:20501478delA	uc002wrz.2	-						RALGAPA2_uc010gcx.2_Intron|RALGAPA2_uc010zsg.1_Intron|RALGAPA2_uc002wsa.1_Intron	NM_020343	NP_065076			akt substrate AS250						activation of Ral GTPase activity	cytosol|nucleus	protein heterodimerization activity|Ral GTPase activator activity			ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	20	22871047	22871048	+	IGR	DEL	AC	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:22871047_22871048delAC								FOXA2 (304946 upstream) : SSTR4 (145009 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	22890672	22890672	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:22890672delA								FOXA2 (324571 upstream) : SSTR4 (125385 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	23189752	23189752	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:23189752delA								CD93 (122775 upstream) : NXT1 (141621 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	23292377	23292378	+	IGR	DEL	TG	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:23292377_23292378delTG								CD93 (225400 upstream) : NXT1 (38995 downstream)																																			---	---	---	---
GZF1	64412	broad.mit.edu	37	20	23351801	23351801	+	3'UTR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:23351801delA	uc010gdb.2	+	7					GZF1_uc002wsy.2_3'UTR|GZF1_uc010zsq.1_3'UTR|GZF1_uc010zsr.1_3'UTR|GZF1_uc002wsz.2_3'UTR	NM_022482	NP_071927			GDNF-inducible zinc finger protein 1						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)																	---	---	---	---
Unknown	0	broad.mit.edu	37	20	24299200	24299201	+	IGR	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:24299200_24299201delAA								GGTLC1 (329784 upstream) : TMEM90B (150634 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	24364184	24364186	+	IGR	DEL	TTT	-	-	rs139185267		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:24364184_24364186delTTT								GGTLC1 (394768 upstream) : TMEM90B (85649 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	24410708	24410708	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:24410708delA								GGTLC1 (441292 upstream) : TMEM90B (39127 downstream)																																			---	---	---	---
TMEM90B	79953	broad.mit.edu	37	20	24546569	24546570	+	Intron	DEL	TG	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:24546569_24546570delTG	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	24861851	24861852	+	IGR	INS	-	TC	TC	rs148173785	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:24861851_24861852insTC								TMEM90B (214684 upstream) : CST7 (68014 downstream)																																			---	---	---	---
ENTPD6	955	broad.mit.edu	37	20	25193333	25193333	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:25193333delT	uc002wuj.2	+						ENTPD6_uc010zsy.1_Intron|ENTPD6_uc010gdj.1_Intron|ENTPD6_uc010zsz.1_Intron|ENTPD6_uc002wum.2_Intron|ENTPD6_uc010zta.1_Intron|ENTPD6_uc002wun.2_Intron|ENTPD6_uc002wuk.2_Intron|ENTPD6_uc002wul.2_Intron|ENTPD6_uc010ztb.1_Intron|ENTPD6_uc010ztc.1_Intron|ENTPD6_uc002wuo.2_Intron|ENTPD6_uc010ztd.1_Intron	NM_001247	NP_001238			ectonucleoside triphosphate diphosphohydrolase 6							Golgi membrane|integral to membrane	nucleoside-diphosphatase activity				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	20	25589546	25589546	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:25589546delA								NINL (23393 upstream) : NANP (4029 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	25651820	25651822	+	Intron	DEL	AAA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:25651820_25651822delAAA	uc002wuz.2	+											Homo sapiens zinc finger protein 337, mRNA (cDNA clone IMAGE:4826085).																														---	---	---	---
Unknown	0	broad.mit.edu	37	20	25862448	25862449	+	IGR	DEL	GA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:25862448_25862449delGA								FAM182B (13662 upstream) : LOC100134868 (127986 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	25868895	25868896	+	IGR	INS	-	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:25868895_25868896insA								FAM182B (20109 upstream) : LOC100134868 (121539 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	25984477	25984477	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:25984477delA								FAM182B (135691 upstream) : LOC100134868 (5958 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	26074256	26074257	+	IGR	INS	-	TC	TC	rs141028126	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:26074256_26074257insTC								FAM182A (6704 upstream) : C20orf191 (9796 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	26107939	26107940	+	IGR	INS	-	TG	TG			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:26107939_26107940insTG								C20orf191 (13262 upstream) : MIR663 (80882 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	26241519	26241519	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:26241519delT								MIR663 (52605 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	29477213	29477213	+	IGR	DEL	A	-	-	rs34037072		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:29477213delA								None (None upstream) : FRG1B (134666 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	29586151	29586152	+	IGR	INS	-	AG	AG	rs145760211	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:29586151_29586152insAG								None (None upstream) : FRG1B (25727 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	29588801	29588801	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:29588801delA								None (None upstream) : FRG1B (23078 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	29600972	29600972	+	IGR	DEL	A	-	-	rs112429825		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:29600972delA								None (None upstream) : FRG1B (10907 downstream)																																			---	---	---	---
FRG1B	284802	broad.mit.edu	37	20	29616441	29616442	+	Intron	INS	-	T	T	rs138561282		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:29616441_29616442insT	uc010ztk.1	+						FRG1B_uc002wvm.1_Intron|FRG1B_uc010ztj.1_Intron|FRG1B_uc010gdr.1_Intron					RecName: Full=Protein FRG1B;												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	20	29964256	29964259	+	IGR	DEL	AAAA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:29964256_29964259delAAAA								DEFB118 (3093 upstream) : DEFB119 (709 downstream)																																			---	---	---	---
DEFB119	245932	broad.mit.edu	37	20	29969614	29969614	+	Intron	DEL	A	-	-	rs76336761		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:29969614delA	uc002wvt.2	-						DEFB119_uc002wvs.2_Intron	NM_153289	NP_695021			defensin, beta 119 isoform a precursor						defense response to bacterium	extracellular region					0	all_hematologic(12;0.158)		Colorectal(19;0.00254)|COAD - Colon adenocarcinoma(19;0.0347)															---	---	---	---
HM13	81502	broad.mit.edu	37	20	30122889	30122889	+	Intron	DEL	A	-	-	rs78990622		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:30122889delA	uc002wwe.2	+						HM13_uc002wwc.2_Intron|HM13_uc002wwd.2_Intron|HM13_uc002wwb.1_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)															---	---	---	---
Unknown	0	broad.mit.edu	37	20	30232801	30232801	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:30232801delA								COX4I2 (1 upstream) : BCL2L1 (19462 downstream)																																			---	---	---	---
BCL2L1	598	broad.mit.edu	37	20	30273535	30273535	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:30273535delT	uc002wwl.2	-						BCL2L1_uc002wwk.2_Intron|BCL2L1_uc002wwm.2_Intron|BCL2L1_uc002wwn.2_Intron	NM_138578	NP_612815			BCL2-like 1 isoform 1						induction of apoptosis by intracellular signals|negative regulation of establishment of protein localization in plasma membrane|negative regulation of survival gene product expression|regulation of mitochondrial membrane permeability|regulation of mitochondrial membrane potential|release of cytochrome c from mitochondria|response to cytokine stimulus	integral to membrane|mitochondrial outer membrane|nuclear membrane	BH3 domain binding|identical protein binding			lung(1)|central_nervous_system(1)	2	all_cancers(5;3.47e-06)|all_epithelial(3;1.83e-06)|Lung NSC(7;2.08e-06)|all_lung(7;3.63e-06)|all_hematologic(12;0.158)|Ovarian(7;0.198)		Epithelial(4;2.97e-06)|all cancers(5;3.21e-05)|OV - Ovarian serous cystadenocarcinoma(3;0.00052)|Colorectal(19;0.0055)|COAD - Colon adenocarcinoma(19;0.0264)															---	---	---	---
TTLL9	164395	broad.mit.edu	37	20	30506184	30506184	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:30506184delT	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|TTLL9_uc010ztq.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	30535697	30535698	+	Intron	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:30535697_30535698delAA	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)															---	---	---	---
C20orf160	140706	broad.mit.edu	37	20	30608978	30608978	+	Intron	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:30608978delG	uc002wxf.2	+						C20orf160_uc002wxg.2_5'Flank	NM_080625	NP_542192			hypothetical protein LOC140706											central_nervous_system(3)|ovary(1)	4																		---	---	---	---
TM9SF4	9777	broad.mit.edu	37	20	30732738	30732738	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:30732738delA	uc002wxj.2	+						TM9SF4_uc010ztr.1_Intron|TM9SF4_uc010zts.1_Intron|TM9SF4_uc002wxk.2_Intron|TM9SF4_uc010gdz.2_Intron	NM_014742	NP_055557			transmembrane 9 superfamily protein member 4							integral to membrane				central_nervous_system(1)|pancreas(1)	2			UCEC - Uterine corpus endometrioid carcinoma (5;0.0241)															---	---	---	---
Unknown	0	broad.mit.edu	37	20	31131421	31131421	+	IGR	DEL	A	-	-	rs75594465		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:31131421delA								C20orf112 (7221 upstream) : C20orf203 (89241 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	31144077	31144079	+	Intron	DEL	GGG	-	-	rs71993407		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:31144077_31144079delGGG	uc002wxx.2	-											SubName: Full=LOC284804 protein; Flags: Fragment;																														---	---	---	---
Unknown	0	broad.mit.edu	37	20	31182115	31182115	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:31182115delA	uc002wxy.2	+											RecName: Full=Putative uncharacterized protein MGC163334;																														---	---	---	---
DNMT3B	1789	broad.mit.edu	37	20	31354186	31354187	+	Intron	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:31354186_31354187delTT	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																		---	---	---	---
MAPRE1	22919	broad.mit.edu	37	20	31424716	31424717	+	Intron	INS	-	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:31424716_31424717insT	uc002wyh.2	+							NM_012325	NP_036457			microtubule-associated protein, RP/EB family,						cell division|cell proliferation|G2/M transition of mitotic cell cycle|mitotic prometaphase|negative regulation of microtubule polymerization|protein localization to microtubule	centrosome|cortical microtubule cytoskeleton|cytosol	microtubule plus-end binding|protein C-terminus binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	20	31527502	31527502	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:31527502delT	uc010zub.1	+							NM_001143967	NP_001137439			EF-hand calcium binding domain 8																														---	---	---	---
C20orf186	149954	broad.mit.edu	37	20	31695008	31695009	+	Intron	DEL	AA	-	-	rs78640132		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:31695008_31695009delAA	uc010zue.1	+							NM_182519	NP_872325			antimicrobial peptide RY2G5 precursor							cytoplasm|extracellular region	lipid binding				0																		---	---	---	---
CDK5RAP1	51654	broad.mit.edu	37	20	31981970	31981972	+	Intron	DEL	CTT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:31981970_31981972delCTT	uc010gek.2	-						CDK5RAP1_uc002wyy.2_Intron|CDK5RAP1_uc002wyz.2_Intron|CDK5RAP1_uc002wza.2_Intron|CDK5RAP1_uc010gel.2_Intron|CDK5RAP1_uc010gem.2_Intron|CDK5RAP1_uc002wzc.1_Intron|CDK5RAP1_uc010gen.2_Intron	NM_016408	NP_057492			CDK5 regulatory subunit associated protein 1						brain development|negative regulation of cyclin-dependent protein kinase activity|regulation of neuron differentiation|tRNA modification	cytoplasm	4 iron, 4 sulfur cluster binding|metal ion binding|neuronal Cdc2-like kinase binding|transferase activity			ovary(2)|skin(2)|lung(1)	5																		---	---	---	---
ZNF341	84905	broad.mit.edu	37	20	32338192	32338192	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:32338192delT	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																		---	---	---	---
CHMP4B	128866	broad.mit.edu	37	20	32402629	32402629	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:32402629delT	uc002xaa.2	+							NM_176812	NP_789782			chromatin modifying protein 4B						cellular membrane organization|endosome transport|protein transport	cytosol|late endosome membrane	protein binding			ovary(1)|central_nervous_system(1)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	20	32735437	32735437	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:32735437delT								EIF2S2 (35352 upstream) : ASIP (112734 downstream)																																			---	---	---	---
ITCH	83737	broad.mit.edu	37	20	32996717	32996719	+	Intron	DEL	TTT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:32996717_32996719delTTT	uc010geu.1	+						ITCH_uc002xak.2_Intron|ITCH_uc010zuj.1_Intron	NM_031483	NP_113671			itchy homolog E3 ubiquitin protein ligase						apoptosis|entry of virus into host cell|inflammatory response|innate immune response|negative regulation of apoptosis|negative regulation of defense response to virus|negative regulation of JNK cascade|negative regulation of NF-kappaB transcription factor activity|negative regulation of type I interferon production|protein K29-linked ubiquitination|protein K48-linked ubiquitination|protein K63-linked ubiquitination|protein ubiquitination involved in ubiquitin-dependent protein catabolic process|regulation of cell growth|regulation of protein deubiquitination|response to virus	cytosol|nucleus|plasma membrane	CXCR chemokine receptor binding|ribonucleoprotein binding|ubiquitin-protein ligase activity			breast(4)|lung(1)|central_nervous_system(1)	6																		---	---	---	---
ITCH	83737	broad.mit.edu	37	20	33037410	33037410	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:33037410delT	uc010geu.1	+						ITCH_uc002xak.2_Intron|ITCH_uc010zuj.1_Intron	NM_031483	NP_113671			itchy homolog E3 ubiquitin protein ligase						apoptosis|entry of virus into host cell|inflammatory response|innate immune response|negative regulation of apoptosis|negative regulation of defense response to virus|negative regulation of JNK cascade|negative regulation of NF-kappaB transcription factor activity|negative regulation of type I interferon production|protein K29-linked ubiquitination|protein K48-linked ubiquitination|protein K63-linked ubiquitination|protein ubiquitination involved in ubiquitin-dependent protein catabolic process|regulation of cell growth|regulation of protein deubiquitination|response to virus	cytosol|nucleus|plasma membrane	CXCR chemokine receptor binding|ribonucleoprotein binding|ubiquitin-protein ligase activity			breast(4)|lung(1)|central_nervous_system(1)	6																		---	---	---	---
ITCH	83737	broad.mit.edu	37	20	33069165	33069165	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:33069165delT	uc010geu.1	+						ITCH_uc002xak.2_Intron|ITCH_uc010zuj.1_Intron	NM_031483	NP_113671			itchy homolog E3 ubiquitin protein ligase						apoptosis|entry of virus into host cell|inflammatory response|innate immune response|negative regulation of apoptosis|negative regulation of defense response to virus|negative regulation of JNK cascade|negative regulation of NF-kappaB transcription factor activity|negative regulation of type I interferon production|protein K29-linked ubiquitination|protein K48-linked ubiquitination|protein K63-linked ubiquitination|protein ubiquitination involved in ubiquitin-dependent protein catabolic process|regulation of cell growth|regulation of protein deubiquitination|response to virus	cytosol|nucleus|plasma membrane	CXCR chemokine receptor binding|ribonucleoprotein binding|ubiquitin-protein ligase activity			breast(4)|lung(1)|central_nervous_system(1)	6																		---	---	---	---
NCOA6	23054	broad.mit.edu	37	20	33311143	33311143	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:33311143delA	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																		---	---	---	---
Unknown	0	broad.mit.edu	37	20	33429950	33429950	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:33429950delA								HMGB3L1 (7685 upstream) : GGT7 (2574 downstream)																																			---	---	---	---
ACSS2	55902	broad.mit.edu	37	20	33494929	33494929	+	Intron	DEL	T	-	-	rs78154982		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:33494929delT	uc002xbd.2	+						ACSS2_uc002xbc.2_Intron|ACSS2_uc010zum.1_Intron|ACSS2_uc010gey.2_Intron|ACSS2_uc002xbe.2_Intron|ACSS2_uc002xbf.2_Intron	NM_018677	NP_061147			acyl-CoA synthetase short-chain family member 2						ethanol oxidation|lipid biosynthetic process|xenobiotic metabolic process	cytosol|nucleus	acetate-CoA ligase activity|ATP binding|protein binding				0					Adenosine monophosphate(DB00131)|Adenosine triphosphate(DB00171)													---	---	---	---
TRPC4AP	26133	broad.mit.edu	37	20	33619038	33619039	+	Intron	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:33619038_33619039delTT	uc002xbk.2	-						TRPC4AP_uc010zuq.1_Intron|TRPC4AP_uc002xbl.2_Intron|TRPC4AP_uc010zur.1_Intron|TRPC4AP_uc002xbm.1_Intron	NM_015638	NP_056453			TRPC4-associated protein isoform a						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)															---	---	---	---
EDEM2	55741	broad.mit.edu	37	20	33732856	33732857	+	Intron	INS	-	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:33732856_33732857insA	uc002xbo.2	-						EDEM2_uc010zuv.1_Intron|EDEM2_uc010zus.1_5'UTR|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)															---	---	---	---
EDEM2	55741	broad.mit.edu	37	20	33799824	33799824	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:33799824delA	uc010zuv.1	-							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)															---	---	---	---
GDF5	8200	broad.mit.edu	37	20	33935201	33935201	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-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	33971656	33971656	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:33971656delA	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)															---	---	---	---
NFS1	9054	broad.mit.edu	37	20	34284029	34284029	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:34284029delA	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	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)													---	---	---	---
PHF20	51230	broad.mit.edu	37	20	34381224	34381225	+	Intron	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:34381224_34381225delTT	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)																	---	---	---	---
EPB41L1	2036	broad.mit.edu	37	20	34726805	34726805	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:34726805delT	uc002xev.2	+						EPB41L1_uc002xeu.2_Intron|EPB41L1_uc010zvo.1_Intron|EPB41L1_uc002xew.2_Intron|EPB41L1_uc002xex.2_Intron|EPB41L1_uc002xey.2_Intron|EPB41L1_uc002xez.2_Intron	NM_012156	NP_036288			erythrocyte membrane protein band 4.1-like 1						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)															OREG0025898	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
C20orf4	25980	broad.mit.edu	37	20	34839346	34839346	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:34839346delT	uc002xfc.1	+						C20orf4_uc002xfd.1_Intron|C20orf4_uc002xfe.1_Intron	NM_015511	NP_056326			hypothetical protein LOC25980												0	Breast(12;0.0162)	Myeloproliferative disorder(115;0.0393)																---	---	---	---
DLGAP4	22839	broad.mit.edu	37	20	35103623	35103624	+	Intron	INS	-	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:35103623_35103624insT	uc002xff.2	+						DLGAP4_uc010zvp.1_Intron|DLGAP4_uc002xfg.2_Intron|DLGAP4_uc002xfh.2_Intron	NM_014902	NP_055717			disks large-associated protein 4 isoform a						cell-cell signaling	membrane	protein binding			skin(2)|ovary(1)	3	Breast(12;0.0192)	Myeloproliferative disorder(115;0.00878)																---	---	---	---
C20orf24	55969	broad.mit.edu	37	20	35239841	35239842	+	Intron	DEL	AA	-	-	rs80108840		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:35239841_35239842delAA	uc002xfq.2	+						C20orf24_uc002xfo.2_Intron|C20orf24_uc002xfp.2_Intron|C20orf24_uc002xft.2_Intron|C20orf24_uc002xfr.2_Intron|C20orf24_uc002xfs.2_Intron	NM_018840	NP_061328			RAB5-interacting protein isoform a								protein binding				0	Breast(12;0.114)	Myeloproliferative disorder(115;0.00878)																---	---	---	---
RBL1	5933	broad.mit.edu	37	20	35647453	35647453	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:35647453delT	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-4200-01A-01D-1126-08	TCGA-BR-4200-11A-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	35696592	35696592	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:35696592delA	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	35769349	35769350	+	Intron	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:35769349_35769350delAA	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)																---	---	---	---
VSTM2L	128434	broad.mit.edu	37	20	36532356	36532357	+	Intron	DEL	CA	-	-	rs55675337	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:36532356_36532357delCA	uc002xhk.3	+							NM_080607	NP_542174			V-set and transmembrane domain containing 2 like											ovary(1)|central_nervous_system(1)	2		Myeloproliferative disorder(115;0.00878)																---	---	---	---
VSTM2L	128434	broad.mit.edu	37	20	36553524	36553524	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:36553524delT	uc002xhk.3	+							NM_080607	NP_542174			V-set and transmembrane domain containing 2 like											ovary(1)|central_nervous_system(1)	2		Myeloproliferative disorder(115;0.00878)																---	---	---	---
VSTM2L	128434	broad.mit.edu	37	20	36562049	36562049	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:36562049delA	uc002xhk.3	+							NM_080607	NP_542174			V-set and transmembrane domain containing 2 like											ovary(1)|central_nervous_system(1)	2		Myeloproliferative disorder(115;0.00878)																---	---	---	---
Unknown	0	broad.mit.edu	37	20	37071902	37071903	+	IGR	INS	-	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:37071902_37071903insA								LOC388796 (7884 upstream) : SNHG11 (3394 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	37079599	37079599	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:37079599delT								SNHG11 (35 upstream) : RALGAPB (21887 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	37243006	37243006	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:37243006delT								ADIG (25902 upstream) : SLC32A1 (110099 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	37263530	37263532	+	IGR	DEL	TTT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:37263530_37263532delTTT								ADIG (46426 upstream) : SLC32A1 (89573 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	37425865	37425865	+	IGR	DEL	G	-	-	rs73622049		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:37425865delG								ACTR5 (24776 upstream) : PPP1R16B (8483 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	37729405	37729405	+	IGR	DEL	A	-	-	rs143784489		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:37729405delA								DHX35 (61042 upstream) : LOC339568 (113019 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	37860516	37860517	+	IGR	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:37860516_37860517delAA								LOC339568 (7125 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	38258947	38258948	+	IGR	INS	-	ATGGA	ATGGA	rs140838940	by1000genomes;byFrequency	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:38258947_38258948insATGGA								LOC339568 (405556 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	38320401	38320401	+	IGR	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:38320401delG								LOC339568 (467010 upstream) : MAFB (994118 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	38578715	38578716	+	IGR	INS	-	CATT	CATT			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:38578715_38578716insCATT								LOC339568 (725324 upstream) : MAFB (735803 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	39061877	39061877	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:39061877delA								None (None upstream) : MAFB (252642 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	39085642	39085642	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:39085642delA								None (None upstream) : MAFB (228877 downstream)																																			---	---	---	---
ZHX3	23051	broad.mit.edu	37	20	39868643	39868645	+	Intron	DEL	TTT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:39868643_39868645delTTT	uc002xjs.1	-						ZHX3_uc002xjq.1_Intron|ZHX3_uc002xjr.1_Intron|ZHX3_uc002xjt.1_Intron|ZHX3_uc002xju.1_Intron|ZHX3_uc002xjv.1_Intron|ZHX3_uc002xjw.1_Intron	NM_015035	NP_055850			zinc fingers and homeoboxes 3						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)																---	---	---	---
CHD6	84181	broad.mit.edu	37	20	40054993	40054993	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:40054993delT	uc002xka.1	-							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	40335366	40335366	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:40335366delA								CHD6 (88233 upstream) : PTPRT (366027 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	40375302	40375302	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:40375302delT								CHD6 (128169 upstream) : PTPRT (326091 downstream)																																			---	---	---	---
PTPRT	11122	broad.mit.edu	37	20	40783500	40783500	+	Intron	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:40783500delG	uc002xkg.2	-						PTPRT_uc010ggj.2_Intron|PTPRT_uc010ggi.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	40880357	40880358	+	Intron	INS	-	A	A	rs144524028	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:40880357_40880358insA	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	41227335	41227336	+	Intron	DEL	AA	-	-	rs113294204		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:41227335_41227336delAA	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	41623079	41623080	+	Intron	DEL	CT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:41623079_41623080delCT	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	41859347	41859347	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:41859347delA								PTPRT (40790 upstream) : SFRS6 (227157 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	42038293	42038293	+	IGR	DEL	T	-	-	rs148204885		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:42038293delT								PTPRT (219736 upstream) : SFRS6 (48211 downstream)																																			---	---	---	---
IFT52	51098	broad.mit.edu	37	20	42246724	42246724	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:42246724delT	uc002xkw.2	+						IFT52_uc010zwi.1_Intron|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)															---	---	---	---
IFT52	51098	broad.mit.edu	37	20	42247856	42247857	+	Intron	DEL	GA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:42247856_42247857delGA	uc002xkw.2	+						IFT52_uc010zwi.1_Intron|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	42363672	42363673	+	IGR	INS	-	T	T	rs112274752		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:42363672_42363673insT								GTSF1L (8030 upstream) : TOX2 (179819 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	42700038	42700038	+	IGR	DEL	C	-	-	rs6031338	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:42700038delC								TOX2 (1786 upstream) : JPH2 (40299 downstream)																																			---	---	---	---
C20orf111	51526	broad.mit.edu	37	20	42831809	42831809	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:42831809delT	uc002xlk.2	-							NM_016470	NP_057554			oxidative stress responsive 1												0		Myeloproliferative disorder(115;0.028)	COAD - Colon adenocarcinoma(18;0.00189)															---	---	---	---
Unknown	0	broad.mit.edu	37	20	42864314	42864314	+	IGR	DEL	T	-	-	rs33936998		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:42864314delT								C20orf111 (24883 upstream) : GDAP1L1 (11594 downstream)																																			---	---	---	---
PKIG	11142	broad.mit.edu	37	20	43160868	43160868	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:43160868delA	uc002xmg.2	+						PKIG_uc002xmh.2_Intron|PKIG_uc002xmi.2_Intron	NM_181805	NP_861521			cAMP-dependent protein kinase inhibitor gamma								cAMP-dependent protein kinase inhibitor activity|protein binding				0		Myeloproliferative disorder(115;0.0122)	Colorectal(3;0.001)|COAD - Colon adenocarcinoma(18;0.00189)															---	---	---	---
PKIG	11142	broad.mit.edu	37	20	43205759	43205759	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:43205759delT	uc002xmg.2	+						PKIG_uc002xmh.2_Intron|PKIG_uc002xmi.2_Intron	NM_181805	NP_861521			cAMP-dependent protein kinase inhibitor gamma								cAMP-dependent protein kinase inhibitor activity|protein binding				0		Myeloproliferative disorder(115;0.0122)	Colorectal(3;0.001)|COAD - Colon adenocarcinoma(18;0.00189)															---	---	---	---
RIMS4	140730	broad.mit.edu	37	20	43402131	43402132	+	Intron	INS	-	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:43402131_43402132insC	uc002xms.2	-						RIMS4_uc010ggu.2_Intron	NM_182970	NP_892015			regulating synaptic membrane exocytosis 4						exocytosis|neurotransmitter transport	cell junction|synapse				ovary(4)|central_nervous_system(1)	5		Myeloproliferative disorder(115;0.0122)																---	---	---	---
RIMS4	140730	broad.mit.edu	37	20	43412283	43412284	+	Intron	INS	-	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:43412283_43412284insA	uc002xms.2	-						RIMS4_uc010ggu.2_Intron	NM_182970	NP_892015			regulating synaptic membrane exocytosis 4						exocytosis|neurotransmitter transport	cell junction|synapse				ovary(4)|central_nervous_system(1)	5		Myeloproliferative disorder(115;0.0122)																---	---	---	---
Unknown	0	broad.mit.edu	37	20	43871969	43871971	+	IGR	DEL	TTT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:43871969_43871971delTTT								SEMG2 (18871 upstream) : SLPI (8908 downstream)																																			---	---	---	---
MATN4	8785	broad.mit.edu	37	20	43926078	43926080	+	Intron	DEL	AAA	-	-	rs141550810		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:43926078_43926080delAAA	uc002xnn.2	-						MATN4_uc002xno.2_Intron|MATN4_uc002xnp.2_Intron|MATN4_uc010zwr.1_Intron|MATN4_uc002xnr.1_Intron	NM_003833	NP_003824			matrilin 4 isoform 1 precursor							extracellular region	protein binding				0		Myeloproliferative disorder(115;0.0122)																---	---	---	---
MATN4	8785	broad.mit.edu	37	20	43930504	43930506	+	Intron	DEL	AAA	-	-	rs148022349		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:43930504_43930506delAAA	uc002xnn.2	-						MATN4_uc002xno.2_Intron|MATN4_uc002xnp.2_Intron|MATN4_uc010zwr.1_Intron|MATN4_uc002xnr.1_Intron	NM_003833	NP_003824			matrilin 4 isoform 1 precursor							extracellular region	protein binding				0		Myeloproliferative disorder(115;0.0122)																---	---	---	---
RBPJL	11317	broad.mit.edu	37	20	43945874	43945875	+	3'UTR	DEL	CT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:43945874_43945875delCT	uc002xns.2	+	12					RBPJL_uc002xnt.2_3'UTR	NM_014276	NP_055091			recombining binding protein L						signal transduction	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity			ovary(1)	1		Myeloproliferative disorder(115;0.0122)																---	---	---	---
ZNF335	63925	broad.mit.edu	37	20	44586695	44586695	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:44586695delT	uc002xqw.2	-						ZNF335_uc010zxk.1_Intron	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)																---	---	---	---
Unknown	0	broad.mit.edu	37	20	44733707	44733707	+	IGR	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:44733707delC								NCOA5 (15127 upstream) : CD40 (13199 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	44771335	44771336	+	IGR	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:44771335_44771336delTT								CD40 (12951 upstream) : CDH22 (31040 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	45331895	45331896	+	IGR	DEL	AA	-	-	rs34627132		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:45331895_45331896delAA								TP53RK (13619 upstream) : SLC2A10 (6383 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	45483849	45483849	+	IGR	DEL	A	-	-	rs11479319		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:45483849delA								SLC2A10 (118866 upstream) : EYA2 (39414 downstream)																																			---	---	---	---
EYA2	2139	broad.mit.edu	37	20	45599229	45599229	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:45599229delA	uc002xsm.2	+						EYA2_uc010ghp.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)																---	---	---	---
EYA2	2139	broad.mit.edu	37	20	45789429	45789429	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:45789429delT	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	45890816	45890817	+	Intron	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:45890816_45890817delAA	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_uc002xtg.2_Intron|ZMYND8_uc010ghs.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	46109871	46109871	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:46109871delT								ZMYND8 (124397 upstream) : NCOA3 (20786 downstream)																																			---	---	---	---
NCOA3	8202	broad.mit.edu	37	20	46160194	46160194	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:46160194delA	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	46282985	46282985	+	3'UTR	DEL	T	-	-	rs71798379		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:46282985delT	uc002xtk.2	+	23					NCOA3_uc002xtl.2_3'UTR|NCOA3_uc002xtm.2_3'UTR|NCOA3_uc002xtn.2_3'UTR|NCOA3_uc010zyc.1_3'UTR	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																		---	---	---	---
Unknown	0	broad.mit.edu	37	20	46470181	46470181	+	IGR	DEL	T	-	-	rs112868976		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:46470181delT								SULF2 (54821 upstream) : LOC284749 (518473 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	46479192	46479192	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:46479192delA								SULF2 (63832 upstream) : LOC284749 (509462 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	46758423	46758426	+	IGR	DEL	TTTT	-	-	rs77298788		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:46758423_46758426delTTTT								SULF2 (343063 upstream) : LOC284749 (230228 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	47020827	47020827	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:47020827delA								LOC284749 (21446 upstream) : PREX1 (219966 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	47044127	47044130	+	IGR	DEL	CAGT	-	-	rs11469146		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:47044127_47044130delCAGT								LOC284749 (44746 upstream) : PREX1 (196663 downstream)																																			---	---	---	---
PREX1	57580	broad.mit.edu	37	20	47334125	47334125	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:47334125delA	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)															---	---	---	---
STAU1	6780	broad.mit.edu	37	20	47734962	47734962	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:47734962delA	uc002xud.2	-						STAU1_uc002xua.2_Intron|STAU1_uc002xub.2_Intron|STAU1_uc002xuc.2_Intron|STAU1_uc002xue.2_Intron|STAU1_uc002xuf.2_Intron|STAU1_uc002xug.2_Intron	NM_017453	NP_059347			staufen isoform b							microtubule associated complex|rough endoplasmic reticulum|stress granule	double-stranded RNA binding			ovary(4)|kidney(1)	5			BRCA - Breast invasive adenocarcinoma(12;0.000644)|Colorectal(8;0.198)															---	---	---	---
STAU1	6780	broad.mit.edu	37	20	47755041	47755041	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:47755041delT	uc002xud.2	-						STAU1_uc002xua.2_Intron|STAU1_uc002xub.2_Intron|STAU1_uc002xuc.2_Intron|STAU1_uc002xue.2_Intron|STAU1_uc002xuf.2_Intron|STAU1_uc002xug.2_Intron	NM_017453	NP_059347			staufen isoform b							microtubule associated complex|rough endoplasmic reticulum|stress granule	double-stranded RNA binding			ovary(4)|kidney(1)	5			BRCA - Breast invasive adenocarcinoma(12;0.000644)|Colorectal(8;0.198)															---	---	---	---
Unknown	0	broad.mit.edu	37	20	48118840	48118840	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:48118840delA								KCNB1 (18350 upstream) : PTGIS (1573 downstream)																																			---	---	---	---
PTGIS	5740	broad.mit.edu	37	20	48161972	48161973	+	Intron	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:48161972_48161973delAA	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)													---	---	---	---
PTGIS	5740	broad.mit.edu	37	20	48180420	48180421	+	Intron	DEL	CA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:48180420_48180421delCA	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)													---	---	---	---
SLC9A8	23315	broad.mit.edu	37	20	48472144	48472144	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:48472144delT	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)															---	---	---	---
RNF114	55905	broad.mit.edu	37	20	48565629	48565629	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:48565629delT	uc002xux.2	+						RNF114_uc010zyo.1_Intron|RNF114_uc002xuy.2_Intron	NM_018683	NP_061153			zinc finger protein 313						cell differentiation|multicellular organismal development|spermatogenesis	intracellular	zinc ion binding			ovary(1)|central_nervous_system(1)	2																		---	---	---	---
BCAS4	55653	broad.mit.edu	37	20	49464417	49464417	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:49464417delA	uc002xvq.2	+						BCAS4_uc002xvr.2_Intron|BCAS4_uc002xvs.2_Intron	NM_017843	NP_060313			breast carcinoma amplified sequence 4 isoform a							cytoplasm					0																		---	---	---	---
BCAS4	55653	broad.mit.edu	37	20	49471296	49471297	+	Intron	INS	-	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:49471296_49471297insC	uc002xvq.2	+						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	49511115	49511115	+	Intron	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:49511115delC	uc002xvt.1	-						ADNP_uc002xvu.1_Intron	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																		---	---	---	---
Unknown	0	broad.mit.edu	37	20	49715448	49715449	+	IGR	DEL	AA	-	-	rs11428327		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:49715448_49715449delAA								KCNG1 (75773 upstream) : NFATC2 (292317 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	49903416	49903416	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:49903416delA								KCNG1 (263741 upstream) : NFATC2 (104350 downstream)																																			---	---	---	---
ATP9A	10079	broad.mit.edu	37	20	50304303	50304304	+	Intron	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:50304303_50304304delAA	uc002xwg.1	-						ATP9A_uc010gih.1_Intron|ATP9A_uc002xwf.1_Intron	NM_006045	NP_006036			ATPase, class II, type 9A						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																		---	---	---	---
Unknown	0	broad.mit.edu	37	20	50528107	50528108	+	IGR	DEL	TA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:50528107_50528108delTA								SALL4 (109059 upstream) : ZFP64 (172443 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	50873340	50873340	+	IGR	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:50873340delG								ZFP64 (64816 upstream) : TSHZ2 (715537 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	50878141	50878141	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:50878141delA								ZFP64 (69617 upstream) : TSHZ2 (710736 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	51288059	51288059	+	IGR	DEL	A	-	-	rs77112193		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:51288059delA								ZFP64 (479535 upstream) : TSHZ2 (300818 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	51478614	51478615	+	IGR	INS	-	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:51478614_51478615insA								ZFP64 (670090 upstream) : TSHZ2 (110262 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	51568229	51568230	+	IGR	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:51568229_51568230delAA								ZFP64 (759705 upstream) : TSHZ2 (20647 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	52389643	52389643	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:52389643delA								ZNF217 (178842 upstream) : SUMO1P1 (101399 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	52530623	52530634	+	IGR	DEL	ATCTATCTATCT	-	-	rs68078939	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:52530623_52530634delATCTATCTATCT								SUMO1P1 (38375 upstream) : BCAS1 (29445 downstream)																																			---	---	---	---
DOK5	55816	broad.mit.edu	37	20	53137726	53137726	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:53137726delT	uc002xwy.2	+						DOK5_uc010gin.2_Intron|DOK5_uc002xwz.2_Intron	NM_018431	NP_060901			docking protein 5								insulin receptor binding			ovary(1)	1			Colorectal(105;0.202)															---	---	---	---
DOK5	55816	broad.mit.edu	37	20	53238228	53238229	+	Intron	DEL	AA	-	-	rs11483914		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:53238228_53238229delAA	uc002xwy.2	+						DOK5_uc010gin.2_Intron|DOK5_uc002xwz.2_Intron	NM_018431	NP_060901			docking protein 5								insulin receptor binding			ovary(1)	1			Colorectal(105;0.202)															---	---	---	---
Unknown	0	broad.mit.edu	37	20	53705893	53705893	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:53705893delT								DOK5 (438184 upstream) : CBLN4 (866604 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	54340777	54340778	+	IGR	DEL	AA	-	-	rs74181030		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:54340777_54340778delAA								None (None upstream) : CBLN4 (231719 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	54350554	54350554	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:54350554delT								None (None upstream) : CBLN4 (221943 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	54506829	54506831	+	IGR	DEL	AAA	-	-	rs112530511		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:54506829_54506831delAAA								None (None upstream) : CBLN4 (65666 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	54737715	54737715	+	IGR	DEL	T	-	-	rs139601934		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:54737715delT								CBLN4 (157703 upstream) : MC3R (86073 downstream)																																			---	---	---	---
MC3R	4159	broad.mit.edu	37	20	54823640	54823641	+	5'Flank	DEL	CT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:54823640_54823641delCT	uc002xxb.2	+							NM_019888	NP_063941			melanocortin 3 receptor						activation of phospholipase C activity by G-protein coupled receptor protein signaling pathway coupled to IP3 second messenger|positive regulation of cAMP biosynthetic process	integral to plasma membrane	melanocyte-stimulating hormone receptor activity|neuropeptide binding|protein binding			ovary(2)|breast(2)	4			Colorectal(105;0.202)															---	---	---	---
C20orf43	51507	broad.mit.edu	37	20	55063417	55063417	+	Intron	DEL	A	-	-	rs76214451		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:55063417delA	uc002xxt.2	+						C20orf43_uc010zzf.1_Intron|C20orf43_uc002xxu.2_Intron|C20orf43_uc002xxv.2_Intron	NM_016407	NP_057491			hypothetical protein LOC51507											ovary(1)	1			Colorectal(105;0.202)															---	---	---	---
Unknown	0	broad.mit.edu	37	20	55228830	55228832	+	IGR	DEL	TTT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:55228830_55228832delTTT								TFAP2C (14494 upstream) : BMP7 (514977 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	56023568	56023568	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:56023568delT								RBM38 (39184 upstream) : CTCFL (40312 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	56294992	56294992	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:56294992delT								PMEPA1 (8451 upstream) : C20orf85 (430991 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	56328346	56328346	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:56328346delA								PMEPA1 (41805 upstream) : C20orf85 (397637 downstream)																																			---	---	---	---
PPP4R1L	55370	broad.mit.edu	37	20	56851477	56851477	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:56851477delA	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	56862129	56862129	+	Intron	DEL	T	-	-	rs66635333		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:56862129delT	uc002xyy.1	-						PPP4R1L_uc010gjn.1_Intron					SubName: Full=cDNA FLJ50842, moderately similar to Serine/threonine-protein phosphatase 4regulatory subunit 1;												0																		---	---	---	---
RAB22A	57403	broad.mit.edu	37	20	56898692	56898692	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:56898692delT	uc002xyz.2	+							NM_020673	NP_065724			RAS-related protein RAB-22A						endocytosis|endosome organization|protein transport|small GTPase mediated signal transduction	early endosome|endosome membrane|plasma membrane	GTP binding|GTPase activity|protein binding				0	all_epithelial(3;5.09e-14)|Lung NSC(12;0.000122)|all_lung(29;0.00042)		BRCA - Breast invasive adenocarcinoma(13;6.2e-12)|Epithelial(14;4.73e-08)|all cancers(14;4.83e-07)															---	---	---	---
RAB22A	57403	broad.mit.edu	37	20	56905503	56905503	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:56905503delT	uc002xyz.2	+							NM_020673	NP_065724			RAS-related protein RAB-22A						endocytosis|endosome organization|protein transport|small GTPase mediated signal transduction	early endosome|endosome membrane|plasma membrane	GTP binding|GTPase activity|protein binding				0	all_epithelial(3;5.09e-14)|Lung NSC(12;0.000122)|all_lung(29;0.00042)		BRCA - Breast invasive adenocarcinoma(13;6.2e-12)|Epithelial(14;4.73e-08)|all cancers(14;4.83e-07)															---	---	---	---
VAPB	9217	broad.mit.edu	37	20	57014633	57014635	+	Intron	DEL	AGC	-	-	rs71968610		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:57014633_57014635delAGC	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	57034413	57034414	+	IGR	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:57034413_57034414delTT								VAPB (12452 upstream) : APCDD1L (12 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	57107867	57107867	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:57107867delT	uc002xzg.1	+											Homo sapiens cDNA FLJ30075 fis, clone BGGI11000285.																														---	---	---	---
CTSZ	1522	broad.mit.edu	37	20	57584587	57584588	+	5'Flank	DEL	TT	-	-	rs71971092		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:57584587_57584588delTT	uc002yai.2	-						CTSZ_uc002yaj.3_5'Flank	NM_001336	NP_001327			cathepsin Z preproprotein						proteolysis	endoplasmic reticulum|extracellular space|lysosome	cysteine-type endopeptidase activity			kidney(1)	1	all_lung(29;0.00711)		Colorectal(105;0.109)															---	---	---	---
ZNF831	128611	broad.mit.edu	37	20	57803689	57803690	+	Intron	DEL	GA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:57803689_57803690delGA	uc002yan.2	+							NM_178457	NP_848552			zinc finger protein 831							intracellular	nucleic acid binding|zinc ion binding			skin(13)|ovary(1)	14	all_lung(29;0.0085)																	---	---	---	---
Unknown	0	broad.mit.edu	37	20	58113012	58113012	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:58113012delA								EDN3 (211966 upstream) : PHACTR3 (39552 downstream)																																			---	---	---	---
PHACTR3	116154	broad.mit.edu	37	20	58416343	58416343	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:58416343delT	uc002yau.2	+						PHACTR3_uc002yat.2_Intron|PHACTR3_uc010zzw.1_Intron|PHACTR3_uc002yav.2_Intron|PHACTR3_uc002yaw.2_Intron|PHACTR3_uc002yax.2_Intron|PHACTR3_uc002yay.2_Intron	NM_080672	NP_542403			phosphatase and actin regulator 3 isoform 1							nuclear matrix	actin binding|protein phosphatase inhibitor activity			ovary(2)|pancreas(1)	3	all_lung(29;0.00344)		BRCA - Breast invasive adenocarcinoma(7;2.76e-09)															---	---	---	---
SYCP2	10388	broad.mit.edu	37	20	58456449	58456449	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:58456449delA	uc002yaz.2	-							NM_014258	NP_055073			synaptonemal complex protein 2						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)															---	---	---	---
Unknown	0	broad.mit.edu	37	20	58822848	58822849	+	Intron	DEL	TC	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:58822848_58822849delTC	uc002ybl.2	+						uc010gjw.1_Intron					Homo sapiens cDNA FLJ35486 fis, clone SMINT2008491.																														---	---	---	---
Unknown	0	broad.mit.edu	37	20	59018435	59018435	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:59018435delT	uc010gjw.1	+											Homo sapiens cDNA FLJ35486 fis, clone SMINT2008491.																														---	---	---	---
Unknown	0	broad.mit.edu	37	20	59778272	59778272	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:59778272delA								MIR646 (894647 upstream) : CDH4 (49287 downstream)																																			---	---	---	---
CDH4	1002	broad.mit.edu	37	20	60412818	60412818	+	Intron	DEL	C	-	-	rs66497535		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:60412818delC	uc002ybn.1	+						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)															---	---	---	---
CDH4	1002	broad.mit.edu	37	20	60464350	60464353	+	Intron	DEL	ATGG	-	-	rs113089640		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:60464350_60464353delATGG	uc002ybn.1	+						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	60689219	60689219	+	IGR	DEL	A	-	-	rs5842374		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:60689219delA								TAF4 (48353 upstream) : LSM14B (8298 downstream)																																			---	---	---	---
PSMA7	5688	broad.mit.edu	37	20	60713607	60713611	+	Intron	DEL	TTTTT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:60713607_60713611delTTTTT	uc002ybx.1	-						PSMA7_uc002yby.1_Intron	NM_002792	NP_002783			proteasome alpha 7 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, alpha-subunit complex	identical protein binding|threonine-type endopeptidase activity				0	Breast(26;3.97e-09)		BRCA - Breast invasive adenocarcinoma(19;1.28e-07)															---	---	---	---
GTPBP5	26164	broad.mit.edu	37	20	60759426	60759427	+	Intron	DEL	AA	-	-	rs111552705		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:60759426_60759427delAA	uc002yce.3	+						GTPBP5_uc011aab.1_Intron|GTPBP5_uc011aac.1_Intron|GTPBP5_uc011aad.1_Intron|GTPBP5_uc011aae.1_Intron|GTPBP5_uc011aaf.1_Intron	NM_015666	NP_056481			GTP binding protein 5						ribosome biogenesis	mitochondrion	GTP binding|GTPase activity|magnesium ion binding				0	Breast(26;3.52e-09)		BRCA - Breast invasive adenocarcinoma(19;2.5e-08)															---	---	---	---
Unknown	0	broad.mit.edu	37	20	61079519	61079521	+	IGR	DEL	TCA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:61079519_61079521delTCA								GATA5 (28493 upstream) : C20orf200 (62034 downstream)																																			---	---	---	---
C20orf166	128826	broad.mit.edu	37	20	61155664	61155665	+	Intron	INS	-	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:61155664_61155665insG	uc011aaj.1	+							NM_178463	NP_848558			hypothetical protein LOC128826												0	Breast(26;1.04e-08)		BRCA - Breast invasive adenocarcinoma(19;7.17e-06)															---	---	---	---
Unknown	0	broad.mit.edu	37	20	61180381	61180382	+	IGR	INS	-	ATCT	ATCT	rs145678881	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:61180381_61180382insATCT								C20orf166 (12411 upstream) : SLCO4A1 (93415 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	61717431	61717434	+	IGR	DEL	TGTG	-	-	rs71924787		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:61717431_61717434delTGTG								NCRNA00029 (49051 upstream) : HAR1B (9411 downstream)																																			---	---	---	---
ZGPAT	84619	broad.mit.edu	37	20	62364034	62364035	+	Intron	INS	-	TG	TG	rs150623660	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:62364034_62364035insTG	uc002ygk.2	+						ZGPAT_uc002ygi.2_Intron|ZGPAT_uc002ygj.2_Intron|ZGPAT_uc010gkk.1_Intron|ZGPAT_uc010gkl.1_Intron|ZGPAT_uc002ygm.2_Intron|ZGPAT_uc002ygn.3_Intron	NM_032527	NP_115916			zinc finger, CCCH-type with G patch domain						negative regulation of epidermal growth factor receptor activity|negative regulation of transcription, DNA-dependent	nucleus	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding				0	all_cancers(38;1.13e-12)|all_epithelial(29;2.64e-14)|Lung NSC(23;4.79e-10)|all_lung(23;1.7e-09)																	---	---	---	---
PRPF6	24148	broad.mit.edu	37	20	62648293	62648297	+	Intron	DEL	TTTTT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:62648293_62648297delTTTTT	uc002yho.2	+						PRPF6_uc002yhp.2_Intron	NM_012469	NP_036601			PRP6 pre-mRNA processing factor 6 homolog						assembly of spliceosomal tri-snRNP|positive regulation of transcription from RNA polymerase II promoter|spliceosome assembly	catalytic step 2 spliceosome|nucleoplasm|U4/U6 snRNP|U4/U6 x U5 tri-snRNP complex|U5 snRNP	androgen receptor binding|ribonucleoprotein binding|transcription coactivator activity			ovary(2)	2	all_cancers(38;6.47e-12)|all_epithelial(29;1.26e-13)|Lung NSC(23;9.37e-10)|all_lung(23;3.23e-09)																	---	---	---	---
NPBWR2	2832	broad.mit.edu	37	20	62740390	62740390	+	5'Flank	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:62740390delG	uc011abt.1	-							NM_005286	NP_005277			neuropeptides B/W receptor 2							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)																	---	---	---	---
Unknown	0	broad.mit.edu	37	21	9414623	9414624	+	IGR	INS	-	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:9414623_9414624insG								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	21	9416165	9416165	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:9416165delT								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	21	9583567	9583567	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:9583567delA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	21	9833722	9833723	+	IGR	INS	-	AA	AA			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:9833722_9833723insAA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	21	10431232	10431232	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:10431232delT								None (None upstream) : TPTE (475511 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	21	10561378	10561378	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:10561378delA	uc011abv.1	-											Homo sapiens cDNA, FLJ18615.																														---	---	---	---
Unknown	0	broad.mit.edu	37	21	10633109	10633109	+	IGR	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:10633109delC								None (None upstream) : TPTE (273634 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	21	10745377	10745379	+	IGR	DEL	TCT	-	-	rs143093237		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:10745377_10745379delTCT								None (None upstream) : TPTE (161364 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	21	10786132	10786133	+	IGR	INS	-	AAATG	AAATG			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:10786132_10786133insAAATG								None (None upstream) : TPTE (120610 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	21	10808907	10808907	+	IGR	DEL	G	-	-	rs111619895		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:10808907delG								None (None upstream) : TPTE (97836 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	21	10826832	10826833	+	IGR	INS	-	AATGG	AATGG	rs78495047		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:10826832_10826833insAATGG								None (None upstream) : TPTE (79910 downstream)																																			---	---	---	---
TPTE	7179	broad.mit.edu	37	21	10910947	10910947	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:10910947delT	uc002yip.1	-						TPTE_uc002yis.1_Intron|TPTE_uc002yiq.1_Intron|TPTE_uc002yir.1_Intron|TPTE_uc010gkv.1_Intron	NM_199261	NP_954870			transmembrane phosphatase with tensin homology						signal transduction	integral to membrane	ion channel activity|protein tyrosine phosphatase activity|protein tyrosine/serine/threonine phosphatase activity			ovary(2)|lung(1)|breast(1)|skin(1)	5			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)														---	---	---	---
TPTE	7179	broad.mit.edu	37	21	10936620	10936620	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:10936620delT	uc002yip.1	-						TPTE_uc002yis.1_Intron|TPTE_uc002yiq.1_Intron|TPTE_uc002yir.1_Intron|TPTE_uc010gkv.1_Intron	NM_199261	NP_954870			transmembrane phosphatase with tensin homology						signal transduction	integral to membrane	ion channel activity|protein tyrosine phosphatase activity|protein tyrosine/serine/threonine phosphatase activity			ovary(2)|lung(1)|breast(1)|skin(1)	5			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)														---	---	---	---
TPTE	7179	broad.mit.edu	37	21	10969701	10969702	+	Intron	DEL	AA	-	-	rs3049903		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:10969701_10969702delAA	uc002yip.1	-						TPTE_uc002yis.1_Intron|TPTE_uc002yiq.1_Intron|TPTE_uc002yir.1_Intron|TPTE_uc010gkv.1_Intron	NM_199261	NP_954870			transmembrane phosphatase with tensin homology						signal transduction	integral to membrane	ion channel activity|protein tyrosine phosphatase activity|protein tyrosine/serine/threonine phosphatase activity			ovary(2)|lung(1)|breast(1)|skin(1)	5			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)														---	---	---	---
BAGE2	85319	broad.mit.edu	37	21	11089714	11089716	+	Intron	DEL	TTT	-	-	rs111488490		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:11089714_11089716delTTT	uc002yit.1	-						BAGE_uc002yix.2_Intron	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	11106521	11106521	+	IGR	DEL	A	-	-	rs141335131		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:11106521delA								BAGE (7584 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	21	14383819	14383819	+	IGR	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:14383819delC								None (None upstream) : C21orf99 (26668 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	21	15212521	15212521	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:15212521delT								POTED (198615 upstream) : C21orf15 (2934 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	21	15243882	15243882	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:15243882delT								C21orf15 (23197 upstream) : C21orf81 (72214 downstream)																																			---	---	---	---
RBM11	54033	broad.mit.edu	37	21	15592145	15592145	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:15592145delA	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)														---	---	---	---
NRIP1	8204	broad.mit.edu	37	21	16366105	16366105	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:16366105delA	uc002yjx.2	-							NM_003489	NP_003480			nuclear receptor interacting protein 1						androgen receptor signaling pathway|negative regulation of transcription from RNA polymerase II promoter|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent		androgen receptor binding|estrogen receptor binding|glucocorticoid receptor binding|transcription coactivator activity|transcription corepressor activity				0				Epithelial(23;1.19e-05)|all cancers(11;4.64e-05)|COAD - Colon adenocarcinoma(22;0.000232)|Colorectal(24;0.0006)|OV - Ovarian serous cystadenocarcinoma(11;0.00418)|Lung(58;0.199)|LUSC - Lung squamous cell carcinoma(23;0.24)														---	---	---	---
NRIP1	8204	broad.mit.edu	37	21	16378497	16378497	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:16378497delA	uc002yjx.2	-							NM_003489	NP_003480			nuclear receptor interacting protein 1						androgen receptor signaling pathway|negative regulation of transcription from RNA polymerase II promoter|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent		androgen receptor binding|estrogen receptor binding|glucocorticoid receptor binding|transcription coactivator activity|transcription corepressor activity				0				Epithelial(23;1.19e-05)|all cancers(11;4.64e-05)|COAD - Colon adenocarcinoma(22;0.000232)|Colorectal(24;0.0006)|OV - Ovarian serous cystadenocarcinoma(11;0.00418)|Lung(58;0.199)|LUSC - Lung squamous cell carcinoma(23;0.24)														---	---	---	---
Unknown	0	broad.mit.edu	37	21	16811894	16811894	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:16811894delT								NRIP1 (374768 upstream) : USP25 (290602 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	21	16959797	16959798	+	IGR	DEL	TT	-	-	rs112256067		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:16959797_16959798delTT								NRIP1 (522671 upstream) : USP25 (142698 downstream)																																			---	---	---	---
USP25	29761	broad.mit.edu	37	21	17206756	17206757	+	Intron	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:17206756_17206757delTT	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)														---	---	---	---
Unknown	0	broad.mit.edu	37	21	18389384	18389384	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:18389384delA								C21orf34 (407290 upstream) : CXADR (495946 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	21	18988586	18988586	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:18988586delA								BTG3 (3318 upstream) : C21orf91 (161137 downstream)																																			---	---	---	---
CHODL	140578	broad.mit.edu	37	21	19415229	19415230	+	Intron	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:19415229_19415230delTT	uc002ykt.2	+						CHODL_uc002ykr.2_Intron|CHODL_uc002yks.2_Intron|CHODL_uc002yku.2_Intron					RecName: Full=Chondrolectin; AltName: Full=Transmembrane protein MT75; Flags: 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)														---	---	---	---
TMPRSS15	5651	broad.mit.edu	37	21	19725395	19725395	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:19725395delA	uc002ykw.2	-							NM_002772	NP_002763			enterokinase precursor						proteolysis	brush border|integral to membrane	scavenger receptor activity|serine-type endopeptidase activity			ovary(5)|upper_aerodigestive_tract(1)|breast(1)|skin(1)	8																		---	---	---	---
Unknown	0	broad.mit.edu	37	21	19876381	19876382	+	IGR	INS	-	A	A	rs147460674	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:19876381_19876382insA								TMPRSS15 (100411 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	21	20357342	20357342	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:20357342delT								TMPRSS15 (581372 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	21	20580083	20580083	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:20580083delT								TMPRSS15 (804113 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	21	22185502	22185502	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:22185502delT								C21orf131 (10076 upstream) : NCAM2 (185131 downstream)																																			---	---	---	---
NCAM2	4685	broad.mit.edu	37	21	22367708	22367709	+	5'Flank	DEL	TC	-	-	rs10552573		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:22367708_22367709delTC	uc002yld.1	+						NCAM2_uc011acb.1_5'Flank	NM_004540	NP_004531			neural cell adhesion molecule 2 precursor						neuron cell-cell adhesion	integral to membrane|plasma membrane				ovary(4)	4		Lung NSC(9;0.195)		all cancers(11;0.00102)|OV - Ovarian serous cystadenocarcinoma(11;0.00121)|Epithelial(23;0.00147)|Colorectal(24;0.174)														---	---	---	---
NCAM2	4685	broad.mit.edu	37	21	22379605	22379605	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:22379605delT	uc002yld.1	+						NCAM2_uc011acb.1_Intron	NM_004540	NP_004531			neural cell adhesion molecule 2 precursor						neuron cell-cell adhesion	integral to membrane|plasma membrane				ovary(4)	4		Lung NSC(9;0.195)		all cancers(11;0.00102)|OV - Ovarian serous cystadenocarcinoma(11;0.00121)|Epithelial(23;0.00147)|Colorectal(24;0.174)														---	---	---	---
Unknown	0	broad.mit.edu	37	21	23216260	23216261	+	IGR	DEL	GA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:23216260_23216261delGA								NCAM2 (305046 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	21	23553078	23553078	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:23553078delT								NCAM2 (641864 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	21	23628964	23628964	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:23628964delA								NCAM2 (717750 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	21	23649087	23649088	+	IGR	DEL	TA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:23649087_23649088delTA								NCAM2 (737873 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	21	23959126	23959126	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:23959126delA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	21	24190292	24190292	+	IGR	DEL	A	-	-	rs144019030	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:24190292delA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	21	26185042	26185042	+	IGR	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:26185042delG								None (None upstream) : NCRNA00158 (573092 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	21	26291493	26291493	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:26291493delA								None (None upstream) : NCRNA00158 (466641 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	21	26328368	26328368	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:26328368delT								None (None upstream) : NCRNA00158 (429766 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	21	26583325	26583325	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:26583325delA								None (None upstream) : NCRNA00158 (174809 downstream)																																			---	---	---	---
MRPL39	54148	broad.mit.edu	37	21	26959265	26959265	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:26959265delT	uc002ylo.2	-						MRPL39_uc002yln.2_Intron	NM_017446	NP_059142			mitochondrial ribosomal protein L39 isoform a							mitochondrial ribosome	nucleotide binding				0																		---	---	---	---
MRPL39	54148	broad.mit.edu	37	21	26976400	26976402	+	Intron	DEL	AAA	-	-	rs11303574		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:26976400_26976402delAAA	uc002ylo.2	-						MRPL39_uc002yln.2_Intron	NM_017446	NP_059142			mitochondrial ribosomal protein L39 isoform a							mitochondrial ribosome	nucleotide binding				0																		---	---	---	---
APP	351	broad.mit.edu	37	21	27258483	27258483	+	Intron	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:27258483delG	uc002ylz.2	-						APP_uc011acg.1_Intron|APP_uc010glk.2_Intron|APP_uc002yma.2_Intron|APP_uc011ach.1_Intron|APP_uc002ymb.2_Intron|APP_uc010glj.2_Intron|APP_uc011aci.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)																---	---	---	---
APP	351	broad.mit.edu	37	21	27394038	27394038	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:27394038delA	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	27651200	27651200	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:27651200delT								APP (107754 upstream) : CYYR1 (187329 downstream)																																			---	---	---	---
CYYR1	116159	broad.mit.edu	37	21	27852395	27852395	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:27852395delA	uc002ymd.2	-						CYYR1_uc011ack.1_Intron|CYYR1_uc002yme.2_Intron	NM_052954	NP_443186			cysteine and tyrosine-rich 1 protein precursor							integral to membrane					0																		---	---	---	---
Unknown	0	broad.mit.edu	37	21	28279577	28279577	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:28279577delA								ADAMTS1 (61849 upstream) : ADAMTS5 (10655 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	21	28403085	28403085	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:28403085delA								ADAMTS5 (63646 upstream) : NCRNA00113 (691613 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	21	28409524	28409525	+	IGR	INS	-	A	A	rs138156826	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:28409524_28409525insA								ADAMTS5 (70085 upstream) : NCRNA00113 (685173 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	21	28854969	28854969	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:28854969delT								ADAMTS5 (515530 upstream) : NCRNA00113 (239729 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	21	29610045	29610046	+	IGR	DEL	AA	-	-	rs79193101		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:29610045_29610046delAA								C21orf94 (214517 upstream) : NCRNA00161 (301594 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	21	29750680	29750681	+	IGR	INS	-	A	A	rs138956968	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:29750680_29750681insA								C21orf94 (355152 upstream) : NCRNA00161 (160959 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	21	29812939	29812939	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:29812939delA								C21orf94 (417411 upstream) : NCRNA00161 (98701 downstream)																																			---	---	---	---
RNF160	26046	broad.mit.edu	37	21	30332708	30332708	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:30332708delA	uc002ymr.2	-							NM_015565	NP_056380			zinc finger protein 294								ligase activity|zinc ion binding				0																		---	---	---	---
USP16	10600	broad.mit.edu	37	21	30412900	30412901	+	Intron	INS	-	TA	TA			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:30412900_30412901insTA	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																		---	---	---	---
USP16	10600	broad.mit.edu	37	21	30416118	30416118	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:30416118delT	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																		---	---	---	---
NCRNA00189	193629	broad.mit.edu	37	21	30633762	30633762	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:30633762delT	uc002ynh.2	+						NCRNA00189_uc002yni.2_Intron	NR_027072				Homo sapiens chromosome 21 open reading frame 109 (C21orf109) mRNA, complete cds.												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	21	30875994	30875995	+	IGR	DEL	GT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:30875994_30875995delGT								BACH1 (141777 upstream) : GRIK1 (33261 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	21	30891903	30891903	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:30891903delT								BACH1 (157686 upstream) : GRIK1 (17353 downstream)																																			---	---	---	---
GRIK1	2897	broad.mit.edu	37	21	30961067	30961067	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:30961067delA	uc002yno.1	-						GRIK1_uc002ynn.2_Intron|GRIK1_uc011acs.1_Intron|GRIK1_uc011act.1_Intron|GRIK1_uc010glq.1_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	31003282	31003282	+	Intron	DEL	T	-	-	rs77556113		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:31003282delT	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	31411978	31411979	+	IGR	INS	-	A	A	rs139797347	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:31411978_31411979insA								GRIK1 (99696 upstream) : CLDN17 (126284 downstream)																																			---	---	---	---
KRTAP13-2	337959	broad.mit.edu	37	21	31744777	31744777	+	5'Flank	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:31744777delT	uc002ynz.3	-							NM_181621	NP_853652			keratin associated protein 13-2							intermediate filament					0																		---	---	---	---
Unknown	0	broad.mit.edu	37	21	31823382	31823382	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:31823382delT								KRTAP15-1 (10285 upstream) : KRTAP19-1 (28984 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	21	32211097	32211097	+	IGR	DEL	A	-	-	rs72022616		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:32211097delA								KRTAP7-1 (9046 upstream) : KRTAP11-1 (41869 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	21	32402895	32402895	+	IGR	DEL	T	-	-	rs72135201		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:32402895delT								KRTAP11-1 (149021 upstream) : KRTAP19-8 (7584 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	21	32453802	32453803	+	IGR	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:32453802_32453803delAA								KRTAP19-8 (43007 upstream) : TIAM1 (36933 downstream)																																			---	---	---	---
TIAM1	7074	broad.mit.edu	37	21	32672700	32672701	+	Intron	INS	-	A	A	rs147275118	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:32672700_32672701insA	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	32851683	32851686	+	Intron	DEL	TGGA	-	-	rs72301045		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:32851683_32851686delTGGA	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	32873630	32873630	+	Intron	DEL	T	-	-	rs74969453		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:32873630delT	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																		---	---	---	---
SFRS15	57466	broad.mit.edu	37	21	33063986	33063993	+	Intron	DEL	AAAAAAAA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:33063986_33063993delAAAAAAAA	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	33074758	33074758	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:33074758delA	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	33185366	33185366	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:33185366delT								SFRS15 (80935 upstream) : HUNK (60262 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	21	33433922	33433925	+	IGR	DEL	TGAG	-	-	rs142441310		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:33433922_33433925delTGAG								HUNK (57546 upstream) : NCRNA00159 (18704 downstream)																																			---	---	---	---
NCRNA00159	54070	broad.mit.edu	37	21	33526721	33526722	+	Intron	INS	-	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:33526721_33526722insC	uc011adm.1	+							NR_024352				Homo sapiens non-protein coding RNA 159 (NCRNA00159), non-coding RNA.												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	21	33622058	33622058	+	IGR	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:33622058delC								NCRNA00159 (93242 upstream) : C21orf45 (18474 downstream)																																			---	---	---	---
URB1	9875	broad.mit.edu	37	21	33749844	33749844	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:33749844delA	uc002ypn.2	-						SNORA80_uc002ypo.2_5'Flank	NM_014825	NP_055640			URB1 ribosome biogenesis 1 homolog							nucleolus	protein binding				0																		---	---	---	---
C21orf63	59271	broad.mit.edu	37	21	33798734	33798734	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:33798734delT	uc002ypr.1	+						C21orf63_uc002ypq.1_Intron|C21orf63_uc002yps.1_Intron|C21orf63_uc010glw.1_Intron|C21orf63_uc002ypt.1_Intron	NM_058187	NP_478067			hypothetical protein LOC59271 precursor							integral to membrane	sugar binding			ovary(2)|pancreas(1)	3																		---	---	---	---
C21orf63	59271	broad.mit.edu	37	21	33811548	33811548	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:33811548delA	uc002ypr.1	+						C21orf63_uc002ypq.1_Intron|C21orf63_uc002yps.1_Intron|C21orf63_uc010glw.1_Intron|C21orf63_uc002ypt.1_Intron	NM_058187	NP_478067			hypothetical protein LOC59271 precursor							integral to membrane	sugar binding			ovary(2)|pancreas(1)	3																		---	---	---	---
C21orf63	59271	broad.mit.edu	37	21	33865020	33865020	+	Intron	DEL	T	-	-	rs112341937		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:33865020delT	uc002ypr.1	+						C21orf63_uc002yps.1_Intron|C21orf63_uc010glw.1_Intron|C21orf63_uc002ypt.1_Intron|C21orf63_uc002ypu.1_Intron|C21orf63_uc011adq.1_5'Flank	NM_058187	NP_478067			hypothetical protein LOC59271 precursor							integral to membrane	sugar binding			ovary(2)|pancreas(1)	3																		---	---	---	---
SYNJ1	8867	broad.mit.edu	37	21	34056204	34056204	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:34056204delA	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																		---	---	---	---
SYNJ1	8867	broad.mit.edu	37	21	34064886	34064886	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:34064886delA	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	34174160	34174160	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:34174160delA	uc010glz.2	-						C21orf62_uc011adt.1_Intron|C21orf62_uc011adu.1_Intron	NM_001162495	NP_001155967			hypothetical protein LOC56245											ovary(1)	1		Myeloproliferative disorder(46;0.0255)																---	---	---	---
C21orf54	728409	broad.mit.edu	37	21	34542325	34542326	+	Intron	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:34542325_34542326delAA	uc002yra.2	-							NR_024102				Homo sapiens cDNA clone IMAGE:8144118.												0																		---	---	---	---
IFNAR1	3454	broad.mit.edu	37	21	34712066	34712066	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:34712066delA	uc002yrn.2	+						IFNAR1_uc011adv.1_Intron	NM_000629	NP_000620			interferon-alpha receptor 1 precursor						JAK-STAT cascade|regulation of type I interferon-mediated signaling pathway|response to virus|type I interferon-mediated signaling pathway	integral to plasma membrane	type I interferon receptor activity			central_nervous_system(1)|skin(1)	2					Interferon Alfa-2a, Recombinant(DB00034)|Interferon Alfa-2b, Recombinant(DB00105)|Interferon alfa-n1(DB00011)|Interferon alfa-n3(DB00018)|Interferon alfacon-1(DB00069)|Interferon beta-1b(DB00068)|Peginterferon alfa-2a(DB00008)|Peginterferon alfa-2b(DB00022)													---	---	---	---
IFNAR1	3454	broad.mit.edu	37	21	34717524	34717524	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:34717524delT	uc002yrn.2	+						IFNAR1_uc011adv.1_Intron	NM_000629	NP_000620			interferon-alpha receptor 1 precursor						JAK-STAT cascade|regulation of type I interferon-mediated signaling pathway|response to virus|type I interferon-mediated signaling pathway	integral to plasma membrane	type I interferon receptor activity			central_nervous_system(1)|skin(1)	2					Interferon Alfa-2a, Recombinant(DB00034)|Interferon Alfa-2b, Recombinant(DB00105)|Interferon alfa-n1(DB00011)|Interferon alfa-n3(DB00018)|Interferon alfacon-1(DB00069)|Interferon beta-1b(DB00068)|Peginterferon alfa-2a(DB00008)|Peginterferon alfa-2b(DB00022)													---	---	---	---
IFNAR1	3454	broad.mit.edu	37	21	34721820	34721821	+	Frame_Shift_Ins	INS	-	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:34721820_34721821insT	uc002yrn.2	+	8	1261_1262	c.1114_1115insT	c.(1114-1116)ATTfs	p.I372fs	IFNAR1_uc011adv.1_Frame_Shift_Ins_p.I303fs	NM_000629	NP_000620	P17181	INAR1_HUMAN	interferon-alpha receptor 1 precursor	372	Fibronectin type-III 3.|Extracellular (Potential).				JAK-STAT cascade|regulation of type I interferon-mediated signaling pathway|response to virus|type I interferon-mediated signaling pathway	integral to plasma membrane	type I interferon receptor activity			central_nervous_system(1)|skin(1)	2					Interferon Alfa-2a, Recombinant(DB00034)|Interferon Alfa-2b, Recombinant(DB00105)|Interferon alfa-n1(DB00011)|Interferon alfa-n3(DB00018)|Interferon alfacon-1(DB00069)|Interferon beta-1b(DB00068)|Peginterferon alfa-2a(DB00008)|Peginterferon alfa-2b(DB00022)													---	---	---	---
GART	2618	broad.mit.edu	37	21	34903299	34903299	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:34903299delT	uc002yrx.2	-						GART_uc002yrz.2_Intron|GART_uc010gmd.2_Intron|GART_uc002yry.2_Intron|GART_uc002ysa.2_Intron	NM_000819	NP_000810			phosphoribosylglycinamide formyltransferase,						'de novo' IMP biosynthetic process|purine base biosynthetic process	cytosol	ATP binding|metal ion binding|methyltransferase activity|phosphoribosylamine-glycine ligase activity|phosphoribosylformylglycinamidine cyclo-ligase activity|phosphoribosylglycinamide formyltransferase activity|protein binding			ovary(1)	1					Pemetrexed(DB00642)													---	---	---	---
GART	2618	broad.mit.edu	37	21	34910710	34910710	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:34910710delT	uc002yrx.2	-						GART_uc002yrz.2_Intron|GART_uc010gmd.2_Intron|GART_uc002yry.2_Intron|GART_uc002ysa.2_Intron	NM_000819	NP_000810			phosphoribosylglycinamide formyltransferase,						'de novo' IMP biosynthetic process|purine base biosynthetic process	cytosol	ATP binding|metal ion binding|methyltransferase activity|phosphoribosylamine-glycine ligase activity|phosphoribosylformylglycinamidine cyclo-ligase activity|phosphoribosylglycinamide formyltransferase activity|protein binding			ovary(1)	1					Pemetrexed(DB00642)													---	---	---	---
Unknown	0	broad.mit.edu	37	21	35306052	35306052	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:35306052delA	uc002ytn.2	+											Homo sapiens cDNA, FLJ18587.																														---	---	---	---
Unknown	0	broad.mit.edu	37	21	35578892	35578892	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:35578892delT								C21orf82 (16672 upstream) : KCNE2 (157431 downstream)																																			---	---	---	---
RUNX1	861	broad.mit.edu	37	21	36341697	36341697	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-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	36575656	36575656	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-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	36703787	36703787	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:36703787delT	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	37093697	37093699	+	Intron	DEL	TTT	-	-	rs72079523		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:37093697_37093699delTTT	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	37114149	37114149	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:37114149delT	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	37300872	37300880	+	Intron	DEL	AAAAAAAAA	-	-	rs112464038	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:37300872_37300880delAAAAAAAAA	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	37397308	37397308	+	IGR	DEL	A	-	-	rs114064678	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:37397308delA								RUNX1 (40261 upstream) : SETD4 (9532 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	21	37518894	37518894	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:37518894delT	uc002yvc.1	-						uc002yvd.1_Intron|uc002yvf.1_Intron					Homo sapiens mRNA expressed in placenta, clone IMAGE:139776.																														---	---	---	---
DOPEY2	9980	broad.mit.edu	37	21	37571346	37571346	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:37571346delT	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	37606150	37606151	+	Intron	INS	-	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:37606150_37606151insT	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	37629063	37629064	+	Intron	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:37629063_37629064delAA	uc002yvg.2	+						DOPEY2_uc011aeb.1_Intron|DOPEY2_uc002yvh.2_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	37660989	37660990	+	Intron	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:37660989_37660990delAA	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																		---	---	---	---
CLDN14	23562	broad.mit.edu	37	21	37833060	37833060	+	3'UTR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:37833060delT	uc002yvk.1	-	2					CLDN14_uc002yvn.1_3'UTR|CLDN14_uc002yvo.1_3'UTR|CLDN14_uc002yvl.1_3'UTR|CLDN14_uc002yvm.1_3'UTR	NM_012130	NP_036262			claudin 14						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																		---	---	---	---
Unknown	0	broad.mit.edu	37	21	37955740	37955740	+	IGR	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:37955740delG								CLDN14 (6873 upstream) : SIM2 (116251 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	21	38023463	38023464	+	IGR	INS	-	TCCA	TCCA			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:38023463_38023464insTCCA								CLDN14 (74596 upstream) : SIM2 (48527 downstream)																																			---	---	---	---
SIM2	6493	broad.mit.edu	37	21	38114303	38114303	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:38114303delT	uc002yvr.2	+						SIM2_uc002yvq.2_Intron	NM_005069	NP_005060			single-minded homolog 2 long isoform						cell differentiation|nervous system development	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|signal transducer activity			central_nervous_system(1)	1																		---	---	---	---
HLCS	3141	broad.mit.edu	37	21	38205340	38205343	+	Intron	DEL	TTTT	-	-	rs113372337		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:38205340_38205343delTTTT	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	38555250	38555250	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:38555250delA	uc002yvz.2	+						TTC3_uc002ywa.2_Intron|TTC3_uc002ywb.2_Intron|TTC3_uc010gnf.2_Intron|TTC3_uc002ywc.2_Intron|TTC3_uc002ywd.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)																---	---	---	---
Unknown	0	broad.mit.edu	37	21	38989400	38989401	+	IGR	INS	-	TCTA	TCTA	rs142454858	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:38989400_38989401insTCTA								DYRK1A (101722 upstream) : KCNJ6 (7385 downstream)																																			---	---	---	---
KCNJ6	3763	broad.mit.edu	37	21	39006599	39006599	+	Intron	DEL	C	-	-	rs138586823		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:39006599delC	uc011aej.1	-						KCNJ6_uc002ywo.2_Intron	NM_002240	NP_002231			potassium inwardly-rectifying channel J6						synaptic transmission	Golgi apparatus|voltage-gated potassium channel complex	G-protein activated inward rectifier potassium channel activity|protein binding			skin(1)	1					Halothane(DB01159)													---	---	---	---
Unknown	0	broad.mit.edu	37	21	39384168	39384168	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:39384168delT								KCNJ6 (95472 upstream) : DSCR4 (42146 downstream)																																			---	---	---	---
DSCR4	10281	broad.mit.edu	37	21	39472222	39472222	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:39472222delA	uc002ywp.2	-							NM_005867	NP_005858			Down syndrome critical region protein 4											ovary(1)	1																		---	---	---	---
KCNJ15	3772	broad.mit.edu	37	21	39667470	39667470	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:39667470delT	uc002ywv.2	+						KCNJ15_uc002yww.2_Intron|KCNJ15_uc002ywx.2_Intron	NM_002243	NP_002234			potassium inwardly-rectifying channel J15						synaptic transmission	integral to plasma membrane	inward rectifier potassium channel activity			ovary(2)|skin(2)|breast(1)|central_nervous_system(1)	6																		---	---	---	---
Unknown	0	broad.mit.edu	37	21	40384785	40384786	+	IGR	DEL	CA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:40384785_40384786delCA								ETS2 (187909 upstream) : PSMG1 (162604 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	21	40525380	40525380	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:40525380delA								ETS2 (328504 upstream) : PSMG1 (22010 downstream)																																			---	---	---	---
BRWD1	54014	broad.mit.edu	37	21	40590392	40590393	+	Intron	INS	-	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:40590392_40590393insA	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	40630644	40630645	+	Intron	INS	-	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:40630644_40630645insA	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)																---	---	---	---
Unknown	0	broad.mit.edu	37	21	41039438	41039439	+	IGR	DEL	TG	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:41039438_41039439delTG								B3GALT5 (4623 upstream) : IGSF5 (77895 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	21	41306514	41306514	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:41306514delA								PCP4 (5194 upstream) : DSCAM (77829 downstream)																																			---	---	---	---
DSCAM	1826	broad.mit.edu	37	21	41789760	41789760	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:41789760delA	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	41910227	41910228	+	Intron	INS	-	A	A	rs148481369	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:41910227_41910228insA	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	42011836	42011836	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:42011836delA	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	42053997	42053997	+	Intron	DEL	T	-	-	rs77359915		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:42053997delT	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	42229104	42229107	+	IGR	DEL	ACAC	-	-	rs72325967		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:42229104_42229107delACAC								DSCAM (10065 upstream) : C21orf130 (284320 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	21	42666452	42666453	+	IGR	INS	-	TG	TG			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:42666452_42666453insTG								BACE2 (17929 upstream) : FAM3B (9724 downstream)																																			---	---	---	---
MX2	4600	broad.mit.edu	37	21	42780024	42780024	+	Frame_Shift_Del	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:42780024delA	uc002yzf.1	+	14	2116	c.2012delA	c.(2011-2013)GAAfs	p.E671fs	MX2_uc002yzg.1_Frame_Shift_Del_p.E394fs|MX2_uc010gop.1_Frame_Shift_Del_p.E153fs	NM_002463	NP_002454	P20592	MX2_HUMAN	myxovirus resistance protein 2	671	GED.				response to virus|type I interferon-mediated signaling pathway	cytoplasm|nucleus	GTP binding|GTPase activity			ovary(2)	2		Prostate(19;1.57e-07)|all_epithelial(19;0.0222)																---	---	---	---
MX1	4599	broad.mit.edu	37	21	42814056	42814056	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:42814056delA	uc002yzh.2	+						MX1_uc002yzi.2_Intron|MX1_uc010goq.2_Intron	NM_001144925	NP_001138397			myxovirus resistance protein 1						induction of apoptosis|response to virus|type I interferon-mediated signaling pathway	cytosol	GTP binding|GTPase activity|protein binding			ovary(1)	1		Prostate(19;3.18e-07)|all_epithelial(19;0.0277)																---	---	---	---
Unknown	0	broad.mit.edu	37	21	43154974	43154975	+	IGR	DEL	TT	-	-	rs113818525		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:43154974_43154975delTT								NCRNA00112 (17233 upstream) : RIPK4 (4554 downstream)																																			---	---	---	---
PRDM15	63977	broad.mit.edu	37	21	43258311	43258311	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:43258311delA	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																		---	---	---	---
Unknown	0	broad.mit.edu	37	21	43389636	43389636	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:43389636delT								C2CD2 (15637 upstream) : ZNF295 (17305 downstream)																																			---	---	---	---
UMODL1	89766	broad.mit.edu	37	21	43541382	43541382	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:43541382delT	uc002zaf.1	+						UMODL1_uc002zad.1_Intron|UMODL1_uc002zae.1_Intron|UMODL1_uc002zag.1_Intron|UMODL1_uc002zal.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																		---	---	---	---
Unknown	0	broad.mit.edu	37	21	43766375	43766376	+	IGR	DEL	AC	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:43766375_43766376delAC								TFF3 (30669 upstream) : TFF2 (93 downstream)																																			---	---	---	---
CBS	875	broad.mit.edu	37	21	44476001	44476002	+	Intron	DEL	TT	-	-	rs79861734		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:44476001_44476002delTT	uc002zcu.2	-						CBS_uc002zcs.1_Intron|CBS_uc002zct.2_Intron|CBS_uc002zcw.3_Intron|CBS_uc002zcv.2_Intron|CBS_uc002zcx.2_3'UTR	NM_000071	NP_000062			cystathionine-beta-synthase						cysteine biosynthetic process from serine|cysteine biosynthetic process via cystathionine|homocysteine catabolic process|hydrogen sulfide biosynthetic process|L-cysteine catabolic process|L-serine catabolic process	cytosol|nucleolus	cystathionine beta-synthase activity|heme binding|protein homodimerization activity|pyridoxal phosphate binding|ubiquitin protein ligase binding				0					L-Cysteine(DB00151)|L-Serine(DB00133)|Pyridoxal Phosphate(DB00114)|Pyridoxine(DB00165)|S-Adenosylmethionine(DB00118)													---	---	---	---
CRYAA	1409	broad.mit.edu	37	21	44589263	44589263	+	Frame_Shift_Del	DEL	C	-	-	rs61729442	byFrequency;by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:44589263delC	uc002zdd.1	+	1	123	c.54delC	c.(52-54)TACfs	p.Y18fs		NM_000394	NP_000385	P02489	CRYAA_HUMAN	crystallin, alpha A	18		Susceptible to oxidation.			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																		---	---	---	---
C21orf84	114038	broad.mit.edu	37	21	44895730	44895730	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:44895730delA	uc002zdh.1	-							NR_026863				Homo sapiens C21orf84 protein (C21orf84) mRNA, complete cds.												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	21	45117597	45117598	+	IGR	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:45117597_45117598delAA								RRP1B (1639 upstream) : PDXK (21380 downstream)																																			---	---	---	---
PDXK	8566	broad.mit.edu	37	21	45163445	45163445	+	Intron	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:45163445delC	uc002zdm.3	+						PDXK_uc010gpj.2_Intron|PDXK_uc002zdn.3_Intron|PDXK_uc002zdq.3_Intron	NM_003681	NP_003672			pyridoxal kinase						cell proliferation|pyridoxal 5'-phosphate salvage	cytosol	ATP binding|lithium ion binding|magnesium ion binding|potassium ion binding|protein homodimerization activity|pyridoxal kinase activity|pyridoxal phosphate binding|sodium ion binding|zinc ion binding				0				Colorectal(79;0.109)|READ - Rectum adenocarcinoma(84;0.161)|STAD - Stomach adenocarcinoma(101;0.18)	Pyridoxal(DB00147)|Pyridoxine(DB00165)													---	---	---	---
Unknown	0	broad.mit.edu	37	21	45426680	45426680	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:45426680delA								AGPAT3 (19206 upstream) : TRAPPC10 (5526 downstream)																																			---	---	---	---
TRAPPC10	7109	broad.mit.edu	37	21	45437619	45437619	+	Intron	DEL	T	-	-	rs76982460		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:45437619delT	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																		---	---	---	---
PFKL	5211	broad.mit.edu	37	21	45725486	45725486	+	Intron	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:45725486delC	uc002zel.2	+						PFKL_uc002zek.2_Intron|PFKL_uc011afd.1_Intron	NM_002626	NP_002617			liver phosphofructokinase						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)												OREG0026250	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
TRPM2	7226	broad.mit.edu	37	21	45783127	45783127	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:45783127delT	uc002zet.1	+						TRPM2_uc002zeu.1_Intron|TRPM2_uc002zew.1_Intron|TRPM2_uc010gpt.1_Intron	NM_003307	NP_003298			transient receptor potential cation channel,							integral to plasma membrane	ADP-ribose diphosphatase activity|calcium channel activity|sodium channel activity			ovary(1)|central_nervous_system(1)|pancreas(1)	3																		---	---	---	---
TRPM2	7226	broad.mit.edu	37	21	45819251	45819251	+	Frame_Shift_Del	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:45819251delG	uc002zet.1	+	15	2348	c.2135delG	c.(2134-2136)TGGfs	p.W712fs	TRPM2_uc002zeu.1_Frame_Shift_Del_p.W712fs|TRPM2_uc002zew.1_Frame_Shift_Del_p.W712fs|TRPM2_uc010gpt.1_Frame_Shift_Del_p.W712fs|TRPM2_uc002zex.1_Frame_Shift_Del_p.W498fs|TRPM2_uc002zey.1_Frame_Shift_Del_p.W225fs	NM_003307	NP_003298	O94759	TRPM2_HUMAN	transient receptor potential cation channel,	712	Cytoplasmic (Potential).					integral to plasma membrane	ADP-ribose diphosphatase activity|calcium channel activity|sodium channel activity			ovary(1)|central_nervous_system(1)|pancreas(1)	3																		---	---	---	---
PTTG1IP	754	broad.mit.edu	37	21	46280730	46280730	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:46280730delT	uc002zgb.1	-						PTTG1IP_uc011afj.1_Intron|PTTG1IP_uc011afk.1_Intron	NM_004339	NP_004330			pituitary tumor-transforming gene 1						protein import into nucleus	cytoplasm|integral to membrane|nucleus				ovary(1)	1				Colorectal(79;0.0659)														---	---	---	---
C21orf70	85395	broad.mit.edu	37	21	46361370	46361371	+	Intron	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:46361370_46361371delTT	uc002zgl.2	+						C21orf67_uc011afm.1_5'Flank|C21orf67_uc002zgj.3_5'Flank|C21orf67_uc002zgk.3_5'Flank|C21orf70_uc002zgm.2_Intron	NM_058190	NP_478070			hypothetical protein LOC85395												0				Colorectal(79;0.248)														---	---	---	---
ADARB1	104	broad.mit.edu	37	21	46596876	46596876	+	Intron	DEL	C	-	-	rs10713294		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:46596876delC	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	46764604	46764604	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:46764604delA								LOC642852 (47336 upstream) : COL18A1 (60493 downstream)																																			---	---	---	---
SLC19A1	6573	broad.mit.edu	37	21	46947149	46947149	+	Intron	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:46947149delG	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	47263044	47263044	+	Intron	DEL	T	-	-	rs141356928		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:47263044delT	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	47301013	47301013	+	Intron	DEL	T	-	-	rs141878412	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:47301013delT	uc002zhq.1	+						PCBP3_uc010gqb.2_Intron|PCBP3_uc002zhp.1_Intron|PCBP3_uc010gqc.1_Intron|PCBP3_uc002zhs.1_Intron|PCBP3_uc002zhr.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	47445668	47445668	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:47445668delT								COL6A1 (20705 upstream) : COL6A2 (72365 downstream)																																			---	---	---	---
LSS	4047	broad.mit.edu	37	21	47609268	47609269	+	Intron	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:47609268_47609269delAA	uc002zij.2	-						LSS_uc011afv.1_3'UTR|LSS_uc002zil.2_3'UTR|LSS_uc002zik.2_3'UTR	NM_001001438	NP_001001438			lanosterol synthase isoform 1						cholesterol biosynthetic process	endoplasmic reticulum membrane	lanosterol synthase activity				0	Breast(49;0.214)																	---	---	---	---
MCM3AP	8888	broad.mit.edu	37	21	47683902	47683903	+	Intron	DEL	TG	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:47683902_47683903delTG	uc002zir.1	-						MCM3AP_uc002ziq.1_Intron	NM_003906	NP_003897			minichromosome maintenance complex component 3						DNA replication|protein import into nucleus	cytosol|nucleus	DNA binding|nucleotide binding			large_intestine(2)|lung(1)|ovary(1)|skin(1)	5	Breast(49;0.112)																	---	---	---	---
PCNT	5116	broad.mit.edu	37	21	47746590	47746590	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:47746590delT	uc002zji.3	+						PCNT_uc002zjj.2_Intron|C21orf58_uc011afx.1_5'Flank|C21orf58_uc002zjf.2_5'Flank|C21orf58_uc010gqj.1_5'Flank|C21orf58_uc002zjg.1_5'Flank	NM_006031	NP_006022			pericentrin						cilium assembly|G2/M transition of mitotic cell cycle	cytosol|microtubule	calmodulin binding			ovary(4)|breast(2)|pancreas(2)	8	Breast(49;0.112)																	---	---	---	---
DIP2A	23181	broad.mit.edu	37	21	47976820	47976820	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:47976820delT	uc002zjo.2	+						DIP2A_uc011afz.1_Intron|DIP2A_uc002zjr.2_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)														---	---	---	---
Unknown	0	broad.mit.edu	37	22	16419352	16419352	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:16419352delT								POTEH (131415 upstream) : OR11H1 (29474 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	22	16920274	16920275	+	IGR	DEL	AT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:16920274_16920275delAT								OR11H1 (470470 upstream) : CCT8L2 (151373 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	22	17021742	17021742	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:17021742delA								OR11H1 (571938 upstream) : CCT8L2 (49906 downstream)																																			---	---	---	---
GAB4	128954	broad.mit.edu	37	22	17444567	17444567	+	Intron	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:17444567delC	uc002zlw.2	-							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)																---	---	---	---
CECR7	100130418	broad.mit.edu	37	22	17528434	17528434	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:17528434delT	uc002zlx.1	+							NR_015352				Homo sapiens cDNA FLJ40726 fis, clone TKIDN1000164.												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	22	17548246	17548249	+	IGR	DEL	AAAA	-	-	rs71825697		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:17548246_17548249delAAAA								CECR7 (8564 upstream) : IL17RA (17600 downstream)																																			---	---	---	---
CECR1	51816	broad.mit.edu	37	22	17694046	17694046	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:17694046delA	uc010gqu.1	-						CECR1_uc011agi.1_Intron|CECR1_uc011agj.1_Intron	NM_017424	NP_059120			cat eye syndrome critical region protein 1						adenosine catabolic process|hypoxanthine salvage|inosine biosynthetic process|multicellular organismal development|purine ribonucleoside monophosphate biosynthetic process	extracellular space|Golgi apparatus	adenosine deaminase activity|adenosine receptor binding|growth factor activity|heparin binding|protein homodimerization activity|proteoglycan binding|zinc ion binding			ovary(1)	1		all_epithelial(15;0.0152)|Lung NSC(13;0.0875)|all_lung(157;0.106)																---	---	---	---
BCL2L13	23786	broad.mit.edu	37	22	18112585	18112586	+	Intron	DEL	AC	-	-	rs112377267		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:18112585_18112586delAC	uc002zmu.2	+						ATP6V1E1_uc002zmr.1_5'Flank|ATP6V1E1_uc002zms.1_5'Flank|ATP6V1E1_uc002zmt.1_5'Flank	NM_015367	NP_056182			BCL2-like 13 (apoptosis facilitator)						induction of apoptosis	integral to membrane|mitochondrial membrane|nucleus	caspase activator activity			ovary(1)|lung(1)|central_nervous_system(1)|skin(1)	4		all_epithelial(15;0.123)		Lung(27;0.199)														---	---	---	---
MICAL3	57553	broad.mit.edu	37	22	18477501	18477501	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:18477501delA	uc002zng.3	-						MICAL3_uc002znh.2_Intron|MICAL3_uc002znl.1_Intron|MICAL3_uc010grf.2_Intron|MICAL3_uc011agm.1_Intron	NM_015241	NP_056056			microtubule associated monoxygenase, calponin							cytoplasm|cytoskeleton	monooxygenase activity|zinc ion binding				0		all_epithelial(15;0.198)		Lung(27;0.0427)														---	---	---	---
CLTCL1	8218	broad.mit.edu	37	22	19246388	19246388	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:19246388delA	uc002zpb.2	-						CLTCL1_uc011agv.1_Intron|CLTCL1_uc011agw.1_Intron	NM_007098	NP_009029			clathrin, heavy polypeptide-like 1 isoform 1						anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis	clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network	protein binding|signal transducer activity|structural molecule activity			ovary(4)|central_nervous_system(1)	5	Colorectal(54;0.0993)							T	?	ALCL								---	---	---	---
HIRA	7290	broad.mit.edu	37	22	19421294	19421294	+	5'Flank	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:19421294delT	uc002zpf.1	-						HIRA_uc011agx.1_5'Flank|HIRA_uc010grn.1_5'Flank|HIRA_uc010gro.1_Intron|HIRA_uc010grp.2_Intron|MRPL40_uc002zpg.2_Intron|MRPL40_uc002zph.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	19424345	19424345	+	Intron	DEL	A	-	-	rs68015924		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:19424345delA	uc010gro.1	-						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)																	---	---	---	---
Unknown	0	broad.mit.edu	37	22	19589247	19589247	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:19589247delT								LOC150185 (34885 upstream) : SEPT5 (112740 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	22	19688548	19688549	+	IGR	INS	-	AGAAA	AGAAA	rs144491945	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:19688548_19688549insAGAAA								LOC150185 (134186 upstream) : SEPT5 (13438 downstream)																																			---	---	---	---
TBX1	6899	broad.mit.edu	37	22	19760153	19760153	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:19760153delT	uc002zqb.2	+						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)																---	---	---	---
TBX1	6899	broad.mit.edu	37	22	19769088	19769091	+	Intron	DEL	TATT	-	-	rs41298040		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:19769088_19769091delTATT	uc002zqc.2	+							NM_005992	NP_005983			T-box 1 isoform B						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)																---	---	---	---
C22orf25	128989	broad.mit.edu	37	22	20045553	20045554	+	Intron	INS	-	A	A	rs142445559		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:20045553_20045554insA	uc010grw.1	+						C22orf25_uc002zrb.1_Intron|C22orf25_uc002zrc.1_Intron|C22orf25_uc002zrd.1_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|C22orf25_uc010gry.1_Intron|C22orf25_uc002zrh.1_Intron	NM_152906	NP_690870			hypothetical protein LOC128989												0	Colorectal(54;0.0533)																	---	---	---	---
DGCR8	54487	broad.mit.edu	37	22	20087600	20087600	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:20087600delT	uc002zri.2	+						DGCR8_uc010grz.2_Intron|DGCR8_uc002zrj.2_Intron	NM_022720	NP_073557			DiGeorge syndrome critical region gene 8						primary miRNA processing	cytoplasm|cytoplasm|microtubule cytoskeleton|nucleolus|nucleoplasm	double-stranded RNA binding|metal ion binding|protein binding				0	Colorectal(54;0.0993)																	---	---	---	---
SCARF2	91179	broad.mit.edu	37	22	20781214	20781214	+	Intron	DEL	A	-	-	rs75169814		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:20781214delA	uc002zsj.1	-						SCARF2_uc002zsk.1_Intron	NM_153334	NP_699165			scavenger receptor class F, member 2 isoform 1						cell adhesion	integral to membrane	protein binding|receptor activity			breast(1)	1	Melanoma(16;0.000465)|Ovarian(15;0.00167)|Colorectal(54;0.0221)|all_neural(72;0.219)	Lung SC(17;0.0262)	LUSC - Lung squamous cell carcinoma(15;0.00102)|Lung(15;0.0173)															---	---	---	---
SCARF2	91179	broad.mit.edu	37	22	20781411	20781411	+	Intron	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:20781411delC	uc002zsj.1	-						SCARF2_uc002zsk.1_Intron	NM_153334	NP_699165			scavenger receptor class F, member 2 isoform 1						cell adhesion	integral to membrane	protein binding|receptor activity			breast(1)	1	Melanoma(16;0.000465)|Ovarian(15;0.00167)|Colorectal(54;0.0221)|all_neural(72;0.219)	Lung SC(17;0.0262)	LUSC - Lung squamous cell carcinoma(15;0.00102)|Lung(15;0.0173)															---	---	---	---
KLHL22	84861	broad.mit.edu	37	22	20822952	20822953	+	Intron	INS	-	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:20822952_20822953insT	uc002zsl.1	-						KLHL22_uc011ahr.1_Intron|KLHL22_uc002zsm.1_Intron	NM_032775	NP_116164			kelch-like						cell division	Cul3-RING ubiquitin ligase complex				lung(1)	1	Melanoma(16;0.000465)|Ovarian(15;0.00167)|Colorectal(54;0.0221)|all_neural(72;0.142)	Lung SC(17;0.0262)	LUSC - Lung squamous cell carcinoma(15;0.00102)|Lung(15;0.0173)															---	---	---	---
PI4KA	5297	broad.mit.edu	37	22	21189421	21189421	+	Intron	DEL	T	-	-	rs112694123		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:21189421delT	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)															---	---	---	---
PI4KA	5297	broad.mit.edu	37	22	21208717	21208717	+	Intron	DEL	T	-	-	rs79413619		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:21208717delT	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	21244556	21244557	+	3'UTR	INS	-	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:21244556_21244557insA	uc011ahw.1	+	5						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	21963192	21963192	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:21963192delT	uc002zva.1	+						UBE2L3_uc011aig.1_Intron|UBE2L3_uc002zuz.1_Intron|UBE2L3_uc010gti.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	22347716	22347716	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:22347716delA	uc002zvu.2	-											Homo sapiens cDNA FLJ16327 fis, clone SYNOV1000256, weakly  similar to Human preferentially expressed antigen of melanoma (PRAME) mRNA.																														---	---	---	---
LOC96610	96610	broad.mit.edu	37	22	22554617	22554617	+	Intron	DEL	T	-	-	rs34093423		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:22554617delT	uc011aim.1	+											Parts of antibodies, mostly variable regions.												0																		---	---	---	---
LOC96610	96610	broad.mit.edu	37	22	23206609	23206609	+	Intron	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:23206609delG	uc011aim.1	+											Parts of antibodies, mostly variable regions.												0																		---	---	---	---
LOC96610	96610	broad.mit.edu	37	22	23238030	23238030	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:23238030delT	uc011aim.1	+						uc002zws.2_Intron					Parts of antibodies, mostly variable regions.												0																		---	---	---	---
RAB36	9609	broad.mit.edu	37	22	23496568	23496568	+	Intron	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:23496568delC	uc002zwv.1	+						RAB36_uc010gtw.1_Intron	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)														---	---	---	---
RAB36	9609	broad.mit.edu	37	22	23500611	23500611	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:23500611delA	uc002zwv.1	+						RAB36_uc010gtw.1_Intron	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	23615254	23615255	+	Intron	DEL	CT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:23615254_23615255delCT	uc002zww.2	+						BCR_uc002zwx.2_Intron|BCR_uc011aiy.1_Intron|BCR_uc010gtx.1_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	23712779	23712779	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:23712779delA								BCR (52556 upstream) : ZDHHC8P1 (20014 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	22	23714092	23714092	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:23714092delA								BCR (53869 upstream) : ZDHHC8P1 (18701 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	22	23793932	23793932	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:23793932delA								ZDHHC8P1 (49133 upstream) : IGLL1 (121383 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	22	23892382	23892384	+	IGR	DEL	CTC	-	-	rs57083156		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:23892382_23892384delCTC								ZDHHC8P1 (147583 upstream) : IGLL1 (22931 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	22	24064407	24064407	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:24064407delA								LOC91316 (4797 upstream) : ZNF70 (16463 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	22	24595359	24595360	+	IGR	DEL	TT	-	-	rs113948438		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:24595359_24595360delTT								SUSD2 (10285 upstream) : GGT5 (20263 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	22	24614987	24614988	+	IGR	DEL	AA	-	-	rs111267378		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:24614987_24614988delAA								SUSD2 (29913 upstream) : GGT5 (635 downstream)																																			---	---	---	---
CYTSA	23384	broad.mit.edu	37	22	24725772	24725772	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:24725772delT	uc002zzw.2	+						CYTSA_uc002zzv.3_Intron|CYTSA_uc011ajq.1_Intron	NM_015330	NP_056145			cytospin A						cell cycle|cell division						0																		---	---	---	---
CYTSA	23384	broad.mit.edu	37	22	24806146	24806146	+	Intron	DEL	G	-	-	rs115288288	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:24806146delG	uc002zzw.2	+						CYTSA_uc002zzv.3_Intron|CYTSA_uc011ajq.1_Intron	NM_015330	NP_056145			cytospin A						cell cycle|cell division						0																		---	---	---	---
Unknown	0	broad.mit.edu	37	22	25060625	25060625	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:25060625delT								POM121L10P (5511 upstream) : PIWIL3 (54376 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	22	25676911	25676911	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:25676911delA								CRYBB2 (49075 upstream) : IGLL3 (36977 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	22	25724572	25724572	+	IGR	DEL	T	-	-	rs113290048		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:25724572delT								IGLL3 (8381 upstream) : LRP5L (22814 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	22	25838268	25838270	+	IGR	DEL	TTT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:25838268_25838270delTTT								LRP5L (60724 upstream) : ADRBK2 (122591 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	22	25843810	25843811	+	5'Flank	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:25843810_25843811delAA	uc003abt.2	+						uc003abu.2_5'Flank					Homo sapiens cDNA clone IMAGE:3542716, partial cds.																														---	---	---	---
MYO18B	84700	broad.mit.edu	37	22	26359076	26359077	+	Intron	DEL	TC	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:26359076_26359077delTC	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																		---	---	---	---
MYO18B	84700	broad.mit.edu	37	22	26368938	26368944	+	Intron	DEL	AAAAAAG	-	-	rs71723499		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:26368938_26368944delAAAAAAG	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																		---	---	---	---
MYO18B	84700	broad.mit.edu	37	22	26397046	26397046	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:26397046delT	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																		---	---	---	---
SEZ6L	23544	broad.mit.edu	37	22	26567475	26567475	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:26567475delA	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																		---	---	---	---
SEZ6L	23544	broad.mit.edu	37	22	26649402	26649402	+	Intron	DEL	C	-	-	rs67702930		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:26649402delC	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																		---	---	---	---
SEZ6L	23544	broad.mit.edu	37	22	26692088	26692089	+	Intron	DEL	AC	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:26692088_26692089delAC	uc003acb.2	+						SEZ6L_uc003acc.2_Intron|SEZ6L_uc011akc.1_Intron|SEZ6L_uc003acd.2_Intron|SEZ6L_uc011akd.1_Intron|SEZ6L_uc003ace.2_Intron|SEZ6L_uc003acf.1_Intron|SEZ6L_uc010gvc.1_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																		---	---	---	---
SEZ6L	23544	broad.mit.edu	37	22	26736199	26736200	+	Intron	INS	-	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:26736199_26736200insA	uc003acb.2	+						SEZ6L_uc003acc.2_Intron|SEZ6L_uc011akc.1_Intron|SEZ6L_uc003acd.2_Intron|SEZ6L_uc011akd.1_Intron|SEZ6L_uc003ace.2_Intron|SEZ6L_uc003acf.1_Intron|SEZ6L_uc010gvc.1_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																		---	---	---	---
Unknown	0	broad.mit.edu	37	22	27189389	27189389	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:27189389delT								MIAT (74440 upstream) : MN1 (954877 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	22	27213011	27213011	+	IGR	DEL	T	-	-	rs142131790		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:27213011delT								MIAT (98062 upstream) : MN1 (931255 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	22	27352841	27352841	+	IGR	DEL	T	-	-	rs66688813		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:27352841delT								MIAT (237892 upstream) : MN1 (791425 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	22	27509610	27509610	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:27509610delT								MIAT (394661 upstream) : MN1 (634656 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	22	28021638	28021638	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:28021638delT								MIAT (906689 upstream) : MN1 (122628 downstream)																																			---	---	---	---
TTC28	23331	broad.mit.edu	37	22	28838104	28838104	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:28838104delT	uc003adp.3	-							NM_001145418	NP_001138890			tetratricopeptide repeat domain 28								binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	22	29211107	29211107	+	IGR	DEL	T	-	-	rs144220518	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:29211107delT								XBP1 (14547 upstream) : ZNRF3 (68783 downstream)																																			---	---	---	---
ZNRF3	84133	broad.mit.edu	37	22	29300074	29300075	+	Intron	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:29300074_29300075delAA	uc003aeg.2	+							NM_032173	NP_115549			zinc and ring finger 3							integral to membrane	zinc ion binding			ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	22	29454246	29454246	+	IGR	DEL	A	-	-	rs112508764		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:29454246delA								ZNRF3 (771 upstream) : C22orf31 (414 downstream)																																			---	---	---	---
KREMEN1	83999	broad.mit.edu	37	22	29549958	29549959	+	Intron	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:29549958_29549959delAA	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																		---	---	---	---
EWSR1	2130	broad.mit.edu	37	22	29687622	29687622	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:29687622delA	uc003aet.2	+						EWSR1_uc003aev.2_Intron|EWSR1_uc003aew.2_Intron|EWSR1_uc003aex.2_Intron|EWSR1_uc003aey.2_Intron|EWSR1_uc003aez.2_5'UTR	NM_005243	NP_005234			Ewing sarcoma breakpoint region 1 isoform 2						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								---	---	---	---
AP1B1	162	broad.mit.edu	37	22	29741057	29741057	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:29741057delT	uc003afj.2	-						AP1B1_uc003afi.2_Intron|AP1B1_uc003afk.2_Intron|AP1B1_uc003afl.2_Intron|AP1B1_uc011ako.1_Intron	NM_001127	NP_001118			adaptor-related protein complex 1 beta 1 subunit						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	protein binding|protein transporter activity			ovary(1)|skin(1)	2																		---	---	---	---
RFPL1	5988	broad.mit.edu	37	22	29835329	29835329	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:29835329delA	uc003afn.2	+						RFPL1S_uc003afm.1_RNA	NM_021026	NP_066306			ret finger protein-like 1								zinc ion binding				0																		---	---	---	---
THOC5	8563	broad.mit.edu	37	22	29938753	29938753	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:29938753delA	uc003afr.2	-						THOC5_uc003afs.2_Intron|THOC5_uc003aft.2_Intron|THOC5_uc003afu.2_Intron|THOC5_uc010gvo.2_Intron|THOC5_uc003afv.1_Intron|THOC5_uc003afw.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																		---	---	---	---
NF2	4771	broad.mit.edu	37	22	30038626	30038627	+	Intron	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:30038626_30038627delTT	uc003age.3	+						NF2_uc003afy.3_Intron|NF2_uc003afz.3_Intron|NF2_uc003agf.3_Intron|NF2_uc003agb.3_Intron|NF2_uc003agc.3_Intron|NF2_uc003agd.3_Intron|NF2_uc003agg.3_Intron|NF2_uc003aga.3_Intron|NF2_uc003agh.3_Intron|NF2_uc003agi.3_Intron|NF2_uc003agj.3_Intron|NF2_uc003agk.3_Intron	NM_000268	NP_000259			neurofibromin 2 isoform 1						actin cytoskeleton organization|negative regulation of cell migration|negative regulation of cell proliferation|negative regulation of cell-cell adhesion|negative regulation of cell-matrix adhesion|negative regulation of DNA replication|negative regulation of tyrosine phosphorylation of Stat3 protein|negative regulation of tyrosine phosphorylation of Stat5 protein|positive regulation of stress fiber assembly|regulation of hippo signaling cascade|Schwann cell proliferation	cytoskeleton|early endosome|extrinsic to membrane|filopodium membrane|nucleolus|perinuclear region of cytoplasm|ruffle membrane	cytoskeletal protein binding|protein binding			meninges(372)|soft_tissue(284)|central_nervous_system(20)|kidney(10)|pleura(9)|skin(7)|large_intestine(5)|breast(5)|urinary_tract(3)|thyroid(2)|endometrium(2)|ovary(2)|lung(2)|stomach(2)|bone(2)|pituitary(1)	728								D|Mis|N|F|S|O		meningioma|acoustic neuroma|renal 	meningioma|acoustic neuroma			Neurofibromatosis_type_2				---	---	---	---
Unknown	0	broad.mit.edu	37	22	30180154	30180154	+	IGR	DEL	T	-	-	rs66907006		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:30180154delT								UQCR10 (13752 upstream) : ASCC2 (4449 downstream)																																			---	---	---	---
ASCC2	84164	broad.mit.edu	37	22	30232559	30232559	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:30232559delT	uc003agr.2	-						ASCC2_uc003ags.2_Intron|ASCC2_uc003agt.2_Intron|ASCC2_uc011akr.1_Intron	NM_032204	NP_115580			activating signal cointegrator 1 complex subunit						regulation of transcription, DNA-dependent|transcription, DNA-dependent						0			OV - Ovarian serous cystadenocarcinoma(5;0.000103)|Epithelial(10;0.0169)|all cancers(5;0.0259)															---	---	---	---
Unknown	0	broad.mit.edu	37	22	30655500	30655500	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:30655500delA								LIF (12704 upstream) : OSM (3321 downstream)																																			---	---	---	---
SEC14L2	23541	broad.mit.edu	37	22	30795503	30795511	+	Intron	DEL	AAAAAAAAA	-	-	rs67636496		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:30795503_30795511delAAAAAAAAA	uc003ahr.2	+						SEC14L2_uc003ahq.2_Intron|SEC14L2_uc011akx.1_Intron|SEC14L2_uc003ahs.2_Intron|SEC14L2_uc011aky.1_Intron	NM_012429	NP_036561			SEC14-like 2 isoform 1						positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	integral to membrane|nucleus	phospholipid binding|transporter activity|vitamin E binding				0					Vitamin E(DB00163)													---	---	---	---
MORC2	22880	broad.mit.edu	37	22	31329912	31329912	+	Intron	DEL	G	-	-	rs71740454		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-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																		---	---	---	---
MORC2	22880	broad.mit.edu	37	22	31358194	31358196	+	Intron	DEL	AAA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:31358194_31358196delAAA	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	31752219	31752219	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:31752219delT								PATZ1 (9970 upstream) : DRG1 (43320 downstream)																																			---	---	---	---
PISD	23761	broad.mit.edu	37	22	32034441	32034442	+	Intron	INS	-	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:32034441_32034442insG	uc003alm.3	-						PISD_uc011alr.1_5'UTR|PISD_uc003aln.3_Intron	NM_014338	NP_055153			phosphatidylserine decarboxylase						phospholipid biosynthetic process	mitochondrion	phosphatidylserine decarboxylase activity			central_nervous_system(2)|ovary(1)	3					Phosphatidylserine(DB00144)													---	---	---	---
Unknown	0	broad.mit.edu	37	22	32061604	32061604	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:32061604delA								PISD (3403 upstream) : C22orf30 (10638 downstream)																																			---	---	---	---
C22orf30	253143	broad.mit.edu	37	22	32109175	32109176	+	Frame_Shift_Ins	INS	-	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:32109175_32109176insA	uc003alp.3	-	4	4842_4843	c.4649_4650insT	c.(4648-4650)TTAfs	p.L1550fs	C22orf30_uc003alo.1_Frame_Shift_Ins_p.L1349fs|C22orf30_uc010gwj.1_Frame_Shift_Ins_p.L1349fs	NM_173566	NP_775837	Q5THK1	PR14L_HUMAN	hypothetical protein LOC253143	1550											0																OREG0003533	type=REGULATORY REGION|Gene=BC040859|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay	---	---	---	---
DEPDC5	9681	broad.mit.edu	37	22	32205968	32205968	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:32205968delA	uc003als.2	+						DEPDC5_uc011als.1_Intron|DEPDC5_uc011alu.1_Intron|DEPDC5_uc011alv.1_Intron|DEPDC5_uc003alt.2_Intron|DEPDC5_uc003alr.1_Intron|DEPDC5_uc011alt.1_Intron	NM_014662	NP_055477			DEP domain containing 5 isoform 1						intracellular signal transduction					ovary(4)|central_nervous_system(3)|pancreas(1)	8																		---	---	---	---
C22orf24	25775	broad.mit.edu	37	22	32331017	32331020	+	Intron	DEL	GGAA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:32331017_32331020delGGAA	uc003aly.2	-						C22orf24_uc003alx.2_Intron	NM_015372	NP_056187			hypothetical protein LOC25775							integral to membrane				central_nervous_system(1)	1																		---	---	---	---
C22orf24	25775	broad.mit.edu	37	22	32333385	32333385	+	Intron	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:32333385delG	uc003aly.2	-						C22orf24_uc003alx.2_Intron	NM_015372	NP_056187			hypothetical protein LOC25775							integral to membrane				central_nervous_system(1)	1																		---	---	---	---
SLC5A1	6523	broad.mit.edu	37	22	32481283	32481283	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:32481283delT	uc003amc.2	+						SLC5A1_uc011alz.1_Intron	NM_000343	NP_000334			solute carrier family 5 (sodium/glucose						carbohydrate metabolic process	integral to plasma membrane	glucose:sodium symporter activity|protein binding			skin(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	22	32705642	32705643	+	IGR	DEL	AC	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:32705642_32705643delAC								SLC5A4 (54324 upstream) : RFPL3 (45229 downstream)																																			---	---	---	---
C22orf28	51493	broad.mit.edu	37	22	32794130	32794130	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:32794130delT	uc003amm.2	-						C22orf28_uc011ama.1_Intron	NM_014306	NP_055121			hypothetical protein LOC51493						cell-matrix adhesion|substrate adhesion-dependent cell spreading|tRNA splicing, via endonucleolytic cleavage and ligation	cytoplasm|tRNA-splicing ligase complex	ATP binding|metal ion binding|RNA ligase (ATP) activity|vinculin binding				0																		---	---	---	---
SYN3	8224	broad.mit.edu	37	22	33357305	33357306	+	Intron	DEL	TC	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:33357305_33357306delTC	uc003amx.2	-						SYN3_uc003amy.2_Intron|SYN3_uc003amz.2_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	33596168	33596168	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:33596168delA								SYN3 (141791 upstream) : LARGE (72895 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	22	33662137	33662137	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:33662137delA								SYN3 (207760 upstream) : LARGE (6926 downstream)																																			---	---	---	---
LARGE	9215	broad.mit.edu	37	22	33863026	33863027	+	Intron	INS	-	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:33863026_33863027insA	uc003and.3	-						LARGE_uc011amd.1_Intron|LARGE_uc003ane.3_Intron|LARGE_uc010gwp.2_Intron|LARGE_uc011ame.1_Intron|LARGE_uc011amf.1_Intron|LARGE_uc010gwq.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	34269967	34269968	+	Intron	DEL	CT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:34269967_34269968delCT	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	35018857	35018857	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:35018857delA								LARGE (700273 upstream) : ISX (443272 downstream)																																			---	---	---	---
ISX	91464	broad.mit.edu	37	22	35476430	35476431	+	Intron	INS	-	AC	AC	rs148108966	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:35476430_35476431insAC	uc003anj.2	+						ISX_uc011amg.1_Intron	NM_001008494	NP_001008494			intestine-specific homeobox							nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			ovary(3)|skin(2)	5																		---	---	---	---
TOM1	10043	broad.mit.edu	37	22	35739287	35739288	+	Intron	INS	-	AC	AC	rs142063849		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:35739287_35739288insAC	uc003ann.2	+						TOM1_uc011ami.1_Intron|TOM1_uc011amj.1_Intron|TOM1_uc003ans.2_Intron|TOM1_uc011amk.1_Intron|TOM1_uc003anp.2_Intron|TOM1_uc011aml.1_Intron|TOM1_uc003ano.2_Intron|TOM1_uc003anq.2_Intron|TOM1_uc003anr.2_Intron	NM_005488	NP_005479			target of myb1 isoform 1						endocytosis|endosome transport|intracellular protein transport	cytosol|early endosome|membrane	protein binding			ovary(1)	1																		---	---	---	---
RBM9	23543	broad.mit.edu	37	22	36263125	36263126	+	Intron	INS	-	CA	CA	rs139224464	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:36263125_36263126insCA	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	36691388	36691389	+	Intron	DEL	AG	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:36691388_36691389delAG	uc003apg.2	-							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	37025841	37025842	+	Intron	DEL	TC	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:37025841_37025842delTC	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	37244819	37244819	+	IGR	DEL	A	-	-	rs72334498		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:37244819delA								PVALB (29302 upstream) : NCF4 (12211 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	22	37620901	37620901	+	IGR	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:37620901delC								SSTR3 (12548 upstream) : RAC2 (411 downstream)																																			---	---	---	---
CYTH4	27128	broad.mit.edu	37	22	37691420	37691421	+	Intron	DEL	CA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:37691420_37691421delCA	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																		---	---	---	---
CYTH4	27128	broad.mit.edu	37	22	37694414	37694415	+	Intron	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:37694414_37694415delAA	uc003arf.2	+						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																		---	---	---	---
ELFN2	114794	broad.mit.edu	37	22	37808951	37808951	+	Intron	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:37808951delC	uc003asq.3	-							NM_052906	NP_443138			leucine rich repeat containing 62							cell surface|integral to membrane				upper_aerodigestive_tract(1)|ovary(1)	2	Melanoma(58;0.0574)																	---	---	---	---
CARD10	29775	broad.mit.edu	37	22	37901524	37901524	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:37901524delA	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)																	---	---	---	---
C22orf23	84645	broad.mit.edu	37	22	38343084	38343084	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:38343084delA	uc003auj.1	-						C22orf23_uc003auk.1_Intron	NM_032561	NP_115950			hypothetical protein LOC84645												0	Melanoma(58;0.045)																	---	---	---	---
C22orf23	84645	broad.mit.edu	37	22	38347219	38347219	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:38347219delA	uc003auj.1	-						C22orf23_uc003auk.1_Intron|POLR2F_uc010gxi.2_5'Flank|POLR2F_uc003aul.2_5'Flank|POLR2F_uc003aum.2_5'Flank	NM_032561	NP_115950			hypothetical protein LOC84645												0	Melanoma(58;0.045)																	---	---	---	---
Unknown	0	broad.mit.edu	37	22	38412669	38412669	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:38412669delT								POLR2F (28328 upstream) : PICK1 (40593 downstream)																																			---	---	---	---
TMEM184B	25829	broad.mit.edu	37	22	38646949	38646950	+	Intron	INS	-	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:38646949_38646950insT	uc003avf.1	-						TMEM184B_uc003avg.1_Intron|TMEM184B_uc003avh.1_Intron|TMEM184B_uc010gxl.1_Intron	NM_012264	NP_036396			transmembrane protein 184B							integral to membrane					0	Melanoma(58;0.045)																	---	---	---	---
Unknown	0	broad.mit.edu	37	22	38804442	38804442	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:38804442delA								LOC400927 (9511 upstream) : KCNJ4 (17891 downstream)																																			---	---	---	---
KDELR3	11015	broad.mit.edu	37	22	38875190	38875190	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:38875190delA	uc003avv.2	+						KDELR3_uc003avu.2_Intron	NM_006855	NP_006846			KDEL receptor 3 isoform a						protein retention in ER lumen|protein transport|vesicle-mediated transport	endoplasmic reticulum membrane|integral to membrane	ER retention sequence binding|receptor activity			ovary(2)	2	Melanoma(58;0.0286)																	---	---	---	---
DMC1	11144	broad.mit.edu	37	22	38954737	38954737	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:38954737delA	uc003avz.1	-						DMC1_uc011anv.1_Intron|DMC1_uc003awa.1_Intron	NM_007068	NP_008999			DMC1 dosage suppressor of mck1 homolog						reciprocal meiotic recombination	condensed nuclear chromosome	ATP binding|DNA binding|DNA-dependent ATPase activity|protein binding			ovary(1)	1	Melanoma(58;0.0286)												Homologous_recombination					---	---	---	---
LOC646851	646851	broad.mit.edu	37	22	39045873	39045874	+	Intron	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:39045873_39045874delAA	uc011anx.1	-						LOC646851_uc011anw.1_Intron					SubName: Full=Putative uncharacterized protein ENSP00000348086;												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	22	39073812	39073813	+	Intron	INS	-	T	T	rs143269069	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:39073812_39073813insT	uc003awd.2	-											Homo sapiens PKD2 interactor, golgi and endoplasmic reticulum associated 1, mRNA (cDNA clone IMAGE:4120338).																														---	---	---	---
Unknown	0	broad.mit.edu	37	22	39199612	39199615	+	IGR	DEL	CTTC	-	-	rs12161027	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:39199612_39199615delCTTC								SUN2 (9451 upstream) : NPTXR (14843 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	22	39283130	39283131	+	IGR	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:39283130_39283131delTT								CBX6 (14872 upstream) : APOBEC3A (70396 downstream)																																			---	---	---	---
APOBEC3D	140564	broad.mit.edu	37	22	39395197	39395198	+	Intron	INS	-	CCTT	CCTT	rs140904169	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:39395197_39395198insCCTT	uc011aoe.1	+						APOBEC3D_uc011aod.1_Intron|APOBEC3D_uc011aof.1_Intron	NM_152426	NP_689639			apolipoprotein B mRNA editing enzyme, catalytic						negative regulation of transposition		hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amidines|zinc ion binding				0	Melanoma(58;0.04)																	---	---	---	---
Unknown	0	broad.mit.edu	37	22	39948831	39948831	+	IGR	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:39948831delC								RPS19BP1 (19971 upstream) : CACNA1I (17927 downstream)																																			---	---	---	---
CACNA1I	8911	broad.mit.edu	37	22	40052231	40052231	+	Intron	DEL	T	-	-	rs11418217		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:40052231delT	uc003ayc.2	+						CACNA1I_uc003ayd.2_Intron|CACNA1I_uc003aye.2_Intron|CACNA1I_uc003ayf.2_Intron	NM_021096	NP_066919			calcium channel, voltage-dependent, T type,						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)													---	---	---	---
GRAP2	9402	broad.mit.edu	37	22	40379191	40379191	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:40379191delA	uc003ayi.2	+							NM_004810				GRB2-related adaptor protein 2						cell-cell signaling|Ras protein signal transduction|T cell costimulation|T cell receptor signaling pathway	cytosol	SH3/SH2 adaptor activity			upper_aerodigestive_tract(1)|central_nervous_system(1)	2																		---	---	---	---
TNRC6B	23112	broad.mit.edu	37	22	40597448	40597448	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:40597448delT	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																		---	---	---	---
SGSM3	27352	broad.mit.edu	37	22	40798383	40798383	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:40798383delT	uc003ayu.1	+						SGSM3_uc010gyc.1_Intron|SGSM3_uc011aos.1_Intron|SGSM3_uc011aot.1_Intron|SGSM3_uc010gyd.1_Intron	NM_015705	NP_056520			small G protein signaling modulator 3						cell cycle arrest|Rap protein signal transduction	cytoplasm	Rab GTPase activator activity|Rab GTPase binding			ovary(2)	2																		---	---	---	---
MKL1	57591	broad.mit.edu	37	22	40965334	40965335	+	Intron	INS	-	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:40965334_40965335insC	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	41084876	41084877	+	IGR	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:41084876_41084877delTT								MCHR1 (6059 upstream) : SLC25A17 (80764 downstream)																																			---	---	---	---
DNAJB7	150353	broad.mit.edu	37	22	41256021	41256021	+	3'UTR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:41256021delA	uc003azj.2	-	1					XPNPEP3_uc011aox.1_Intron|XPNPEP3_uc003azh.2_Intron|XPNPEP3_uc003azi.2_Intron|XPNPEP3_uc011aoy.1_5'Flank|XPNPEP3_uc003azg.1_Intron|XPNPEP3_uc003azf.1_Intron|XPNPEP3_uc010gyh.1_5'Flank	NM_145174	NP_660157			DnaJ (Hsp40) homolog, subfamily B, member 7						protein folding		heat shock protein binding|unfolded protein binding			ovary(1)	1																		---	---	---	---
XPNPEP3	63929	broad.mit.edu	37	22	41264850	41264850	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:41264850delA	uc003azh.2	+						XPNPEP3_uc011aox.1_Intron|XPNPEP3_uc003azi.2_Intron|XPNPEP3_uc011aoy.1_Intron|XPNPEP3_uc010gyh.1_Intron	NM_022098	NP_071381			X-prolyl aminopeptidase (aminopeptidase P) 3,						cellular process	mitochondrion	aminopeptidase activity|manganese ion binding|metallopeptidase activity				0																		---	---	---	---
XPNPEP3	63929	broad.mit.edu	37	22	41303425	41303425	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:41303425delA	uc003azh.2	+						XPNPEP3_uc011aox.1_Intron|XPNPEP3_uc003azi.2_Intron|XPNPEP3_uc011aoy.1_Intron	NM_022098	NP_071381			X-prolyl aminopeptidase (aminopeptidase P) 3,						cellular process	mitochondrion	aminopeptidase activity|manganese ion binding|metallopeptidase activity				0																		---	---	---	---
EP300	2033	broad.mit.edu	37	22	41502632	41502633	+	Intron	INS	-	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:41502632_41502633insT	uc003azl.3	+							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				---	---	---	---
EP300	2033	broad.mit.edu	37	22	41572224	41572224	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:41572224delA	uc003azl.3	+							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	41605111	41605111	+	Intron	DEL	T	-	-	rs67934576		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:41605111delT	uc003azo.2	+						L3MBTL2_uc010gyi.1_Intron|L3MBTL2_uc003azn.2_Intron	NM_031488	NP_113676			l(3)mbt-like 2						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																		---	---	---	---
ZC3H7B	23264	broad.mit.edu	37	22	41751783	41751785	+	In_Frame_Del	DEL	CTT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:41751783_41751785delCTT	uc003azw.2	+	19	2407_2409	c.2191_2193delCTT	c.(2191-2193)CTTdel	p.L732del	ZC3H7B_uc010gyl.1_Intron	NM_017590	NP_060060	Q9UGR2	Z3H7B_HUMAN	zinc finger CCCH-type containing 7B	748					interspecies interaction between organisms	nucleus	nucleic acid binding|protein binding|zinc ion binding			central_nervous_system(1)	1																		---	---	---	---
MEI1	150365	broad.mit.edu	37	22	42107188	42107188	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:42107188delT	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																		---	---	---	---
CENPM	79019	broad.mit.edu	37	22	42342581	42342581	+	Intron	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:42342581delG	uc003bbn.2	-						WBP2NL_uc011ape.1_Intron|LOC339674_uc003bba.1_Intron|CENPM_uc003bbm.2_5'UTR|CENPM_uc003bbo.2_Intron|CENPM_uc003bbp.1_Intron	NM_024053	NP_076958			centromere protein M isoform a						mitotic prometaphase	condensed chromosome kinetochore|cytosol|nucleus					0																OREG0026600	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
CYP2D6	1565	broad.mit.edu	37	22	42525717	42525718	+	Intron	DEL	TC	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:42525717_42525718delTC	uc003bce.2	-						uc003bcd.1_Intron|CYP2D6_uc010gyu.2_Intron|CYP2D6_uc003bcf.2_Intron	NM_000106	NP_000097			cytochrome P450, family 2, subfamily D,								electron carrier activity|heme binding|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			breast(1)|skin(1)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	22	43127012	43127012	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:43127012delA								A4GALT (9726 upstream) : ARFGAP3 (65520 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	22	43180583	43180583	+	IGR	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:43180583delC								A4GALT (63297 upstream) : ARFGAP3 (11949 downstream)																																			---	---	---	---
TTLL1	25809	broad.mit.edu	37	22	43451914	43451914	+	Intron	DEL	T	-	-	rs11326597		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:43451914delT	uc003bdi.2	-						TTLL1_uc010gzh.2_Intron|TTLL1_uc003bdj.2_Intron|TTLL1_uc003bdh.2_Intron	NM_012263	NP_036395			tubulin tyrosine ligase-like family, member 1						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)														---	---	---	---
BIK	638	broad.mit.edu	37	22	43515826	43515826	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:43515826delA	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)																---	---	---	---
BIK	638	broad.mit.edu	37	22	43522706	43522706	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:43522706delT	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)																---	---	---	---
TTLL12	23170	broad.mit.edu	37	22	43563473	43563474	+	3'UTR	DEL	CT	-	-	rs36105550		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:43563473_43563474delCT	uc003bdq.2	-	14					TTLL12_uc003bdp.2_3'UTR|TTLL12_uc003bdr.1_Intron	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)																---	---	---	---
SCUBE1	80274	broad.mit.edu	37	22	43602657	43602658	+	Intron	INS	-	AAG	AAG	rs138016510	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:43602657_43602658insAAG	uc003bdt.1	-							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)																---	---	---	---
Unknown	0	broad.mit.edu	37	22	43749846	43749848	+	IGR	DEL	TTT	-	-	rs5759298	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:43749846_43749848delTTT								SCUBE1 (10491 upstream) : MPPED1 (58172 downstream)																																			---	---	---	---
MPPED1	758	broad.mit.edu	37	22	43852693	43852694	+	Intron	DEL	GT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:43852693_43852694delGT	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)																---	---	---	---
EFCAB6	64800	broad.mit.edu	37	22	44109043	44109044	+	Intron	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:44109043_44109044delAA	uc003bdy.1	-						EFCAB6_uc003bdz.1_Intron|EFCAB6_uc010gzi.1_Intron|EFCAB6_uc010gzk.1_Intron|EFCAB6_uc011aqa.1_Intron|EFCAB6_uc003bea.1_Intron	NM_022785	NP_073622			CAP-binding protein complex interacting protein						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)																---	---	---	---
EFCAB6	64800	broad.mit.edu	37	22	44167521	44167521	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:44167521delT	uc003bdy.1	-						EFCAB6_uc003bdz.1_Intron|EFCAB6_uc010gzi.1_Intron|EFCAB6_uc011aqa.1_Intron|EFCAB6_uc003bea.1_Intron|EFCAB6_uc003beb.3_Intron	NM_022785	NP_073622			CAP-binding protein complex interacting protein						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)																---	---	---	---
EFCAB6	64800	broad.mit.edu	37	22	44175645	44175645	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:44175645delA	uc003bdy.1	-						EFCAB6_uc003bdz.1_Intron|EFCAB6_uc010gzi.1_Intron|EFCAB6_uc011aqa.1_Intron|EFCAB6_uc003bea.1_Intron|EFCAB6_uc003beb.3_Intron	NM_022785	NP_073622			CAP-binding protein complex interacting protein						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)																---	---	---	---
PRR5	55615	broad.mit.edu	37	22	45082228	45082228	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:45082228delT	uc010gzt.1	+						PRR5_uc003bew.1_Intron|PRR5_uc003bex.1_Intron|PRR5_uc010gzu.1_Intron|PRR5_uc003bey.1_Intron|PRR5_uc003bez.1_Intron	NM_001017530	NP_001017530			proline rich 5 (renal) isoform 3						cell cycle					skin(1)	1		all_neural(38;0.00409)|Ovarian(80;0.024)|Glioma(61;0.0647)		UCEC - Uterine corpus endometrioid carcinoma (28;0.168)														---	---	---	---
PHF21B	112885	broad.mit.edu	37	22	45392536	45392537	+	Intron	DEL	AC	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:45392536_45392537delAC	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)														---	---	---	---
SMC1B	27127	broad.mit.edu	37	22	45754477	45754477	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:45754477delA	uc003bgc.2	-						SMC1B_uc003bgd.2_Intron	NM_148674	NP_683515			SMC1 structural maintenance of chromosomes						chromosome organization|meiosis	chromosome, centromeric region|cytoplasm|meiotic cohesin complex|nucleus	ATP binding			ovary(2)	2		Ovarian(80;0.00965)|all_neural(38;0.0416)		UCEC - Uterine corpus endometrioid carcinoma (28;0.0182)														---	---	---	---
SMC1B	27127	broad.mit.edu	37	22	45790203	45790203	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:45790203delA	uc003bgc.2	-						SMC1B_uc003bgd.2_Intron|SMC1B_uc003bge.1_Intron	NM_148674	NP_683515			SMC1 structural maintenance of chromosomes						chromosome organization|meiosis	chromosome, centromeric region|cytoplasm|meiotic cohesin complex|nucleus	ATP binding			ovary(2)	2		Ovarian(80;0.00965)|all_neural(38;0.0416)		UCEC - Uterine corpus endometrioid carcinoma (28;0.0182)														---	---	---	---
RIBC2	26150	broad.mit.edu	37	22	45811578	45811578	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:45811578delT	uc011aqs.1	+						SMC1B_uc003bgc.2_5'Flank|SMC1B_uc003bgd.2_5'Flank	NM_015653	NP_056468			RIB43A domain with coiled-coils 2												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	45852037	45852038	+	IGR	DEL	AA	-	-	rs67827864		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:45852037_45852038delAA								RIBC2 (23744 upstream) : FBLN1 (46681 downstream)																																			---	---	---	---
FBLN1	2192	broad.mit.edu	37	22	45939157	45939157	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-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)														---	---	---	---
WNT7B	7477	broad.mit.edu	37	22	46369778	46369779	+	Intron	INS	-	T	T	rs141228167	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:46369778_46369779insT	uc003bgo.2	-						WNT7B_uc010haa.2_5'Flank	NM_058238	NP_478679			wingless-type MMTV integration site family,						activation of JUN kinase activity|anterior/posterior pattern formation|axis specification|axonogenesis|canonical Wnt receptor signaling pathway|cell-cell signaling|cellular response to retinoic acid|central nervous system vasculogenesis|chorio-allantoic fusion|developmental growth involved in morphogenesis|embryonic placenta morphogenesis|establishment or maintenance of polarity of embryonic epithelium|fibroblast proliferation|forebrain regionalization|inner medullary collecting duct development|lens fiber cell development|lobar bronchus development|lung epithelium development|lung morphogenesis|lung-associated mesenchyme development|mammary gland epithelium development|metanephric collecting duct development|metanephric loop of Henle development|metanephros morphogenesis|negative regulation of smoothened signaling pathway|outer medullary collecting duct development|oxygen homeostasis|positive regulation of JNK cascade|positive regulation of osteoblast differentiation|renal inner medulla development|renal outer medulla development|stem cell proliferation|synapse organization|trachea cartilage morphogenesis|Wnt receptor signaling pathway, calcium modulating pathway	extracellular space|plasma membrane|proteinaceous extracellular matrix	extracellular matrix structural constituent|frizzled binding|signal transducer activity			lung(1)	1		Ovarian(80;0.00965)|all_neural(38;0.0416)		UCEC - Uterine corpus endometrioid carcinoma (28;0.0178)|LUAD - Lung adenocarcinoma(64;0.247)														---	---	---	---
CELSR1	9620	broad.mit.edu	37	22	46805624	46805624	+	Intron	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:46805624delG	uc003bhw.1	-						CELSR1_uc011arc.1_5'Flank	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	46845207	46845210	+	Intron	DEL	CATC	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:46845207_46845210delCATC	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)														---	---	---	---
Unknown	0	broad.mit.edu	37	22	47717228	47717228	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:47717228delT								TBC1D22A (147506 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	22	48066424	48066424	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:48066424delA	uc003bik.1	+											Homo sapiens cDNA FLJ35788 fis, clone TESTI2005683.																														---	---	---	---
Unknown	0	broad.mit.edu	37	22	48276923	48276923	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:48276923delT								TBC1D22A (707201 upstream) : FAM19A5 (608365 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	22	48512757	48512758	+	IGR	INS	-	A	A	rs143662266	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:48512757_48512758insA								TBC1D22A (943035 upstream) : FAM19A5 (372530 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	22	48745432	48745433	+	IGR	DEL	CT	-	-	rs34869237		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:48745432_48745433delCT								None (None upstream) : FAM19A5 (139855 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	22	48752308	48752309	+	IGR	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:48752308_48752309delTT								None (None upstream) : FAM19A5 (132979 downstream)																																			---	---	---	---
FAM19A5	25817	broad.mit.edu	37	22	48915332	48915332	+	Intron	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:48915332delG	uc003bim.3	+							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	49365274	49365274	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:49365274delT								FAM19A5 (217532 upstream) : C22orf34 (442902 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	22	49426719	49426719	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:49426719delA								FAM19A5 (278977 upstream) : C22orf34 (381457 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	22	49706160	49706160	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:49706160delA								FAM19A5 (558418 upstream) : C22orf34 (102016 downstream)																																			---	---	---	---
TTLL8	164714	broad.mit.edu	37	22	50467073	50467074	+	Intron	INS	-	C	C	rs149258291	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:50467073_50467074insC	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	50467139	50467140	+	Intron	INS	-	C	C	rs66811361		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:50467139_50467140insC	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)														---	---	---	---
Unknown	0	broad.mit.edu	37	22	50777239	50777240	+	IGR	DEL	GT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:50777239_50777240delGT								FAM116B (11750 upstream) : SAPS2 (4520 downstream)																																			---	---	---	---
SBF1	6305	broad.mit.edu	37	22	50906382	50906382	+	Intron	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:50906382delC	uc003blh.2	-						SBF1_uc011arx.1_5'Flank|SBF1_uc003bli.2_Intron	NM_002972	NP_002963			SET binding factor 1						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)														---	---	---	---
ODF3B	440836	broad.mit.edu	37	22	50973947	50973948	+	5'Flank	INS	-	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:50973947_50973948insA	uc003bmh.2	-							NM_001014440	NP_001014440			outer dense fiber of sperm tails 3B												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	X	820456	820457	+	IGR	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:820456_820457delTT								SHOX (200311 upstream) : CRLF2 (494430 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	1218739	1218740	+	IGR	DEL	AG	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:1218739_1218740delAG								SHOX (598594 upstream) : CRLF2 (96147 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	1231650	1231650	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:1231650delA								SHOX (611505 upstream) : CRLF2 (83237 downstream)																																			---	---	---	---
CRLF2	64109	broad.mit.edu	37	X	1315114	1315114	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:1315114delT	uc004cpm.1	-											Homo sapiens mRNA for IL-XR, complete cds.							extracellular region|integral to membrane|plasma membrane	receptor activity			haematopoietic_and_lymphoid_tissue(7)	7		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)						Mis|T	P2RY8|IGH@	B-ALL|Downs associated ALL								---	---	---	---
Unknown	0	broad.mit.edu	37	X	2029086	2029087	+	IGR	DEL	CT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:2029086_2029087delCT								ASMT (267113 upstream) : DHRSX (108470 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	2505116	2505118	+	IGR	DEL	AAA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:2505116_2505118delAAA								DHRSX (86101 upstream) : CD99 (104110 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	3226525	3226525	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:3226525delT								ARSF (195778 upstream) : MXRA5 (86 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	4188276	4188276	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:4188276delA								PRKX (556615 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	5564271	5564274	+	IGR	DEL	CATC	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:5564271_5564274delCATC								None (None upstream) : NLGN4X (243810 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	5786881	5786882	+	IGR	INS	-	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:5786881_5786882insT								None (None upstream) : NLGN4X (21202 downstream)																																			---	---	---	---
NLGN4X	57502	broad.mit.edu	37	X	6092988	6092988	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:6092988delA	uc010ndh.2	-						NLGN4X_uc004crq.2_Intron|NLGN4X_uc010ndi.2_Intron|NLGN4X_uc004crr.2_Intron|NLGN4X_uc010ndj.2_Intron	NM_181332	NP_851849			X-linked neuroligin 4 precursor						brainstem development|cell adhesion|cell-cell junction organization|cerebellum development|male courtship behavior|positive regulation of organ growth|regulation of excitatory postsynaptic membrane potential|social behavior|synapse assembly|territorial aggressive behavior|vocalization behavior	cell surface|dendrite|integral to plasma membrane|synapse	chloride ion binding|neurexin binding|protein homodimerization activity|receptor activity			skin(2)|large_intestine(1)|ovary(1)	4																		---	---	---	---
STS	412	broad.mit.edu	37	X	7073210	7073211	+	Intron	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:7073210_7073211delTT	uc004crw.2	+						STS_uc011mhp.1_Intron|STS_uc004crx.1_Intron					Homo sapiens cDNA, FLJ94694, highly similar to Homo sapiens steroid sulfatase (microsomal), arylsulfatase C,isozyme S (STS), mRNA.						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				---	---	---	---
KAL1	3730	broad.mit.edu	37	X	8698187	8698187	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:8698187delA	uc004csf.2	-							NM_000216	NP_000207			Kallmann syndrome 1 protein precursor						axon guidance|cell adhesion|cellular component movement	extracellular space|plasma membrane|proteinaceous extracellular matrix	extracellular matrix structural constituent|heparin binding|serine-type endopeptidase inhibitor activity			ovary(3)|pancreas(1)	4																		---	---	---	---
Unknown	0	broad.mit.edu	37	X	9143833	9143833	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:9143833delT								FAM9B (11186 upstream) : TBL1X (287502 downstream)																																			---	---	---	---
TBL1X	6907	broad.mit.edu	37	X	9570397	9570398	+	Intron	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:9570397_9570398delTT	uc010ndq.2	+						TBL1X_uc004csq.3_Intron|TBL1X_uc010ndr.2_Intron|TBL1X_uc004csr.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)																---	---	---	---
SHROOM2	357	broad.mit.edu	37	X	9804525	9804526	+	Intron	DEL	TC	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:9804525_9804526delTC	uc004csu.1	+							NM_001649	NP_001640			apical protein of Xenopus-like						apical protein localization|brain development|cell migration|cell morphogenesis|cellular pigment accumulation|ear development|establishment of melanosome localization|eye pigment granule organization|lens morphogenesis in camera-type eye|melanosome organization	apical plasma membrane|cell-cell adherens junction|microtubule|tight junction	actin filament binding|beta-catenin binding|ligand-gated sodium channel activity			ovary(3)|skin(3)|upper_aerodigestive_tract(1)|breast(1)	8		Hepatocellular(5;0.000888)																---	---	---	---
SHROOM2	357	broad.mit.edu	37	X	9829773	9829773	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:9829773delT	uc004csu.1	+							NM_001649	NP_001640			apical protein of Xenopus-like						apical protein localization|brain development|cell migration|cell morphogenesis|cellular pigment accumulation|ear development|establishment of melanosome localization|eye pigment granule organization|lens morphogenesis in camera-type eye|melanosome organization	apical plasma membrane|cell-cell adherens junction|microtubule|tight junction	actin filament binding|beta-catenin binding|ligand-gated sodium channel activity			ovary(3)|skin(3)|upper_aerodigestive_tract(1)|breast(1)	8		Hepatocellular(5;0.000888)																---	---	---	---
ARHGAP6	395	broad.mit.edu	37	X	11239456	11239456	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:11239456delT	uc004cup.1	-						ARHGAP6_uc004cuo.1_Intron|ARHGAP6_uc004cur.1_Intron|ARHGAP6_uc004cum.1_Intron|ARHGAP6_uc004cun.1_Intron|ARHGAP6_uc010neb.1_Intron|ARHGAP6_uc011mif.1_Intron	NM_013427	NP_038286			Rho GTPase activating protein 6 isoform 1						actin filament polymerization|activation of phospholipase C activity|negative regulation of focal adhesion assembly|negative regulation of stress fiber assembly|Rho protein signal transduction	actin filament|cytosol	phospholipase activator activity|phospholipase binding|Rho GTPase activator activity|SH3 domain binding|SH3/SH2 adaptor activity			urinary_tract(1)|lung(1)	2																		---	---	---	---
MSL3	10943	broad.mit.edu	37	X	11778972	11778974	+	In_Frame_Del	DEL	AAG	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:11778972_11778974delAAG	uc004cuw.2	+	4	403_405	c.298_300delAAG	c.(298-300)AAGdel	p.K102del	MSL3_uc004cuv.1_In_Frame_Del_p.K102del|MSL3_uc004cux.2_In_Frame_Del_p.K43del|MSL3_uc011mig.1_5'UTR|MSL3_uc011mih.1_In_Frame_Del_p.K90del|MSL3_uc004cuy.2_5'UTR|MSL3_uc011mii.1_5'UTR	NM_078629	NP_523353	Q8N5Y2	MS3L1_HUMAN	male-specific lethal 3-like 1 isoform a	102					histone H4-K16 acetylation|multicellular organismal development|transcription from RNA polymerase II promoter	MSL complex	DNA binding|methylated histone residue binding|sequence-specific DNA binding transcription factor activity			ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	X	11884577	11884577	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:11884577delA								MSL3 (90707 upstream) : FRMPD4 (272008 downstream)																																			---	---	---	---
FRMPD4	9758	broad.mit.edu	37	X	12399633	12399633	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:12399633delT	uc004cuz.1	+						FRMPD4_uc011mij.1_Intron	NM_014728	NP_055543			FERM and PDZ domain containing 4						positive regulation of synapse structural plasticity	cytoskeleton|dendritic spine	phosphatidylinositol-4,5-bisphosphate binding|protein binding			central_nervous_system(5)|ovary(3)|skin(2)|large_intestine(1)|lung(1)|pancreas(1)	13																		---	---	---	---
Unknown	0	broad.mit.edu	37	X	13196512	13196512	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:13196512delT								FAM9C (133712 upstream) : ATXN3L (140258 downstream)																																			---	---	---	---
OFD1	8481	broad.mit.edu	37	X	13787350	13787350	+	3'UTR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-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																		---	---	---	---
GPM6B	2824	broad.mit.edu	37	X	13931444	13931444	+	Intron	DEL	T	-	-	rs35452542		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:13931444delT	uc004cvx.2	-						GPM6B_uc011min.1_Intron|GPM6B_uc004cwa.2_Intron	NM_001001994	NP_001001994			glycoprotein M6B isoform 4						cell differentiation|nervous system development	integral to membrane					0																		---	---	---	---
GLRA2	2742	broad.mit.edu	37	X	14692230	14692230	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:14692230delA	uc010nep.2	+						GLRA2_uc010neq.2_Intron|GLRA2_uc004cwe.3_Intron|GLRA2_uc011mio.1_Intron|GLRA2_uc011mip.1_Intron	NM_001118885	NP_001112357			glycine receptor, alpha 2 isoform A						neuropeptide signaling pathway	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(1)|lung(1)	2	Hepatocellular(33;0.128)				Ethanol(DB00898)|Glycine(DB00145)													---	---	---	---
AP1S2	8905	broad.mit.edu	37	X	15863649	15863649	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:15863649delA	uc004cxi.2	-						AP1S2_uc004cxh.2_Intron|AP1S2_uc010nex.2_Intron|AP1S2_uc011mis.1_Intron|AP1S2_uc011mit.1_Intron|AP1S2_uc011miu.1_Intron	NM_003916	NP_003907			adaptor-related protein complex 1 sigma 2						endocytosis|intracellular protein transport|post-Golgi vesicle-mediated transport|regulation of defense response to virus by virus|viral reproduction	AP-type membrane coat adaptor complex|coated pit|cytoplasmic vesicle membrane|cytosol|Golgi membrane|lysosomal membrane	protein transporter activity				0	Hepatocellular(33;0.183)																	---	---	---	---
Unknown	0	broad.mit.edu	37	X	15911850	15911851	+	IGR	INS	-	AGAA	AGAA	rs11798819		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:15911850_15911851insAGAA								AP1S2 (38750 upstream) : GRPR (229573 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	16796120	16796121	+	IGR	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:16796120_16796121delAA								SYAP1 (16787 upstream) : TXLNG (8439 downstream)																																			---	---	---	---
REPS2	9185	broad.mit.edu	37	X	16974192	16974192	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:16974192delA	uc004cxv.1	+						REPS2_uc004cxw.1_Intron	NM_004726	NP_004717			RALBP1 associated Eps domain containing 2						epidermal growth factor receptor signaling pathway|protein complex assembly	cytoplasm	calcium ion binding|protein binding			skin(2)|central_nervous_system(1)	3	Hepatocellular(33;0.183)																	---	---	---	---
BEND2	139105	broad.mit.edu	37	X	18194275	18194275	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:18194275delT	uc004cyj.3	-						BEND2_uc010nfb.2_Intron	NM_153346	NP_699177			BEN domain containing 2											ovary(3)|kidney(1)|central_nervous_system(1)	5																		---	---	---	---
CDKL5	6792	broad.mit.edu	37	X	18498978	18498981	+	Intron	DEL	TTTT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:18498978_18498981delTTTT	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)																	---	---	---	---
PDHA1	5160	broad.mit.edu	37	X	19375562	19375562	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:19375562delA	uc004czg.3	+						PDHA1_uc004czh.3_Intron|PDHA1_uc011mjc.1_Intron|PDHA1_uc011mjd.1_Intron|PDHA1_uc010nfk.2_Intron|PDHA1_uc010nfl.2_Intron	NM_000284	NP_000275			pyruvate dehydrogenase E1 alpha 1 precursor						glycolysis|pyruvate metabolic process|regulation of acetyl-CoA biosynthetic process from pyruvate	mitochondrial matrix	protein binding|pyruvate dehydrogenase (acetyl-transferring) activity			ovary(1)	1	Hepatocellular(33;0.183)				NADH(DB00157)													---	---	---	---
EIF1AX	1964	broad.mit.edu	37	X	20161378	20161378	+	5'Flank	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:20161378delA	uc004czt.2	-							NM_001412	NP_001403			X-linked eukaryotic translation initiation							cytosol	translation initiation factor activity			ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	X	20564899	20564899	+	IGR	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:20564899delC								RPS6KA3 (279376 upstream) : CNKSR2 (828081 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	20859883	20859883	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:20859883delT								RPS6KA3 (574360 upstream) : CNKSR2 (533097 downstream)																																			---	---	---	---
CNKSR2	22866	broad.mit.edu	37	X	21581709	21581709	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:21581709delA	uc004czx.1	+						CNKSR2_uc004czw.2_Intron|CNKSR2_uc011mjn.1_Intron|CNKSR2_uc011mjo.1_Intron|CNKSR2_uc004czy.2_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																		---	---	---	---
Unknown	0	broad.mit.edu	37	X	21942292	21942293	+	IGR	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:21942292_21942293delAA								MBTPS2 (38752 upstream) : SMS (16549 downstream)																																			---	---	---	---
SMS	6611	broad.mit.edu	37	X	21995605	21995606	+	Intron	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:21995605_21995606delAA	uc004dag.2	+						SMS_uc011mjq.1_Intron|SMS_uc004daf.1_Intron|SMS_uc010nfs.2_5'Flank|SMS_uc010nft.2_5'Flank	NM_004595	NP_004586			spermine synthase						methionine metabolic process|spermine biosynthetic process	cytosol	spermidine synthase activity|spermine synthase activity			ovary(1)	1					Spermine(DB00127)													---	---	---	---
SMS	6611	broad.mit.edu	37	X	22007853	22007853	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:22007853delT	uc004dag.2	+						SMS_uc010nfs.2_Intron|SMS_uc010nft.2_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)													---	---	---	---
PHEX	5251	broad.mit.edu	37	X	22151761	22151761	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:22151761delA	uc004dah.2	+						PHEX_uc011mjr.1_Intron|PHEX_uc011mjs.1_Intron	NM_000444	NP_000435			phosphate-regulating neutral endopeptidase						biomineral tissue development|cell-cell signaling|protein modification process|proteolysis|skeletal system development	integral to plasma membrane	aminopeptidase activity|metalloendopeptidase activity|zinc ion binding			ovary(2)|lung(1)	3																		---	---	---	---
Unknown	0	broad.mit.edu	37	X	22878407	22878407	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:22878407delA								ZNF645 (585833 upstream) : DDX53 (139680 downstream)																																			---	---	---	---
CXorf58	254158	broad.mit.edu	37	X	23945136	23945136	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:23945136delA	uc004daz.1	+						CXorf58_uc011mju.1_Intron	NM_152761	NP_689974			hypothetical protein LOC254158												0																		---	---	---	---
ZFX	7543	broad.mit.edu	37	X	24217378	24217379	+	Intron	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:24217378_24217379delTT	uc004dbf.2	+						ZFX_uc004dbd.1_Intron|ZFX_uc010nfx.1_Intron|ZFX_uc004dbe.2_Intron|ZFX_uc011mjv.1_Intron|ZFX_uc010nfy.1_Intron	NM_003410	NP_003401			zinc finger protein, X-linked						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|transcription coactivator activity|zinc ion binding			ovary(2)	2																		---	---	---	---
ZFX	7543	broad.mit.edu	37	X	24225362	24225368	+	Intron	DEL	ATTTTTT	-	-	rs62796264		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:24225362_24225368delATTTTTT	uc004dbf.2	+						ZFX_uc004dbd.1_Intron|ZFX_uc010nfx.1_Intron|ZFX_uc004dbe.2_Intron|ZFX_uc011mjv.1_Intron|ZFX_uc010nfy.1_Intron|ZFX_uc010nfz.2_5'Flank	NM_003410	NP_003401			zinc finger protein, X-linked						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|transcription coactivator activity|zinc ion binding			ovary(2)	2																		---	---	---	---
PDK3	5165	broad.mit.edu	37	X	24541023	24541024	+	Intron	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:24541023_24541024delAA	uc004dbg.2	+						PDK3_uc004dbh.2_Intron	NM_005391	NP_005382			pyruvate dehydrogenase kinase 3 isoform 2						glucose metabolic process|peptidyl-histidine phosphorylation|pyruvate metabolic process|regulation of acetyl-CoA biosynthetic process from pyruvate	mitochondrial matrix	ATP binding|protein binding|pyruvate dehydrogenase (acetyl-transferring) kinase activity|two-component sensor activity			lung(4)|upper_aerodigestive_tract(1)|ovary(1)	6																		---	---	---	---
Unknown	0	broad.mit.edu	37	X	25483186	25483186	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:25483186delT								ARX (449121 upstream) : MAGEB18 (673277 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	27768909	27768909	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:27768909delT								DCAF8L2 (1972 upstream) : MAGEB10 (57216 downstream)																																			---	---	---	---
IL1RAPL1	11141	broad.mit.edu	37	X	29301000	29301000	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:29301000delT	uc004dby.2	+							NM_014271	NP_055086			interleukin 1 receptor accessory protein-like 1						innate immune response|negative regulation of calcium ion transport via voltage-gated calcium channel activity|negative regulation of exocytosis|regulation of neuron projection development	cytoplasm|integral to membrane|plasma membrane	protein binding|transmembrane receptor activity			ovary(3)|lung(1)|pancreas(1)	5																		---	---	---	---
IL1RAPL1	11141	broad.mit.edu	37	X	29810884	29810885	+	Intron	INS	-	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:29810884_29810885insA	uc004dby.2	+							NM_014271	NP_055086			interleukin 1 receptor accessory protein-like 1						innate immune response|negative regulation of calcium ion transport via voltage-gated calcium channel activity|negative regulation of exocytosis|regulation of neuron projection development	cytoplasm|integral to membrane|plasma membrane	protein binding|transmembrane receptor activity			ovary(3)|lung(1)|pancreas(1)	5																		---	---	---	---
IL1RAPL1	11141	broad.mit.edu	37	X	29850823	29850827	+	Intron	DEL	TTTTT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:29850823_29850827delTTTTT	uc004dby.2	+							NM_014271	NP_055086			interleukin 1 receptor accessory protein-like 1						innate immune response|negative regulation of calcium ion transport via voltage-gated calcium channel activity|negative regulation of exocytosis|regulation of neuron projection development	cytoplasm|integral to membrane|plasma membrane	protein binding|transmembrane receptor activity			ovary(3)|lung(1)|pancreas(1)	5																		---	---	---	---
Unknown	0	broad.mit.edu	37	X	31002501	31002501	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:31002501delA								TAB3 (9300 upstream) : FTHL17 (86857 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	31046877	31046877	+	IGR	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:31046877delC								TAB3 (53676 upstream) : FTHL17 (42481 downstream)																																			---	---	---	---
DMD	1756	broad.mit.edu	37	X	31329603	31329603	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:31329603delT	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	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)																---	---	---	---
DMD	1756	broad.mit.edu	37	X	31437057	31437057	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:31437057delT	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	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)																---	---	---	---
DMD	1756	broad.mit.edu	37	X	31671124	31671124	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:31671124delA	uc004dda.1	-						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	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)																---	---	---	---
DMD	1756	broad.mit.edu	37	X	32252583	32252583	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:32252583delA	uc004dda.1	-						DMD_uc004dcw.2_Intron|DMD_uc004dcx.2_Intron|DMD_uc004dcz.2_Intron|DMD_uc004dcy.1_Intron|DMD_uc004ddb.1_Intron|DMD_uc010ngo.1_Intron|DMD_uc010ngn.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)																---	---	---	---
DMD	1756	broad.mit.edu	37	X	32364014	32364014	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:32364014delA	uc004dda.1	-						DMD_uc004dcw.2_Intron|DMD_uc004dcx.2_Intron|DMD_uc004dcz.2_Intron|DMD_uc004dcy.1_Intron|DMD_uc004ddb.1_Intron|DMD_uc010ngo.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)																---	---	---	---
DMD	1756	broad.mit.edu	37	X	32366648	32366648	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:32366648delA	uc004dda.1	-						DMD_uc004dcw.2_Intron|DMD_uc004dcx.2_Intron|DMD_uc004dcz.2_Intron|DMD_uc004dcy.1_Intron|DMD_uc004ddb.1_Intron|DMD_uc010ngo.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)																---	---	---	---
DMD	1756	broad.mit.edu	37	X	32463461	32463461	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:32463461delA	uc004dda.1	-						DMD_uc004dcz.2_Intron|DMD_uc004dcy.1_Intron|DMD_uc004ddb.1_Intron|DMD_uc010ngo.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)																---	---	---	---
Unknown	0	broad.mit.edu	37	X	33456915	33456915	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:33456915delA								DMD (99189 upstream) : FAM47A (690960 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	33862030	33862031	+	IGR	INS	-	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:33862030_33862031insA								DMD (504304 upstream) : FAM47A (285844 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	34480421	34480421	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:34480421delT								FAM47A (329993 upstream) : TMEM47 (164762 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	35281157	35281157	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:35281157delT								FAM47B (318123 upstream) : MAGEB16 (535302 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	36443468	36443468	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:36443468delA								CXorf30 (40035 upstream) : FAM47C (583002 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	36472065	36472066	+	IGR	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:36472065_36472066delAA								CXorf30 (68632 upstream) : FAM47C (554404 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	37774411	37774412	+	IGR	DEL	GC	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:37774411_37774412delGC								DYNLT3 (67522 upstream) : CXorf27 (75658 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	38851536	38851537	+	IGR	DEL	AC	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:38851536_38851537delAC								MID1IP1 (185755 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	39305020	39305021	+	IGR	DEL	AC	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:39305020_39305021delAC								MID1IP1 (639239 upstream) : BCOR (605480 downstream)																																	OREG0019731	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	39728411	39728412	+	IGR	DEL	CA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:39728411_39728412delCA								None (None upstream) : BCOR (182089 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	40790201	40790201	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:40790201delA								LOC100132831 (97752 upstream) : USP9X (154687 downstream)																																			---	---	---	---
DDX3X	1654	broad.mit.edu	37	X	41207100	41207101	+	3'UTR	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:41207100_41207101delTT	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	41270119	41270119	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:41270119delT								DDX3X (46395 upstream) : NYX (36594 downstream)																																			---	---	---	---
GPR34	2857	broad.mit.edu	37	X	41556044	41556045	+	3'UTR	INS	-	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:41556044_41556045insA	uc004dfp.3	+	3					CASK_uc004dfl.3_Intron|CASK_uc004dfm.3_Intron|CASK_uc004dfn.3_Intron|GPR34_uc004dfq.3_3'UTR|GPR34_uc010nhg.2_3'UTR|GPR34_uc004dfr.3_3'UTR	NM_001097579	NP_001091048			G protein-coupled receptor 34							integral to plasma membrane	purinergic nucleotide receptor activity, G-protein coupled			ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	X	42073571	42073571	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:42073571delT								CASK (291284 upstream) : PPP1R2P9 (563048 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	42709002	42709002	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:42709002delT								PPP1R2P9 (71516 upstream) : MAOA (806407 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	43024884	43024884	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:43024884delT								PPP1R2P9 (387398 upstream) : MAOA (490525 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	43140038	43140038	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:43140038delT								PPP1R2P9 (502552 upstream) : MAOA (375371 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	43380591	43380591	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:43380591delA								PPP1R2P9 (743105 upstream) : MAOA (134818 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	45092266	45092266	+	IGR	DEL	T	-	-	rs5902354		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:45092266delT								CXorf36 (32120 upstream) : MIR221 (513319 downstream)																																			---	---	---	---
ZNF674	641339	broad.mit.edu	37	X	46375286	46375286	+	Intron	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:46375286delC	uc004dgr.2	-						ZNF674_uc011mlg.1_Intron	NM_001039891	NP_001034980			zinc finger family member 674 isoform 1						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			breast(2)	2																		---	---	---	---
SLC9A7	84679	broad.mit.edu	37	X	46598884	46598885	+	Intron	DEL	TC	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:46598884_46598885delTC	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																		---	---	---	---
PHF16	9767	broad.mit.edu	37	X	46785693	46785693	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:46785693delT	uc004dgx.2	+						PHF16_uc004dgy.2_Intron	NM_001077445	NP_001070913			PHD finger protein 16						histone H3 acetylation|histone H4-K12 acetylation|histone H4-K5 acetylation|histone H4-K8 acetylation	histone acetyltransferase complex	zinc ion binding				0																		---	---	---	---
PHF16	9767	broad.mit.edu	37	X	46866367	46866367	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:46866367delT	uc004dgx.2	+						PHF16_uc004dgy.2_Intron	NM_001077445	NP_001070913			PHD finger protein 16						histone H3 acetylation|histone H4-K12 acetylation|histone H4-K5 acetylation|histone H4-K8 acetylation	histone acetyltransferase complex	zinc ion binding				0																		---	---	---	---
PHF16	9767	broad.mit.edu	37	X	46884358	46884358	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:46884358delT	uc004dgx.2	+						PHF16_uc004dgy.2_Intron	NM_001077445	NP_001070913			PHD finger protein 16						histone H3 acetylation|histone H4-K12 acetylation|histone H4-K5 acetylation|histone H4-K8 acetylation	histone acetyltransferase complex	zinc ion binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	X	46922107	46922107	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:46922107delT								PHF16 (1467 upstream) : RGN (15668 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	48184092	48184092	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:48184092delT								SSX1 (57213 upstream) : SSX3 (21771 downstream)																																			---	---	---	---
SSX3	10214	broad.mit.edu	37	X	48216743	48216744	+	5'Flank	DEL	GA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:48216743_48216744delGA	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																		---	---	---	---
CACNA1F	778	broad.mit.edu	37	X	49083786	49083786	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:49083786delT	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)													---	---	---	---
DGKK	139189	broad.mit.edu	37	X	50211856	50211857	+	Intron	INS	-	TG	TG	rs145971796		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:50211856_50211857insTG	uc010njr.1	-							NM_001013742	NP_001013764			diacylglycerol kinase kappa						activation of protein kinase C activity by G-protein coupled receptor protein signaling pathway|diacylglycerol metabolic process|intracellular signal transduction|platelet activation|response to oxidative stress	cytoplasm|plasma membrane	ATP binding|diacylglycerol kinase activity|metal ion binding			ovary(1)|kidney(1)	2	Ovarian(276;0.236)																	---	---	---	---
SHROOM4	57477	broad.mit.edu	37	X	50336318	50336318	+	3'UTR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:50336318delT	uc004dpe.2	-	9					SHROOM4_uc004dpd.3_Intron|uc004dpc.1_5'Flank	NM_020717	NP_065768			shroom family member 4						actin filament organization|brain development|cell morphogenesis|cognition	apical plasma membrane|basal plasma membrane|internal side of plasma membrane|nucleus	actin filament binding			upper_aerodigestive_tract(1)	1	Ovarian(276;0.236)																	---	---	---	---
TSPYL2	64061	broad.mit.edu	37	X	53113546	53113547	+	Intron	DEL	AT	-	-	rs146708183	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:53113546_53113547delAT	uc004drw.2	+						TSPYL2_uc004drv.2_Intron|TSPYL2_uc004drx.1_5'Flank	NM_022117	NP_071400			TSPY-like 2						cell cycle|chromatin modification|negative regulation of cell cycle|negative regulation of cell growth|negative regulation of DNA replication|nucleosome assembly|regulation of protein kinase activity|regulation of signal transduction|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleolus	protein binding|rDNA binding				0																		---	---	---	---
KDM5C	8242	broad.mit.edu	37	X	53248345	53248345	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:53248345delT	uc004drz.2	-						KDM5C_uc011moc.1_Intron|KDM5C_uc011mod.1_Intron|KDM5C_uc004dsa.2_Intron	NM_004187	NP_004178			jumonji, AT rich interactive domain 1C isoform						chromatin modification|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|protein binding|zinc ion binding			kidney(9)|ovary(5)|salivary_gland(1)|autonomic_ganglia(1)|haematopoietic_and_lymphoid_tissue(1)|oesophagus(1)	18								N|F|S		clear cell renal carcinoma								---	---	---	---
Unknown	0	broad.mit.edu	37	X	54397347	54397347	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:54397347delT								WNK3 (12909 upstream) : TSR2 (69506 downstream)																																			---	---	---	---
ITIH5L	347365	broad.mit.edu	37	X	54802615	54802616	+	Intron	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:54802615_54802616delAA	uc004dtj.2	-							NM_198510	NP_940912			inter-alpha (globulin) inhibitor H5-like						hyaluronan metabolic process	extracellular region	serine-type endopeptidase inhibitor activity			lung(2)|skin(2)|ovary(1)|breast(1)	6																		---	---	---	---
Unknown	0	broad.mit.edu	37	X	54934802	54934802	+	IGR	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:54934802delG								MAGED2 (92357 upstream) : TRO (12447 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	55511428	55511428	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:55511428delA								MAGEH1 (31430 upstream) : USP51 (1534 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	55669134	55669135	+	IGR	INS	-	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:55669134_55669135insA								FOXR2 (17377 upstream) : RRAGB (74975 downstream)																																			---	---	---	---
KLF8	11279	broad.mit.edu	37	X	56259443	56259443	+	5'UTR	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:56259443delG	uc004dur.2	+	1					KLF8_uc010nkg.2_5'UTR|KLF8_uc011mop.1_Intron|KLF8_uc010nkh.2_5'Flank	NM_007250	NP_009181			Kruppel-like factor 8 isoform 1						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	X	56606566	56606566	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:56606566delT								UBQLN2 (13197 upstream) : LOC550643 (149152 downstream)																																			---	---	---	---
LOC550643	550643	broad.mit.edu	37	X	56809150	56809151	+	Intron	INS	-	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:56809150_56809151insT	uc004dut.3	+							NR_015367				Homo sapiens hypothetical protein LOC550643, mRNA (cDNA clone IMAGE:5285100).												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	X	57068550	57068551	+	IGR	INS	-	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:57068550_57068551insT								SPIN3 (46562 upstream) : SPIN2B (77565 downstream)																																			---	---	---	---
FAAH2	158584	broad.mit.edu	37	X	57442777	57442778	+	Intron	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:57442777_57442778delTT	uc004dvc.2	+							NM_174912	NP_777572			fatty acid amide hydrolase 2							integral to membrane	carbon-nitrogen ligase activity, with glutamine as amido-N-donor|hydrolase activity			ovary(3)	3															HNSCC(52;0.14)			---	---	---	---
Unknown	0	broad.mit.edu	37	X	57905897	57905897	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:57905897delA								ZXDB (281991 upstream) : ZXDA (28301 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	57998659	57998659	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:57998659delT								ZXDA (61592 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	61795772	61795773	+	IGR	INS	-	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:61795772_61795773insT								None (None upstream) : SPIN4 (771335 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	61806595	61806596	+	IGR	INS	-	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:61806595_61806596insA								None (None upstream) : SPIN4 (760512 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	61834345	61834345	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:61834345delT								None (None upstream) : SPIN4 (732763 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	62620543	62620543	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:62620543delT								SPIN4 (49325 upstream) : LOC92249 (25896 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	63105501	63105501	+	IGR	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:63105501delC								MIR1468 (99534 upstream) : FAM123B (299497 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	64368930	64368930	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:64368930delT								ZC4H2 (114337 upstream) : ZC3H12B (339776 downstream)																																			---	---	---	---
ZC3H12B	340554	broad.mit.edu	37	X	64722149	64722150	+	Frame_Shift_Ins	INS	-	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:64722149_64722150insT	uc010nko.2	+	5	1547_1548	c.1538_1539insT	c.(1537-1539)CATfs	p.H513fs		NM_001010888	NP_001010888	Q5HYM0	ZC12B_HUMAN	zinc finger CCCH-type containing 12B	513							endonuclease activity|nucleic acid binding|zinc ion binding			lung(1)|kidney(1)|pancreas(1)	3																		---	---	---	---
Unknown	0	broad.mit.edu	37	X	65887236	65887236	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:65887236delA								EDA2R (28128 upstream) : AR (876638 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	65915744	65915745	+	IGR	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:65915744_65915745delTT								EDA2R (56636 upstream) : AR (848129 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	66256726	66256726	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:66256726delA								EDA2R (397618 upstream) : AR (507148 downstream)																																			---	---	---	---
AR	367	broad.mit.edu	37	X	66943842	66943842	+	3'UTR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:66943842delT	uc004dwu.1	+	8					AR_uc004dwv.1_3'UTR	NM_000044	NP_000035			androgen receptor isoform 1						cell death|cell growth|cell proliferation|cell-cell signaling|negative regulation of apoptosis|negative regulation of integrin biosynthetic process|positive regulation of cell proliferation|positive regulation of integrin biosynthetic process|positive regulation of NF-kappaB transcription factor activity|positive regulation of phosphorylation|positive regulation of transcription from RNA polymerase II promoter|positive regulation of transcription from RNA polymerase III promoter|regulation of establishment of protein localization in plasma membrane|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor|transport	cytoplasm|nuclear chromatin|nucleoplasm	androgen binding|androgen receptor activity|beta-catenin binding|enzyme binding|ligand-regulated transcription factor activity|protein dimerization activity|sequence-specific DNA binding transcription factor activity|transcription factor binding|transcription regulatory region DNA binding|zinc ion binding			ovary(3)|lung(2)|breast(2)|central_nervous_system(1)	8	all_cancers(1;0.173)|Prostate(1;2.27e-16)|all_epithelial(1;0.102)	all_lung(315;1.3e-11)			Bicalutamide(DB01128)|Cyproterone(DB04839)|Dromostanolone(DB00858)|Finasteride(DB01216)|Fluoxymesterone(DB01185)|Flutamide(DB00499)|Nandrolone(DB00984)|Nilutamide(DB00665)|Oxandrolone(DB00621)|Testosterone(DB00624)									Androgen_Insensitivity_Syndrome				---	---	---	---
OPHN1	4983	broad.mit.edu	37	X	67403899	67403900	+	Intron	INS	-	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:67403899_67403900insG	uc004dww.3	-						OPHN1_uc011mpg.1_Intron	NM_002547	NP_002538			oligophrenin 1						axon guidance|endocytosis|filopodium assembly|small GTPase mediated signal transduction|substrate-dependent cell migration, cell extension	axon|cell junction|cytosol|dendritic spine|synapse	cytoskeletal adaptor activity|Rho GTPase activator activity|SH3 domain binding			ovary(2)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	X	67683780	67683780	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:67683780delA								OPHN1 (30481 upstream) : YIPF6 (35106 downstream)																																			---	---	---	---
STARD8	9754	broad.mit.edu	37	X	67894612	67894613	+	Intron	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:67894612_67894613delTT	uc004dxa.2	+						STARD8_uc004dxb.2_Intron	NM_014725	NP_055540			StAR-related lipid transfer (START) domain						regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol|focal adhesion	GTPase activator activity			breast(3)|ovary(2)|pancreas(1)	6																		---	---	---	---
EFNB1	1947	broad.mit.edu	37	X	68059472	68059480	+	Intron	DEL	CTGACTTCT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:68059472_68059480delCTGACTTCT	uc004dxd.3	+						EFNB1_uc004dxe.2_Intron	NM_004429	NP_004420			ephrin-B1 precursor						cell adhesion|cell-cell signaling	integral to plasma membrane|soluble fraction|synapse	ephrin receptor binding				0																		---	---	---	---
IGBP1	3476	broad.mit.edu	37	X	69367273	69367273	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:69367273delA	uc004dxv.2	+						IGBP1_uc004dxw.2_Intron	NM_001551	NP_001542			immunoglobulin binding protein 1						B cell activation|negative regulation of caspase activity|negative regulation of stress-activated MAPK cascade|negative regulation of transcription from RNA polymerase II promoter|regulation of microtubule-based movement|response to interleukin-1|response to tumor necrosis factor|signal transduction	cytoplasm	protein phosphatase type 2A regulator activity			kidney(1)|pancreas(1)	2																		---	---	---	---
ARR3	407	broad.mit.edu	37	X	69497769	69497769	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:69497769delA	uc004dyb.2	+						ARR3_uc004dya.2_Intron	NM_004312	NP_004303			arrestin 3, retinal (X-arrestin)						signal transduction|visual perception	cytoplasm|soluble fraction				large_intestine(2)|ovary(2)	4																		---	---	---	---
KIF4A	24137	broad.mit.edu	37	X	69547855	69547855	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:69547855delA	uc004dyg.2	+						KIF4A_uc010nkw.2_Intron|KIF4A_uc004dyf.1_Intron	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	69774440	69774440	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:69774440delA	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)																	---	---	---	---
TEX11	56159	broad.mit.edu	37	X	70026650	70026650	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:70026650delA	uc004dyl.2	-						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)																	---	---	---	---
TEX11	56159	broad.mit.edu	37	X	70127618	70127618	+	5'UTR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:70127618delA	uc004dyl.2	-	2					TEX11_uc004dym.2_Frame_Shift_Del_p.S8fs	NM_001003811	NP_001003811			testis expressed sequence 11 isoform 1								protein binding			ovary(3)|breast(1)|skin(1)	5	Renal(35;0.156)																	---	---	---	---
TAF1	6872	broad.mit.edu	37	X	70643256	70643256	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:70643256delT	uc004dzu.3	+						BCYRN1_uc011mpt.1_Intron|TAF1_uc004dzt.3_Intron|TAF1_uc004dzv.3_Intron|TAF1_uc010nld.1_Intron|TAF1_uc010nle.1_Intron|TAF1_uc010nlf.1_Intron|TAF1_uc004dzx.2_Intron|TAF1_uc004dzy.2_Intron|TAF1_uc004dzw.1_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	71289268	71289269	+	Intron	DEL	AG	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:71289268_71289269delAG	uc011mqa.1	+							NM_001013627	NP_001013649			NHS-like 2												0	Renal(35;0.156)																	---	---	---	---
Unknown	0	broad.mit.edu	37	X	71492424	71492424	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:71492424delA								PIN4 (7612 upstream) : RPS4X (30 downstream)																																			---	---	---	---
HDAC8	55869	broad.mit.edu	37	X	71742492	71742492	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:71742492delT	uc004eau.2	-						HDAC8_uc011mqe.1_Intron|HDAC8_uc011mqf.1_Intron|HDAC8_uc011mqg.1_Intron|HDAC8_uc011mqh.1_Intron|HDAC8_uc010nlk.1_Intron|HDAC8_uc004eav.2_Intron|HDAC8_uc004eaw.2_Intron	NM_018486	NP_060956			histone deacetylase 8						chromatin assembly or disassembly|negative regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	cytoplasm|histone deacetylase complex|nuclear chromosome	histone deacetylase activity (H3-K16 specific)|metal ion 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 factor binding				0	Renal(35;0.156)				Vorinostat(DB02546)													---	---	---	---
PHKA1	5255	broad.mit.edu	37	X	71880269	71880269	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:71880269delT	uc004eax.3	-						PHKA1_uc004eay.3_Intron|PHKA1_uc011mqi.1_Intron	NM_002637	NP_002628			phosphorylase kinase, alpha 1 (muscle) isoform						glucose metabolic process|glycogen catabolic process	cytosol|plasma membrane	calmodulin binding|glucan 1,4-alpha-glucosidase activity|phosphorylase kinase activity			ovary(3)|skin(1)	4	Renal(35;0.156)																	---	---	---	---
PHKA1	5255	broad.mit.edu	37	X	71899695	71899695	+	Intron	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:71899695delG	uc004eax.3	-						PHKA1_uc004eay.3_Intron|PHKA1_uc011mqi.1_Intron	NM_002637	NP_002628			phosphorylase kinase, alpha 1 (muscle) isoform						glucose metabolic process|glycogen catabolic process	cytosol|plasma membrane	calmodulin binding|glucan 1,4-alpha-glucosidase activity|phosphorylase kinase activity			ovary(3)|skin(1)	4	Renal(35;0.156)																	---	---	---	---
TSIX	9383	broad.mit.edu	37	X	73042890	73042890	+	RNA	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:73042890delT	uc004ebn.2	+	1		c.30851delT			XIST_uc004ebm.1_RNA	NR_003255				Homo sapiens XIST antisense RNA (non-protein coding) (TSIX), non-coding RNA.												0																		---	---	---	---
TSIX	9383	broad.mit.edu	37	X	73046080	73046080	+	RNA	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-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																		---	---	---	---
NCRNA00182	100302692	broad.mit.edu	37	X	73427257	73427258	+	Intron	DEL	GG	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:73427257_73427258delGG	uc010nlq.1	-						uc004ebq.1_Intron					Homo sapiens cDNA FLJ33139 fis, clone UTERU1000109.												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	X	74155263	74155263	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:74155263delA								KIAA2022 (9976 upstream) : ABCB7 (117844 downstream)																																			---	---	---	---
ABCB7	22	broad.mit.edu	37	X	74284697	74284697	+	Intron	DEL	A	-	-	rs71999133		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:74284697delA	uc004eca.2	-						ABCB7_uc004ebz.2_Intron|ABCB7_uc011mqn.1_Intron|ABCB7_uc010nls.2_Intron|ABCB7_uc010nlt.2_Intron	NM_004299	NP_004290			ATP-binding cassette, sub-family B, member 7						cellular iron ion homeostasis	integral to membrane|mitochondrial inner membrane	ATP binding|ATPase activity, coupled to transmembrane movement of substances|heme transporter activity			ovary(1)	1																		---	---	---	---
ZDHHC15	158866	broad.mit.edu	37	X	74670546	74670546	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:74670546delA	uc004ecg.2	-						ZDHHC15_uc004ech.2_Intron|ZDHHC15_uc011mqo.1_Intron|ZDHHC15_uc004eci.2_3'UTR	NM_144969	NP_659406			zinc finger, DHHC-type containing 15 isoform 1							integral to membrane	zinc ion binding			ovary(2)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	X	74964980	74964981	+	IGR	INS	-	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:74964980_74964981insT								ZDHHC15 (221643 upstream) : MAGEE2 (37842 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	75445320	75445320	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:75445320delT								CXorf26 (47287 upstream) : MAGEE1 (202797 downstream)																																			---	---	---	---
ATRX	546	broad.mit.edu	37	X	76928018	76928018	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:76928018delA	uc004ecp.3	-						ATRX_uc004ecq.3_Intron|ATRX_uc004eco.3_Intron|ATRX_uc004ecr.2_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	77280723	77280723	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:77280723delA	uc004ecx.3	+							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																		---	---	---	---
Unknown	0	broad.mit.edu	37	X	77320610	77320610	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:77320610delT								ATP7A (14719 upstream) : PGK1 (39056 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	77614498	77614498	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:77614498delA								CYSLTR1 (31411 upstream) : ZCCHC5 (297068 downstream)																																			---	---	---	---
TBX22	50945	broad.mit.edu	37	X	79272529	79272530	+	Intron	INS	-	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:79272529_79272530insA	uc010nmg.1	+						TBX22_uc004edi.1_Intron	NM_001109878	NP_001103348			T-box 22 isoform 1						multicellular organismal development|negative regulation of transcription from RNA polymerase II promoter	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity			lung(7)|large_intestine(3)|central_nervous_system(2)|breast(1)|skin(1)|ovary(1)	15																		---	---	---	---
BRWD3	254065	broad.mit.edu	37	X	79947491	79947491	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:79947491delA	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																		---	---	---	---
Unknown	0	broad.mit.edu	37	X	80223649	80223649	+	IGR	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:80223649delG								BRWD3 (158416 upstream) : HMGN5 (145551 downstream)																																			---	---	---	---
SH3BGRL	6451	broad.mit.edu	37	X	80469097	80469098	+	Intron	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:80469097_80469098delTT	uc004eef.2	+						SH3BGRL_uc011mqs.1_Intron|SH3BGRL_uc010nml.2_Intron|SH3BGRL_uc010nmm.2_Intron|SH3BGRL_uc010nmn.2_Intron	NM_003022	NP_003013			SH3 domain binding glutamic acid-rich protein							cytoplasm|nucleus	SH3 domain binding|SH3/SH2 adaptor activity			ovary(1)	1		all_lung(315;5.94e-05)																---	---	---	---
Unknown	0	broad.mit.edu	37	X	80699251	80699251	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:80699251delT								SH3BGRL (145209 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	82035796	82035796	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:82035796delA								None (None upstream) : POU3F4 (727473 downstream)																																			---	---	---	---
CYLC1	1538	broad.mit.edu	37	X	83128981	83128981	+	Frame_Shift_Del	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:83128981delA	uc004eei.1	+	4	1286	c.1265delA	c.(1264-1266)GAAfs	p.E422fs	CYLC1_uc004eeh.1_Frame_Shift_Del_p.E421fs	NM_021118	NP_066941	P35663	CYLC1_HUMAN	cylicin, basic protein of sperm head	422	5.				cell differentiation|multicellular organismal development|spermatogenesis	acrosomal matrix|cytoskeletal calyx	structural molecule activity			ovary(4)|skin(1)	5																		---	---	---	---
Unknown	0	broad.mit.edu	37	X	83315898	83315899	+	IGR	INS	-	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:83315898_83315899insA								CYLC1 (174272 upstream) : RPS6KA6 (3085 downstream)																																			---	---	---	---
RPS6KA6	27330	broad.mit.edu	37	X	83371300	83371300	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:83371300delA	uc004eej.1	-						RPS6KA6_uc011mqt.1_Intron|RPS6KA6_uc011mqu.1_Intron	NM_014496	NP_055311			ribosomal protein S6 kinase polypeptide 6						axon guidance|central nervous system development|intracellular protein kinase cascade|synaptic transmission	cytosol|nucleoplasm	ATP binding|magnesium ion binding|protein serine/threonine kinase activity			lung(5)|stomach(1)|central_nervous_system(1)|skin(1)	8																		---	---	---	---
ZNF711	7552	broad.mit.edu	37	X	84524388	84524388	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:84524388delT	uc004eeo.2	+						ZNF711_uc004eep.2_Intron|ZNF711_uc004eeq.2_Intron|ZNF711_uc011mqy.1_Intron	NM_021998	NP_068838			zinc finger protein 711						positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	protein binding|sequence-specific DNA binding|zinc ion binding			ovary(3)|skin(1)	4																		---	---	---	---
Unknown	0	broad.mit.edu	37	X	85114202	85114205	+	IGR	DEL	GGAG	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:85114202_85114205delGGAG								MIR1321 (23339 upstream) : CHM (1981 downstream)																																			---	---	---	---
DACH2	117154	broad.mit.edu	37	X	86087097	86087097	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-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	86336248	86336248	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:86336248delT								DACH2 (248643 upstream) : KLHL4 (436467 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	87325811	87325811	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:87325811delA								KLHL4 (400761 upstream) : CPXCR1 (676415 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	87352266	87352266	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:87352266delT								KLHL4 (427216 upstream) : CPXCR1 (649960 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	87912707	87912707	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:87912707delA								KLHL4 (987657 upstream) : CPXCR1 (89519 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	88459638	88459639	+	IGR	INS	-	GTC	GTC	rs67326256		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:88459638_88459639insGTC								CPXCR1 (449855 upstream) : TGIF2LX (717301 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	89611656	89611657	+	IGR	INS	-	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:89611656_89611657insT								TGIF2LX (433776 upstream) : None (None downstream)																																			---	---	---	---
DIAPH2	1730	broad.mit.edu	37	X	96504063	96504064	+	Intron	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:96504063_96504064delTT	uc004efu.3	+						DIAPH2_uc004eft.3_Intron	NM_006729	NP_006720			diaphanous 2 isoform 156						cell differentiation|cytokinesis|multicellular organismal development|oogenesis	cytosol|early endosome|Golgi apparatus|mitochondrion|nucleolus	receptor binding|Rho GTPase binding			ovary(3)|lung(1)	4																		---	---	---	---
Unknown	0	broad.mit.edu	37	X	98278772	98278772	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:98278772delT								None (None upstream) : LOC442459 (437828 downstream)																																			---	---	---	---
SRPX2	27286	broad.mit.edu	37	X	99906192	99906192	+	Intron	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:99906192delG	uc004egb.2	+							NM_014467	NP_055282			sushi-repeat-containing protein, X-linked 2						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																		---	---	---	---
NOX1	27035	broad.mit.edu	37	X	100103281	100103281	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:100103281delT	uc004egj.2	-						NOX1_uc004egl.3_Intron|NOX1_uc010nne.2_Intron	NM_007052	NP_008983			NADPH oxidase 1 isoform long						angiogenesis|cell migration|electron transport chain|FADH2 metabolic process|hydrogen peroxide metabolic process|inflammatory response|intracellular pH elevation|positive regulation of integrin biosynthetic process|positive regulation of smooth muscle cell proliferation|positive regulation vascular endothelial growth factor production|respiratory burst|response to pH|signal transduction|superoxide anion generation	cell junction|early endosome|invadopodium membrane|NADPH oxidase complex	electron carrier activity|flavin adenine dinucleotide binding|iron ion binding|Rac GTPase binding|superoxide-generating NADPH oxidase activity|voltage-gated proton channel activity			ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	X	100131835	100131836	+	Intron	DEL	TT	-	-	rs60444250		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:100131835_100131836delTT	uc010nnf.2	-						NOX1_uc004egj.2_5'Flank|NOX1_uc004egl.3_5'Flank|NOX1_uc010nne.2_5'Flank					full-length cDNA clone CS0DA010YB10 of Neuroblastoma of Homo sapiens (human).																														---	---	---	---
CENPI	2491	broad.mit.edu	37	X	100357486	100357487	+	Intron	DEL	AC	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:100357486_100357487delAC	uc004egx.2	+						CENPI_uc011mrg.1_Intron|CENPI_uc004egy.2_Intron	NM_006733	NP_006724			centromere protein I						CenH3-containing nucleosome assembly at centromere|mitotic prometaphase	cytosol|kinetochore|nucleoplasm	protein binding			skin(1)	1																		---	---	---	---
TAF7L	54457	broad.mit.edu	37	X	100537679	100537679	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:100537679delT	uc004ehb.2	-						TAF7L_uc004eha.2_Intron|TAF7L_uc004ehc.1_Intron	NM_024885	NP_079161			TATA box binding protein-associated factor, RNA						cell differentiation|multicellular organismal development|regulation of transcription, DNA-dependent|spermatogenesis|transcription initiation from RNA polymerase II promoter	cytoplasm|transcription factor TFIID complex	binding			breast(1)	1																		---	---	---	---
BTK	695	broad.mit.edu	37	X	100614140	100614140	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:100614140delA	uc004ehg.2	-						BTK_uc004ehf.2_5'Flank|BTK_uc010nnh.2_5'Flank|BTK_uc010nni.2_5'Flank|BTK_uc004ehe.2_5'Flank|BTK_uc010nnj.2_5'Flank|BTK_uc010nnk.2_5'Flank|BTK_uc010nnl.2_5'Flank|BTK_uc010nnm.2_5'Flank|BTK_uc010nnn.2_Intron|BTK_uc010nno.2_Intron|BTK_uc004ehh.1_5'Flank|BTK_uc004ehi.2_Intron	NM_000061	NP_000052			Bruton agammaglobulinemia tyrosine kinase						calcium-mediated signaling|induction of apoptosis by extracellular signals|mesoderm development	cytosol|membrane raft|nucleus|plasma membrane	ATP binding|identical protein binding|metal ion binding|non-membrane spanning protein tyrosine kinase activity|phosphatidylinositol-3,4,5-trisphosphate binding			lung(3)|central_nervous_system(2)|ovary(1)	6														Agammaglobulinemia_X-linked				---	---	---	---
NXF5	55998	broad.mit.edu	37	X	101093566	101093566	+	Intron	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:101093566delG	uc011mrk.1	-						NXF5_uc004eih.1_Intron|NXF5_uc004eii.1_Intron|NXF5_uc004eij.1_Intron|NXF5_uc004eik.1_Intron|NXF5_uc004eil.1_Intron	NM_032946	NP_116564			nuclear RNA export factor 5						mRNA export from nucleus|multicellular organismal development	actin cytoskeleton|cytoplasm|nucleus	nucleocytoplasmic transporter activity|nucleotide binding|protein binding|RNA binding			central_nervous_system(1)	1																		---	---	---	---
ZMAT1	84460	broad.mit.edu	37	X	101138375	101138378	+	3'UTR	DEL	ACTG	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:101138375_101138378delACTG	uc004eim.2	-	2					ZMAT1_uc011mrl.1_3'UTR|ZMAT1_uc004ein.2_3'UTR|ZMAT1_uc011mrm.1_3'UTR	NM_032441	NP_115817			zinc finger, matrin type 1 isoform 3							nucleus	zinc ion binding			ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	X	102874616	102874616	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:102874616delA								TCEAL3 (9762 upstream) : TCEAL1 (9032 downstream)																																			---	---	---	---
TMSB15B	286527	broad.mit.edu	37	X	103220212	103220212	+	3'UTR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:103220212delT	uc010noz.2	+	3					TMSB15B_uc004elo.3_RNA|TMSB15B_uc004elq.3_RNA	NM_194324	NP_919305			thymosin beta15b						actin cytoskeleton organization|sequestering of actin monomers	cytoplasm|cytoskeleton	actin binding			skin(1)	1																		---	---	---	---
MCART6	401612	broad.mit.edu	37	X	103362657	103362657	+	Intron	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:103362657delC	uc004elu.2	-							NM_001012755	NP_001012773			mitochondrial carrier triple repeat 6						transport	integral to membrane|mitochondrial inner membrane					0																		---	---	---	---
MCART6	401612	broad.mit.edu	37	X	103373461	103373464	+	Intron	DEL	ACAC	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:103373461_103373464delACAC	uc004elu.2	-							NM_001012755	NP_001012773			mitochondrial carrier triple repeat 6						transport	integral to membrane|mitochondrial inner membrane					0																		---	---	---	---
IL1RAPL2	26280	broad.mit.edu	37	X	104615636	104615636	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:104615636delT	uc004elz.1	+							NM_017416	NP_059112			interleukin 1 receptor accessory protein-like 2						central nervous system development|innate immune response	integral to membrane	interleukin-1, Type II, blocking receptor activity			breast(2)|ovary(1)	3																		---	---	---	---
Unknown	0	broad.mit.edu	37	X	105220272	105220272	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:105220272delA								NRK (17676 upstream) : SERPINA7 (56925 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	105453018	105453021	+	IGR	DEL	ACAC	-	-	rs71772605		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:105453018_105453021delACAC								MUM1L1 (70 upstream) : CXorf57 (402139 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	105698343	105698343	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:105698343delA								MUM1L1 (245395 upstream) : CXorf57 (156817 downstream)																																			---	---	---	---
TBC1D8B	54885	broad.mit.edu	37	X	106082478	106082478	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:106082478delT	uc004emo.2	+						MORC4_uc004emp.3_Intron|TBC1D8B_uc004emn.2_Intron	NM_017752	NP_060222			TBC1 domain family, member 8B (with GRAM domain)							intracellular	calcium ion binding|Rab GTPase activator activity			ovary(2)|central_nervous_system(1)|skin(1)	4																		---	---	---	---
CXorf41	139212	broad.mit.edu	37	X	106486388	106486388	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:106486388delT	uc004enc.2	+						CXorf41_uc004end.2_Intron	NM_173494	NP_775765			hypothetical protein LOC139212												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	X	106755271	106755272	+	IGR	INS	-	CA	CA			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:106755271_106755272insCA								CXorf41 (267799 upstream) : PRPS1 (116382 downstream)																																			---	---	---	---
ATG4A	115201	broad.mit.edu	37	X	107350319	107350319	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:107350319delT	uc004enr.2	+						ATG4A_uc004ent.2_Intron|ATG4A_uc004ens.2_Intron|ATG4A_uc011msl.1_Intron|ATG4A_uc010npi.2_Intron	NM_052936	NP_443168			autophagy-related cysteine endopeptidase 2						autophagy|protein transport|proteolysis	cytoplasm	cysteine-type peptidase activity			pancreas(1)	1																		---	---	---	---
COL4A6	1288	broad.mit.edu	37	X	107405630	107405632	+	Intron	DEL	AAG	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:107405630_107405632delAAG	uc004enw.3	-						COL4A6_uc004env.3_Intron|COL4A6_uc011msn.1_Intron|COL4A6_uc010npk.2_Intron|COL4A6_uc011msm.1_5'Flank|COL4A6_uc010npj.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	107433735	107433735	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:107433735delA	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-4200-01A-01D-1126-08	TCGA-BR-4200-11A-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)													---	---	---	---
Unknown	0	broad.mit.edu	37	X	109215193	109215194	+	IGR	INS	-	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:109215193_109215194insT								ACSL4 (238572 upstream) : TMEM164 (30669 downstream)																																			---	---	---	---
RGAG1	57529	broad.mit.edu	37	X	109610674	109610674	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:109610674delT	uc011msr.1	+						AMMECR1_uc004eoq.2_Intron	NM_020769	NP_065820			retrotransposon gag domain containing 1											lung(2)|upper_aerodigestive_tract(1)|ovary(1)	4																		---	---	---	---
PAK3	5063	broad.mit.edu	37	X	110406780	110406781	+	Intron	INS	-	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:110406780_110406781insT	uc004epa.2	+						PAK3_uc010npt.1_Intron|PAK3_uc010npu.1_Intron|PAK3_uc004eoy.1_5'UTR|PAK3_uc004eoz.2_Intron|PAK3_uc011mst.1_Intron|PAK3_uc010npv.1_Intron|PAK3_uc010npw.1_Intron	NM_001128173	NP_001121645			p21-activated kinase 3 isoform d						multicellular organismal development		ATP binding|metal ion binding|protein serine/threonine kinase activity|SH3 domain binding			lung(6)|ovary(3)|large_intestine(1)	10															TSP Lung(19;0.15)			---	---	---	---
ZCCHC16	340595	broad.mit.edu	37	X	111562983	111562983	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:111562983delT	uc004epo.1	+							NM_001004308	NP_001004308			zinc finger, CCHC domain containing 16								nucleic acid binding|zinc ion binding			ovary(1)	1																		---	---	---	---
ZCCHC16	340595	broad.mit.edu	37	X	111646364	111646364	+	Intron	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:111646364delC	uc004epo.1	+							NM_001004308	NP_001004308			zinc finger, CCHC domain containing 16								nucleic acid binding|zinc ion binding			ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	X	116590208	116590208	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:116590208delT								CXorf61 (996071 upstream) : KLHL13 (441569 downstream)																																			---	---	---	---
DOCK11	139818	broad.mit.edu	37	X	117718660	117718660	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:117718660delT	uc004eqp.2	+						DOCK11_uc004eqq.2_Intron	NM_144658	NP_653259			dedicator of cytokinesis 11						blood coagulation	cytosol	GTP binding			ovary(3)	3																		---	---	---	---
Unknown	0	broad.mit.edu	37	X	118076175	118076175	+	IGR	DEL	A	-	-	rs111400980		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:118076175delA								ZCCHC12 (115245 upstream) : LONRF3 (32538 downstream)																																			---	---	---	---
SEPT6	23157	broad.mit.edu	37	X	118781447	118781448	+	Intron	DEL	TT	-	-	rs112764543		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:118781447_118781448delTT	uc004erv.2	-						SEPT6_uc010nqk.2_Intron|SEPT6_uc004ers.2_Intron|SEPT6_uc004ert.2_Intron|SEPT6_uc004eru.2_Intron|SEPT6_uc004erw.2_Intron|SEPT6_uc011mtv.1_Intron|SEPT6_uc011mtw.1_Intron|MIR766_hsa-mir-766|MI0003836_5'Flank	NM_015129	NP_055944			septin 6 isoform B						cell cycle|cytokinesis|interspecies interaction between organisms	cleavage furrow|condensed chromosome kinetochore|midbody|septin complex|spindle	GTP binding|protein binding			lung(1)|ovary(1)|prostate(1)|kidney(1)	4																		---	---	---	---
NKAP	79576	broad.mit.edu	37	X	119070412	119070412	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:119070412delA	uc004esh.2	-						NKAP_uc004esg.2_Intron	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	119580084	119580084	+	Intron	DEL	C	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:119580084delC	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																		---	---	---	---
CUL4B	8450	broad.mit.edu	37	X	119680348	119680348	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:119680348delT	uc004esw.2	-						CUL4B_uc010nqq.2_Intron|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																		---	---	---	---
Unknown	0	broad.mit.edu	37	X	120224002	120224003	+	IGR	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:120224002_120224003delTT								GLUD2 (40208 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	120365233	120365234	+	IGR	INS	-	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:120365233_120365234insT								GLUD2 (181439 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	121516723	121516724	+	IGR	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:121516723_121516724delAA								None (None upstream) : GRIA3 (801372 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	122100012	122100013	+	IGR	INS	-	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:122100012_122100013insA								None (None upstream) : GRIA3 (218083 downstream)																																			---	---	---	---
ODZ1	10178	broad.mit.edu	37	X	123970160	123970162	+	Intron	DEL	AGA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:123970160_123970162delAGA	uc004euj.2	-						ODZ1_uc011muj.1_Intron|ODZ1_uc010nqy.2_Intron	NM_014253	NP_055068			odz, odd Oz/ten-m homolog 1 isoform 3						immune response|negative regulation of cell proliferation|nervous system development|signal transduction	extracellular region	heparin binding			ovary(11)|breast(4)|large_intestine(2)|skin(2)|pancreas(2)|upper_aerodigestive_tract(1)|lung(1)	23																		---	---	---	---
Unknown	0	broad.mit.edu	37	X	127564492	127564492	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:127564492delT								ACTRT1 (378110 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	129012710	129012710	+	IGR	DEL	A	-	-	rs28565068		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:129012710delA								ZDHHC9 (34586 upstream) : UTP14A (27449 downstream)																																			---	---	---	---
BCORL1	63035	broad.mit.edu	37	X	129145787	129145787	+	Intron	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:129145787delG	uc004evb.1	+						BCORL1_uc010nrd.1_5'Flank	NM_021946	NP_068765			BCL6 co-repressor-like 1						chromatin modification|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus				ovary(4)|breast(2)|lung(1)	7																		---	---	---	---
BCORL1	63035	broad.mit.edu	37	X	129171119	129171119	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:129171119delA	uc004evb.1	+						BCORL1_uc004evc.1_Intron	NM_021946	NP_068765			BCL6 co-repressor-like 1						chromatin modification|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus				ovary(4)|breast(2)|lung(1)	7																		---	---	---	---
Unknown	0	broad.mit.edu	37	X	129434364	129434365	+	IGR	DEL	AC	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:129434364_129434365delAC								ZNF280C (31491 upstream) : SLC25A14 (39545 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	129686117	129686118	+	IGR	DEL	TT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:129686117_129686118delTT								FAM45B (55385 upstream) : ENOX2 (71241 downstream)																																			---	---	---	---
ARHGAP36	158763	broad.mit.edu	37	X	130215479	130215479	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:130215479delT	uc004evz.2	+						ARHGAP36_uc004ewa.2_Intron|ARHGAP36_uc004ewb.2_Intron|ARHGAP36_uc004ewc.2_5'Flank	NM_144967	NP_659404			hypothetical protein LOC158763 precursor						regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol	GTPase activator activity			ovary(3)	3																		---	---	---	---
Unknown	0	broad.mit.edu	37	X	130769665	130769665	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:130769665delT								IGSF1 (56792 upstream) : LOC286467 (67014 downstream)																																			---	---	---	---
RAP2C	57826	broad.mit.edu	37	X	131351076	131351076	+	Frame_Shift_Del	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:131351076delT	uc004ewp.2	-	2	1005	c.221delA	c.(220-222)AACfs	p.N74fs	uc004ewr.1_5'Flank|RAP2C_uc004ewo.2_Frame_Shift_Del_p.N8fs|RAP2C_uc010nrk.2_RNA|RAP2C_uc004ewq.3_Frame_Shift_Del_p.N74fs	NM_021183	NP_067006	Q9Y3L5	RAP2C_HUMAN	RAP2C, member of RAS oncogene family precursor	74					negative regulation of cell migration|positive regulation of protein autophosphorylation|Rap protein signal transduction|regulation of protein tyrosine kinase activity	recycling endosome membrane	GTP binding|GTPase activity			ovary(1)	1	Acute lymphoblastic leukemia(192;0.000127)																	---	---	---	---
Unknown	0	broad.mit.edu	37	X	132381028	132381028	+	IGR	DEL	G	-	-	rs78453418		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:132381028delG								TFDP3 (28652 upstream) : GPC4 (54036 downstream)																																			---	---	---	---
GPC3	2719	broad.mit.edu	37	X	132816753	132816753	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:132816753delA	uc004exe.1	-						GPC3_uc004exd.1_Intron|GPC3_uc010nrn.1_Intron|GPC3_uc011mvh.1_Intron|GPC3_uc010nro.1_Intron	NM_004484	NP_004475			glypican 3 isoform 2 precursor							extracellular space|integral to plasma membrane|proteinaceous extracellular matrix	heparan sulfate proteoglycan binding|peptidyl-dipeptidase inhibitor activity			lung(2)|prostate(1)|breast(1)|skin(1)	5	Acute lymphoblastic leukemia(192;0.000127)							T|D|Mis|N|F|S			Wilms tumour			Simpson-Golabi-Behmel_syndrome				---	---	---	---
GPC3	2719	broad.mit.edu	37	X	133034255	133034255	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:133034255delT	uc004exe.1	-						GPC3_uc010nrn.1_Intron|GPC3_uc011mvh.1_Intron|GPC3_uc010nro.1_Intron|GPC3_uc010nrp.1_Intron	NM_004484	NP_004475			glypican 3 isoform 2 precursor							extracellular space|integral to plasma membrane|proteinaceous extracellular matrix	heparan sulfate proteoglycan binding|peptidyl-dipeptidase inhibitor activity			lung(2)|prostate(1)|breast(1)|skin(1)	5	Acute lymphoblastic leukemia(192;0.000127)							T|D|Mis|N|F|S			Wilms tumour			Simpson-Golabi-Behmel_syndrome				---	---	---	---
PHF6	84295	broad.mit.edu	37	X	133548080	133548080	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-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)																	---	---	---	---
Unknown	0	broad.mit.edu	37	X	135162167	135162167	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:135162167delT								SLC9A6 (32741 upstream) : FHL1 (66694 downstream)																																			---	---	---	---
MAP7D3	79649	broad.mit.edu	37	X	135322706	135322706	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:135322706delA	uc004ezt.2	-						MAP7D3_uc004ezs.2_Intron|MAP7D3_uc011mwc.1_Intron|MAP7D3_uc010nsa.1_Intron	NM_024597	NP_078873			MAP7 domain containing 3							cytoplasm|spindle				ovary(2)|central_nervous_system(1)|skin(1)	4	Acute lymphoblastic leukemia(192;0.000127)																	---	---	---	---
Unknown	0	broad.mit.edu	37	X	135502792	135502792	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:135502792delA								GPR112 (3745 upstream) : BRS3 (67333 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	135887475	135887475	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:135887475delA								ARHGEF6 (23972 upstream) : RBMX (63878 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	136601625	136601626	+	IGR	DEL	AA	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:136601625_136601626delAA								GPR101 (487792 upstream) : ZIC3 (46720 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	137004114	137004114	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:137004114delT								ZIC3 (349857 upstream) : LOC158696 (692778 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	137019796	137019796	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:137019796delA								ZIC3 (365539 upstream) : LOC158696 (677096 downstream)																																			---	---	---	---
MCF2	4168	broad.mit.edu	37	X	138708237	138708237	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:138708237delT	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	138834350	138834351	+	Intron	DEL	CT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:138834350_138834351delCT	uc004faz.2	-						ATP11C_uc004fax.2_Intron|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)																	---	---	---	---
ATP11C	286410	broad.mit.edu	37	X	138840030	138840030	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:138840030delA	uc004faz.2	-						ATP11C_uc004fax.2_Intron|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)																	---	---	---	---
Unknown	0	broad.mit.edu	37	X	139006117	139006117	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:139006117delT								ATP11C (91670 upstream) : MIR505 (190 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	139970984	139970985	+	IGR	DEL	GT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:139970984_139970985delGT								CDR1 (104261 upstream) : MIR320D2 (37352 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	140267804	140267805	+	IGR	DEL	AC	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:140267804_140267805delAC								SPANXB2 (181934 upstream) : LDOC1 (2135 downstream)																																			---	---	---	---
SPANXC	64663	broad.mit.edu	37	X	140414272	140414272	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:140414272delA	uc004fbl.2	-											Homo sapiens nuclear-associated protein SPAN-Xa (SPANX) mRNA, complete cds.							cytoplasm|nucleus					0	Acute lymphoblastic leukemia(192;7.65e-05)																	---	---	---	---
Unknown	0	broad.mit.edu	37	X	140815241	140815241	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:140815241delT								SPANXE (28586 upstream) : MAGEC3 (110861 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	141695205	141695205	+	IGR	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:141695205delG								MAGEC2 (402129 upstream) : SPANXN4 (418499 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	143001844	143001844	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:143001844delA								UBE2NL (33489 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	144622471	144622471	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:144622471delT								SPANXN1 (284743 upstream) : SLITRK2 (276876 downstream)																																			---	---	---	---
FMR1	2332	broad.mit.edu	37	X	147011446	147011446	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:147011446delT	uc010nst.2	+						FMR1_uc011mwz.1_Intron|FMR1_uc004fcj.2_Intron|FMR1_uc004fck.3_Intron|FMR1_uc004fcl.3_Intron|FMR1_uc011mxa.1_5'Flank	NM_002024	NP_002015			fragile X mental retardation 1						mRNA transport|negative regulation of translational initiation	cytoplasm|mRNA cap binding complex|nucleolus|nucleoplasm|soluble fraction	mRNA binding|protein binding			ovary(2)|pancreas(1)	3	Acute lymphoblastic leukemia(192;6.56e-05)													Fragile_X_syndrome				---	---	---	---
FMR1	2332	broad.mit.edu	37	X	147026629	147026630	+	Intron	INS	-	TG	TG			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:147026629_147026630insTG	uc010nst.2	+						FMR1_uc004fcj.2_Intron|FMR1_uc004fck.3_Intron|FMR1_uc004fcl.3_Intron|FMR1_uc011mxa.1_Intron	NM_002024	NP_002015			fragile X mental retardation 1						mRNA transport|negative regulation of translational initiation	cytoplasm|mRNA cap binding complex|nucleolus|nucleoplasm|soluble fraction	mRNA binding|protein binding			ovary(2)|pancreas(1)	3	Acute lymphoblastic leukemia(192;6.56e-05)													Fragile_X_syndrome				---	---	---	---
IDS	3423	broad.mit.edu	37	X	148574533	148574533	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:148574533delA	uc011mxe.1	-						IDS_uc011mxd.1_5'Flank|IDS_uc011mxf.1_Intron|IDS_uc011mxg.1_Intron|IDS_uc010nsu.1_Intron|IDS_uc004fcw.3_Intron|IDS_uc011mxh.1_Intron|IDS_uc011mxi.1_Intron	NM_000202	NP_000193			iduronate-2-sulfatase isoform a precursor							lysosome	iduronate-2-sulfatase activity|metal ion binding				0	Acute lymphoblastic leukemia(192;6.56e-05)|Colorectal(9;0.0662)																	---	---	---	---
MAGEA11	4110	broad.mit.edu	37	X	148797911	148797911	+	Frame_Shift_Del	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:148797911delT	uc004fdq.2	+	5	867	c.765delT	c.(763-765)AATfs	p.N255fs	HSFX2_uc004fdl.2_Intron|HSFX1_uc004fdm.2_Intron|MAGEA11_uc004fdr.2_Frame_Shift_Del_p.N226fs	NM_005366	NP_005357	P43364	MAGAB_HUMAN	melanoma antigen family A, 11 isoform a	255	MAGE.					cytoplasm|nucleus	protein binding			ovary(2)	2	Acute lymphoblastic leukemia(192;6.56e-05)|Colorectal(9;0.0662)																	---	---	---	---
MTM1	4534	broad.mit.edu	37	X	149767039	149767039	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:149767039delT	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	149807261	149807261	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:149807261delT	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)																	---	---	---	---
MTMR1	8776	broad.mit.edu	37	X	149898766	149898766	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:149898766delT	uc004fei.2	+						MTMR1_uc011mya.1_Intron|MTMR1_uc004feg.1_Intron|MTMR1_uc004feh.1_Intron|MTMR1_uc004fej.2_Intron|MTMR1_uc010ntf.2_Intron	NM_003828	NP_003819			myotubularin-related protein 1							plasma membrane	protein tyrosine phosphatase activity			ovary(1)	1	Acute lymphoblastic leukemia(192;6.56e-05)																	---	---	---	---
Unknown	0	broad.mit.edu	37	X	150653232	150653232	+	IGR	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:150653232delG								VMA21 (75397 upstream) : PASD1 (78775 downstream)																																			---	---	---	---
GABRE	2564	broad.mit.edu	37	X	151142547	151142547	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:151142547delA	uc004ffi.2	-						GABRE_uc011myd.1_Intron|GABRE_uc011mye.1_Intron	NM_004961	NP_004952			gamma-aminobutyric acid (GABA) A receptor,						gamma-aminobutyric acid signaling pathway	cell junction|chloride channel complex|integral to plasma membrane|postsynaptic membrane	chloride channel activity|extracellular ligand-gated ion channel activity|GABA-A receptor activity			ovary(2)	2	Acute lymphoblastic leukemia(192;6.56e-05)																	---	---	---	---
Unknown	0	broad.mit.edu	37	X	151787057	151787059	+	IGR	DEL	TTT	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:151787057_151787059delTTT								GABRA3 (167226 upstream) : GABRQ (19578 downstream)																																			---	---	---	---
CSAG1	158511	broad.mit.edu	37	X	151909222	151909223	+	3'UTR	INS	-	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:151909222_151909223insA	uc004fge.2	+	5					CSAG1_uc004fgf.2_3'UTR|CSAG1_uc004fgd.2_RNA	NM_153478	NP_705611			chondrosarcoma associated gene 1 precursor											ovary(1)	1	Acute lymphoblastic leukemia(192;6.56e-05)																	---	---	---	---
Unknown	0	broad.mit.edu	37	X	152362615	152362616	+	IGR	INS	-	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:152362615_152362616insT								PNMA6A (119214 upstream) : MAGEA1 (118906 downstream)																																			---	---	---	---
DKC1	1736	broad.mit.edu	37	X	153994771	153994771	+	Intron	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:153994771delA	uc004fmm.2	+						DKC1_uc010nvf.2_Intron|SNORA36A_uc004fmn.2_5'Flank	NM_001363	NP_001354			dyskerin isoform 1						cell proliferation|pseudouridine synthesis|rRNA processing|telomere maintenance via telomerase	Cajal body|nucleolus|telomerase holoenzyme complex	protein binding|pseudouridine synthase activity|RNA binding|telomerase activity				0	all_cancers(53;8.15e-17)|all_epithelial(53;1.1e-10)|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)													Congenital_Dyskeratosis				---	---	---	---
F8	2157	broad.mit.edu	37	X	154130095	154130095	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:154130095delT	uc004fmt.2	-						F8_uc010nvi.1_Intron	NM_000132	NP_000123			coagulation factor VIII isoform a precursor						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)													---	---	---	---
VBP1	7411	broad.mit.edu	37	X	154463483	154463483	+	Intron	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:154463483delT	uc004fnc.2	+						VBP1_uc004fnd.2_Intron	NM_003372	NP_003363			von Hippel-Lindau binding protein 1						'de novo' posttranslational protein folding	nucleus|prefoldin complex	unfolded 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	154616718	154616718	+	IGR	DEL	T	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:154616718delT								CLIC2 (52732 upstream) : TMLHE (103055 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	154959485	154959485	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:154959485delA								TMLHE (116868 upstream) : SPRY3 (37966 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	Y	9978056	9978056	+	IGR	DEL	G	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrY:9978056delG								TTTY22 (327202 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	Y	9992532	9992532	+	IGR	DEL	A	-	-			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrY:9992532delA								TTTY22 (341678 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	Y	59002856	59002857	+	IGR	INS	-	AGA	AGA	rs10648088		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrY:59002856_59002857insAGA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	Y	59006978	59006978	+	IGR	DEL	A	-	-	rs140439618		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrY:59006978delA								None (None upstream) : None (None downstream)																																			---	---	---	---
AGRN	375790	broad.mit.edu	37	1	979278	979278	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:979278A>G	uc001ack.1	+	10	1924	c.1874A>G	c.(1873-1875)CAC>CGC	p.H625R		NM_198576	NP_940978	O00468	AGRIN_HUMAN	agrin precursor	625	Kazal-like 7.				axon guidance|clustering of voltage-gated sodium channels|muscarinic acetylcholine receptor signaling pathway|receptor clustering	basal lamina	laminin binding|structural constituent of cytoskeleton			central_nervous_system(2)|breast(1)	3	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;0.00462)|Epithelial(90;5.98e-38)|OV - Ovarian serous cystadenocarcinoma(86;5.43e-23)|Colorectal(212;5.97e-05)|COAD - Colon adenocarcinoma(227;0.000201)|Kidney(185;0.0024)|BRCA - Breast invasive adenocarcinoma(365;0.00246)|STAD - Stomach adenocarcinoma(132;0.00645)|KIRC - Kidney renal clear cell carcinoma(229;0.0354)|Lung(427;0.201)														---	---	---	---
SDF4	51150	broad.mit.edu	37	1	1159259	1159259	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:1159259A>G	uc001adh.3	-	3	745	c.416T>C	c.(415-417)ATG>ACG	p.M139T	SDF4_uc001adg.2_5'Flank|SDF4_uc001adi.3_Missense_Mutation_p.M139T|SDF4_uc009vjv.2_Missense_Mutation_p.M17T|SDF4_uc009vjw.2_RNA|SDF4_uc001adj.1_Missense_Mutation_p.M17T	NM_016176	NP_057260	Q9BRK5	CAB45_HUMAN	stromal cell derived factor 4 isoform 2	139	EF-hand 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)														---	---	---	---
UBE2J2	118424	broad.mit.edu	37	1	1190778	1190778	+	Silent	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:1190778C>T	uc001adn.2	-	7	895	c.585G>A	c.(583-585)ACG>ACA	p.T195T	UBE2J2_uc001adm.2_Silent_p.T160T|UBE2J2_uc001ado.2_Silent_p.T211T|UBE2J2_uc001adp.2_Silent_p.T195T|UBE2J2_uc001adq.2_Silent_p.T143T|UBE2J2_uc001adr.2_Silent_p.T143T|UBE2J2_uc001ads.2_Silent_p.T143T	NM_194458	NP_919440	Q8N2K1	UB2J2_HUMAN	ubiquitin conjugating enzyme E2, J2 isoform 3	195	Cytoplasmic (Potential).				response to unfolded protein	endoplasmic reticulum membrane|integral to membrane	ATP binding|ubiquitin-protein ligase 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;6.66e-35)|OV - Ovarian serous cystadenocarcinoma(86;3.53e-21)|Colorectal(212;0.00019)|COAD - Colon adenocarcinoma(227;0.000215)|Kidney(185;0.00255)|BRCA - Breast invasive adenocarcinoma(365;0.00266)|STAD - Stomach adenocarcinoma(132;0.00645)|KIRC - Kidney renal clear cell carcinoma(229;0.0371)|Lung(427;0.205)														---	---	---	---
CCNL2	81669	broad.mit.edu	37	1	1333657	1333657	+	Silent	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:1333657G>A	uc001afi.2	-	3	461	c.429C>T	c.(427-429)GAC>GAT	p.D143D	CCNL2_uc001afg.1_Translation_Start_Site|CCNL2_uc001afh.2_Silent_p.D143D|CCNL2_uc001afj.2_Silent_p.D143D|CCNL2_uc001afk.2_Silent_p.D143D|LOC148413_uc001afm.2_5'Flank|LOC148413_uc001afn.1_5'Flank|LOC148413_uc009vkc.1_5'Flank|LOC148413_uc009vkd.2_5'Flank	NM_030937	NP_112199	Q96S94	CCNL2_HUMAN	cyclin L2 isoform A	143	Cyclin-like 1.				regulation of cyclin-dependent protein kinase activity|regulation of transcription, DNA-dependent|RNA processing|transcription, DNA-dependent	nuclear speck	protein kinase binding			ovary(2)|central_nervous_system(1)	3	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;2.03e-36)|OV - Ovarian serous cystadenocarcinoma(86;4.17e-22)|Colorectal(212;0.000159)|COAD - Colon adenocarcinoma(227;0.000193)|Kidney(185;0.0023)|BRCA - Breast invasive adenocarcinoma(365;0.00465)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0342)|Lung(427;0.146)														---	---	---	---
MRPL20	55052	broad.mit.edu	37	1	1337471	1337471	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:1337471A>G	uc001afo.3	-	4	538	c.442T>C	c.(442-444)TAC>CAC	p.Y148H	CCNL2_uc001afh.2_5'Flank|CCNL2_uc001afj.2_5'Flank|CCNL2_uc001afk.2_5'Flank|CCNL2_uc001afi.2_5'Flank|LOC148413_uc001afn.1_RNA	NM_017971	NP_060441	Q9BYC9	RM20_HUMAN	mitochondrial ribosomal protein L20 precursor	148							protein binding|rRNA binding				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;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)														---	---	---	---
ATAD3A	55210	broad.mit.edu	37	1	1455652	1455652	+	Missense_Mutation	SNP	G	A	A	rs2767471		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:1455652G>A	uc001afz.1	+	6	884	c.790G>A	c.(790-792)GCC>ACC	p.A264T	ATAD3A_uc001aga.1_Missense_Mutation_p.A216T|ATAD3A_uc001agb.1_Missense_Mutation_p.A137T	NM_018188	NP_060658	Q9NVI7	ATD3A_HUMAN	ATPase family, AAA domain containing 3A	264	Potential.						ATP binding|nucleoside-triphosphatase activity|protein binding			skin(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;1.12e-36)|OV - Ovarian serous cystadenocarcinoma(86;2.18e-22)|Colorectal(212;0.000164)|COAD - Colon adenocarcinoma(227;0.000195)|Kidney(185;0.00233)|BRCA - Breast invasive adenocarcinoma(365;0.00469)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0347)|Lung(427;0.147)														---	---	---	---
NADK	65220	broad.mit.edu	37	1	1686884	1686884	+	Missense_Mutation	SNP	A	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:1686884A>C	uc009vkw.2	-	7	738	c.617T>G	c.(616-618)CTG>CGG	p.L206R	NADK_uc001aic.2_Missense_Mutation_p.L206R|NADK_uc001aid.3_Missense_Mutation_p.L206R|NADK_uc001aie.2_Missense_Mutation_p.L351R|NADK_uc010nyv.1_Missense_Mutation_p.L174R|NADK_uc009vkx.1_Missense_Mutation_p.L84R	NM_023018	NP_075394	O95544	NADK_HUMAN	NAD kinase	206					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	2288976	2288976	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:2288976C>A	uc001ajb.1	-	10	952	c.931G>T	c.(931-933)GCT>TCT	p.A311S	MORN1_uc009vld.2_Missense_Mutation_p.A287S|MORN1_uc001ajd.1_Missense_Mutation_p.A311S	NM_024848	NP_079124	Q5T089	MORN1_HUMAN	MORN repeat containing 1	311										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)														---	---	---	---
ACTRT2	140625	broad.mit.edu	37	1	2939334	2939334	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:2939334G>A	uc001ajz.2	+	1	1289	c.1084G>A	c.(1084-1086)GCA>ACA	p.A362T		NM_080431	NP_536356	Q8TDY3	ACTT2_HUMAN	actin-related protein M2	362						cytoplasm|cytoskeleton					0	all_cancers(77;0.00205)|all_epithelial(69;0.0011)|Ovarian(185;0.0634)|Lung NSC(156;0.0893)|all_lung(157;0.0909)	all_epithelial(116;2.66e-20)|all_lung(118;1.56e-08)|Lung NSC(185;2.54e-06)|Breast(487;0.00156)|Renal(390;0.00183)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0308)|Lung SC(97;0.0847)|Medulloblastoma(700;0.123)		Epithelial(90;7.19e-38)|OV - Ovarian serous cystadenocarcinoma(86;5.15e-22)|GBM - Glioblastoma multiforme(42;1.1e-12)|Colorectal(212;3.98e-05)|COAD - Colon adenocarcinoma(227;0.000193)|Kidney(185;0.000329)|BRCA - Breast invasive adenocarcinoma(365;0.000949)|KIRC - Kidney renal clear cell carcinoma(229;0.00544)|STAD - Stomach adenocarcinoma(132;0.00644)|Lung(427;0.125)														---	---	---	---
PRDM16	63976	broad.mit.edu	37	1	3328738	3328738	+	Silent	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:3328738G>A	uc001akf.2	+	9	2057	c.1977G>A	c.(1975-1977)CCG>CCA	p.P659P	PRDM16_uc001akc.2_Silent_p.P659P|PRDM16_uc001akd.2_Silent_p.P659P|PRDM16_uc001ake.2_Silent_p.P659P|PRDM16_uc009vlh.2_Silent_p.P360P	NM_022114	NP_071397	Q9HAZ2	PRD16_HUMAN	PR domain containing 16 isoform 1	659					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	3334522	3334522	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:3334522A>G	uc001akf.2	+	11	2902	c.2822A>G	c.(2821-2823)GAC>GGC	p.D941G	PRDM16_uc001akc.2_Missense_Mutation_p.D940G|PRDM16_uc001akd.2_Missense_Mutation_p.D940G|PRDM16_uc001ake.2_Missense_Mutation_p.D941G|PRDM16_uc009vlh.2_Missense_Mutation_p.D641G	NM_022114	NP_071397	Q9HAZ2	PRD16_HUMAN	PR domain containing 16 isoform 1	941	Mediates interaction with SKI and regulation of TGF-beta signaling.|Interaction with CTBP1 and CTBP2 (By similarity).				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								---	---	---	---
ARHGEF16	27237	broad.mit.edu	37	1	3397090	3397090	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:3397090G>A	uc001akg.3	+	15	2317	c.2069G>A	c.(2068-2070)CGT>CAT	p.R690H	ARHGEF16_uc001aki.2_Missense_Mutation_p.R402H|ARHGEF16_uc001akj.2_Missense_Mutation_p.R402H|ARHGEF16_uc010nzh.1_Missense_Mutation_p.R394H	NM_014448	NP_055263	Q5VV41	ARHGG_HUMAN	Rho guanine exchange factor 16	690					activation of Cdc42 GTPase activity|activation of Rac GTPase activity|apoptosis|cell chemotaxis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|positive regulation of establishment of protein localization in plasma membrane|small GTPase mediated signal transduction	cytosol	PDZ domain binding|receptor tyrosine kinase binding|Rho GTPase binding|Rho guanyl-nucleotide exchange factor activity			ovary(1)	1	all_cancers(77;0.00276)|all_epithelial(69;0.00102)|Ovarian(185;0.0634)|Lung NSC(156;0.0969)|all_lung(157;0.101)	all_epithelial(116;7.14e-21)|all_lung(118;2.24e-08)|Lung NSC(185;3.55e-06)|Breast(487;0.000765)|Renal(390;0.00121)|Hepatocellular(190;0.0046)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0308)|Lung SC(97;0.0847)|Medulloblastoma(700;0.211)		Epithelial(90;8.62e-38)|OV - Ovarian serous cystadenocarcinoma(86;3.62e-22)|GBM - Glioblastoma multiforme(42;2.49e-12)|Colorectal(212;4.25e-05)|COAD - Colon adenocarcinoma(227;0.000196)|Kidney(185;0.000342)|BRCA - Breast invasive adenocarcinoma(365;0.000681)|KIRC - Kidney renal clear cell carcinoma(229;0.00549)|STAD - Stomach adenocarcinoma(132;0.00644)|Lung(427;0.201)														---	---	---	---
CCDC27	148870	broad.mit.edu	37	1	3686456	3686456	+	Intron	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:3686456A>G	uc001akv.2	+						LOC388588_uc001akw.3_5'Flank	NM_152492	NP_689705			coiled-coil domain containing 27											skin(1)	1	all_cancers(77;0.0385)|Ovarian(185;0.0634)|Lung NSC(156;0.21)|all_lung(157;0.218)	all_epithelial(116;5.52e-17)|all_lung(118;1.04e-06)|Lung NSC(185;0.000214)|Renal(390;0.00357)|Breast(487;0.00446)|Hepatocellular(190;0.0218)|Lung SC(97;0.0367)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.127)		Epithelial(90;1.11e-38)|OV - Ovarian serous cystadenocarcinoma(86;1.35e-22)|GBM - Glioblastoma multiforme(42;3.46e-16)|Colorectal(212;1.17e-05)|COAD - Colon adenocarcinoma(227;5.76e-05)|Kidney(185;0.00036)|BRCA - Breast invasive adenocarcinoma(365;0.000696)|KIRC - Kidney renal clear cell carcinoma(229;0.00558)|STAD - Stomach adenocarcinoma(132;0.00645)|Lung(427;0.203)														---	---	---	---
LRRC47	57470	broad.mit.edu	37	1	3703770	3703770	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:3703770C>A	uc001akx.1	-	2	748	c.720G>T	c.(718-720)AAG>AAT	p.K240N		NM_020710	NP_065761	Q8N1G4	LRC47_HUMAN	leucine rich repeat containing 47	240	LRR 7.				translation		phenylalanine-tRNA ligase activity|RNA binding			large_intestine(1)|ovary(1)	2	all_cancers(77;0.0375)|Ovarian(185;0.0634)|all_lung(157;0.208)|Lung NSC(156;0.21)	all_epithelial(116;1.34e-16)|all_lung(118;2.53e-06)|Lung NSC(185;0.00028)|Renal(390;0.00357)|Breast(487;0.00446)|Hepatocellular(190;0.0218)|Myeloproliferative disorder(586;0.0393)|Lung SC(97;0.0743)|Ovarian(437;0.127)		Epithelial(90;5.49e-39)|OV - Ovarian serous cystadenocarcinoma(86;1.43e-22)|GBM - Glioblastoma multiforme(42;3.69e-16)|Colorectal(212;1.21e-05)|COAD - Colon adenocarcinoma(227;5.87e-05)|Kidney(185;0.000367)|BRCA - Breast invasive adenocarcinoma(365;0.000704)|KIRC - Kidney renal clear cell carcinoma(229;0.00567)|STAD - Stomach adenocarcinoma(132;0.00645)|Lung(427;0.124)														---	---	---	---
NPHP4	261734	broad.mit.edu	37	1	5927118	5927118	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:5927118G>A	uc001alq.1	-	25	3796	c.3530C>T	c.(3529-3531)CCG>CTG	p.P1177L	NPHP4_uc001alr.1_Missense_Mutation_p.P119L	NM_015102	NP_055917	O75161	NPHP4_HUMAN	nephroretinin	1177					actin cytoskeleton organization|cell-cell adhesion|signal transduction|visual behavior	cell-cell junction|centrosome|cilium|microtubule basal body	protein binding|structural molecule activity			pancreas(1)	1	Ovarian(185;0.0634)	all_cancers(23;7.53e-41)|all_epithelial(116;3.96e-23)|all_lung(118;5.12e-09)|all_hematologic(16;5.45e-07)|Lung NSC(185;5.49e-07)|all_neural(13;3.21e-06)|Acute lymphoblastic leukemia(12;3.44e-05)|Breast(487;0.000601)|Renal(390;0.0007)|Colorectal(325;0.00113)|Hepatocellular(190;0.00213)|Glioma(11;0.00223)|Myeloproliferative disorder(586;0.0256)|Ovarian(437;0.04)|Lung SC(97;0.128)|Medulloblastoma(700;0.213)		Epithelial(90;1.69e-36)|GBM - Glioblastoma multiforme(13;5.07e-29)|OV - Ovarian serous cystadenocarcinoma(86;1.05e-19)|Colorectal(212;4.54e-07)|COAD - Colon adenocarcinoma(227;3.14e-05)|Kidney(185;0.00012)|BRCA - Breast invasive adenocarcinoma(365;0.00102)|KIRC - Kidney renal clear cell carcinoma(229;0.00179)|STAD - Stomach adenocarcinoma(132;0.00472)|READ - Rectum adenocarcinoma(331;0.0649)														---	---	---	---
NPHP4	261734	broad.mit.edu	37	1	5935038	5935038	+	Silent	SNP	C	T	T	rs146948888	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:5935038C>T	uc001alq.1	-	21	3206	c.2940G>A	c.(2938-2940)ACG>ACA	p.T980T		NM_015102	NP_055917	O75161	NPHP4_HUMAN	nephroretinin	980					actin cytoskeleton organization|cell-cell adhesion|signal transduction|visual behavior	cell-cell junction|centrosome|cilium|microtubule basal body	protein binding|structural molecule activity			pancreas(1)	1	Ovarian(185;0.0634)	all_cancers(23;7.53e-41)|all_epithelial(116;3.96e-23)|all_lung(118;5.12e-09)|all_hematologic(16;5.45e-07)|Lung NSC(185;5.49e-07)|all_neural(13;3.21e-06)|Acute lymphoblastic leukemia(12;3.44e-05)|Breast(487;0.000601)|Renal(390;0.0007)|Colorectal(325;0.00113)|Hepatocellular(190;0.00213)|Glioma(11;0.00223)|Myeloproliferative disorder(586;0.0256)|Ovarian(437;0.04)|Lung SC(97;0.128)|Medulloblastoma(700;0.213)		Epithelial(90;1.69e-36)|GBM - Glioblastoma multiforme(13;5.07e-29)|OV - Ovarian serous cystadenocarcinoma(86;1.05e-19)|Colorectal(212;4.54e-07)|COAD - Colon adenocarcinoma(227;3.14e-05)|Kidney(185;0.00012)|BRCA - Breast invasive adenocarcinoma(365;0.00102)|KIRC - Kidney renal clear cell carcinoma(229;0.00179)|STAD - Stomach adenocarcinoma(132;0.00472)|READ - Rectum adenocarcinoma(331;0.0649)														---	---	---	---
CHD5	26038	broad.mit.edu	37	1	6206455	6206455	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:6206455C>T	uc001amb.1	-	11	1719	c.1619G>A	c.(1618-1620)CGC>CAC	p.R540H	CHD5_uc001ama.1_5'Flank|CHD5_uc001amc.1_RNA	NM_015557	NP_056372	Q8TDI0	CHD5_HUMAN	chromodomain helicase DNA binding protein 5	540	Chromo 1.				chromatin modification|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	ATP binding|ATP-dependent helicase activity|DNA binding|zinc ion binding			central_nervous_system(3)|breast(3)|ovary(2)|upper_aerodigestive_tract(1)|lung(1)|skin(1)|pancreas(1)	12	Ovarian(185;0.0634)	all_cancers(23;5.36e-32)|all_epithelial(116;2.32e-17)|all_neural(13;3.68e-06)|all_lung(118;3.94e-06)|all_hematologic(16;2.39e-05)|Lung NSC(185;5.33e-05)|Acute lymphoblastic leukemia(12;0.000372)|Glioma(11;0.00127)|Renal(390;0.00188)|Colorectal(325;0.00342)|Breast(487;0.00373)|Hepatocellular(190;0.0218)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.15)		Epithelial(90;3.08e-37)|GBM - Glioblastoma multiforme(13;1.36e-31)|OV - Ovarian serous cystadenocarcinoma(86;7.7e-19)|Colorectal(212;9.97e-08)|COAD - Colon adenocarcinoma(227;1.07e-05)|Kidney(185;6.16e-05)|KIRC - Kidney renal clear cell carcinoma(229;0.00109)|BRCA - Breast invasive adenocarcinoma(365;0.0012)|STAD - Stomach adenocarcinoma(132;0.00346)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.193)														---	---	---	---
HES3	390992	broad.mit.edu	37	1	6304462	6304462	+	Silent	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:6304462C>T	uc009vly.1	+	2	92	c.37C>T	c.(37-39)CTG>TTG	p.L13L		NM_001024598	NP_001019769	Q5TGS1	HES3_HUMAN	hairy and enhancer of split 3	13	Helix-loop-helix motif.				transcription, DNA-dependent	nucleus	DNA binding				0	Ovarian(185;0.0634)	all_cancers(23;2.48e-32)|all_epithelial(116;1.14e-17)|all_lung(118;2.85e-06)|all_neural(13;3.68e-06)|all_hematologic(16;2.39e-05)|Lung NSC(185;3.77e-05)|Acute lymphoblastic leukemia(12;0.000372)|Glioma(11;0.00127)|Renal(390;0.00188)|Colorectal(325;0.00342)|Breast(487;0.00475)|Hepatocellular(190;0.0218)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.15)		Epithelial(90;1.2e-37)|GBM - Glioblastoma multiforme(13;3.2e-29)|OV - Ovarian serous cystadenocarcinoma(86;2.52e-19)|Colorectal(212;1.19e-07)|COAD - Colon adenocarcinoma(227;1.3e-05)|Kidney(185;4.88e-05)|KIRC - Kidney renal clear cell carcinoma(229;0.000871)|BRCA - Breast invasive adenocarcinoma(365;0.00105)|STAD - Stomach adenocarcinoma(132;0.00308)|READ - Rectum adenocarcinoma(331;0.0642)|Lung(427;0.241)														---	---	---	---
TAS1R1	80835	broad.mit.edu	37	1	6635050	6635050	+	Silent	SNP	C	T	T	rs150390485	byFrequency;by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:6635050C>T	uc001ant.2	+	3	858	c.858C>T	c.(856-858)TCC>TCT	p.S286S	TAS1R1_uc001anu.2_Intron|TAS1R1_uc001anv.2_Intron|TAS1R1_uc001anw.2_Silent_p.S286S	NM_138697	NP_619642	Q7RTX1	TS1R1_HUMAN	sweet taste receptor T1r isoform b	286	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)														---	---	---	---
CAMTA1	23261	broad.mit.edu	37	1	7527904	7527904	+	Silent	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:7527904C>T	uc001aoi.2	+	6	660	c.453C>T	c.(451-453)TGC>TGT	p.C151C		NM_015215	NP_056030	Q9Y6Y1	CMTA1_HUMAN	calmodulin-binding transcription activator 1	151	CG-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	7724061	7724061	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:7724061C>T	uc001aoi.2	+	9	1661	c.1454C>T	c.(1453-1455)CCC>CTC	p.P485L		NM_015215	NP_056030	Q9Y6Y1	CMTA1_HUMAN	calmodulin-binding transcription activator 1	485					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)														---	---	---	---
SLC45A1	50651	broad.mit.edu	37	1	8385970	8385970	+	Silent	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:8385970C>T	uc001apb.2	+	3	583	c.583C>T	c.(583-585)CTG>TTG	p.L195L		NM_001080397	NP_001073866	Q9Y2W3	S45A1_HUMAN	DNB5	195	Helical; (Potential).				carbohydrate transport	integral to membrane	symporter activity			central_nervous_system(2)|pancreas(1)|skin(1)	4	Ovarian(185;0.0661)|all_lung(157;0.127)	all_epithelial(116;1.22e-15)|all_lung(118;0.000147)|Lung NSC(185;0.000251)|Renal(390;0.000469)|Colorectal(325;0.00578)|Breast(348;0.00686)|Hepatocellular(190;0.0228)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.11)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|all cancers(8;3.95e-66)|GBM - Glioblastoma multiforme(8;5.93e-33)|Colorectal(212;2.86e-07)|COAD - Colon adenocarcinoma(227;3.11e-05)|Kidney(185;5.33e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000513)|KIRC - Kidney renal clear cell carcinoma(229;0.000979)|STAD - Stomach adenocarcinoma(132;0.00199)|READ - Rectum adenocarcinoma(331;0.0649)														---	---	---	---
SLC2A5	6518	broad.mit.edu	37	1	9101897	9101897	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:9101897C>T	uc001apo.2	-	5	810	c.518G>A	c.(517-519)GGC>GAC	p.G173D	SLC2A5_uc010nzy.1_Missense_Mutation_p.G114D|SLC2A5_uc010nzz.1_Missense_Mutation_p.G58D|SLC2A5_uc010oaa.1_Missense_Mutation_p.G129D|SLC2A5_uc010oab.1_Missense_Mutation_p.G173D|SLC2A5_uc010oac.1_3'UTR|SLC2A5_uc001app.3_Missense_Mutation_p.G173D	NM_003039	NP_003030	P22732	GTR5_HUMAN	solute carrier family 2 (facilitated	173	Helical; Name=5; (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	9427513	9427513	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:9427513C>T	uc010oae.1	+	3	1040	c.701C>T	c.(700-702)CCG>CTG	p.P234L	SPSB1_uc001apv.2_Missense_Mutation_p.P234L	NM_025106	NP_079382	Q96BD6	SPSB1_HUMAN	splA/ryanodine receptor domain and SOCS box	234	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)														---	---	---	---
KIF1B	23095	broad.mit.edu	37	1	10386323	10386323	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:10386323G>A	uc001aqx.3	+	27	3032	c.2830G>A	c.(2830-2832)GGC>AGC	p.G944S	KIF1B_uc001aqw.3_Missense_Mutation_p.G898S|KIF1B_uc001aqy.2_Missense_Mutation_p.G918S|KIF1B_uc001aqz.2_Missense_Mutation_p.G944S|KIF1B_uc001ara.2_Missense_Mutation_p.G904S|KIF1B_uc001arb.2_Missense_Mutation_p.G930S	NM_015074	NP_055889	O60333	KIF1B_HUMAN	kinesin family member 1B isoform b	944					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)														---	---	---	---
CASZ1	54897	broad.mit.edu	37	1	10702948	10702948	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:10702948C>T	uc001aro.2	-	20	4450	c.4130G>A	c.(4129-4131)AGC>AAC	p.S1377N		NM_001079843	NP_001073312	Q86V15	CASZ1_HUMAN	castor homolog 1, zinc finger isoform a	1377					regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	DNA binding|zinc ion binding			skin(1)	1	Ovarian(185;0.203)|all_lung(157;0.204)	Lung NSC(185;4.96e-06)|all_lung(284;1.22e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00212)|Hepatocellular(190;0.00913)|Ovarian(437;0.0229)|Myeloproliferative disorder(586;0.0255)	STAD - Stomach adenocarcinoma(5;0.0224)	UCEC - Uterine corpus endometrioid carcinoma (279;0.0265)|Colorectal(212;3.54e-08)|COAD - Colon adenocarcinoma(227;9.56e-06)|BRCA - Breast invasive adenocarcinoma(304;0.000219)|Kidney(185;0.00142)|KIRC - Kidney renal clear cell carcinoma(229;0.00381)|READ - Rectum adenocarcinoma(331;0.0419)|STAD - Stomach adenocarcinoma(132;0.0623)														---	---	---	---
MTOR	2475	broad.mit.edu	37	1	11199366	11199366	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:11199366G>A	uc001asd.2	-	36	5246	c.5125C>T	c.(5125-5127)CGC>TGC	p.R1709C		NM_004958	NP_004949	P42345	MTOR_HUMAN	FK506 binding protein 12-rapamycin associated	1709	FAT.				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	11300569	11300569	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:11300569C>T	uc001asd.2	-	11	1698	c.1577G>A	c.(1576-1578)CGT>CAT	p.R526H		NM_004958	NP_004949	P42345	MTOR_HUMAN	FK506 binding protein 12-rapamycin associated	526					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																		---	---	---	---
MAD2L2	10459	broad.mit.edu	37	1	11737626	11737626	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:11737626G>A	uc001asp.2	-	4	393	c.205C>T	c.(205-207)CAC>TAC	p.H69Y	MAD2L2_uc009vnc.2_Missense_Mutation_p.H69Y|MAD2L2_uc001asq.3_Missense_Mutation_p.H69Y	NM_006341	NP_006332	Q9UI95	MD2L2_HUMAN	MAD2 homolog	69	Mediates interaction with REV1 and REV3L and homodimerization.|HORMA.				cell division|DNA damage response, signal transduction resulting in transcription|double-strand break repair|mitosis|mitotic cell cycle spindle assembly checkpoint|negative regulation of mitotic anaphase-promoting complex activity|positive regulation of peptidyl-serine phosphorylation|positive regulation of transcription, DNA-dependent|regulation of cell growth|transcription, DNA-dependent	cytoplasm|nucleoplasm|spindle|zeta DNA polymerase complex	JUN kinase binding				0	Ovarian(185;0.249)	Lung NSC(185;4.15e-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;5.04e-06)|COAD - Colon adenocarcinoma(227;0.000245)|BRCA - Breast invasive adenocarcinoma(304;0.000295)|Kidney(185;0.000733)|KIRC - Kidney renal clear cell carcinoma(229;0.00258)|STAD - Stomach adenocarcinoma(313;0.0072)|READ - Rectum adenocarcinoma(331;0.0649)									DNA_polymerases_(catalytic_subunits)|Direct_reversal_of_damage					---	---	---	---
VPS13D	55187	broad.mit.edu	37	1	12328836	12328836	+	Silent	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:12328836G>A	uc001atv.2	+	16	2016	c.1875G>A	c.(1873-1875)CGG>CGA	p.R625R	VPS13D_uc001atw.2_Silent_p.R625R	NM_015378	NP_056193	Q5THJ4	VP13D_HUMAN	vacuolar protein sorting 13D isoform 1	625					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)														---	---	---	---
PRAMEF1	65121	broad.mit.edu	37	1	12854536	12854536	+	Missense_Mutation	SNP	C	T	T	rs1063777		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:12854536C>T	uc001auj.1	+	3	863	c.760C>T	c.(760-762)CGG>TGG	p.R254W		NM_023013	NP_075389	O95521	PRAM1_HUMAN	PRAME family member 1	254											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)														---	---	---	---
LOC649330	649330	broad.mit.edu	37	1	12907889	12907889	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:12907889G>A	uc009vno.2	-	1	349	c.254C>T	c.(253-255)GCT>GTT	p.A85V	HNRNPCL1_uc010obf.1_Missense_Mutation_p.A85V	NM_001146181	NP_001139653	B7ZW38	B7ZW38_HUMAN	heterogeneous nuclear ribonucleoprotein C-like	85							nucleic acid binding|nucleotide binding				0																		---	---	---	---
CELA2B	51032	broad.mit.edu	37	1	15808817	15808817	+	Silent	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:15808817C>T	uc001awl.2	+	4	310	c.285C>T	c.(283-285)TCC>TCT	p.S95S		NM_015849	NP_056933	P08218	CEL2B_HUMAN	elastase 2B preproprotein	95	Peptidase S1.				proteolysis	extracellular region	serine-type endopeptidase activity			ovary(1)	1																		---	---	---	---
TMEM82	388595	broad.mit.edu	37	1	16073452	16073452	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:16073452G>A	uc001axc.2	+	5	986	c.848G>A	c.(847-849)GGT>GAT	p.G283D		NM_001013641	NP_001013663	A0PJX8	TMM82_HUMAN	transmembrane protein 82	283	Leu-rich.|Helical; (Potential).					integral to membrane				breast(1)|central_nervous_system(1)	2		Colorectal(325;0.00108)|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;0.0798)		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	16202925	16202925	+	Silent	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:16202925G>A	uc001axk.1	+	3	837	c.633G>A	c.(631-633)CTG>CTA	p.L211L	SPEN_uc010obp.1_Silent_p.L170L	NM_015001	NP_055816	Q96T58	MINT_HUMAN	spen homolog, transcriptional regulator	211	Arg-rich.|By similarity.				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)														---	---	---	---
CLCNKA	1187	broad.mit.edu	37	1	16358975	16358975	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:16358975C>T	uc001axu.2	+	18	1963	c.1883C>T	c.(1882-1884)ACG>ATG	p.T628M	CLCNKA_uc001axt.2_RNA|CLCNKA_uc001axv.2_Missense_Mutation_p.T627M|CLCNKA_uc010obw.1_Missense_Mutation_p.T585M|CLCNKB_uc001axw.3_Intron	NM_004070	NP_004061	P51800	CLCKA_HUMAN	chloride channel Ka isoform 1	628	CBS 2.				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)											OREG0013132	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
NBPF1	55672	broad.mit.edu	37	1	16907295	16907295	+	Silent	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:16907295A>G	uc009vos.1	-	16	2424	c.1536T>C	c.(1534-1536)GTT>GTC	p.V512V	NBPF1_uc009vot.1_Intron|NBPF1_uc001ayz.1_Intron|NBPF1_uc010oce.1_Silent_p.V241V	NM_017940	NP_060410	Q3BBV0	NBPF1_HUMAN	hypothetical protein LOC55672	512	NBPF 2.					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)														---	---	---	---
SDHB	6390	broad.mit.edu	37	1	17349104	17349104	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:17349104T>C	uc001bae.2	-	7	915	c.764A>G	c.(763-765)AAG>AGG	p.K255R		NM_003000	NP_002991	P21912	DHSB_HUMAN	succinate dehydrogenase complex, subunit B, iron	255					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				---	---	---	---
PADI1	29943	broad.mit.edu	37	1	17570627	17570627	+	Silent	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:17570627C>T	uc001bah.1	+	16	1973	c.1881C>T	c.(1879-1881)TGC>TGT	p.C627C	PADI1_uc010oco.1_Silent_p.C184C|PADI1_uc010ocp.1_Silent_p.C142C|PADI1_uc010ocq.1_Silent_p.C98C|PADI1_uc009vpb.1_Missense_Mutation_p.A21V	NM_013358	NP_037490	Q9ULC6	PADI1_HUMAN	peptidylarginine deiminase type I	627					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)													---	---	---	---
PADI4	23569	broad.mit.edu	37	1	17690206	17690206	+	Missense_Mutation	SNP	C	T	T	rs147723249	byFrequency;by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:17690206C>T	uc001baj.2	+	16	1976	c.1948C>T	c.(1948-1950)CGC>TGC	p.R650C		NM_012387	NP_036519	Q9UM07	PADI4_HUMAN	peptidyl arginine deiminase, type IV	650					chromatin modification|peptidyl-citrulline biosynthetic process from peptidyl-arginine|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	calcium ion binding|protein-arginine deiminase activity			ovary(1)|skin(1)	2		Colorectal(325;3.46e-05)|Breast(348;0.000162)|all_lung(284;0.000338)|Lung NSC(340;0.00042)|Renal(390;0.000518)|Ovarian(437;0.00409)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00537)|BRCA - Breast invasive adenocarcinoma(304;8.54e-06)|COAD - Colon adenocarcinoma(227;1.33e-05)|Kidney(64;0.000223)|KIRC - Kidney renal clear cell carcinoma(64;0.00313)|STAD - Stomach adenocarcinoma(196;0.00707)|READ - Rectum adenocarcinoma(331;0.0689)|Lung(427;0.199)	L-Citrulline(DB00155)													---	---	---	---
RCC2	55920	broad.mit.edu	37	1	17743115	17743115	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:17743115G>A	uc001bal.2	-	7	934	c.887C>T	c.(886-888)GCC>GTC	p.A296V	RCC2_uc001bam.2_Missense_Mutation_p.A296V	NM_001136204	NP_001129676	Q9P258	RCC2_HUMAN	regulator of chromosome condensation 2	296	RCC1 4.				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)														---	---	---	---
RCC2	55920	broad.mit.edu	37	1	17755676	17755676	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:17755676C>T	uc001bal.2	-	2	352	c.305G>A	c.(304-306)TGC>TAC	p.C102Y	RCC2_uc001bam.2_Missense_Mutation_p.C102Y	NM_001136204	NP_001129676	Q9P258	RCC2_HUMAN	regulator of chromosome condensation 2	102					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)														---	---	---	---
UBR4	23352	broad.mit.edu	37	1	19484348	19484348	+	Silent	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:19484348C>T	uc001bbi.2	-	40	5725	c.5721G>A	c.(5719-5721)GGG>GGA	p.G1907G	UBR4_uc001bbl.1_5'Flank|UBR4_uc001bbm.1_Silent_p.G1118G	NM_020765	NP_065816	Q5T4S7	UBR4_HUMAN	retinoblastoma-associated factor 600	1907					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	19557424	19557424	+	Nonsense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:19557424G>A	uc001bbo.2	-	17	2021	c.1978C>T	c.(1978-1980)CGA>TGA	p.R660*	KIAA0090_uc001bbp.2_Nonsense_Mutation_p.R659*|KIAA0090_uc001bbq.2_Nonsense_Mutation_p.R659*|KIAA0090_uc001bbr.2_Nonsense_Mutation_p.R638*	NM_015047	NP_055862	Q8N766	K0090_HUMAN	hypothetical protein LOC23065 precursor	660	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)														---	---	---	---
AKR7L	246181	broad.mit.edu	37	1	19595104	19595104	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:19595104C>T	uc010ocx.1	-	7	796	c.796G>A	c.(796-798)GCC>ACC	p.A266T	AKR7L_uc010ocy.1_Missense_Mutation_p.G200D	NM_201252	NP_957704			aflatoxin B1 aldehyde reductase 3 isoform 1												0																		---	---	---	---
AKR7A3	22977	broad.mit.edu	37	1	19609370	19609370	+	Missense_Mutation	SNP	G	A	A	rs144760570	byFrequency	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:19609370G>A	uc001bbv.1	-	7	928	c.851C>T	c.(850-852)GCG>GTG	p.A284V		NM_012067	NP_036199	O95154	ARK73_HUMAN	aldo-keto reductase family 7, member A3	284					cellular aldehyde metabolic process	cytosol	aldo-keto reductase (NADP) activity|electron carrier activity				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;0.00459)|BRCA - Breast invasive adenocarcinoma(304;1.78e-05)|Kidney(64;0.00016)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|GBM - Glioblastoma multiforme(114;0.00276)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)														---	---	---	---
UBXN10	127733	broad.mit.edu	37	1	20517071	20517071	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:20517071C>A	uc001bdb.2	+	2	101	c.17C>A	c.(16-18)CCT>CAT	p.P6H		NM_152376	NP_689589	Q96LJ8	UBX10_HUMAN	UBX domain protein 10	6										ovary(1)	1																		---	---	---	---
KIF17	57576	broad.mit.edu	37	1	21044070	21044070	+	Missense_Mutation	SNP	C	T	T	rs146128405	byFrequency	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:21044070C>T	uc001bdr.3	-	1	248	c.130G>A	c.(130-132)GCC>ACC	p.A44T	KIF17_uc001bds.3_Missense_Mutation_p.A44T	NM_020816	NP_065867	Q9P2E2	KIF17_HUMAN	kinesin family member 17 isoform a	44	Kinesin-motor.				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	21106929	21106929	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:21106929G>A	uc001bdw.1	-	2	145	c.5C>T	c.(4-6)GCG>GTG	p.A2V	HP1BP3_uc001bdv.1_5'UTR|HP1BP3_uc010odh.1_Intron|HP1BP3_uc001bdy.1_Missense_Mutation_p.A2V|HP1BP3_uc001bdz.2_RNA|HP1BP3_uc001bea.2_Missense_Mutation_p.A2V|HP1BP3_uc001beb.2_Missense_Mutation_p.A2V	NM_016287	NP_057371	Q5SSJ5	HP1B3_HUMAN	HP1-BP74	2					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)														---	---	---	---
NBPF3	84224	broad.mit.edu	37	1	21809758	21809758	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:21809758C>T	uc001ber.2	+	15	2131	c.1781C>T	c.(1780-1782)GCC>GTC	p.A594V	NBPF3_uc001bes.2_Missense_Mutation_p.A538V|NBPF3_uc009vqb.2_Missense_Mutation_p.A582V|NBPF3_uc010odm.1_Missense_Mutation_p.A524V	NM_032264	NP_115640	Q9H094	NBPF3_HUMAN	neuroblastoma breakpoint family, member 3	594	NBPF 5.					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)														---	---	---	---
WNT4	54361	broad.mit.edu	37	1	22447752	22447752	+	Silent	SNP	C	T	T	rs143835757		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:22447752C>T	uc001bfs.3	-	4	644	c.540G>A	c.(538-540)TCG>TCA	p.S180S	WNT4_uc010odt.1_Silent_p.S117S	NM_030761	NP_110388	P56705	WNT4_HUMAN	wingless-type MMTV integration site family,	180					adrenal gland development|androgen biosynthetic process|anterior/posterior pattern formation|axis specification|branching involved in ureteric bud morphogenesis|canonical Wnt receptor signaling pathway|cellular response to transforming growth factor beta stimulus|dermatome development|endoderm development|epithelial to mesenchymal transition|establishment of protein localization in plasma membrane|female gonad development|female sex determination|liver development|male gonad development|mesonephric tubule development|metanephric mesenchymal cell differentiation|negative regulation of canonical Wnt receptor signaling pathway|negative regulation of fibroblast growth factor receptor signaling pathway|negative regulation of male gonad development|negative regulation of testicular blood vessel morphogenesis|negative regulation of testosterone biosynthetic process|negative regulation of transcription, DNA-dependent|oocyte development|paramesonephric duct development|positive regulation of aldosterone biosynthetic process|positive regulation of bone mineralization|positive regulation of canonical Wnt receptor signaling pathway|positive regulation of collagen biosynthetic process|positive regulation of cortisol biosynthetic process|positive regulation of osteoblast differentiation|positive regulation of transcription, DNA-dependent|protein palmitoylation|renal vesicle formation|smooth muscle cell differentiation|somatotropin secreting cell differentiation|tertiary branching involved in mammary gland duct morphogenesis|thyroid-stimulating hormone-secreting cell differentiation|Wnt receptor signaling pathway, calcium modulating pathway	cell surface|extracellular space|Golgi apparatus|plasma membrane|proteinaceous extracellular matrix	extracellular matrix structural constituent|signal transducer activity|transcription corepressor activity			ovary(1)	1		Colorectal(325;3.46e-05)|all_lung(284;5.94e-05)|Lung NSC(340;6.55e-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;9.02e-26)|Colorectal(126;1.71e-07)|COAD - Colon adenocarcinoma(152;1.17e-05)|GBM - Glioblastoma multiforme(114;2.01e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000568)|KIRC - Kidney renal clear cell carcinoma(1967;0.00277)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.138)														---	---	---	---
EPHB2	2048	broad.mit.edu	37	1	23189588	23189588	+	Silent	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:23189588C>T	uc009vqj.1	+	4	1015	c.870C>T	c.(868-870)CCC>CCT	p.P290P	EPHB2_uc001bge.2_Silent_p.P290P|EPHB2_uc001bgf.2_Silent_p.P290P|EPHB2_uc010odu.1_Silent_p.P290P	NM_017449	NP_059145	P29323	EPHB2_HUMAN	ephrin receptor EphB2 isoform 1 precursor	290	Extracellular (Potential).|Cys-rich.				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				---	---	---	---
LUZP1	7798	broad.mit.edu	37	1	23418023	23418023	+	Missense_Mutation	SNP	C	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:23418023C>G	uc001bgk.2	-	4	3116	c.2732G>C	c.(2731-2733)GGC>GCC	p.G911A	LUZP1_uc010odv.1_Missense_Mutation_p.G911A|LUZP1_uc001bgl.2_Missense_Mutation_p.G911A|LUZP1_uc001bgm.1_Missense_Mutation_p.G911A	NM_033631	NP_361013	Q86V48	LUZP1_HUMAN	leucine zipper protein 1	911						nucleus					0		Colorectal(325;3.46e-05)|Lung NSC(340;4.15e-05)|all_lung(284;6.64e-05)|Renal(390;0.000219)|Ovarian(437;0.00373)|Breast(348;0.00815)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|OV - Ovarian serous cystadenocarcinoma(117;4.88e-27)|Colorectal(126;8.36e-08)|COAD - Colon adenocarcinoma(152;4.31e-06)|GBM - Glioblastoma multiforme(114;8.64e-05)|BRCA - Breast invasive adenocarcinoma(304;0.00112)|KIRC - Kidney renal clear cell carcinoma(1967;0.00176)|STAD - Stomach adenocarcinoma(196;0.0146)|READ - Rectum adenocarcinoma(331;0.0686)|Lung(427;0.0967)|LUSC - Lung squamous cell carcinoma(448;0.199)														---	---	---	---
ASAP3	55616	broad.mit.edu	37	1	23765231	23765231	+	Intron	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:23765231A>G	uc001bha.2	-						ASAP3_uc001bgy.1_5'Flank|ASAP3_uc001bgz.1_5'Flank|ASAP3_uc010odz.1_Intron|ASAP3_uc010oea.1_Intron|ASAP3_uc001bhb.2_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																		---	---	---	---
RHD	6007	broad.mit.edu	37	1	25611120	25611120	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:25611120T>C	uc001bjz.2	+	2	263	c.205T>C	c.(205-207)TTC>CTC	p.F69L	RHD_uc010oep.1_Missense_Mutation_p.F69L|RHD_uc001bkc.2_Missense_Mutation_p.F69L|RHD_uc009vrm.2_5'UTR|RHD_uc001bka.2_Missense_Mutation_p.F69L|RHD_uc001bkb.2_Missense_Mutation_p.F69L|RHD_uc009vrn.2_Missense_Mutation_p.F69L|RHD_uc009vro.2_Missense_Mutation_p.F69L|RHD_uc009vrp.2_Missense_Mutation_p.F69L	NM_016124	NP_057208	Q02161	RHD_HUMAN	Rh blood group D antigen isoform 1	69						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)														---	---	---	---
TMEM50A	23585	broad.mit.edu	37	1	25678175	25678175	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:25678175G>T	uc001bke.2	+	4	415	c.265G>T	c.(265-267)GGT>TGT	p.G89C	TMEM50A_uc010oeq.1_Missense_Mutation_p.G89C|TMEM50A_uc009vrr.2_RNA|TMEM50A_uc009vrs.2_RNA	NM_014313	NP_055128	O95807	TM50A_HUMAN	small membrane protein 1	89						endoplasmic reticulum|integral to 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;0.0422)|OV - Ovarian serous cystadenocarcinoma(117;3.47e-27)|Colorectal(126;1.1e-08)|COAD - Colon adenocarcinoma(152;7.48e-07)|STAD - Stomach adenocarcinoma(196;0.00035)|BRCA - Breast invasive adenocarcinoma(304;0.00047)|KIRC - Kidney renal clear cell carcinoma(1967;0.000755)|GBM - Glioblastoma multiforme(114;0.00106)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.204)														---	---	---	---
SLC30A2	7780	broad.mit.edu	37	1	26365752	26365752	+	Missense_Mutation	SNP	G	A	A	rs35623192	byFrequency	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:26365752G>A	uc001blh.1	-	7	1088	c.871C>T	c.(871-873)CGC>TGC	p.R291C	SLC30A2_uc001blg.1_Missense_Mutation_p.R340C	NM_032513	NP_115902	Q9BRI3	ZNT2_HUMAN	solute carrier family 30, member 2 isoform 2	291	Vacuolar (Potential).				positive regulation of sequestering of zinc ion|zinc ion transport	integral to membrane|late endosome|lysosomal membrane	cation transmembrane transporter activity				0		Colorectal(325;3.46e-05)|Lung NSC(340;6.18e-05)|all_lung(284;9.43e-05)|Renal(390;0.0007)|Ovarian(437;0.00473)|Breast(348;0.0155)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0298)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|OV - Ovarian serous cystadenocarcinoma(117;7.09e-26)|Colorectal(126;2.96e-08)|COAD - Colon adenocarcinoma(152;1.7e-06)|KIRC - Kidney renal clear cell carcinoma(1967;0.000728)|BRCA - Breast invasive adenocarcinoma(304;0.000969)|STAD - Stomach adenocarcinoma(196;0.00151)|GBM - Glioblastoma multiforme(114;0.00614)|READ - Rectum adenocarcinoma(331;0.0649)														---	---	---	---
NUDC	10726	broad.mit.edu	37	1	27271928	27271928	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:27271928G>T	uc001bng.1	+	7	905	c.789G>T	c.(787-789)GAG>GAT	p.E263D	NUDC_uc001bnh.1_Missense_Mutation_p.E320D|NUDC_uc009vsq.1_Missense_Mutation_p.E237D	NM_006600	NP_006591	Q9Y266	NUDC_HUMAN	nuclear distribution gene C homolog	263					cell proliferation|cytokinesis|mitotic prometaphase|multicellular organismal development	cytosol|microtubule|nucleoplasm	protein binding			ovary(1)	1				UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|Epithelial(14;6.1e-51)|OV - Ovarian serous cystadenocarcinoma(117;2.87e-29)|Colorectal(126;5.74e-09)|COAD - Colon adenocarcinoma(152;9.31e-07)|BRCA - Breast invasive adenocarcinoma(304;0.000281)|STAD - Stomach adenocarcinoma(196;0.000604)|KIRC - Kidney renal clear cell carcinoma(1967;0.000739)|READ - Rectum adenocarcinoma(331;0.0421)														---	---	---	---
FCN3	8547	broad.mit.edu	37	1	27695849	27695849	+	Nonsense_Mutation	SNP	G	A	A	rs141468956		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:27695849G>A	uc001boa.2	-	8	784	c.778C>T	c.(778-780)CGA>TGA	p.R260*	MAP3K6_uc001bny.1_5'Flank|MAP3K6_uc009vsw.1_5'Flank|FCN3_uc001bob.2_Nonsense_Mutation_p.R249*	NM_003665	NP_003656	O75636	FCN3_HUMAN	ficolin 3 isoform 1 precursor	260	Fibrinogen C-terminal.				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	27736517	27736517	+	Silent	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:27736517T>C	uc001bof.1	-	8	1224	c.1008A>G	c.(1006-1008)CCA>CCG	p.P336P	WASF2_uc010ofl.1_Intron	NM_006990	NP_008921	Q9Y6W5	WASF2_HUMAN	WAS protein family, member 2	336	Poly-Pro.				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)														---	---	---	---
WASF2	10163	broad.mit.edu	37	1	27736694	27736694	+	Silent	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:27736694T>C	uc001bof.1	-	8	1047	c.831A>G	c.(829-831)CCA>CCG	p.P277P	WASF2_uc010ofl.1_Intron	NM_006990	NP_008921	Q9Y6W5	WASF2_HUMAN	WAS protein family, member 2	277					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)														---	---	---	---
AHDC1	27245	broad.mit.edu	37	1	27875650	27875650	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:27875650C>T	uc009vsy.2	-	6	3946	c.2977G>A	c.(2977-2979)GCT>ACT	p.A993T	AHDC1_uc009vsz.1_Missense_Mutation_p.A993T	NM_001029882	NP_001025053	Q5TGY3	AHDC1_HUMAN	AT hook, DNA binding motif, containing 1	993							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)														---	---	---	---
AHDC1	27245	broad.mit.edu	37	1	27876945	27876945	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:27876945G>T	uc009vsy.2	-	6	2651	c.1682C>A	c.(1681-1683)CCC>CAC	p.P561H	AHDC1_uc009vsz.1_Missense_Mutation_p.P561H	NM_001029882	NP_001025053	Q5TGY3	AHDC1_HUMAN	AT hook, DNA binding motif, containing 1	561							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	28282557	28282557	+	Silent	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:28282557G>A	uc001bpg.2	+	7	1160	c.969G>A	c.(967-969)CGG>CGA	p.R323R	SMPDL3B_uc001bpf.2_Silent_p.R323R|SMPDL3B_uc010ofq.1_Silent_p.R117R|SMPDL3B_uc010ofr.1_Silent_p.R275R	NM_014474	NP_055289	Q92485	ASM3B_HUMAN	acid sphingomyelinase-like phosphodiesterase 3B	323					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)														---	---	---	---
EYA3	2140	broad.mit.edu	37	1	28384511	28384511	+	Silent	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:28384511C>T	uc001bpi.1	-	2	192	c.27G>A	c.(25-27)GAG>GAA	p.E9E	EYA3_uc010ofs.1_5'UTR|EYA3_uc010oft.1_Silent_p.E9E|EYA3_uc001bpj.2_Silent_p.E9E|EYA3_uc001bpk.1_RNA|EYA3_uc010ofu.1_RNA	NM_001990	NP_001981	Q99504	EYA3_HUMAN	eyes absent 3	9					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)														---	---	---	---
PHACTR4	65979	broad.mit.edu	37	1	28818302	28818302	+	Intron	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:28818302A>G	uc001bpw.2	+						PHACTR4_uc001bpv.1_Intron|PHACTR4_uc001bpx.2_Intron|PHACTR4_uc001bpy.2_Intron|PHACTR4_uc001bpz.2_Intron	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)														---	---	---	---
SFRS4	6429	broad.mit.edu	37	1	29481275	29481275	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:29481275T>C	uc001bro.2	-	4	884	c.511A>G	c.(511-513)AGA>GGA	p.R171G	SFRS4_uc010ofy.1_Intron|SFRS4_uc009vtp.2_RNA	NM_005626	NP_005617	Q08170	SRSF4_HUMAN	splicing factor, arginine/serine-rich 4	171	RRM 2.				mRNA 3'-end processing|mRNA export from nucleus|nuclear mRNA splicing, via spliceosome|termination of RNA polymerase II transcription	nuclear speck	nucleotide binding|RNA binding				0		Colorectal(325;0.00161)|Breast(348;0.0364)|Myeloproliferative disorder(586;0.0393)|all_neural(195;0.0529)|Lung NSC(340;0.0654)|all_lung(284;0.074)|Ovarian(437;0.104)|Medulloblastoma(700;0.151)		Colorectal(126;1.01e-07)|COAD - Colon adenocarcinoma(152;6.21e-06)|STAD - Stomach adenocarcinoma(196;0.0196)|BRCA - Breast invasive adenocarcinoma(304;0.0531)|READ - Rectum adenocarcinoma(331;0.0649)|KIRC - Kidney renal clear cell carcinoma(1967;0.138)														---	---	---	---
PTPRU	10076	broad.mit.edu	37	1	29587339	29587339	+	Silent	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:29587339C>T	uc001bru.2	+	7	1178	c.1068C>T	c.(1066-1068)AGC>AGT	p.S356S	PTPRU_uc001brv.2_Silent_p.S356S|PTPRU_uc001brw.2_Silent_p.S356S|PTPRU_uc009vtq.2_Silent_p.S356S|PTPRU_uc009vtr.2_Silent_p.S356S	NM_005704	NP_005695	Q92729	PTPRU_HUMAN	protein tyrosine phosphatase, receptor type, U	356	Fibronectin type-III 1.|Extracellular (Potential).				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)														---	---	---	---
PTPRU	10076	broad.mit.edu	37	1	29587353	29587353	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:29587353G>A	uc001bru.2	+	7	1192	c.1082G>A	c.(1081-1083)CGT>CAT	p.R361H	PTPRU_uc001brv.2_Missense_Mutation_p.R361H|PTPRU_uc001brw.2_Missense_Mutation_p.R361H|PTPRU_uc009vtq.2_Missense_Mutation_p.R361H|PTPRU_uc009vtr.2_Missense_Mutation_p.R361H	NM_005704	NP_005695	Q92729	PTPRU_HUMAN	protein tyrosine phosphatase, receptor type, U	361	Fibronectin type-III 1.|Extracellular (Potential).				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)														---	---	---	---
PUM1	9698	broad.mit.edu	37	1	31478691	31478691	+	Intron	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:31478691C>T	uc001bsi.1	-						PUM1_uc001bsg.1_Intron|PUM1_uc001bsh.1_Intron|PUM1_uc001bsj.1_Intron|PUM1_uc010oga.1_Intron|PUM1_uc001bsk.1_Intron|PUM1_uc010ogb.1_Intron	NM_014676	NP_055491			pumilio 1 isoform 2						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)														---	---	---	---
HCRTR1	3061	broad.mit.edu	37	1	32085319	32085319	+	Intron	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:32085319C>T	uc009vtx.2	+						HCRTR1_uc001btb.2_Intron|HCRTR1_uc001btc.3_Intron|HCRTR1_uc001btd.2_Intron|HCRTR1_uc010ogl.1_Intron	NM_001525	NP_001516			orexin receptor 1						feeding behavior|neuropeptide signaling pathway|synaptic transmission	integral to plasma membrane				ovary(1)	1		Ovarian(437;0.0221)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0837)|Breast(348;0.116)		STAD - Stomach adenocarcinoma(196;0.053)														---	---	---	---
PEF1	553115	broad.mit.edu	37	1	32098126	32098126	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:32098126C>A	uc001bth.1	-	4	607	c.595G>T	c.(595-597)GGC>TGC	p.G199C	PEF1_uc001bte.1_Missense_Mutation_p.G38C|PEF1_uc001btf.1_Missense_Mutation_p.G38C|PEF1_uc001btg.1_Missense_Mutation_p.G129C	NM_012392	NP_036524	Q9UBV8	PEF1_HUMAN	penta-EF-hand domain containing 1	199	EF-hand 3.|2 (Potential).				response to calcium ion	cytoplasm|membrane	calcium ion binding|protein heterodimerization activity				0		Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.104)|all_neural(195;0.186)		STAD - Stomach adenocarcinoma(196;0.0546)														---	---	---	---
ZBTB8A	653121	broad.mit.edu	37	1	33060695	33060695	+	Silent	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:33060695A>G	uc001bvn.2	+	4	1349	c.864A>G	c.(862-864)ACA>ACG	p.T288T	ZBTB8A_uc001bvk.2_RNA|ZBTB8A_uc001bvm.2_Silent_p.T288T	NM_001040441	NP_001035531	Q96BR9	ZBT8A_HUMAN	zinc finger and BTB domain containing 8A	288	C2H2-type 1.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0																		---	---	---	---
RNF19B	127544	broad.mit.edu	37	1	33404010	33404010	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:33404010T>C	uc010oho.1	-	8	1733	c.1733A>G	c.(1732-1734)AAC>AGC	p.N578S	RNF19B_uc001bwm.3_Missense_Mutation_p.N577S|RNF19B_uc010ohp.1_Missense_Mutation_p.N577S	NM_153341	NP_699172	Q6ZMZ0	RN19B_HUMAN	ring finger protein 19B isoform a	578						integral to membrane	ligase activity|protein binding|zinc ion binding				0		Myeloproliferative disorder(586;0.0393)|all_neural(195;0.186)																---	---	---	---
TRIM62	55223	broad.mit.edu	37	1	33623872	33623872	+	Missense_Mutation	SNP	A	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:33623872A>T	uc001bxb.2	-	4	1497	c.859T>A	c.(859-861)TTC>ATC	p.F287I		NM_018207	NP_060677	Q9BVG3	TRI62_HUMAN	tripartite motif-containing 62	287	B30.2/SPRY.					intracellular	zinc ion binding				0		Myeloproliferative disorder(586;0.0393)																---	---	---	---
ZSCAN20	7579	broad.mit.edu	37	1	33956970	33956970	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:33956970G>A	uc001bxj.3	+	6	1279	c.1112G>A	c.(1111-1113)CGG>CAG	p.R371Q	ZSCAN20_uc001bxk.2_Missense_Mutation_p.R317Q|ZSCAN20_uc009vui.2_Missense_Mutation_p.R371Q	NM_145238	NP_660281	P17040	ZSC20_HUMAN	zinc finger protein 31	371					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	34090854	34090854	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:34090854G>A	uc001bxn.1	-	34	5206	c.5177C>T	c.(5176-5178)GCG>GTG	p.A1726V	CSMD2_uc001bxm.1_Missense_Mutation_p.A1766V|CSMD2_uc001bxo.1_Missense_Mutation_p.A639V	NM_052896	NP_443128	Q7Z408	CSMD2_HUMAN	CUB and Sushi multiple domains 2	1726	Extracellular (Potential).|CUB 10.					integral to membrane|plasma membrane	protein binding			ovary(6)|skin(5)|pancreas(1)	12		Myeloproliferative disorder(586;0.0294)|all_neural(195;0.249)																---	---	---	---
C1orf212	113444	broad.mit.edu	37	1	35320792	35320792	+	Missense_Mutation	SNP	G	A	A	rs138978598		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:35320792G>A	uc001byb.2	-	2	907	c.490C>T	c.(490-492)CAC>TAC	p.H164Y		NM_138428	NP_612437			hypothetical protein LOC113444												0		Myeloproliferative disorder(586;0.0393)																---	---	---	---
C1orf216	127703	broad.mit.edu	37	1	36181557	36181557	+	Silent	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:36181557G>A	uc001bzh.1	-	2	854	c.366C>T	c.(364-366)AGC>AGT	p.S122S		NM_152374	NP_689587	Q8TAB5	CA216_HUMAN	hypothetical protein LOC127703	122										skin(1)	1		Myeloproliferative disorder(586;0.0393)|all_neural(195;0.196)														OREG0013357	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
CLSPN	63967	broad.mit.edu	37	1	36226732	36226732	+	Silent	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:36226732C>T	uc001bzi.2	-	7	1049	c.969G>A	c.(967-969)CGG>CGA	p.R323R	CLSPN_uc009vux.2_Silent_p.R323R	NM_022111	NP_071394	Q9HAW4	CLSPN_HUMAN	claspin	323					activation of protein kinase activity|cell cycle|cellular component disassembly involved in apoptosis|DNA repair|DNA replication|G2/M transition DNA damage checkpoint|mitotic cell cycle DNA replication checkpoint|peptidyl-serine phosphorylation	nucleoplasm	anaphase-promoting complex binding|DNA binding			breast(2)|ovary(2)|central_nervous_system(1)|lung(1)|skin(1)|kidney(1)	8		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0887)																---	---	---	---
THRAP3	9967	broad.mit.edu	37	1	36759545	36759545	+	Intron	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:36759545T>C	uc001cae.3	+						THRAP3_uc001caf.3_Intron	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								---	---	---	---
CSF3R	1441	broad.mit.edu	37	1	36935380	36935380	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:36935380C>A	uc001caw.1	-	11	1525	c.1347G>T	c.(1345-1347)TGG>TGT	p.W449C	CSF3R_uc001cat.1_Missense_Mutation_p.W12C|CSF3R_uc009vvc.1_Missense_Mutation_p.W12C|CSF3R_uc001cau.1_5'UTR|CSF3R_uc001cav.1_Missense_Mutation_p.W449C|CSF3R_uc001cax.1_Missense_Mutation_p.W449C|CSF3R_uc001cay.1_Missense_Mutation_p.W449C	NM_000760	NP_000751	Q99062	CSF3R_HUMAN	colony stimulating factor 3 receptor isoform a	449	Extracellular (Potential).|Fibronectin type-III 4.				cell adhesion|defense response	extracellular region|integral to plasma membrane	cytokine receptor activity			central_nervous_system(2)|ovary(1)	3		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.164)			Filgrastim(DB00099)|Pegfilgrastim(DB00019)													---	---	---	---
GNL2	29889	broad.mit.edu	37	1	38041276	38041276	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:38041276G>A	uc001cbk.2	-	10	1226	c.1063C>T	c.(1063-1065)CGT>TGT	p.R355C		NM_013285	NP_037417	Q13823	NOG2_HUMAN	guanine nucleotide binding protein-like 2	355	G.				ribosome biogenesis	nucleolus	GTP binding|GTPase activity|protein binding			ovary(1)|central_nervous_system(1)	2		Myeloproliferative disorder(586;0.0393)																---	---	---	---
EPHA10	284656	broad.mit.edu	37	1	38185704	38185704	+	Silent	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:38185704G>A	uc009vvi.2	-	14	2525	c.2439C>T	c.(2437-2439)GCC>GCT	p.A813A	EPHA10_uc001cbt.2_RNA|EPHA10_uc009vvh.1_RNA|EPHA10_uc001cbu.2_RNA|EPHA10_uc001cbv.1_RNA	NM_001099439	NP_001092909	Q5JZY3	EPHAA_HUMAN	EPH receptor A10 isofom 3	813	Cytoplasmic (Potential).|Protein kinase.					extracellular region|integral to membrane|integral to plasma membrane	ATP binding|ephrin receptor activity|protein binding|transmembrane-ephrin receptor activity			breast(4)|stomach(3)|lung(1)	8	Acute lymphoblastic leukemia(166;0.074)|all_hematologic(146;0.197)	Myeloproliferative disorder(586;0.0255)|all_neural(195;0.164)																---	---	---	---
KIAA0754	643314	broad.mit.edu	37	1	39876410	39876410	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:39876410C>T	uc009vvt.1	+	1	1235	c.473C>T	c.(472-474)GCT>GTT	p.A158V	MACF1_uc010ois.1_Intron|MACF1_uc001cda.1_Intron|MACF1_uc001cdc.1_Intron|MACF1_uc010oiu.1_Intron	NM_015038	NP_055853	O94854	K0754_HUMAN	hypothetical protein LOC643314	22	13 X 13 AA approximate tandem repeat of P-T-S-P-A-A-A-V-P-T-P-E-E.										0	Lung NSC(20;5.57e-06)|Ovarian(52;0.00769)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0393)	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	39988080	39988080	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:39988080G>A	uc001cdi.2	+	5	1220	c.874G>A	c.(874-876)GTC>ATC	p.V292I	PPIEL_uc001cdj.1_RNA|PPIEL_uc001cdk.2_RNA	NM_181809	NP_861525	Q7Z5Y6	BMP8A_HUMAN	bone morphogenetic protein 8A precursor	292					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)															---	---	---	---
BMP8B	656	broad.mit.edu	37	1	40229458	40229458	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:40229458C>T	uc001cdz.1	-	5	1250	c.874G>A	c.(874-876)GTC>ATC	p.V292I	BMP8B_uc001cea.1_Missense_Mutation_p.V317I|PPIE_uc001cdv.2_3'UTR|PPIE_uc001cdw.2_3'UTR	NM_001720	NP_001711	P34820	BMP8B_HUMAN	bone morphogenetic protein 8B preproprotein	292					cartilage development|cell differentiation|growth|ossification	extracellular space	cytokine activity|growth factor activity				0	all_cancers(7;5.56e-14)|all_lung(5;3.88e-17)|all_epithelial(6;3.78e-16)|Lung NSC(20;7.03e-07)|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;1.87e-18)|Epithelial(16;1.92e-17)|all cancers(16;4.03e-16)|LUSC - Lung squamous cell carcinoma(16;0.000261)|Lung(16;0.000457)															---	---	---	---
COL9A2	1298	broad.mit.edu	37	1	40770177	40770177	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:40770177C>T	uc001cfh.1	-	23	1256	c.1186G>A	c.(1186-1188)GTG>ATG	p.V396M	COL9A2_uc001cfi.1_Missense_Mutation_p.V215M	NM_001852	NP_001843	Q14055	CO9A2_HUMAN	alpha 2 type IX collagen precursor	396	Triple-helical region 3 (COL3).				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)															---	---	---	---
HIVEP3	59269	broad.mit.edu	37	1	42047227	42047227	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:42047227G>A	uc001cgz.3	-	4	4455	c.3242C>T	c.(3241-3243)GCC>GTC	p.A1081V	HIVEP3_uc001cha.3_Missense_Mutation_p.A1081V|HIVEP3_uc001cgy.2_RNA	NM_024503	NP_078779	Q5T1R4	ZEP3_HUMAN	human immunodeficiency virus type I enhancer	1081					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)																---	---	---	---
RIMKLA	284716	broad.mit.edu	37	1	42875732	42875732	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:42875732C>A	uc001chi.2	+	4	697	c.559C>A	c.(559-561)CTG>ATG	p.L187M		NM_173642	NP_775913	Q8IXN7	RIMKA_HUMAN	ribosomal modification protein rimK-like family	187	ATP-grasp.|ATP (By similarity).				protein modification process	cytoplasm	acid-amino acid ligase activity|ATP binding|metal ion binding				0																		---	---	---	---
ZNF691	51058	broad.mit.edu	37	1	43316851	43316851	+	Silent	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:43316851T>C	uc001cih.2	+	2	354	c.303T>C	c.(301-303)CAT>CAC	p.H101H	ZNF691_uc001cig.2_Silent_p.H74H|ZNF691_uc009vwm.2_Silent_p.H94H	NM_015911	NP_056995	Q5VV52	ZN691_HUMAN	zinc finger protein 691	105						nucleus	DNA binding|zinc ion binding			ovary(2)	2	Ovarian(52;0.00769)|all_hematologic(146;0.0977)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0505)																---	---	---	---
KIAA0467	23334	broad.mit.edu	37	1	43897960	43897960	+	Silent	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:43897960T>C	uc001cjk.1	+	22	3057	c.2595T>C	c.(2593-2595)CAT>CAC	p.H865H		NM_015284	NP_056099	Q5T011	SZT2_HUMAN	hypothetical protein LOC23334	1764						peroxisome					0	all_hematologic(146;0.0958)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0505)																---	---	---	---
KDM4A	9682	broad.mit.edu	37	1	44131395	44131395	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:44131395C>T	uc001cjx.2	+	6	818	c.652C>T	c.(652-654)CGG>TGG	p.R218W	KDM4A_uc010oki.1_Missense_Mutation_p.R218W	NM_014663	NP_055478	O75164	KDM4A_HUMAN	jumonji domain containing 2A	218	JmjC.				interspecies interaction between organisms|negative regulation of transcription, DNA-dependent|transcription, DNA-dependent	centrosome|nucleolus	histone demethylase activity (H3-K36 specific)|nucleic acid binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|protein binding|zinc ion binding			skin(1)	1																		---	---	---	---
IPO13	9670	broad.mit.edu	37	1	44432256	44432256	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:44432256C>T	uc001ckx.2	+	16	3202	c.2407C>T	c.(2407-2409)CGG>TGG	p.R803W	IPO13_uc001cky.2_Missense_Mutation_p.R21W	NM_014652	NP_055467	O94829	IPO13_HUMAN	importin 13	803	HEAT 14.				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)																---	---	---	---
SLC6A9	6536	broad.mit.edu	37	1	44475767	44475767	+	Silent	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:44475767G>A	uc001cll.2	-	4	600	c.408C>T	c.(406-408)GGC>GGT	p.G136G	SLC6A9_uc009vxe.2_5'UTR|SLC6A9_uc010okm.1_Silent_p.G63G|SLC6A9_uc001clm.2_Silent_p.G82G|SLC6A9_uc009vxd.2_RNA|SLC6A9_uc010okn.1_Silent_p.G67G|SLC6A9_uc001cln.2_Silent_p.G63G|SLC6A9_uc010oko.1_Intron|SLC6A9_uc010okp.1_RNA	NM_201649	NP_964012	P48067	SC6A9_HUMAN	solute carrier family 6 member 9 isoform 2	136	Helical; Name=2; (Potential).					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)													---	---	---	---
DMAP1	55929	broad.mit.edu	37	1	44685560	44685560	+	Intron	SNP	G	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:44685560G>T	uc001clq.1	+						DMAP1_uc001clr.1_Intron|DMAP1_uc001cls.1_Intron|DMAP1_uc010oku.1_Intron	NM_001034024	NP_001029196			DNA methyltransferase 1 associated protein 1						DNA methylation|histone H2A acetylation|histone H4 acetylation|negative regulation of transcription, DNA-dependent|regulation of growth|transcription, DNA-dependent	NuA4 histone acetyltransferase complex	DNA binding|protein binding				0	Acute lymphoblastic leukemia(166;0.155)																	---	---	---	---
RNF220	55182	broad.mit.edu	37	1	45115397	45115397	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:45115397C>T	uc001clv.1	+	13	1870	c.1510C>T	c.(1510-1512)CGG>TGG	p.R504W	RNF220_uc001clw.1_Missense_Mutation_p.R504W|RNF220_uc010oky.1_Missense_Mutation_p.R291W|RNF220_uc010okz.1_Missense_Mutation_p.R246W|RNF220_uc001clx.1_Missense_Mutation_p.R220W|RNF220_uc001cly.1_Missense_Mutation_p.R184W|RNF220_uc001clz.1_Missense_Mutation_p.R183W|RNF220_uc001cma.1_Missense_Mutation_p.R183W|TMEM53_uc001cmb.1_Intron	NM_018150	NP_060620	Q5VTB9	RN220_HUMAN	ring finger protein 220	504	Potential.				protein autoubiquitination	cytoplasm	ubiquitin-protein ligase activity|zinc ion binding			ovary(2)	2																		---	---	---	---
RPS8	6202	broad.mit.edu	37	1	45242267	45242267	+	Intron	SNP	C	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:45242267C>A	uc001cmi.2	+						SNORD38A_uc009vxi.2_5'Flank|SNORD38B_uc001cml.2_5'Flank	NM_001012	NP_001003			ribosomal protein S8						endocrine pancreas development|maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)|translational elongation|translational termination|viral transcription	cytosolic small ribosomal subunit	protein binding|structural constituent of ribosome			ovary(1)	1	Acute lymphoblastic leukemia(166;0.155)																	---	---	---	---
MMACHC	25974	broad.mit.edu	37	1	45974561	45974561	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:45974561C>T	uc009vxv.2	+	4	672	c.523C>T	c.(523-525)CCA>TCA	p.P175S	MMACHC_uc001cny.2_RNA	NM_015506	NP_056321	Q9Y4U1	MMAC_HUMAN	methylmalonic aciduria (cobalamin deficiency)	175							cobalamin binding				0	Acute lymphoblastic leukemia(166;0.155)				Cyanocobalamin(DB00115)|Hydroxocobalamin(DB00200)													---	---	---	---
IPP	3652	broad.mit.edu	37	1	46184936	46184936	+	Silent	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:46184936C>T	uc001cou.2	-	6	1392	c.1125G>A	c.(1123-1125)TCG>TCA	p.S375S	IPP_uc001cos.3_Silent_p.S375S	NM_005897	NP_005888	Q9Y573	IPP_HUMAN	intracisternal A particle-promoted polypeptide	375	Kelch 2.					actin cytoskeleton|cytoplasm	actin binding			ovary(1)	1	Acute lymphoblastic leukemia(166;0.155)																	---	---	---	---
MAST2	23139	broad.mit.edu	37	1	46500511	46500511	+	Silent	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:46500511G>A	uc001cov.2	+	29	4453	c.4170G>A	c.(4168-4170)CGG>CGA	p.R1390R	MAST2_uc001cow.2_Silent_p.R1389R|MAST2_uc001cpa.2_RNA	NM_015112	NP_055927	Q6P0Q8	MAST2_HUMAN	microtubule associated serine/threonine kinase	1390					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)																	---	---	---	---
CYP4Z1	199974	broad.mit.edu	37	1	47560255	47560255	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:47560255C>T	uc001cqu.1	+	7	793	c.790C>T	c.(790-792)CGG>TGG	p.R264W		NM_178134	NP_835235	Q86W10	CP4Z1_HUMAN	cytochrome P450 4Z1	264	Lumenal (Potential).					endoplasmic reticulum membrane|integral to membrane|microsome	aromatase activity|electron carrier activity|heme binding			skin(1)	1																		---	---	---	---
SPATA6	54558	broad.mit.edu	37	1	48821355	48821355	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:48821355T>C	uc001crr.1	-	11	1346	c.1181A>G	c.(1180-1182)CAA>CGA	p.Q394R	SPATA6_uc001crs.1_Intron|SPATA6_uc010omv.1_Missense_Mutation_p.Q380R	NM_019073	NP_061946	Q9NWH7	SPAT6_HUMAN	spermatogenesis associated 6 precursor	394					cell differentiation|multicellular organismal development|spermatogenesis	extracellular region				ovary(1)	1																		---	---	---	---
AGBL4	84871	broad.mit.edu	37	1	49128851	49128851	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:49128851C>T	uc001cru.2	-	7	855	c.697G>A	c.(697-699)GAA>AAA	p.E233K	AGBL4_uc010omw.1_5'UTR|AGBL4_uc010omx.1_Missense_Mutation_p.E245K|AGBL4_uc001crv.1_Missense_Mutation_p.E86K|AGBL4_uc010omy.1_Intron	NM_032785	NP_116174	Q5VU57	CBPC6_HUMAN	ATP/GTP binding protein-like 4	233		Zinc (By similarity).			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)														---	---	---	---
TTC39A	22996	broad.mit.edu	37	1	51755743	51755743	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:51755743C>T	uc001csl.2	-	16	1640	c.1535G>A	c.(1534-1536)GGC>GAC	p.G512D	TTC39A_uc001csk.2_Missense_Mutation_p.G477D|TTC39A_uc010ond.1_Missense_Mutation_p.G449D|TTC39A_uc010one.1_Missense_Mutation_p.G476D|TTC39A_uc010onf.1_Missense_Mutation_p.G480D|TTC39A_uc001csj.2_Missense_Mutation_p.G113D	NM_001080494	NP_001073963	Q5SRH9	TT39A_HUMAN	tetratricopeptide repeat domain 39A isoform 2	512	TPR 2.						binding			skin(1)	1																		---	---	---	---
ORC1L	4998	broad.mit.edu	37	1	52838863	52838863	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:52838863T>C	uc001ctt.2	-	17	2795	c.2576A>G	c.(2575-2577)AAA>AGA	p.K859R	ORC1L_uc010oni.1_Missense_Mutation_p.K854R|ORC1L_uc001ctu.2_Missense_Mutation_p.K859R|ORC1L_uc009vzd.2_Missense_Mutation_p.K613R	NM_004153	NP_004144	Q13415	ORC1_HUMAN	origin recognition complex, subunit 1	859	Necessary and sufficient for ORC complex assembly.				cell cycle checkpoint|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	cytosol|nuclear origin of replication recognition complex|nucleolus|nucleoplasm|plasma membrane	ATP binding|DNA binding|nucleoside-triphosphatase activity|protein binding				0																		---	---	---	---
ORC1L	4998	broad.mit.edu	37	1	52839002	52839002	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:52839002A>G	uc001ctt.2	-	17	2656	c.2437T>C	c.(2437-2439)TAC>CAC	p.Y813H	ORC1L_uc010oni.1_Missense_Mutation_p.Y808H|ORC1L_uc001ctu.2_Missense_Mutation_p.Y813H|ORC1L_uc009vzd.2_Missense_Mutation_p.Y567H	NM_004153	NP_004144	Q13415	ORC1_HUMAN	origin recognition complex, subunit 1	813	Necessary and sufficient for ORC complex assembly.				cell cycle checkpoint|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	cytosol|nuclear origin of replication recognition complex|nucleolus|nucleoplasm|plasma membrane	ATP binding|DNA binding|nucleoside-triphosphatase activity|protein binding				0																		---	---	---	---
PODN	127435	broad.mit.edu	37	1	53544301	53544301	+	Silent	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:53544301C>T	uc001cuv.2	+	8	1270	c.1263C>T	c.(1261-1263)CGC>CGT	p.R421R	PODN_uc001cuw.2_Silent_p.R402R|PODN_uc010onr.1_Silent_p.R402R|PODN_uc010ons.1_Silent_p.R279R	NM_153703	NP_714914	Q7Z5L7	PODN_HUMAN	podocan	373	LRR 12.				negative regulation of cell migration|negative regulation of cell proliferation	cytoplasm|extracellular space|proteinaceous extracellular matrix	collagen binding			ovary(1)|pancreas(1)	2																		---	---	---	---
LRP8	7804	broad.mit.edu	37	1	53716450	53716450	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:53716450T>C	uc001cvi.1	-	17	2730	c.2588A>G	c.(2587-2589)AAC>AGC	p.N863S	LRP8_uc001cvh.1_Missense_Mutation_p.N416S|LRP8_uc001cvk.1_Missense_Mutation_p.N693S|LRP8_uc001cvj.1_Missense_Mutation_p.N863S|LRP8_uc001cvl.1_Missense_Mutation_p.N659S|LRP8_uc001cvm.1_Missense_Mutation_p.N448S	NM_004631	NP_004622	Q14114	LRP8_HUMAN	low density lipoprotein receptor-related protein	863	Cytoplasmic (Potential).				cytokine-mediated signaling pathway|endocytosis|lipid metabolic process|platelet activation|proteolysis	caveola	calcium ion binding|very-low-density lipoprotein particle receptor activity				0																		---	---	---	---
MRPL37	51253	broad.mit.edu	37	1	54670971	54670971	+	Silent	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:54670971G>A	uc001cxa.3	+	3	611	c.534G>A	c.(532-534)CCG>CCA	p.P178P	MRPL37_uc009vzp.2_Intron|MRPL37_uc001cxb.1_Silent_p.P178P|MRPL37_uc001cxc.3_5'UTR|MRPL37_uc010oob.1_RNA	NM_016491	NP_057575	Q9BZE1	RM37_HUMAN	mitochondrial ribosomal protein L37 precursor	178					translation	mitochondrial ribosome	structural constituent of ribosome				0																		---	---	---	---
C1orf175	374977	broad.mit.edu	37	1	55158102	55158102	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:55158102T>C	uc010ooe.1	+	16	3041	c.2717T>C	c.(2716-2718)GTG>GCG	p.V906A	C1orf175_uc001cxq.2_RNA|C1orf175_uc010ooc.1_Missense_Mutation_p.V474A|C1orf175_uc001cxs.2_RNA|C1orf175_uc010ood.1_Missense_Mutation_p.V424A|C1orf175_uc010oof.1_RNA|C1orf175_uc001cxr.1_RNA|C1orf175_uc010oog.1_Missense_Mutation_p.V906A|C1orf175_uc010ooh.1_RNA|C1orf175_uc009vzq.1_RNA|C1orf175_uc001cxt.1_RNA|C1orf175_uc009vzr.1_Missense_Mutation_p.V108A|C1orf175_uc001cxu.2_Missense_Mutation_p.V52A	NM_001039464	NP_001034553	Q68CQ1	HEAT8_HUMAN	hypothetical protein LOC374977	906						integral to membrane	binding				0																		---	---	---	---
PRKAA2	5563	broad.mit.edu	37	1	57170021	57170021	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:57170021C>T	uc001cyk.3	+	7	1237	c.1166C>T	c.(1165-1167)ACG>ATG	p.T389M		NM_006252	NP_006243	P54646	AAPK2_HUMAN	AMP-activated protein kinase alpha 2 catalytic	389					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																		---	---	---	---
C8B	732	broad.mit.edu	37	1	57397488	57397488	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:57397488C>T	uc001cyp.2	-	11	1683	c.1616G>A	c.(1615-1617)CGG>CAG	p.R539Q	C8B_uc010oon.1_Missense_Mutation_p.R477Q|C8B_uc010ooo.1_Missense_Mutation_p.R487Q	NM_000066	NP_000057	P07358	CO8B_HUMAN	complement component 8, beta polypeptide	539					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	59004457	59004457	+	Intron	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:59004457A>G	uc001cyt.1	-						OMA1_uc001cyx.1_Intron|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																		---	---	---	---
FGGY	55277	broad.mit.edu	37	1	59787280	59787280	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:59787280G>A	uc001czi.3	+	2	271	c.59G>A	c.(58-60)GGC>GAC	p.G20D	FGGY_uc001czg.2_5'UTR|FGGY_uc001czh.2_RNA|FGGY_uc009wac.2_Missense_Mutation_p.G20D|FGGY_uc001czj.3_Missense_Mutation_p.G20D|FGGY_uc001czk.3_Intron|FGGY_uc001czl.3_Missense_Mutation_p.G20D	NM_018291	NP_060761	Q96C11	FGGY_HUMAN	FGGY carbohydrate kinase domain containing	20					carbohydrate metabolic process|cell death|neuron homeostasis		kinase activity|phosphotransferase activity, alcohol group as acceptor			ovary(1)	1	all_cancers(7;7.36e-05)																	---	---	---	---
NFIA	4774	broad.mit.edu	37	1	61824830	61824830	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:61824830G>A	uc001czw.2	+	6	1314	c.830G>A	c.(829-831)CGC>CAC	p.R277H	NFIA_uc001czy.2_Missense_Mutation_p.R269H|NFIA_uc010oos.1_Missense_Mutation_p.R322H|NFIA_uc001czv.2_Missense_Mutation_p.R277H	NM_001134673	NP_001128145	Q12857	NFIA_HUMAN	nuclear factor I/A isoform 1	277					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																		---	---	---	---
USP1	7398	broad.mit.edu	37	1	62916376	62916376	+	Silent	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:62916376G>A	uc001daj.1	+	9	2410	c.2082G>A	c.(2080-2082)GCG>GCA	p.A694A	USP1_uc001dak.1_Silent_p.A694A|USP1_uc001dal.1_Silent_p.A694A	NM_001017415	NP_001017415	O94782	UBP1_HUMAN	ubiquitin specific protease 1	694					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)														---	---	---	---
EFCAB7	84455	broad.mit.edu	37	1	63999133	63999133	+	Silent	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:63999133A>G	uc001dbf.2	+	5	789	c.495A>G	c.(493-495)AAA>AAG	p.K165K		NM_032437	NP_115813	A8K855	EFCB7_HUMAN	EF-hand calcium binding domain 7	165	EF-hand 2.						calcium ion binding				0																		---	---	---	---
EFCAB7	84455	broad.mit.edu	37	1	64021032	64021032	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:64021032T>C	uc001dbf.2	+	9	1354	c.1060T>C	c.(1060-1062)TTT>CTT	p.F354L		NM_032437	NP_115813	A8K855	EFCB7_HUMAN	EF-hand calcium binding domain 7	354							calcium ion binding				0																		---	---	---	---
PGM1	5236	broad.mit.edu	37	1	64102059	64102059	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:64102059G>A	uc001dbh.2	+	6	1241	c.1028G>A	c.(1027-1029)CGG>CAG	p.R343Q	PGM1_uc010ooy.1_Missense_Mutation_p.R146Q|PGM1_uc010ooz.1_Missense_Mutation_p.R361Q	NM_002633	NP_002624	P36871	PGM1_HUMAN	phosphoglucomutase 1	343					cellular calcium ion homeostasis|galactose catabolic process|glucose 1-phosphate metabolic process|glycogen biosynthetic process|glycogen catabolic process	cytosol	magnesium ion binding|phosphoglucomutase activity			ovary(2)|kidney(1)	3																		---	---	---	---
LEPROT	54741	broad.mit.edu	37	1	65895578	65895578	+	Silent	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:65895578C>T	uc001dcf.2	+	3	215	c.126C>T	c.(124-126)CAC>CAT	p.H42H	LEPR_uc001dcg.2_Intron|LEPR_uc001dch.2_Intron|LEPR_uc001dci.2_Intron|LEPR_uc009waq.2_Intron|LEPROT_uc009wap.2_Silent_p.H51H	NM_017526	NP_059996	O15243	OBRG_HUMAN	leptin receptor gene-related protein	42	Helical; (Potential).					endosome membrane|Golgi membrane|integral to plasma membrane					0				OV - Ovarian serous cystadenocarcinoma(397;0.00722)|KIRC - Kidney renal clear cell carcinoma(1967;0.094)														---	---	---	---
LEPR	3953	broad.mit.edu	37	1	66087143	66087143	+	Splice_Site	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:66087143T>C	uc001dci.2	+	18	2799	c.2597_splice	c.e18+2	p.R866_splice	LEPR_uc001dcg.2_Splice_Site_p.R866_splice|LEPR_uc001dch.2_Splice_Site_p.R866_splice|LEPR_uc009waq.2_Intron|LEPR_uc001dcj.2_Splice_Site_p.R866_splice|LEPR_uc001dck.2_Splice_Site_p.R866_splice	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)														---	---	---	---
PDE4B	5142	broad.mit.edu	37	1	66723491	66723491	+	Nonsense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:66723491C>T	uc001dcn.2	+	6	720	c.529C>T	c.(529-531)CGA>TGA	p.R177*	PDE4B_uc009war.2_Nonsense_Mutation_p.R85*|PDE4B_uc001dco.2_Nonsense_Mutation_p.R177*|PDE4B_uc001dcp.2_Nonsense_Mutation_p.R162*	NM_001037341	NP_001032418	Q07343	PDE4B_HUMAN	phosphodiesterase 4B isoform 1	177					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)													---	---	---	---
SGIP1	84251	broad.mit.edu	37	1	67098774	67098774	+	Silent	SNP	A	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:67098774A>T	uc001dcr.2	+	3	313	c.96A>T	c.(94-96)GGA>GGT	p.G32G		NM_032291	NP_115667	Q9BQI5	SGIP1_HUMAN	SH3-domain GRB2-like (endophilin) interacting	32					positive regulation of energy homeostasis|positive regulation of feeding behavior|positive regulation of receptor-mediated endocytosis|response to dietary excess	AP-2 adaptor complex	microtubule binding|phospholipid binding|SH3 domain binding			ovary(3)	3																		---	---	---	---
MIER1	57708	broad.mit.edu	37	1	67452090	67452090	+	3'UTR	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:67452090A>G	uc001dde.2	+	14					MIER1_uc010opf.1_Missense_Mutation_p.I429M|MIER1_uc009way.2_Missense_Mutation_p.I449M|MIER1_uc001ddc.2_Missense_Mutation_p.I465M|MIER1_uc001ddh.2_Missense_Mutation_p.I349M|MIER1_uc001ddf.2_3'UTR|MIER1_uc001ddg.2_3'UTR|MIER1_uc010opg.1_3'UTR|MIER1_uc001ddj.1_3'UTR|MIER1_uc001ddi.2_Missense_Mutation_p.I412M	NM_001077700	NP_001071168			mesoderm induction early response 1 isoform b						positive regulation of I-kappaB kinase/NF-kappaB cascade|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	DNA binding|signal transducer activity			ovary(1)	1																		---	---	---	---
IL23R	149233	broad.mit.edu	37	1	67724620	67724620	+	Missense_Mutation	SNP	G	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:67724620G>C	uc001ddo.2	+	11	1784	c.1699G>C	c.(1699-1701)GTA>CTA	p.V567L	IL23R_uc009waz.2_Missense_Mutation_p.V364L|IL23R_uc010opi.1_RNA|IL23R_uc010opj.1_Missense_Mutation_p.V165L|IL23R_uc010opk.1_3'UTR|IL23R_uc010opl.1_Missense_Mutation_p.V149L|IL23R_uc010opm.1_RNA|IL23R_uc001ddq.2_Missense_Mutation_p.V313L|IL23R_uc010opn.1_Missense_Mutation_p.V412L|IL23R_uc001ddr.2_RNA|IL23R_uc010ops.1_Missense_Mutation_p.V364L|IL23R_uc010opt.1_Missense_Mutation_p.V208L|IL23R_uc010opu.1_Missense_Mutation_p.V263L|IL23R_uc010opv.1_Missense_Mutation_p.V325L|IL23R_uc010opw.1_Missense_Mutation_p.V202L|IL23R_uc010opx.1_Missense_Mutation_p.V208L|IL23R_uc010opy.1_Missense_Mutation_p.V334L|IL23R_uc010opz.1_Missense_Mutation_p.V208L|IL23R_uc010oqa.1_Missense_Mutation_p.V208L|IL23R_uc010oqb.1_Missense_Mutation_p.V396L|IL23R_uc010oqc.1_Missense_Mutation_p.V283L|IL23R_uc010oqd.1_Missense_Mutation_p.V202L|IL23R_uc010oqe.1_Missense_Mutation_p.V165L|IL23R_uc010oqf.1_Missense_Mutation_p.V165L|IL23R_uc010oqg.1_Missense_Mutation_p.V165L|IL23R_uc010oqh.1_Missense_Mutation_p.V208L|IL23R_uc001dds.2_Missense_Mutation_p.V312L|IL23R_uc001ddt.2_Missense_Mutation_p.V165L	NM_144701	NP_653302	Q5VWK5	IL23R_HUMAN	interleukin 23 receptor precursor	567	Cytoplasmic (Potential).				inflammatory response|negative regulation of interleukin-10 production|positive regulation of defense response to virus by host|positive regulation of interferon-gamma production|positive regulation of interleukin-12 production|positive regulation of memory T cell differentiation|positive regulation of T cell mediated cytotoxicity|positive regulation of T-helper 1 type immune response|positive regulation of T-helper 17 cell lineage commitment|positive regulation of T-helper 17 type immune response|response to interferon-gamma|response to lipopolysaccharide	interleukin-23 receptor complex	receptor activity				0																		---	---	---	---
NEGR1	257194	broad.mit.edu	37	1	72241938	72241938	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:72241938T>C	uc001dfw.2	-	3	552	c.452A>G	c.(451-453)AAT>AGT	p.N151S	NEGR1_uc001dfv.2_Missense_Mutation_p.N23S|NEGR1_uc010oqs.1_Missense_Mutation_p.N151S	NM_173808	NP_776169	Q7Z3B1	NEGR1_HUMAN	neuronal growth regulator 1 precursor	151	Ig-like C2-type 2.				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)														---	---	---	---
LRRIQ3	127255	broad.mit.edu	37	1	74506926	74506926	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:74506926C>A	uc001dfy.3	-	7	1881	c.1689G>T	c.(1687-1689)AAG>AAT	p.K563N	LRRIQ3_uc001dfz.3_Intron	NM_001105659	NP_001099129	A6PVS8	LRIQ3_HUMAN	leucine-rich repeats and IQ motif containing 3	563	Potential.									ovary(2)	2																		---	---	---	---
C1orf173	127254	broad.mit.edu	37	1	75072365	75072365	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:75072365G>A	uc001dgg.2	-	10	1628	c.1409C>T	c.(1408-1410)ACT>ATT	p.T470I	uc001dgh.2_Intron|C1orf173_uc001dgi.3_Missense_Mutation_p.T264I	NM_001002912	NP_001002912	Q5RHP9	CA173_HUMAN	hypothetical protein LOC127254	470	Glu-rich.									ovary(3)|upper_aerodigestive_tract(1)|central_nervous_system(1)	5																		---	---	---	---
SLC44A5	204962	broad.mit.edu	37	1	75679417	75679417	+	Silent	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:75679417A>G	uc001dgu.2	-	22	2079	c.1935T>C	c.(1933-1935)TCT>TCC	p.S645S	SLC44A5_uc001dgt.2_Silent_p.S645S|SLC44A5_uc001dgs.2_Silent_p.S603S|SLC44A5_uc001dgr.2_Silent_p.S603S|SLC44A5_uc010oqz.1_Silent_p.S684S|SLC44A5_uc010ora.1_Silent_p.S639S|SLC44A5_uc010orb.1_Silent_p.S515S	NM_152697	NP_689910	Q8NCS7	CTL5_HUMAN	solute carrier family 44, member 5 isoform A	645	Extracellular (Potential).					integral to membrane|plasma membrane	choline transmembrane transporter activity			ovary(2)|skin(2)	4																		---	---	---	---
AK5	26289	broad.mit.edu	37	1	77759572	77759572	+	Missense_Mutation	SNP	G	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:77759572G>C	uc001dhn.2	+	3	599	c.342G>C	c.(340-342)GAG>GAC	p.E114D	AK5_uc001dho.2_Missense_Mutation_p.E88D|AK5_uc001dhm.1_Missense_Mutation_p.E90D	NM_174858	NP_777283	Q9Y6K8	KAD5_HUMAN	adenylate kinase 5 isoform 1	114					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																		---	---	---	---
AK5	26289	broad.mit.edu	37	1	77779534	77779534	+	Intron	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:77779534G>A	uc001dhn.2	+						AK5_uc001dho.2_Intron|AK5_uc001dhm.1_Missense_Mutation_p.A228T	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																		---	---	---	---
ZZZ3	26009	broad.mit.edu	37	1	78034027	78034027	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:78034027A>G	uc001dhq.2	-	13	2932	c.2456T>C	c.(2455-2457)GTG>GCG	p.V819A	ZZZ3_uc001dhr.2_Missense_Mutation_p.V325A|ZZZ3_uc001dhp.2_Missense_Mutation_p.V818A	NM_015534	NP_056349	Q8IYH5	ZZZ3_HUMAN	zinc finger, ZZ-type containing 3	819	ZZ-type.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(4)|large_intestine(1)	5																		---	---	---	---
WDR63	126820	broad.mit.edu	37	1	85550310	85550310	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:85550310A>G	uc001dkt.2	+	6	663	c.472A>G	c.(472-474)AAA>GAA	p.K158E	WDR63_uc009wcl.2_Missense_Mutation_p.K158E	NM_145172	NP_660155	Q8IWG1	WDR63_HUMAN	WD repeat domain 63	158										upper_aerodigestive_tract(2)|ovary(2)|skin(1)	5				all cancers(265;0.00391)|Epithelial(280;0.00922)|Colorectal(170;0.166)														---	---	---	---
SYDE2	84144	broad.mit.edu	37	1	85656152	85656152	+	Silent	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:85656152A>G	uc009wcm.2	-	2	1078	c.1029T>C	c.(1027-1029)TGT>TGC	p.C343C	SYDE2_uc001dku.3_Silent_p.C343C	NM_032184	NP_115560	Q5VT97	SYDE2_HUMAN	synapse defective 1, Rho GTPase, homolog 2	343					activation of Rho GTPase activity|small GTPase mediated signal transduction	cytosol	Rho GTPase activator activity			ovary(1)|central_nervous_system(1)	2				all cancers(265;0.0126)|Epithelial(280;0.0336)														---	---	---	---
CLCA1	1179	broad.mit.edu	37	1	86964503	86964503	+	Intron	SNP	A	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:86964503A>C	uc001dlt.2	+							NM_001285	NP_001276			chloride channel accessory 1 precursor						calcium ion transport	extracellular space|integral to plasma membrane	chloride channel activity			ovary(1)	1		Lung NSC(277;0.239)		all cancers(265;0.0249)|Epithelial(280;0.0476)														---	---	---	---
PKN2	5586	broad.mit.edu	37	1	89226061	89226061	+	Splice_Site	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:89226061T>C	uc001dmn.2	+	3	846	c.504_splice	c.e3+2	p.K168_splice	PKN2_uc001dmm.1_Splice_Site_p.K168_splice|PKN2_uc010osp.1_Splice_Site_p.K168_splice|PKN2_uc010osq.1_Splice_Site_p.K11_splice|PKN2_uc009wcv.2_Splice_Site_p.K168_splice	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)														---	---	---	---
GBP3	2635	broad.mit.edu	37	1	89479012	89479012	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:89479012G>A	uc001dmt.2	-	6	929	c.724C>T	c.(724-726)CGC>TGC	p.R242C	GBP3_uc010oss.1_Missense_Mutation_p.R163C|GBP3_uc001dmu.2_Missense_Mutation_p.R108C|GBP3_uc001dmv.2_RNA	NM_018284	NP_060754	Q9H0R5	GBP3_HUMAN	guanylate binding protein 3	242						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)														---	---	---	---
BRDT	676	broad.mit.edu	37	1	92428306	92428306	+	5'UTR	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:92428306T>C	uc001dok.3	+	2					BRDT_uc001dol.3_5'UTR|BRDT_uc010osz.1_5'UTR|BRDT_uc009wdf.2_Intron|BRDT_uc010ota.1_5'UTR|BRDT_uc010otb.1_5'UTR|BRDT_uc001dom.3_5'UTR	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)														---	---	---	---
ABCA4	24	broad.mit.edu	37	1	94512553	94512553	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:94512553T>C	uc001dqh.2	-	19	2944	c.2840A>G	c.(2839-2841)GAC>GGC	p.D947G	ABCA4_uc010otn.1_Missense_Mutation_p.D873G	NM_000350	NP_000341	P78363	ABCA4_HUMAN	ATP-binding cassette, sub-family A member 4	947	Cytoplasmic.|ABC transporter 1.				phototransduction, visible light|visual perception	integral to plasma membrane|membrane fraction	ATP binding|ATPase activity, coupled to transmembrane movement of substances			ovary(4)|skin(4)|central_nervous_system(2)|upper_aerodigestive_tract(1)|breast(1)	12		all_lung(203;0.000757)|Lung NSC(277;0.00335)		all cancers(265;0.00432)|GBM - Glioblastoma multiforme(16;0.00715)|Epithelial(280;0.171)														---	---	---	---
ABCA4	24	broad.mit.edu	37	1	94528842	94528842	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:94528842T>G	uc001dqh.2	-	12	1690	c.1586A>C	c.(1585-1587)AAT>ACT	p.N529T	ABCA4_uc010otn.1_Missense_Mutation_p.N529T	NM_000350	NP_000341	P78363	ABCA4_HUMAN	ATP-binding cassette, sub-family A member 4	529	Extracellular.				phototransduction, visible light|visual perception	integral to plasma membrane|membrane fraction	ATP binding|ATPase activity, coupled to transmembrane movement of substances			ovary(4)|skin(4)|central_nervous_system(2)|upper_aerodigestive_tract(1)|breast(1)	12		all_lung(203;0.000757)|Lung NSC(277;0.00335)		all cancers(265;0.00432)|GBM - Glioblastoma multiforme(16;0.00715)|Epithelial(280;0.171)														---	---	---	---
ARHGAP29	9411	broad.mit.edu	37	1	94650435	94650435	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:94650435C>T	uc001dqj.3	-	18	2471	c.2102G>A	c.(2101-2103)TGT>TAT	p.C701Y	ARHGAP29_uc009wdq.1_RNA|ARHGAP29_uc001dqk.2_Missense_Mutation_p.C267Y	NM_004815	NP_004806	Q52LW3	RHG29_HUMAN	PTPL1-associated RhoGAP 1	701	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)														---	---	---	---
F3	2152	broad.mit.edu	37	1	95001638	95001638	+	Missense_Mutation	SNP	C	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:95001638C>G	uc001dqr.2	-	3	474	c.295G>C	c.(295-297)GTG>CTG	p.V99L	F3_uc001dqp.2_RNA|F3_uc001dqq.2_RNA|F3_uc001dqs.2_Missense_Mutation_p.V99L	NM_001993	NP_001984	P13726	TF_HUMAN	coagulation factor III precursor	99	Extracellular (Potential).				activation of caspase activity|activation of plasma proteins involved in acute inflammatory response|anti-apoptosis|blood coagulation, extrinsic pathway|positive regulation of angiogenesis|positive regulation of endothelial cell proliferation|positive regulation of platelet-derived growth factor receptor signaling pathway|positive regulation of protein kinase B signaling cascade	extracellular matrix|extracellular space|integral to membrane	cell surface binding|phospholipid binding|protease binding			central_nervous_system(1)	1		all_lung(203;0.00106)|Lung NSC(277;0.00475)		all cancers(265;0.0232)|Epithelial(280;0.121)	Coagulation factor VIIa(DB00036)													---	---	---	---
DPYD	1806	broad.mit.edu	37	1	97981426	97981426	+	Silent	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:97981426G>A	uc001drv.2	-	13	1733	c.1596C>T	c.(1594-1596)GAC>GAT	p.D532D		NM_000110	NP_000101	Q12882	DPYD_HUMAN	dihydropyrimidine dehydrogenase isoform 1	532					'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	98058869	98058869	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:98058869A>G	uc001drv.2	-	10	1170	c.1033T>C	c.(1033-1035)TTT>CTT	p.F345L		NM_000110	NP_000101	Q12882	DPYD_HUMAN	dihydropyrimidine dehydrogenase isoform 1	345	NADP (Potential).				'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)													---	---	---	---
LPPR4	9890	broad.mit.edu	37	1	99764627	99764627	+	Missense_Mutation	SNP	T	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:99764627T>A	uc001dse.2	+	4	681	c.575T>A	c.(574-576)ATT>AAT	p.I192N	LPPR4_uc010oue.1_Missense_Mutation_p.I192N	NM_014839	NP_055654	Q7Z2D5	LPPR4_HUMAN	plasticity related gene 1	192	Helical; (Potential).						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)														---	---	---	---
S1PR1	1901	broad.mit.edu	37	1	101705444	101705444	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:101705444C>T	uc001dud.2	+	2	1418	c.904C>T	c.(904-906)CTC>TTC	p.L302F	S1PR1_uc009weg.2_Missense_Mutation_p.L302F	NM_001400	NP_001391	P21453	S1PR1_HUMAN	sphingosine-1-phosphate receptor 1	302	Helical; Name=7; (By similarity).				cell adhesion	integral to membrane	lysosphingolipid and lysophosphatidic acid receptor activity			ovary(2)|lung(1)	3																		---	---	---	---
AMY2B	280	broad.mit.edu	37	1	104118160	104118160	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:104118160A>G	uc001duq.2	+	9	1715	c.1099A>G	c.(1099-1101)AAC>GAC	p.N367D	AMY2B_uc010ouo.1_RNA|LOC648740_uc001dur.2_Missense_Mutation_p.N367D|AMY2B_uc001dus.1_RNA	NM_020978	NP_066188	P19961	AMY2B_HUMAN	amylase, pancreatic, alpha-2B precursor	367					carbohydrate metabolic process|digestion	extracellular region	alpha-amylase activity|metal ion binding				0		all_epithelial(167;3.05e-05)|all_lung(203;0.000199)|Lung NSC(277;0.000451)		Colorectal(144;0.0669)|all cancers(265;0.083)|Epithelial(280;0.094)|Lung(183;0.112)														---	---	---	---
STXBP3	6814	broad.mit.edu	37	1	109294903	109294903	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:109294903A>G	uc001dvy.2	+	2	149	c.74A>G	c.(73-75)GAC>GGC	p.D25G	STXBP3_uc001dvz.2_RNA	NM_007269	NP_009200	O00186	STXB3_HUMAN	syntaxin binding protein 3	25	Mediates interaction with DOC2B (By similarity).				negative regulation of calcium ion-dependent exocytosis|neutrophil degranulation|platelet aggregation|protein transport|vesicle docking involved in exocytosis	cytosol|nucleus|platelet alpha granule|specific granule|tertiary granule	syntaxin-2 binding			ovary(3)|central_nervous_system(1)	4		all_epithelial(167;0.000154)|all_lung(203;0.00026)|Lung NSC(277;0.000508)		Colorectal(144;0.0386)|Lung(183;0.104)|COAD - Colon adenocarcinoma(174;0.137)|Epithelial(280;0.231)														---	---	---	---
KIAA1324	57535	broad.mit.edu	37	1	109716331	109716331	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:109716331G>A	uc001dwq.2	+	8	960	c.824G>A	c.(823-825)TGC>TAC	p.C275Y	KIAA1324_uc009wex.1_Intron|KIAA1324_uc009wey.2_Intron|KIAA1324_uc010ovg.1_Missense_Mutation_p.C173Y	NM_020775	NP_065826	Q6UXG2	K1324_HUMAN	hypothetical protein LOC57535 precursor	275	Extracellular (Potential).				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)														---	---	---	---
CELSR2	1952	broad.mit.edu	37	1	109811524	109811524	+	Silent	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:109811524C>T	uc001dxa.3	+	19	6586	c.6525C>T	c.(6523-6525)GAC>GAT	p.D2175D		NM_001408	NP_001399	Q9HCU4	CELR2_HUMAN	cadherin EGF LAG seven-pass G-type receptor 2	2175	Extracellular (Potential).				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)														---	---	---	---
GPR61	83873	broad.mit.edu	37	1	110086370	110086370	+	Silent	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:110086370C>T	uc001dxy.2	+	2	1409	c.726C>T	c.(724-726)CAC>CAT	p.H242H		NM_031936	NP_114142	Q9BZJ8	GPR61_HUMAN	G protein-coupled receptor 61	242	Cytoplasmic (Potential).			QH -> PD (in Ref. 1; AAK12637).		integral to membrane|plasma membrane	G-protein coupled receptor activity			central_nervous_system(2)	2		all_epithelial(167;2.83e-05)|all_lung(203;0.00016)|Lung NSC(277;0.000318)|Breast(1374;0.244)		Lung(183;0.0426)|Colorectal(144;0.11)|Epithelial(280;0.128)|all cancers(265;0.132)|LUSC - Lung squamous cell carcinoma(189;0.228)														---	---	---	---
GSTM5	2949	broad.mit.edu	37	1	110255249	110255249	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:110255249G>A	uc001dyn.2	+	2	117	c.46G>A	c.(46-48)GCC>ACC	p.A16T	GSTM5_uc010ovu.1_5'UTR	NM_000851	NP_000842	P46439	GSTM5_HUMAN	glutathione S-transferase mu 5	16	GST N-terminal.				xenobiotic metabolic process	endoplasmic reticulum membrane	glutathione transferase activity			central_nervous_system(6)	6		all_epithelial(167;2.5e-05)|all_lung(203;0.000135)|Lung NSC(277;0.000269)|Breast(1374;0.244)		Colorectal(144;0.0131)|all cancers(265;0.0252)|Epithelial(280;0.0265)|Lung(183;0.0425)|COAD - Colon adenocarcinoma(174;0.0474)|LUSC - Lung squamous cell carcinoma(189;0.228)	Glutathione(DB00143)													---	---	---	---
RBM15	64783	broad.mit.edu	37	1	110884794	110884794	+	Missense_Mutation	SNP	T	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:110884794T>A	uc001dzl.1	+	1	2850	c.2767T>A	c.(2767-2769)TTC>ATC	p.F923I	RBM15_uc001dzm.1_Missense_Mutation_p.F923I	NM_022768	NP_073605	Q96T37	RBM15_HUMAN	RNA binding motif protein 15	923	SPOC.				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	111216190	111216190	+	Silent	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:111216190G>A	uc001dzv.1	-	1	1466	c.1242C>T	c.(1240-1242)AGC>AGT	p.S414S		NM_002232	NP_002223	P22001	KCNA3_HUMAN	potassium voltage-gated channel, shaker-related	414	Helical; Name=Segment S5; (Potential).					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)														---	---	---	---
OVGP1	5016	broad.mit.edu	37	1	111959090	111959090	+	Intron	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:111959090T>C	uc001eba.2	-						OVGP1_uc001eaz.2_Intron|OVGP1_uc010owb.1_Intron	NM_002557	NP_002548			oviductal glycoprotein 1 precursor						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)														---	---	---	---
C1orf183	55924	broad.mit.edu	37	1	112269694	112269694	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:112269694C>A	uc001ebo.1	-	2	948	c.790G>T	c.(790-792)GGC>TGC	p.G264C	C1orf183_uc001ebp.1_Missense_Mutation_p.G249C	NM_019099	NP_061972	Q9NTI7	CA183_HUMAN	hypothetical protein LOC55924 isoform 1	264										ovary(2)	2		all_cancers(81;7.29e-06)|all_epithelial(167;4.98e-06)|all_lung(203;2.44e-05)|Lung NSC(69;4.16e-05)		Lung(183;0.0155)|Colorectal(144;0.0289)|all cancers(265;0.0592)|LUSC - Lung squamous cell carcinoma(189;0.0826)|Epithelial(280;0.0852)|COAD - Colon adenocarcinoma(174;0.113)														---	---	---	---
MOV10	4343	broad.mit.edu	37	1	113232072	113232072	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:113232072T>C	uc001eck.2	+	4	647	c.377T>C	c.(376-378)GTG>GCG	p.V126A	MOV10_uc001ecl.2_Missense_Mutation_p.V126A|MOV10_uc001ecn.2_Missense_Mutation_p.V126A|MOV10_uc001ecm.2_Missense_Mutation_p.V66A|MOV10_uc009wgj.1_Missense_Mutation_p.V66A	NM_001130079	NP_001123551	Q9HCE1	MOV10_HUMAN	Mov10, Moloney leukemia virus 10, homolog	126					mRNA cleavage involved in gene silencing by miRNA|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasmic mRNA processing body	ATP binding|helicase activity|protein binding|RNA binding			ovary(4)|skin(1)	5	Lung SC(450;0.246)	all_cancers(81;3.31e-11)|all_epithelial(167;5.69e-10)|all_lung(203;3.73e-05)|Breast(1374;0.000525)|Lung NSC(69;0.000954)|Ovarian(761;0.0367)|Lung SC(238;0.114)		OV - Ovarian serous cystadenocarcinoma(397;3.99e-67)|all cancers(265;1e-62)|Epithelial(280;4.78e-61)|Lung(183;0.0234)|Colorectal(144;0.0686)|READ - Rectum adenocarcinoma(129;0.0929)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133)|BRCA - Breast invasive adenocarcinoma(282;0.24)														---	---	---	---
PPM1J	333926	broad.mit.edu	37	1	113253637	113253637	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:113253637C>T	uc001ect.1	-	7	1130	c.1103G>A	c.(1102-1104)GGC>GAC	p.G368D	PPM1J_uc009wgl.1_RNA|PPM1J_uc001ecs.1_Missense_Mutation_p.G162D	NM_005167	NP_005158	Q5JR12	PPM1J_HUMAN	protein phosphatase 1J (PP2C domain containing)	368	PP2C-like.									breast(2)|central_nervous_system(1)	3	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)														---	---	---	---
MAGI3	260425	broad.mit.edu	37	1	114201758	114201758	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:114201758A>G	uc001edk.2	+	16	2867	c.2686A>G	c.(2686-2688)AAA>GAA	p.K896E	MAGI3_uc001edh.3_Missense_Mutation_p.K921E|MAGI3_uc001edi.3_Missense_Mutation_p.K896E|MAGI3_uc010owm.1_Missense_Mutation_p.K921E|MAGI3_uc001edj.2_Missense_Mutation_p.K617E	NM_001142782	NP_001136254	Q5TCQ9	MAGI3_HUMAN	membrane-associated guanylate kinase-related  3	921	Interaction with LPAR2 and GRIN2B.|PDZ 5.				apoptosis|interspecies interaction between organisms|intracellular signal transduction	nucleus|tight junction	ATP binding|guanylate kinase activity|protein binding			lung(3)|ovary(2)|central_nervous_system(1)	6	Lung SC(450;0.184)	all_cancers(81;2.34e-09)|all_epithelial(167;7.41e-09)|all_lung(203;7.13e-06)|Lung NSC(69;1.2e-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)														---	---	---	---
MAGI3	260425	broad.mit.edu	37	1	114226552	114226552	+	Silent	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:114226552A>G	uc001edk.2	+	21	4543	c.4362A>G	c.(4360-4362)AAA>AAG	p.K1454K	MAGI3_uc001edi.3_3'UTR|MAGI3_uc010owm.1_3'UTR|MAGI3_uc001edj.2_3'UTR|MAGI3_uc009wgo.2_RNA	NM_001142782	NP_001136254	Q5TCQ9	MAGI3_HUMAN	membrane-associated guanylate kinase-related  3	1479					apoptosis|interspecies interaction between organisms|intracellular signal transduction	nucleus|tight junction	ATP binding|guanylate kinase activity|protein binding			lung(3)|ovary(2)|central_nervous_system(1)	6	Lung SC(450;0.184)	all_cancers(81;2.34e-09)|all_epithelial(167;7.41e-09)|all_lung(203;7.13e-06)|Lung NSC(69;1.2e-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)														---	---	---	---
TRIM33	51592	broad.mit.edu	37	1	114967384	114967384	+	Intron	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:114967384A>G	uc001eew.2	-						TRIM33_uc010owr.1_Intron|TRIM33_uc010ows.1_Intron|TRIM33_uc001eex.2_Intron	NM_015906	NP_056990			tripartite motif-containing 33 protein isoform						negative regulation of BMP signaling pathway|negative regulation of transcription, DNA-dependent|protein ubiquitination|regulation of transforming growth factor beta receptor signaling pathway|transcription, DNA-dependent	nucleus	co-SMAD binding|DNA binding|ligase activity|R-SMAD binding|zinc ion binding			lung(4)|central_nervous_system(3)|large_intestine(1)|breast(1)|skin(1)|ovary(1)	11	all_epithelial(7;0.000132)|all_lung(7;0.00106)|Lung SC(450;0.184)	all_cancers(81;3.03e-08)|all_epithelial(167;3.24e-08)|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)				T	RET	papillary thyroid								---	---	---	---
TSPAN2	10100	broad.mit.edu	37	1	115596047	115596047	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:115596047T>C	uc001eft.2	-	7	615	c.553A>G	c.(553-555)AAG>GAG	p.K185E		NM_005725	NP_005716	O60636	TSN2_HUMAN	tetraspan 2	185	Extracellular (Potential).					integral to membrane					0	Lung SC(450;0.211)	all_cancers(81;2.9e-07)|all_epithelial(167;1.42e-06)|all_lung(203;6.72e-06)|Lung NSC(69;1.13e-05)|Acute lymphoblastic leukemia(138;0.191)		Lung(183;0.0234)|Colorectal(144;0.0686)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133)|all cancers(265;0.159)|Epithelial(280;0.179)														---	---	---	---
SLC22A15	55356	broad.mit.edu	37	1	116562260	116562260	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:116562260A>G	uc001egb.3	+	3	488	c.358A>G	c.(358-360)AGT>GGT	p.S120G	SLC22A15_uc001ega.2_Missense_Mutation_p.S120G	NM_018420	NP_060890	Q8IZD6	S22AF_HUMAN	solute carrier family 22, member 15	120	Helical; (Potential).				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)														---	---	---	---
FAM46C	54855	broad.mit.edu	37	1	118165797	118165797	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:118165797G>A	uc001ehe.2	+	2	506	c.307G>A	c.(307-309)GCA>ACA	p.A103T		NM_017709	NP_060179	Q5VWP2	FA46C_HUMAN	hypothetical protein LOC54855	103											0	Lung SC(450;0.225)	all_cancers(81;0.000101)|all_lung(203;3.4e-06)|all_epithelial(167;4.98e-06)|Lung NSC(69;2.33e-05)		Lung(183;0.0576)|LUSC - Lung squamous cell carcinoma(189;0.192)|Colorectal(144;0.247)											Multiple Myeloma(3;1.13e-06)			---	---	---	---
TBX15	6913	broad.mit.edu	37	1	119428077	119428077	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:119428077A>G	uc001ehl.1	-	8	1084	c.769T>C	c.(769-771)TCT>CCT	p.S257P	TBX15_uc009whj.1_Missense_Mutation_p.S81P	NM_152380	NP_689593	Q96SF7	TBX15_HUMAN	T-box 15	363						nucleus	DNA binding|sequence-specific DNA binding transcription factor activity			large_intestine(1)|pancreas(1)	2	all_neural(166;0.117)	all_cancers(81;0.000692)|all_lung(203;3.05e-06)|Lung NSC(69;2.13e-05)|all_epithelial(167;0.000237)		Lung(183;0.044)|LUSC - Lung squamous cell carcinoma(189;0.141)														---	---	---	---
ZNF697	90874	broad.mit.edu	37	1	120168554	120168554	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:120168554A>G	uc001ehy.1	-	2	284	c.170T>C	c.(169-171)ATG>ACG	p.M57T		NM_001080470	NP_001073939	Q5TEC3	ZN697_HUMAN	zinc finger protein 697	57					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)														---	---	---	---
GJA5	2702	broad.mit.edu	37	1	147231238	147231238	+	Silent	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:147231238G>A	uc001eps.1	-	2	250	c.109C>T	c.(109-111)CTG>TTG	p.L37L	GJA5_uc001ept.1_Silent_p.L37L	NM_181703	NP_859054	P36382	CXA5_HUMAN	connexin 40	37	Helical; (Potential).				angiogenesis|cell-cell junction assembly|muscle contraction	integral to membrane				ovary(1)	1	all_hematologic(923;0.0276)		LUSC - Lung squamous cell carcinoma(543;0.202)															---	---	---	---
NBPF14	25832	broad.mit.edu	37	1	148008581	148008581	+	Silent	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:148008581T>C	uc001eqq.2	-	17	2024	c.2007A>G	c.(2005-2007)TCA>TCG	p.S669S	LOC200030_uc001eqe.2_Intron|LOC200030_uc001eqf.2_Intron|LOC200030_uc001eqg.2_Intron|FLJ39739_uc001eqo.1_Intron|NBPF14_uc010pab.1_Intron|NBPF14_uc010pac.1_Silent_p.S242S|NBPF14_uc001eqx.2_Intron|NBPF14_uc010pad.1_Intron|NBPF14_uc001eqs.1_Intron	NM_015383	NP_056198	Q5TI25	NBPFE_HUMAN	hypothetical protein LOC25832	669	NBPF 7.					cytoplasm				ovary(1)	1	all_hematologic(923;0.032)																	---	---	---	---
LOC200030	200030	broad.mit.edu	37	1	148341928	148341928	+	Intron	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:148341928G>A	uc001eqe.2	-						LOC200030_uc001eqf.2_Silent_p.H215H|LOC200030_uc001eqg.2_Intron|NBPF14_uc009wkf.1_RNA|uc001erd.3_Silent_p.H215H|uc001erc.3_RNA|uc010paj.1_Intron|uc010pau.1_Translation_Start_Site|uc010pav.1_Silent_p.H215H|uc010paw.1_Silent_p.H140H					SubName: Full=cDNA FLJ78770;							cytoplasm					0																		---	---	---	---
HIST2H2AC	8338	broad.mit.edu	37	1	149858826	149858826	+	Missense_Mutation	SNP	T	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:149858826T>A	uc001etd.2	+	1	302	c.302T>A	c.(301-303)GTC>GAC	p.V101D	HIST2H2BE_uc001etc.2_5'Flank	NM_003517	NP_003508	Q16777	H2A2C_HUMAN	histone cluster 2, H2ac	101					nucleosome assembly	nucleosome|nucleus	DNA binding			ovary(1)|skin(1)	2	Breast(34;0.0124)|all_hematologic(923;0.127)		STAD - Stomach adenocarcinoma(528;0.133)|LUSC - Lung squamous cell carcinoma(543;0.221)															---	---	---	---
TARS2	80222	broad.mit.edu	37	1	150471087	150471087	+	Silent	SNP	C	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:150471087C>A	uc001euq.2	+	11	1355	c.1348C>A	c.(1348-1350)CGA>AGA	p.R450R	TARS2_uc010pcd.1_RNA|TARS2_uc001eur.2_Silent_p.R368R|TARS2_uc009wlt.2_Silent_p.R76R|TARS2_uc009wls.2_Silent_p.R320R	NM_025150	NP_079426	Q9BW92	SYTM_HUMAN	threonyl-tRNA synthetase 2, mitochondrial	450					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)													---	---	---	---
ECM1	1893	broad.mit.edu	37	1	150483478	150483478	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:150483478G>A	uc001eus.2	+	6	711	c.512G>A	c.(511-513)CGG>CAG	p.R171Q	ECM1_uc010pce.1_Missense_Mutation_p.R100Q|ECM1_uc010pcf.1_Missense_Mutation_p.R93Q|ECM1_uc001eut.2_Missense_Mutation_p.R171Q|ECM1_uc001euu.2_Missense_Mutation_p.R200Q|ECM1_uc001euv.2_Missense_Mutation_p.R198Q|ECM1_uc009wlu.2_5'UTR	NM_004425	NP_004416	Q16610	ECM1_HUMAN	extracellular matrix protein 1 isoform 1	171	2 X approximate repeats.|1.				angiogenesis|biomineral tissue development|negative regulation of bone mineralization|negative regulation of peptidase activity|ossification|positive regulation of angiogenesis|positive regulation of endothelial cell proliferation|positive regulation of I-kappaB kinase/NF-kappaB cascade	proteinaceous extracellular matrix	laminin binding|protease binding|protein C-terminus binding|signal transducer activity			ovary(2)|central_nervous_system(1)	3	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;1.29e-21)|BRCA - Breast invasive adenocarcinoma(12;0.000734)|LUSC - Lung squamous cell carcinoma(543;0.171)|STAD - Stomach adenocarcinoma(528;0.206)															---	---	---	---
FAM63A	55793	broad.mit.edu	37	1	150974767	150974767	+	Silent	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:150974767A>G	uc001ewf.2	-	3	2011	c.327T>C	c.(325-327)CCT>CCC	p.P109P	FAM63A_uc001ewc.2_5'UTR|FAM63A_uc010pcm.1_Silent_p.P14P|FAM63A_uc001ewd.2_5'UTR|FAM63A_uc001ewe.2_Intron|FAM63A_uc010pcn.1_Silent_p.P157P|FAM63A_uc001ewg.2_Silent_p.P109P	NM_018379	NP_001156731	Q8N5J2	FA63A_HUMAN	hypothetical protein LOC55793 isoform 1	109							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)															---	---	---	---
RFX5	5993	broad.mit.edu	37	1	151318694	151318694	+	Nonsense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:151318694G>A	uc001exv.1	-	3	317	c.103C>T	c.(103-105)CGA>TGA	p.R35*	RFX5_uc001exw.1_Nonsense_Mutation_p.R35*|RFX5_uc009wmr.1_Nonsense_Mutation_p.R35*|RFX5_uc010pcx.1_Nonsense_Mutation_p.R35*	NM_001025603	NP_001020774	P48382	RFX5_HUMAN	regulatory factor X, 5	35	N-terminal domain.					nucleus	DNA binding|protein binding|sequence-specific DNA binding transcription factor activity			ovary(1)	1	Lung SC(34;0.00471)|Ovarian(49;0.0147)|Hepatocellular(266;0.0997)|all_hematologic(923;0.127)|Melanoma(130;0.185)		UCEC - Uterine corpus endometrioid carcinoma (35;0.112)|LUSC - Lung squamous cell carcinoma(543;0.181)															---	---	---	---
SELENBP1	8991	broad.mit.edu	37	1	151338749	151338749	+	Splice_Site	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:151338749A>G	uc001exx.2	-	7	890	c.843_splice	c.e7+1	p.E281_splice	SELENBP1_uc010pcy.1_Splice_Site_p.E323_splice|SELENBP1_uc001exy.2_Splice_Site_p.E178_splice|SELENBP1_uc001exz.2_Splice_Site_p.E178_splice|SELENBP1_uc010pcz.1_Splice_Site_p.E219_splice|SELENBP1_uc009wms.2_Splice_Site_p.E117_splice|SELENBP1_uc009wmt.2_Splice_Site_p.E178_splice|SELENBP1_uc001eya.2_Splice_Site_p.E217_splice|SELENBP1_uc009wmu.2_Splice_Site_p.E178_splice	NM_003944	NP_003935			selenium binding protein 1						protein transport	cytosol|membrane|nucleolus	protein binding|selenium binding				0	Lung SC(34;0.00471)|Ovarian(49;0.00871)|Hepatocellular(266;0.0997)|all_hematologic(923;0.127)|Melanoma(130;0.185)		UCEC - Uterine corpus endometrioid carcinoma (35;0.112)|LUSC - Lung squamous cell carcinoma(543;0.181)															---	---	---	---
CGN	57530	broad.mit.edu	37	1	151491647	151491647	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:151491647C>T	uc009wmw.2	+	2	796	c.652C>T	c.(652-654)CGC>TGC	p.R218C		NM_020770	NP_065821	Q9P2M7	CING_HUMAN	cingulin	212	Interacts with ZO-2.|Head.					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)															---	---	---	---
TCHH	7062	broad.mit.edu	37	1	152080120	152080120	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:152080120C>T	uc001ezp.2	-	2	5573	c.5573G>A	c.(5572-5574)CGT>CAT	p.R1858H	TCHH_uc009wne.1_Missense_Mutation_p.R1858H	NM_007113	NP_009044	Q07283	TRHY_HUMAN	trichohyalin	1858	23 X 26 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)															---	---	---	---
TCHH	7062	broad.mit.edu	37	1	152082320	152082320	+	Silent	SNP	T	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:152082320T>G	uc001ezp.2	-	2	3373	c.3373A>C	c.(3373-3375)AGA>CGA	p.R1125R	TCHH_uc009wne.1_Silent_p.R1125R	NM_007113	NP_009044	Q07283	TRHY_HUMAN	trichohyalin	1125	4-8.|10 X 30 AA 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)															---	---	---	---
TCHH	7062	broad.mit.edu	37	1	152082724	152082724	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:152082724T>C	uc001ezp.2	-	2	2969	c.2969A>G	c.(2968-2970)TAC>TGC	p.Y990C	TCHH_uc009wne.1_Missense_Mutation_p.Y990C	NM_007113	NP_009044	Q07283	TRHY_HUMAN	trichohyalin	990	10 X 30 AA tandem repeats.|4-3.				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)															---	---	---	---
TCHH	7062	broad.mit.edu	37	1	152085352	152085352	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:152085352C>A	uc001ezp.2	-	2	341	c.341G>T	c.(340-342)AGG>ATG	p.R114M	TCHH_uc009wne.1_Missense_Mutation_p.R114M	NM_007113	NP_009044	Q07283	TRHY_HUMAN	trichohyalin	114					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	152188247	152188247	+	Missense_Mutation	SNP	C	T	T	rs144419544	byFrequency	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:152188247C>T	uc001ezt.1	-	3	5934	c.5858G>A	c.(5857-5859)CGA>CAA	p.R1953Q		NM_001009931	NP_001009931	Q86YZ3	HORN_HUMAN	hornerin	1953	22.				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	152278976	152278976	+	Nonsense_Mutation	SNP	C	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:152278976C>A	uc001ezu.1	-	3	8422	c.8386G>T	c.(8386-8388)GGA>TGA	p.G2796*		NM_002016	NP_002007	P20930	FILA_HUMAN	filaggrin	2796	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	152282884	152282884	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:152282884G>A	uc001ezu.1	-	3	4514	c.4478C>T	c.(4477-4479)CCG>CTG	p.P1493L		NM_002016	NP_002007	P20930	FILA_HUMAN	filaggrin	1493	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				---	---	---	---
CRNN	49860	broad.mit.edu	37	1	152383290	152383290	+	Missense_Mutation	SNP	T	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:152383290T>A	uc001ezx.2	-	3	342	c.268A>T	c.(268-270)AGC>TGC	p.S90C		NM_016190	NP_057274	Q9UBG3	CRNN_HUMAN	cornulin	90					cell-cell adhesion|response to heat	cytoplasm|membrane	calcium ion binding			ovary(2)|skin(1)	3	Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		LUSC - Lung squamous cell carcinoma(543;0.206)															---	---	---	---
LCE2D	353141	broad.mit.edu	37	1	152636863	152636863	+	Silent	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:152636863T>C	uc001fag.2	+	2	337	c.282T>C	c.(280-282)AGT>AGC	p.S94S		NM_178430	NP_848517	Q5TA82	LCE2D_HUMAN	late cornified envelope 2D	94	Cys-rich.				keratinization						0	Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		LUSC - Lung squamous cell carcinoma(543;0.206)															---	---	---	---
LCE1D	353134	broad.mit.edu	37	1	152770299	152770299	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:152770299G>A	uc009wnp.2	+	2	72	c.29G>A	c.(28-30)TGC>TAC	p.C10Y		NM_178352	NP_848129	Q5T752	LCE1D_HUMAN	late cornified envelope 1D	10	Cys-rich.				cellular response to calcium ion|keratinization	cornified envelope|perinuclear region of cytoplasm					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;0.206)															---	---	---	---
CREB3L4	148327	broad.mit.edu	37	1	153941397	153941397	+	Intron	SNP	C	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:153941397C>A	uc001fdn.3	+						SLC39A1_uc001fdl.2_5'Flank|CREB3L4_uc010pef.1_Intron|CREB3L4_uc001fdo.3_Intron|CREB3L4_uc001fdm.1_Intron|CREB3L4_uc001fdp.1_Intron|CREB3L4_uc010peg.1_Intron|CREB3L4_uc001fdr.2_Intron|CREB3L4_uc001fdq.2_Intron	NM_130898	NP_570968			cAMP responsive element binding protein 3-like						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)															---	---	---	---
RUSC1	23623	broad.mit.edu	37	1	155291849	155291849	+	Silent	SNP	C	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:155291849C>A	uc001fkj.2	+	2	514	c.285C>A	c.(283-285)GCC>GCA	p.A95A	RAG1AP1_uc010pey.1_Intron|C1orf104_uc001fkh.1_5'Flank|C1orf104_uc001fki.2_Intron|RUSC1_uc001fkk.2_Silent_p.A95A|RUSC1_uc009wqn.1_RNA|RUSC1_uc009wqo.1_5'Flank|RUSC1_uc001fkl.2_5'Flank|RUSC1_uc001fkp.2_5'Flank|RUSC1_uc001fkq.2_5'Flank|RUSC1_uc010pgb.1_5'Flank|RUSC1_uc009wqp.1_5'Flank|RUSC1_uc001fkn.2_5'Flank|RUSC1_uc001fko.2_5'Flank|RUSC1_uc001fkr.2_5'Flank	NM_001105203	NP_001098673	Q9BVN2	RUSC1_HUMAN	RUN and SH3 domain containing 1 isoform a	95						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	155447705	155447705	+	Silent	SNP	A	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:155447705A>C	uc009wqq.2	-	3	5436	c.4956T>G	c.(4954-4956)TCT>TCG	p.S1652S	ASH1L_uc001fkt.2_Silent_p.S1652S|ASH1L_uc009wqr.1_Silent_p.S1652S	NM_018489	NP_060959	Q9NR48	ASH1L_HUMAN	absent, small, or homeotic 1-like	1652	Ser-rich.				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)															---	---	---	---
SEMA4A	64218	broad.mit.edu	37	1	156144956	156144956	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:156144956A>G	uc001fnl.2	+	13	1618	c.1514A>G	c.(1513-1515)GAC>GGC	p.D505G	SEMA4A_uc009wrq.2_Missense_Mutation_p.D505G|SEMA4A_uc001fnm.2_Missense_Mutation_p.D505G|SEMA4A_uc001fnn.2_Missense_Mutation_p.D373G|SEMA4A_uc001fno.2_Missense_Mutation_p.D505G	NM_022367	NP_071762	Q9H3S1	SEM4A_HUMAN	semaphorin B precursor	505	Extracellular (Potential).|PSI.				axon guidance	integral to membrane|plasma membrane	receptor activity			ovary(1)|skin(1)	2	Hepatocellular(266;0.158)																	---	---	---	---
SLC25A44	9673	broad.mit.edu	37	1	156170179	156170179	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:156170179G>A	uc001fnp.2	+	2	863	c.541G>A	c.(541-543)GGC>AGC	p.G181S	SLC25A44_uc010phc.1_Missense_Mutation_p.G72S|SLC25A44_uc009wrr.2_Missense_Mutation_p.G181S|SLC25A44_uc010phd.1_Intron|SLC25A44_uc010phe.1_Intron	NM_014655	NP_055470	Q96H78	S2544_HUMAN	solute carrier family 25, member 44	181	Solcar 2.				transmembrane transport	integral to membrane|mitochondrial inner membrane	binding			ovary(1)	1	Hepatocellular(266;0.158)																	---	---	---	---
IQGAP3	128239	broad.mit.edu	37	1	156509674	156509674	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:156509674G>A	uc001fpf.2	-	24	2923	c.2848C>T	c.(2848-2850)CGG>TGG	p.R950W		NM_178229	NP_839943	Q86VI3	IQGA3_HUMAN	IQ motif containing GTPase activating protein 3	950					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	156532382	156532382	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:156532382T>C	uc001fpf.2	-	9	949	c.874A>G	c.(874-876)AAC>GAC	p.N292D	IQGAP3_uc009wsb.1_Missense_Mutation_p.N249D	NM_178229	NP_839943	Q86VI3	IQGA3_HUMAN	IQ motif containing GTPase activating protein 3	292					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)																	---	---	---	---
BCAN	63827	broad.mit.edu	37	1	156616821	156616821	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:156616821G>A	uc001fpp.2	+	3	656	c.320G>A	c.(319-321)CGC>CAC	p.R107H	BCAN_uc001fpo.2_Missense_Mutation_p.R107H	NM_021948	NP_068767	Q96GW7	PGCB_HUMAN	brevican isoform 1	107	Ig-like V-type.				cell adhesion	anchored to membrane|proteinaceous extracellular matrix	hyaluronic acid binding|sugar binding			ovary(1)|pancreas(1)	2	all_hematologic(923;0.088)|Hepatocellular(266;0.158)																	---	---	---	---
ISG20L2	81875	broad.mit.edu	37	1	156694047	156694047	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:156694047G>A	uc001fps.1	-	2	1102	c.841C>T	c.(841-843)CGT>TGT	p.R281C	ISG20L2_uc001fpt.1_Missense_Mutation_p.R281C	NM_030980	NP_112242	Q9H9L3	I20L2_HUMAN	interferon stimulated exonuclease gene	281	Exonuclease.				ribosome biogenesis	nucleolus	exonuclease activity|nucleic acid binding|protein binding			ovary(1)|central_nervous_system(1)	2	all_hematologic(923;0.088)|Hepatocellular(266;0.158)																	---	---	---	---
NTRK1	4914	broad.mit.edu	37	1	156846291	156846291	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:156846291G>A	uc001fqh.1	+	14	1788	c.1732G>A	c.(1732-1734)GTC>ATC	p.V578I	NTRK1_uc001fqf.1_Missense_Mutation_p.V542I|NTRK1_uc009wsi.1_Missense_Mutation_p.V277I|NTRK1_uc001fqi.1_Missense_Mutation_p.V572I|NTRK1_uc009wsk.1_Missense_Mutation_p.V575I	NM_002529	NP_002520	P04629	NTRK1_HUMAN	neurotrophic tyrosine kinase, receptor, type 1	578	Cytoplasmic (Potential).|Protein kinase.				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	156906770	156906770	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:156906770G>A	uc001fqo.2	-	39	5388	c.4348C>T	c.(4348-4350)CTC>TTC	p.L1450F	ARHGEF11_uc010phu.1_Missense_Mutation_p.L866F|ARHGEF11_uc001fqn.2_Missense_Mutation_p.L1490F|MIR765_hsa-mir-765|MI0005116_5'Flank	NM_014784	NP_055599	O15085	ARHGB_HUMAN	Rho guanine nucleotide exchange factor (GEF) 11	1450					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	156933381	156933381	+	Silent	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:156933381T>C	uc001fqo.2	-	11	1889	c.849A>G	c.(847-849)GTA>GTG	p.V283V	ARHGEF11_uc001fqn.2_Silent_p.V323V	NM_014784	NP_055599	O15085	ARHGB_HUMAN	Rho guanine nucleotide exchange factor (GEF) 11	283					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)																	---	---	---	---
KIRREL	55243	broad.mit.edu	37	1	158064519	158064519	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:158064519C>A	uc001frn.3	+	15	2287	c.1883C>A	c.(1882-1884)CCT>CAT	p.P628H	KIRREL_uc010pib.1_Missense_Mutation_p.P528H|KIRREL_uc009wsq.2_Missense_Mutation_p.P464H|KIRREL_uc001fro.3_Missense_Mutation_p.P442H|uc001frp.2_5'Flank	NM_018240	NP_060710	Q96J84	KIRR1_HUMAN	kin of IRRE like precursor	628	Cytoplasmic (Potential).					integral to membrane				ovary(1)	1	all_hematologic(112;0.0378)																	---	---	---	---
OR10R2	343406	broad.mit.edu	37	1	158450495	158450495	+	Silent	SNP	C	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:158450495C>A	uc010pik.1	+	1	828	c.828C>A	c.(826-828)TCC>TCA	p.S276S	uc001fso.1_RNA	NM_001004472	NP_001004472	Q8NGX6	O10R2_HUMAN	olfactory receptor, family 10, subfamily R,	276	Helical; Name=6; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			pancreas(2)|skin(1)	3	all_hematologic(112;0.0378)																	---	---	---	---
OR10J3	441911	broad.mit.edu	37	1	159283546	159283546	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:159283546C>T	uc010piu.1	-	1	904	c.904G>A	c.(904-906)GCA>ACA	p.A302T		NM_001004467	NP_001004467	Q5JRS4	O10J3_HUMAN	olfactory receptor, family 10, subfamily J,	302	Cytoplasmic (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(2)	2	all_hematologic(112;0.0429)																	---	---	---	---
APCS	325	broad.mit.edu	37	1	159558337	159558337	+	Nonsense_Mutation	SNP	G	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:159558337G>T	uc001ftv.2	+	2	607	c.511G>T	c.(511-513)GGA>TGA	p.G171*		NM_001639	NP_001630	P02743	SAMP_HUMAN	serum amyloid P component precursor	171	Pentaxin.				acute-phase response|chaperone-mediated protein complex assembly|protein folding	extracellular space	metal ion binding|sugar binding|unfolded protein binding			ovary(1)|breast(1)	2	all_hematologic(112;0.0429)																	---	---	---	---
ATP1A2	477	broad.mit.edu	37	1	160104985	160104985	+	Missense_Mutation	SNP	C	T	T	rs145701604		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:160104985C>T	uc001fvc.2	+	15	2147	c.2015C>T	c.(2014-2016)TCG>TTG	p.S672L	ATP1A2_uc001fvb.2_Missense_Mutation_p.S672L|ATP1A2_uc001fvd.2_Missense_Mutation_p.S408L	NM_000702	NP_000693	P50993	AT1A2_HUMAN	Na+/K+ -ATPase alpha 2 subunit proprotein	672	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	160784254	160784254	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:160784254G>T	uc001fwu.2	+	4	825	c.775G>T	c.(775-777)GGG>TGG	p.G259W	LY9_uc010pjs.1_Missense_Mutation_p.G259W|LY9_uc001fwv.2_Missense_Mutation_p.G259W|LY9_uc001fww.2_Missense_Mutation_p.G259W|LY9_uc001fwx.2_Missense_Mutation_p.G259W|LY9_uc001fwy.1_Missense_Mutation_p.G161W|LY9_uc001fwz.2_Translation_Start_Site	NM_002348	NP_002339	Q9HBG7	LY9_HUMAN	lymphocyte antigen 9 isoform a	259	Extracellular (Potential).|Ig-like V-type 2.				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	160851810	160851810	+	Silent	SNP	G	A	A	rs145206585	byFrequency	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:160851810G>A	uc001fxc.2	-	4	458	c.342C>T	c.(340-342)GAC>GAT	p.D114D		NM_017625	NP_060095	Q8WWA0	ITLN1_HUMAN	intelectin precursor	114	Fibrinogen C-terminal.				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)															---	---	---	---
ITLN2	142683	broad.mit.edu	37	1	160914918	160914918	+	3'UTR	SNP	C	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:160914918C>A	uc001fxd.2	-	8					ITLN2_uc009wts.2_3'UTR|ITLN2_uc010pju.1_3'UTR	NM_080878	NP_543154			intelectin 2 precursor						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)															---	---	---	---
ARHGAP30	257106	broad.mit.edu	37	1	161026217	161026217	+	Silent	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:161026217C>T	uc001fxl.2	-	3	652	c.306G>A	c.(304-306)CCG>CCA	p.P102P	ARHGAP30_uc001fxk.2_Silent_p.P102P|ARHGAP30_uc001fxm.2_Intron|ARHGAP30_uc009wtx.2_5'UTR|ARHGAP30_uc001fxn.1_5'UTR	NM_001025598	NP_001020769	Q7Z6I6	RHG30_HUMAN	Rho GTPase activating protein 30 isoform 1	102	Rho-GAP.				regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol	GTPase activator activity			ovary(2)|upper_aerodigestive_tract(1)	3	all_cancers(52;8.05e-20)|Breast(13;0.00188)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.00122)															---	---	---	---
FCRLB	127943	broad.mit.edu	37	1	161693201	161693201	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:161693201A>G	uc001gbh.2	+	5	331	c.97A>G	c.(97-99)ACC>GCC	p.T33A	FCRLB_uc009wus.2_Missense_Mutation_p.T33A|FCRLB_uc001gbj.2_Missense_Mutation_p.T33A|FCRLB_uc001gbk.2_Missense_Mutation_p.T33A|FCRLB_uc001gbl.2_Missense_Mutation_p.T26A|FCRLB_uc001gbm.2_Missense_Mutation_p.T26A|FCRLB_uc001gbi.2_Missense_Mutation_p.T33A|FCRLB_uc001gbn.3_5'Flank	NM_001002901	NP_001002901	Q6BAA4	FCRLB_HUMAN	Fc receptor-like B	33	Ig-like C2-type 1.					endoplasmic reticulum					0	all_hematologic(112;0.0359)		BRCA - Breast invasive adenocarcinoma(70;0.00634)															---	---	---	---
C1orf111	284680	broad.mit.edu	37	1	162344046	162344046	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:162344046G>T	uc001gbx.2	-	3	642	c.578C>A	c.(577-579)CCC>CAC	p.P193H		NM_182581	NP_872387	Q5T0L3	CA111_HUMAN	hypothetical protein LOC284680	193										ovary(1)	1	all_hematologic(112;0.15)		BRCA - Breast invasive adenocarcinoma(70;0.0938)															---	---	---	---
SH2D1B	117157	broad.mit.edu	37	1	162372533	162372533	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:162372533A>G	uc001gbz.1	-	2	316	c.194T>C	c.(193-195)ATA>ACA	p.I65T	SH2D1B_uc001gca.1_Missense_Mutation_p.I65T	NM_053282	NP_444512	O14796	SH21B_HUMAN	SH2 domain containing 1B	65	SH2.									pancreas(1)	1	all_hematologic(112;0.115)		BRCA - Breast invasive adenocarcinoma(70;0.126)															---	---	---	---
PBX1	5087	broad.mit.edu	37	1	164761835	164761835	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:164761835G>A	uc001gct.2	+	3	628	c.370G>A	c.(370-372)GGA>AGA	p.G124R	PBX1_uc010pku.1_Missense_Mutation_p.G124R|PBX1_uc010pkv.1_Missense_Mutation_p.G41R|PBX1_uc001gcs.2_Missense_Mutation_p.G124R|PBX1_uc010pkw.1_Missense_Mutation_p.G14R	NM_002585	NP_002576	P40424	PBX1_HUMAN	pre-B-cell leukemia homeobox 1	124					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								---	---	---	---
ALDH9A1	223	broad.mit.edu	37	1	165649758	165649758	+	Missense_Mutation	SNP	A	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:165649758A>T	uc001gdh.1	-	5	860	c.755T>A	c.(754-756)GTC>GAC	p.V252D	ALDH9A1_uc010pky.1_Missense_Mutation_p.V158D|ALDH9A1_uc010pkz.1_Missense_Mutation_p.V242D|ALDH9A1_uc010pla.1_Missense_Mutation_p.V158D	NM_000696	NP_000687	P49189	AL9A1_HUMAN	aldehyde dehydrogenase 9A1	228					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)													---	---	---	---
ILDR2	387597	broad.mit.edu	37	1	166891928	166891928	+	Silent	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:166891928A>G	uc001gdx.1	-	8	1169	c.1113T>C	c.(1111-1113)CCT>CCC	p.P371P		NM_199351	NP_955383	Q71H61	ILDR2_HUMAN	immunoglobulin-like domain containing receptor	371	Cytoplasmic (Potential).					integral to membrane				ovary(1)	1																		---	---	---	---
MAEL	84944	broad.mit.edu	37	1	166985522	166985522	+	Splice_Site	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:166985522G>A	uc001gdy.1	+	9	979	c.908_splice	c.e9+1	p.A303_splice	MAEL_uc001gdz.1_Splice_Site_p.A272_splice|MAEL_uc009wvf.1_Splice_Site	NM_032858	NP_116247			maelstrom homolog						cell differentiation|DNA methylation involved in gamete generation|gene silencing by RNA|multicellular organismal development|piRNA metabolic process|spermatogenesis	piP-body	DNA binding			skin(1)	1																		---	---	---	---
SCYL3	57147	broad.mit.edu	37	1	169828326	169828326	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:169828326C>T	uc001ggs.2	-	11	1366	c.1168G>A	c.(1168-1170)GAT>AAT	p.D390N	SCYL3_uc010plw.1_Missense_Mutation_p.D36N|SCYL3_uc001ggt.2_Missense_Mutation_p.D390N|SCYL3_uc001ggu.2_RNA	NM_181093	NP_851607	Q8IZE3	PACE1_HUMAN	SCY1-like 3 isoform 2	390	HEAT 4.				cell migration	Golgi apparatus|lamellipodium	ATP binding|protein binding|protein kinase activity			ovary(1)|skin(1)	2	all_hematologic(923;0.0922)|Acute lymphoblastic leukemia(37;0.181)																	---	---	---	---
BAT2L2	23215	broad.mit.edu	37	1	171510150	171510150	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:171510150T>C	uc010pmg.1	+	16	3805	c.3539T>C	c.(3538-3540)TTT>TCT	p.F1180S	BAT2L2_uc010pmh.1_Missense_Mutation_p.F157S	NM_015172	NP_055987	Q9Y520	PRC2C_HUMAN	HBxAg transactivated protein 2	1180							protein C-terminus binding				0																		---	---	---	---
MYOC	4653	broad.mit.edu	37	1	171621252	171621252	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:171621252G>A	uc001ghu.2	-	1	522	c.500C>T	c.(499-501)GCC>GTC	p.A167V	MYOC_uc010pmk.1_Missense_Mutation_p.A109V	NM_000261	NP_000252	Q99972	MYOC_HUMAN	myocilin precursor	167	Potential.				anatomical structure morphogenesis	cilium|extracellular space|rough endoplasmic reticulum	structural molecule activity			lung(1)	1	all_cancers(6;5.47e-10)|all_hematologic(923;0.088)|Acute lymphoblastic leukemia(37;0.181)																	---	---	---	---
C1orf9	51430	broad.mit.edu	37	1	172526438	172526438	+	Silent	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:172526438T>C	uc001giq.3	+	5	778	c.462T>C	c.(460-462)GGT>GGC	p.G154G	C1orf9_uc010pmm.1_Silent_p.G154G|C1orf9_uc009wwd.2_Silent_p.G117G|C1orf9_uc010pmn.1_Silent_p.G117G|C1orf9_uc010pmo.1_RNA	NM_014283	NP_055098	Q9UBS9	OSPT_HUMAN	chromosome 1 open reading frame 9 protein	154					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)														---	---	---	---
C1orf9	51430	broad.mit.edu	37	1	172558743	172558743	+	Silent	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:172558743C>T	uc001giq.3	+	18	2818	c.2502C>T	c.(2500-2502)CCC>CCT	p.P834P	C1orf9_uc010pmm.1_Silent_p.P834P|C1orf9_uc009wwd.2_Silent_p.P790P|C1orf9_uc010pmn.1_Intron|C1orf9_uc010pmo.1_RNA	NM_014283	NP_055098	Q9UBS9	OSPT_HUMAN	chromosome 1 open reading frame 9 protein	834					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)														---	---	---	---
C1orf9	51430	broad.mit.edu	37	1	172579410	172579410	+	3'UTR	SNP	A	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:172579410A>C	uc001giq.3	+	24					C1orf9_uc009wwd.2_3'UTR|C1orf9_uc010pmn.1_3'UTR|C1orf9_uc010pmo.1_RNA	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)														---	---	---	---
RFWD2	64326	broad.mit.edu	37	1	175958556	175958556	+	Nonsense_Mutation	SNP	C	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:175958556C>A	uc001gku.1	-	16	2045	c.1789G>T	c.(1789-1791)GGA>TGA	p.G597*	RFWD2_uc001gkv.1_Nonsense_Mutation_p.G573*|RFWD2_uc001gkw.1_Nonsense_Mutation_p.G357*|RFWD2_uc009wwv.2_Nonsense_Mutation_p.G396*|RFWD2_uc001gkt.1_Nonsense_Mutation_p.G436*	NM_022457	NP_071902	Q8NHY2	RFWD2_HUMAN	ring finger and WD repeat domain 2 isoform a	597	WD 5.				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																		---	---	---	---
PAPPA2	60676	broad.mit.edu	37	1	176526280	176526280	+	Silent	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:176526280G>A	uc001gkz.2	+	2	1986	c.822G>A	c.(820-822)CTG>CTA	p.L274L	PAPPA2_uc001gky.1_Silent_p.L274L|PAPPA2_uc009www.2_RNA	NM_020318	NP_064714	Q9BXP8	PAPP2_HUMAN	pappalysin 2 isoform 1	274					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	176563677	176563677	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:176563677T>C	uc001gkz.2	+	3	2101	c.937T>C	c.(937-939)TCC>CCC	p.S313P	PAPPA2_uc001gky.1_Missense_Mutation_p.S313P|PAPPA2_uc009www.2_RNA	NM_020318	NP_064714	Q9BXP8	PAPP2_HUMAN	pappalysin 2 isoform 1	313					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	176853497	176853497	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:176853497C>T	uc001glc.2	-	19	3416	c.3204G>A	c.(3202-3204)ATG>ATA	p.M1068I	ASTN1_uc001glb.1_Missense_Mutation_p.M1068I|ASTN1_uc001gld.1_Missense_Mutation_p.M1068I	NM_004319	NP_004310	O14525	ASTN1_HUMAN	astrotactin isoform 1	1076	Fibronectin type-III 1.				cell migration|neuron cell-cell adhesion	integral to membrane				ovary(6)|skin(5)|central_nervous_system(2)|large_intestine(1)|lung(1)	15																		---	---	---	---
TOR1AIP1	26092	broad.mit.edu	37	1	179876974	179876974	+	Silent	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:179876974T>C	uc001gnq.2	+	7	1031	c.813T>C	c.(811-813)GCT>GCC	p.A271A	TOR1AIP1_uc001gnp.1_Silent_p.A272A	NM_015602	NP_056417	Q5JTV8	TOIP1_HUMAN	lamina-associated polypeptide 1B	271	Nuclear (Potential).					integral to membrane|nuclear inner membrane				breast(1)|central_nervous_system(1)	2																		---	---	---	---
QSOX1	5768	broad.mit.edu	37	1	180135661	180135661	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:180135661T>C	uc001gnz.2	+	2	376	c.301T>C	c.(301-303)TGT>CGT	p.C101R	QSOX1_uc001gny.2_Missense_Mutation_p.C101R|QSOX1_uc001goa.2_Missense_Mutation_p.C101R	NM_002826	NP_002817	O00391	QSOX1_HUMAN	quiescin Q6 sulfhydryl oxidase 1 isoform a	101	Thioredoxin.				cell redox homeostasis|protein thiol-disulfide exchange	extracellular space|integral to Golgi membrane	flavin-linked sulfhydryl oxidase activity			ovary(1)|central_nervous_system(1)	2																		---	---	---	---
GLUL	2752	broad.mit.edu	37	1	182353670	182353670	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:182353670T>C	uc001gpa.1	-	7	1204	c.992A>G	c.(991-993)CAG>CGG	p.Q331R	GLUL_uc010pnt.1_Missense_Mutation_p.Q118R|GLUL_uc001gpb.1_Missense_Mutation_p.Q331R|GLUL_uc001gpc.1_Missense_Mutation_p.Q331R|GLUL_uc001gpd.1_Missense_Mutation_p.Q331R	NM_001033056	NP_001028228	P15104	GLNA_HUMAN	glutamine synthetase	331					cell proliferation|glutamine biosynthetic process|neurotransmitter uptake	cytosol|Golgi apparatus|mitochondrion	ATP binding|glutamate decarboxylase activity|glutamate-ammonia ligase activity|identical protein binding				0					Asparaginase(DB00023)|L-Glutamic Acid(DB00142)|L-Glutamine(DB00130)|L-Methionine(DB00134)													---	---	---	---
NCF2	4688	broad.mit.edu	37	1	183546848	183546848	+	Intron	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:183546848G>A	uc001gqj.3	-						NCF2_uc010pod.1_Intron|NCF2_uc010poe.1_Intron|NCF2_uc001gqk.3_Intron	NM_000433	NP_000424			neutrophil cytosolic factor 2						cellular defense response|innate immune response|respiratory burst|superoxide anion generation	NADPH oxidase complex|nucleolus	electron carrier activity|protein C-terminus binding			ovary(3)	3																		---	---	---	---
FAM129A	116496	broad.mit.edu	37	1	184853759	184853759	+	Intron	SNP	C	T	T	rs142988649	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:184853759C>T	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																		---	---	---	---
IVNS1ABP	10625	broad.mit.edu	37	1	185269562	185269562	+	Intron	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:185269562C>T	uc001grl.2	-						IVNS1ABP_uc001gri.2_Intron|IVNS1ABP_uc001grj.2_Intron|IVNS1ABP_uc009wyj.2_Intron|IVNS1ABP_uc009wyk.2_Intron|IVNS1ABP_uc001grm.2_Intron	NM_006469	NP_006460			influenza virus NS1A binding protein						interspecies interaction between organisms|response to virus|RNA splicing|transcription from RNA polymerase III promoter	cytoplasm|cytoskeleton|spliceosomal complex|transcription factor complex				ovary(4)|central_nervous_system(1)	5																		---	---	---	---
TPR	7175	broad.mit.edu	37	1	186327670	186327670	+	Intron	SNP	C	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:186327670C>A	uc001grv.2	-						TPR_uc010pop.1_Intron	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								---	---	---	---
PTGS2	5743	broad.mit.edu	37	1	186648497	186648497	+	Silent	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-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)													---	---	---	---
PLA2G4A	5321	broad.mit.edu	37	1	186946862	186946862	+	Silent	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:186946862C>T	uc001gsc.2	+	16	2107	c.1902C>T	c.(1900-1902)TGC>TGT	p.C634C	PLA2G4A_uc010pos.1_Silent_p.C574C	NM_024420	NP_077734	P47712	PA24A_HUMAN	cytosolic phospholipase A2, group IVA	634	PLA2c.			C->A: No effect on phospholipase activity; when associated with A-620.	phospholipid catabolic process|platelet activating factor biosynthetic process|platelet activation	cytosol|endoplasmic reticulum membrane	calcium ion binding|calcium-dependent phospholipid binding|lysophospholipase activity			lung(2)|breast(1)	3					Flunisolide(DB00180)|Fluocinolone Acetonide(DB00591)|Fluocinonide(DB01047)|Fluorometholone(DB00324)|Flurandrenolide(DB00846)|Fluticasone Propionate(DB00588)|Medrysone(DB00253)|Quinacrine(DB01103)													---	---	---	---
CDC73	79577	broad.mit.edu	37	1	193172987	193172987	+	Intron	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:193172987A>G	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				---	---	---	---
CDC73	79577	broad.mit.edu	37	1	193218982	193218982	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:193218982T>C	uc001gtb.2	+	16	1783	c.1540T>C	c.(1540-1542)TTT>CTT	p.F514L		NM_024529	NP_078805	Q6P1J9	CDC73_HUMAN	parafibromin	514					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				---	---	---	---
KCNT2	343450	broad.mit.edu	37	1	196397303	196397303	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:196397303C>T	uc001gtd.1	-	10	976	c.916G>A	c.(916-918)GTC>ATC	p.V306I	KCNT2_uc009wyt.1_RNA|KCNT2_uc001gte.1_Missense_Mutation_p.V306I|KCNT2_uc001gtf.1_Missense_Mutation_p.V306I|KCNT2_uc001gtg.1_Intron|KCNT2_uc009wyu.2_Missense_Mutation_p.V306I|KCNT2_uc009wyv.1_Missense_Mutation_p.V281I	NM_198503	NP_940905	Q6UVM3	KCNT2_HUMAN	potassium channel, subfamily T, member 2	306	Cytoplasmic (Potential).					voltage-gated potassium channel complex	ATP binding|calcium-activated potassium channel activity|voltage-gated potassium channel activity			ovary(5)|breast(1)|skin(1)	7																		---	---	---	---
CFH	3075	broad.mit.edu	37	1	196654278	196654278	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:196654278A>G	uc001gtj.3	+	7	1115	c.875A>G	c.(874-876)TAC>TGC	p.Y292C	CFH_uc001gti.3_Missense_Mutation_p.Y292C|CFH_uc009wyw.2_Missense_Mutation_p.Y292C|CFH_uc009wyx.2_Missense_Mutation_p.Y228C	NM_000186	NP_000177	P08603	CFAH_HUMAN	complement factor H isoform a precursor	292	Sushi 5.				complement activation, alternative pathway	extracellular space				skin(4)|ovary(1)|breast(1)	6																		---	---	---	---
CFHR3	10878	broad.mit.edu	37	1	196744066	196744066	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:196744066A>G	uc001gtl.2	+	1	137	c.50A>G	c.(49-51)AAT>AGT	p.N17S	CFHR3_uc001gtk.2_Missense_Mutation_p.N17S|CFHR3_uc010poy.1_Missense_Mutation_p.N17S	NM_021023	NP_066303	Q02985	FHR3_HUMAN	complement factor H-related 3 precursor	17						extracellular space					0																		---	---	---	---
CFHR1	3078	broad.mit.edu	37	1	196796081	196796081	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:196796081A>G	uc001gtn.2	+	3	490	c.376A>G	c.(376-378)AAC>GAC	p.N126D	CFHR1_uc001gtm.2_Intron	NM_002113	NP_002104	Q03591	FHR1_HUMAN	complement factor H-related 1 precursor	126	Sushi 2.				complement activation	extracellular space					0																		---	---	---	---
ASPM	259266	broad.mit.edu	37	1	197072557	197072557	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:197072557T>C	uc001gtu.2	-	18	6081	c.5824A>G	c.(5824-5826)ATG>GTG	p.M1942V	ASPM_uc001gtv.2_Intron|ASPM_uc001gtw.3_Intron	NM_018136	NP_060606	Q8IZT6	ASPM_HUMAN	asp (abnormal spindle)-like, microcephaly	1942					mitosis	cytoplasm|nucleus	calmodulin binding			ovary(4)|central_nervous_system(2)	6																		---	---	---	---
ZBTB41	360023	broad.mit.edu	37	1	197168912	197168912	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:197168912C>A	uc001gtx.1	-	1	761	c.692G>T	c.(691-693)AGG>ATG	p.R231M	ZBTB41_uc009wyz.1_RNA|CRB1_uc010poz.1_5'Flank	NM_194314	NP_919290	Q5SVQ8	ZBT41_HUMAN	zinc finger and BTB domain containing 41	231					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)|skin(1)	2																		---	---	---	---
PTPRC	5788	broad.mit.edu	37	1	198704361	198704361	+	Nonsense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:198704361C>T	uc001gur.1	+	23	2557	c.2377C>T	c.(2377-2379)CAG>TAG	p.Q793*	PTPRC_uc001gus.1_Nonsense_Mutation_p.Q745*|PTPRC_uc001gut.1_Nonsense_Mutation_p.Q632*|PTPRC_uc010ppg.1_Nonsense_Mutation_p.Q729*	NM_002838	NP_002829	P08575	PTPRC_HUMAN	protein tyrosine phosphatase, receptor type, C	793	Cytoplasmic (Potential).|Tyrosine-protein phosphatase 1.				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																		---	---	---	---
NR5A2	2494	broad.mit.edu	37	1	200143150	200143150	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:200143150G>A	uc001gvb.2	+	8	1644	c.1438G>A	c.(1438-1440)GCC>ACC	p.A480T	NR5A2_uc001gvc.2_Missense_Mutation_p.A434T|NR5A2_uc009wzh.2_Missense_Mutation_p.A440T|NR5A2_uc010pph.1_Missense_Mutation_p.A408T	NM_205860	NP_995582	O00482	NR5A2_HUMAN	nuclear receptor subfamily 5, group A, member 2	480					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)																	---	---	---	---
KIF14	9928	broad.mit.edu	37	1	200561356	200561356	+	Missense_Mutation	SNP	T	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:200561356T>A	uc010ppk.1	-	16	3104	c.2665A>T	c.(2665-2667)ATT>TTT	p.I889F	KIF14_uc010ppj.1_Missense_Mutation_p.I398F	NM_014875	NP_055690	Q15058	KIF14_HUMAN	kinesin family member 14	889	FHA.				microtubule-based movement	cytoplasm|microtubule|nucleus|spindle	ATP binding|microtubule motor activity|protein binding			breast(3)|ovary(2)|skin(2)	7																		---	---	---	---
KIF14	9928	broad.mit.edu	37	1	200571155	200571155	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:200571155A>G	uc010ppk.1	-	11	2460	c.2021T>C	c.(2020-2022)ATG>ACG	p.M674T	KIF14_uc010ppj.1_Missense_Mutation_p.M183T	NM_014875	NP_055690	Q15058	KIF14_HUMAN	kinesin family member 14	674					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	200956032	200956032	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:200956032C>T	uc001gvs.1	-	26	3946	c.3629G>A	c.(3628-3630)CGA>CAA	p.R1210Q	KIF21B_uc001gvr.1_Missense_Mutation_p.R1210Q|KIF21B_uc009wzl.1_Missense_Mutation_p.R1210Q|KIF21B_uc010ppn.1_Missense_Mutation_p.R1210Q	NM_017596	NP_060066	O75037	KI21B_HUMAN	kinesin family member 21B	1210					microtubule-based movement	cytoplasm|microtubule	ATP binding|microtubule motor activity			ovary(3)|skin(3)	6																		---	---	---	---
PPP1R12B	4660	broad.mit.edu	37	1	202391744	202391744	+	Intron	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:202391744G>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)															---	---	---	---
SYT2	127833	broad.mit.edu	37	1	202573576	202573576	+	Intron	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:202573576G>A	uc001gye.2	-						SYT2_uc010pqb.1_Intron|SYT2_uc009xaf.2_Intron	NM_001136504	NP_001129976			synaptotagmin II						neurotransmitter secretion	cell junction|chromaffin granule membrane|endocytic vesicle membrane|integral to membrane|synaptic vesicle membrane	protein binding|transporter activity			ovary(2)|skin(1)	3			BRCA - Breast invasive adenocarcinoma(75;0.169)		Botulinum Toxin Type B(DB00042)													---	---	---	---
KLHL12	59349	broad.mit.edu	37	1	202878176	202878176	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:202878176C>T	uc001gyo.1	-	6	994	c.794G>A	c.(793-795)CGG>CAG	p.R265Q	KLHL12_uc001gym.1_5'UTR|KLHL12_uc001gyn.1_Missense_Mutation_p.R115Q|KLHL12_uc010pqc.1_Missense_Mutation_p.R303Q|KLHL12_uc009xah.1_Missense_Mutation_p.R265Q	NM_021633	NP_067646	Q53G59	KLH12_HUMAN	kelch-like 12	265					Wnt receptor signaling pathway		protein binding				0			BRCA - Breast invasive adenocarcinoma(75;0.166)															---	---	---	---
TMEM183A	92703	broad.mit.edu	37	1	202976929	202976929	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:202976929A>G	uc001gyu.1	+	2	195	c.137A>G	c.(136-138)GAT>GGT	p.D46G	TMEM183A_uc009xai.1_Missense_Mutation_p.D46G|TMEM183A_uc001gyv.1_RNA|TMEM183A_uc001gyw.1_Missense_Mutation_p.D46G|TMEM183A_uc001gyx.1_Missense_Mutation_p.D46G	NM_001079809	NP_001073277	Q8IXX5	T183A_HUMAN	transmembrane protein 183B	46						integral to membrane					0			BRCA - Breast invasive adenocarcinoma(75;0.18)															---	---	---	---
CHI3L1	1116	broad.mit.edu	37	1	203149788	203149788	+	Intron	SNP	G	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:203149788G>T	uc001gzi.2	-						FMOD_uc010pqi.1_Intron|CHI3L1_uc001gzk.1_Intron|CHI3L1_uc001gzj.2_Intron|CHI3L1_uc001gzl.3_5'Flank	NM_001276	NP_001267			chitinase 3-like 1 precursor						chitin catabolic process	extracellular space|proteinaceous extracellular matrix	cation binding|chitinase activity|extracellular matrix structural constituent|sugar binding			pancreas(1)	1																		---	---	---	---
CHI3L1	1116	broad.mit.edu	37	1	203155438	203155438	+	Intron	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:203155438A>G	uc001gzi.2	-						FMOD_uc010pqi.1_Intron|CHI3L1_uc001gzj.2_Intron	NM_001276	NP_001267			chitinase 3-like 1 precursor						chitin catabolic process	extracellular space|proteinaceous extracellular matrix	cation binding|chitinase activity|extracellular matrix structural constituent|sugar binding			pancreas(1)	1																		---	---	---	---
SOX13	9580	broad.mit.edu	37	1	204092845	204092845	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:204092845G>A	uc001ham.2	+	12	1883	c.1288G>A	c.(1288-1290)GCC>ACC	p.A430T	SOX13_uc010pqp.1_Missense_Mutation_p.A429T|SOX13_uc010pqq.1_Missense_Mutation_p.A297T	NM_005686	NP_005677	Q9UN79	SOX13_HUMAN	SRY-box 13	430	HMG box.				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)													OREG0014126	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
ETNK2	55224	broad.mit.edu	37	1	204106317	204106317	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:204106317T>C	uc001hao.3	-	6	1256	c.929A>G	c.(928-930)CAC>CGC	p.H310R	ETNK2_uc010pqr.1_Missense_Mutation_p.H132R|ETNK2_uc001han.3_Missense_Mutation_p.H310R|ETNK2_uc010pqs.1_Missense_Mutation_p.H269R|ETNK2_uc010pqt.1_Missense_Mutation_p.H132R	NM_018208	NP_060678	Q9NVF9	EKI2_HUMAN	ethanolamine kinase 2	310							ATP binding|choline kinase activity|ethanolamine kinase activity			ovary(1)|central_nervous_system(1)	2	all_cancers(21;0.032)|Breast(84;0.116)|all_epithelial(62;0.196)		KIRC - Kidney renal clear cell carcinoma(13;0.0584)|Kidney(21;0.0934)|BRCA - Breast invasive adenocarcinoma(75;0.109)															---	---	---	---
PPP1R15B	84919	broad.mit.edu	37	1	204380400	204380400	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:204380400T>C	uc001hav.3	-	1	545	c.140A>G	c.(139-141)AAC>AGC	p.N47S		NM_032833	NP_116222	Q5SWA1	PR15B_HUMAN	protein phosphatase 1, regulatory subunit 15B	47					regulation of translation					ovary(1)|pancreas(1)	2	all_cancers(21;0.0032)|all_neural(3;0.0218)|Glioma(3;0.0382)|Breast(84;0.179)|all_epithelial(62;0.193)|Prostate(682;0.227)		all cancers(3;1.14e-29)|KIRC - Kidney renal clear cell carcinoma(13;0.0584)|Kidney(21;0.0934)|BRCA - Breast invasive adenocarcinoma(75;0.139)															---	---	---	---
PIK3C2B	5287	broad.mit.edu	37	1	204423850	204423850	+	Silent	SNP	G	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:204423850G>T	uc001haw.2	-	13	2492	c.2013C>A	c.(2011-2013)ACC>ACA	p.T671T	PIK3C2B_uc010pqv.1_Silent_p.T671T|PIK3C2B_uc001hax.1_Silent_p.T671T|PIK3C2B_uc009xbd.1_RNA	NM_002646	NP_002637	O00750	P3C2B_HUMAN	phosphoinositide-3-kinase, class 2 beta	671					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)															---	---	---	---
CDK18	5129	broad.mit.edu	37	1	205495599	205495599	+	Intron	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:205495599C>T	uc001hcr.2	+						CDK18_uc010pri.1_Intron|CDK18_uc001hcp.2_Intron|CDK18_uc001hcq.2_Intron|CDK18_uc010prj.1_Intron|CDK18_uc001hcs.2_Intron|CDK18_uc009xbm.1_Intron|CDK18_uc001hct.2_5'Flank	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																		---	---	---	---
ELK4	2005	broad.mit.edu	37	1	205589075	205589075	+	Intron	SNP	T	C	C	rs140752697	byFrequency	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:205589075T>C	uc001hcy.1	-						ELK4_uc001hcz.2_Missense_Mutation_p.M367V	NM_001973	NP_001964			ELK4 protein isoform a							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								---	---	---	---
PM20D1	148811	broad.mit.edu	37	1	205799469	205799469	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:205799469T>C	uc001hdj.2	-	12	1369	c.1324A>G	c.(1324-1326)AAC>GAC	p.N442D	PM20D1_uc009xbr.2_RNA	NM_152491	NP_689704	Q6GTS8	P20D1_HUMAN	peptidase M20 domain containing 1 precursor	442						extracellular region	metal ion binding|peptidase activity			skin(1)	1	Breast(84;0.201)		BRCA - Breast invasive adenocarcinoma(75;0.0252)															---	---	---	---
DYRK3	8444	broad.mit.edu	37	1	206821384	206821384	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:206821384C>T	uc001hej.2	+	3	1009	c.841C>T	c.(841-843)CGG>TGG	p.R281W	DYRK3_uc001hek.2_Intron|DYRK3_uc001hei.2_Missense_Mutation_p.R261W	NM_003582	NP_003573	O43781	DYRK3_HUMAN	dual-specificity tyrosine-(Y)-phosphorylation	281	Protein kinase.				erythrocyte differentiation	nucleus	ATP binding|magnesium ion binding|protein binding|protein serine/threonine kinase activity|protein tyrosine kinase activity			stomach(2)|central_nervous_system(1)	3	Breast(84;0.183)		BRCA - Breast invasive adenocarcinoma(75;0.166)															---	---	---	---
YOD1	55432	broad.mit.edu	37	1	207222988	207222988	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:207222988C>T	uc001hfe.1	-	2	471	c.424G>A	c.(424-426)GTC>ATC	p.V142I	PFKFB2_uc010psc.1_Intron|YOD1_uc001hff.1_Missense_Mutation_p.V98I	NM_018566	NP_061036	Q5VVQ6	OTU1_HUMAN	YOD1 OTU deubiquinating enzyme 1 homolog	142					cellular amino acid metabolic process|endoplasmic reticulum unfolded protein response|ER-associated protein catabolic process|protein K48-linked deubiquitination|protein K63-linked deubiquitination	intracellular	protein binding|ubiquitin-specific protease activity|zinc ion binding			lung(1)	1	Prostate(682;0.19)																	---	---	---	---
CR1	1378	broad.mit.edu	37	1	207780634	207780634	+	Missense_Mutation	SNP	T	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:207780634T>A	uc001hfy.2	+	28	4639	c.4499T>A	c.(4498-4500)GTC>GAC	p.V1500D	CR1_uc009xcl.1_Missense_Mutation_p.V1050D|CR1_uc001hfx.2_Missense_Mutation_p.V1950D	NM_000573	NP_000564	P17927	CR1_HUMAN	complement receptor 1 isoform F precursor	1500	Extracellular (Potential).|Sushi 23.				complement activation, classical pathway|innate immune response	integral to plasma membrane	complement receptor activity			ovary(3)	3																		---	---	---	---
HSD11B1	3290	broad.mit.edu	37	1	209879231	209879231	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:209879231C>T	uc001hhj.2	+	3	271	c.164C>T	c.(163-165)GCG>GTG	p.A55V	HSD11B1_uc001hhk.2_Missense_Mutation_p.A55V	NM_181755	NP_861420	P28845	DHI1_HUMAN	11-beta-hydroxysteroid dehydrogenase 1	55	Lumenal (Potential).|NADP.				glucocorticoid biosynthetic process	endoplasmic reticulum membrane|integral to membrane	11-beta-hydroxysteroid dehydrogenase (NADP+) activity|11-beta-hydroxysteroid dehydrogenase|binding			breast(1)	1				OV - Ovarian serous cystadenocarcinoma(81;1.04e-55)|Epithelial(68;1.57e-52)|all cancers(67;1.83e-46)|Colorectal(1306;0.115)	NADH(DB00157)													---	---	---	---
LPGAT1	9926	broad.mit.edu	37	1	211956771	211956771	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:211956771C>T	uc001hiu.2	-	5	1340	c.527G>A	c.(526-528)CGA>CAA	p.R176Q	LPGAT1_uc001hiv.2_Missense_Mutation_p.R176Q	NM_014873	NP_055688	Q92604	LGAT1_HUMAN	lysophosphatidylglycerol acyltransferase 1	176					phospholipid biosynthetic process	endoplasmic reticulum membrane|integral to membrane	acyltransferase activity			ovary(1)|skin(1)	2				OV - Ovarian serous cystadenocarcinoma(81;0.00773)|all cancers(67;0.0765)|Epithelial(68;0.114)														---	---	---	---
PPP2R5A	5525	broad.mit.edu	37	1	212530328	212530328	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:212530328G>A	uc001hjb.2	+	10	1589	c.1015G>A	c.(1015-1017)GTC>ATC	p.V339I	PPP2R5A_uc010ptd.1_Missense_Mutation_p.V280I	NM_006243	NP_006234	Q15172	2A5A_HUMAN	protein phosphatase 2, regulatory subunit B	339					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)														---	---	---	---
HHIPL2	79802	broad.mit.edu	37	1	222717499	222717499	+	Silent	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:222717499G>A	uc001hnh.1	-	2	412	c.354C>T	c.(352-354)GAC>GAT	p.D118D		NM_024746	NP_079022	Q6UWX4	HIPL2_HUMAN	HHIP-like 2 precursor	118					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)														---	---	---	---
MIA3	375056	broad.mit.edu	37	1	222798117	222798117	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:222798117G>A	uc001hnl.2	+	3	284	c.275G>A	c.(274-276)CGC>CAC	p.R92H	MIA3_uc009xea.1_5'Flank	NM_198551	NP_940953	Q5JRA6	MIA3_HUMAN	melanoma inhibitory activity family, member 3	92	SH3.|Extracellular (Potential).				exocytosis|negative regulation of cell adhesion|negative regulation of cell migration|positive regulation of leukocyte migration|protein transport|wound healing	endoplasmic reticulum membrane|integral to membrane	protein binding			ovary(4)|central_nervous_system(1)	5				GBM - Glioblastoma multiforme(131;0.0199)														---	---	---	---
MIA3	375056	broad.mit.edu	37	1	222838821	222838821	+	Missense_Mutation	SNP	C	T	T	rs1053368		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:222838821C>T	uc001hnl.2	+	28	5593	c.5584C>T	c.(5584-5586)CCC>TCC	p.P1862S	MIA3_uc001hnm.2_Missense_Mutation_p.P740S	NM_198551	NP_940953	Q5JRA6	MIA3_HUMAN	melanoma inhibitory activity family, member 3	1862	Pro-rich.|Cytoplasmic (Potential).				exocytosis|negative regulation of cell adhesion|negative regulation of cell migration|positive regulation of leukocyte migration|protein transport|wound healing	endoplasmic reticulum membrane|integral to membrane	protein binding			ovary(4)|central_nervous_system(1)	5				GBM - Glioblastoma multiforme(131;0.0199)														---	---	---	---
TLR5	7100	broad.mit.edu	37	1	223285137	223285137	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:223285137T>C	uc001hnv.1	-	4	1683	c.1237A>G	c.(1237-1239)AAT>GAT	p.N413D	TLR5_uc001hnw.1_Missense_Mutation_p.N413D	NM_003268	NP_003259	O60602	TLR5_HUMAN	toll-like receptor 5 precursor	413	Extracellular (Potential).		Missing (in 10% of the population; abolishes flagellin signaling; associated with resistance to SLEB1).		cellular response to mechanical stimulus|inflammatory response|innate immune response|MyD88-dependent toll-like receptor signaling pathway|positive regulation of interleukin-8 production|positive regulation of toll-like receptor signaling pathway	integral to membrane|plasma membrane	interleukin-1 receptor binding|transmembrane receptor activity			ovary(2)|lung(1)|skin(1)	4				GBM - Glioblastoma multiforme(131;0.0851)														---	---	---	---
ACBD3	64746	broad.mit.edu	37	1	226349338	226349338	+	Nonsense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:226349338G>A	uc001hpy.2	-	4	669	c.622C>T	c.(622-624)CAA>TAA	p.Q208*		NM_022735	NP_073572	Q9H3P7	GCP60_HUMAN	acyl-Coenzyme A binding domain containing 3	208	Arg-rich.|Potential.|Glu-rich.				steroid biosynthetic process|transport	Golgi membrane|integral to membrane|mitochondrion	fatty-acyl-CoA binding|protein binding				0	Breast(184;0.158)			GBM - Glioblastoma multiforme(131;0.121)														---	---	---	---
ITPKB	3707	broad.mit.edu	37	1	226829743	226829743	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:226829743T>C	uc010pvo.1	-	5	2670	c.2330A>G	c.(2329-2331)GAC>GGC	p.D777G		NM_002221	NP_002212	P27987	IP3KB_HUMAN	1D-myo-inositol-trisphosphate 3-kinase B	777							ATP binding|calmodulin binding|inositol trisphosphate 3-kinase activity			ovary(4)|central_nervous_system(1)	5		Prostate(94;0.0773)																---	---	---	---
URB2	9816	broad.mit.edu	37	1	229781708	229781708	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:229781708G>A	uc001hts.1	+	6	4034	c.3898G>A	c.(3898-3900)GCT>ACT	p.A1300T	URB2_uc009xfd.1_Missense_Mutation_p.A1300T	NM_014777	NP_055592	Q14146	URB2_HUMAN	URB2 ribosome biogenesis 2 homolog	1300						nucleolus				central_nervous_system(2)|ovary(1)	3																		---	---	---	---
GALNT2	2590	broad.mit.edu	37	1	230398357	230398357	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:230398357A>G	uc010pwa.1	+	12	1247	c.1175A>G	c.(1174-1176)TAC>TGC	p.Y392C	GALNT2_uc010pvy.1_Missense_Mutation_p.Y354C|GALNT2_uc010pvz.1_RNA|GALNT2_uc001htu.2_Missense_Mutation_p.Y4C	NM_004481	NP_004472	Q10471	GALT2_HUMAN	polypeptide N-acetylgalactosaminyltransferase 2	392	Lumenal (Potential).				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)																---	---	---	---
COG2	22796	broad.mit.edu	37	1	230822726	230822726	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:230822726A>G	uc001htw.2	+	13	1577	c.1426A>G	c.(1426-1428)AAA>GAA	p.K476E	COG2_uc001htx.2_Missense_Mutation_p.K476E|COG2_uc010pwc.1_Missense_Mutation_p.K349E	NM_007357	NP_031383	Q14746	COG2_HUMAN	component of oligomeric golgi complex 2 isoform	476					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)																---	---	---	---
TTC13	79573	broad.mit.edu	37	1	231051949	231051949	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:231051949T>C	uc001huf.3	-	18	2114	c.2083A>G	c.(2083-2085)ACA>GCA	p.T695A	TTC13_uc009xfi.2_Missense_Mutation_p.T642A|TTC13_uc009xfj.2_RNA|TTC13_uc001hug.3_Missense_Mutation_p.T641A|TTC13_uc009xfk.1_Missense_Mutation_p.T584A	NM_024525	NP_078801	Q8NBP0	TTC13_HUMAN	tetratricopeptide repeat domain 13 isoform a	695							binding			ovary(1)|skin(1)	2	Breast(184;0.0871)|Ovarian(103;0.183)	Prostate(94;0.167)		COAD - Colon adenocarcinoma(196;0.243)														---	---	---	---
TRIM67	440730	broad.mit.edu	37	1	231333129	231333129	+	Nonsense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:231333129C>T	uc009xfn.1	+	2	1099	c.1057C>T	c.(1057-1059)CAG>TAG	p.Q353*		NM_001004342	NP_001004342	Q6ZTA4	TRI67_HUMAN	tripartite motif-containing 67	353	Potential.					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)																---	---	---	---
SIPA1L2	57568	broad.mit.edu	37	1	232568025	232568025	+	Silent	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:232568025C>T	uc001hvg.2	-	14	4382	c.4224G>A	c.(4222-4224)CCG>CCA	p.P1408P	SIPA1L2_uc001hvf.2_Silent_p.P482P	NM_020808	NP_065859	Q9P2F8	SI1L2_HUMAN	signal-induced proliferation-associated 1 like	1408					regulation of small GTPase mediated signal transduction	intracellular	GTPase activator activity			ovary(2)|central_nervous_system(2)|pancreas(1)|skin(1)	6		all_cancers(173;0.00605)|Prostate(94;0.128)|all_epithelial(177;0.186)																---	---	---	---
SIPA1L2	57568	broad.mit.edu	37	1	232650749	232650749	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:232650749C>T	uc001hvg.2	-	1	495	c.337G>A	c.(337-339)GTC>ATC	p.V113I		NM_020808	NP_065859	Q9P2F8	SI1L2_HUMAN	signal-induced proliferation-associated 1 like	113					regulation of small GTPase mediated signal transduction	intracellular	GTPase activator activity			ovary(2)|central_nervous_system(2)|pancreas(1)|skin(1)	6		all_cancers(173;0.00605)|Prostate(94;0.128)|all_epithelial(177;0.186)																---	---	---	---
KIAA1804	84451	broad.mit.edu	37	1	233515465	233515465	+	Intron	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:233515465C>T	uc001hvt.3	+						KIAA1804_uc001hvu.3_Intron	NM_032435	NP_115811			mixed lineage kinase 4						activation of JUN kinase activity|protein autophosphorylation		ATP binding|MAP kinase kinase kinase activity|protein homodimerization activity			lung(5)|central_nervous_system(2)|skin(1)	8		all_cancers(173;0.000405)|all_epithelial(177;0.0345)|Prostate(94;0.122)																---	---	---	---
IRF2BP2	359948	broad.mit.edu	37	1	234742982	234742982	+	Silent	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:234742982G>A	uc001hwg.2	-	2	1696	c.1665C>T	c.(1663-1665)TGC>TGT	p.C555C	IRF2BP2_uc009xfw.2_Silent_p.C165C|IRF2BP2_uc001hwf.2_Silent_p.C539C	NM_182972	NP_892017	Q7Z5L9	I2BP2_HUMAN	interferon regulatory factor 2 binding protein 2	555					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus					0	Ovarian(103;0.0303)	all_cancers(173;0.0236)|Prostate(94;0.0115)	OV - Ovarian serous cystadenocarcinoma(106;2.86e-05)|Epithelial(3;6.2e-05)															---	---	---	---
HEATR1	55127	broad.mit.edu	37	1	236715331	236715331	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:236715331T>C	uc001hyd.1	-	44	6439	c.6314A>G	c.(6313-6315)GAA>GGA	p.E2105G	HEATR1_uc009xgh.1_Missense_Mutation_p.E1267G	NM_018072	NP_060542	Q9H583	HEAT1_HUMAN	protein BAP28	2105					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)															---	---	---	---
ACTN2	88	broad.mit.edu	37	1	236849986	236849986	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:236849986G>A	uc001hyf.2	+	1	217	c.13G>A	c.(13-15)GAG>AAG	p.E5K	ACTN2_uc001hyg.2_5'UTR|ACTN2_uc009xgi.1_Missense_Mutation_p.E5K	NM_001103	NP_001094	P35609	ACTN2_HUMAN	actinin, alpha 2	5	Actin-binding.				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)															---	---	---	---
ACTN2	88	broad.mit.edu	37	1	236917269	236917269	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:236917269G>A	uc001hyf.2	+	16	2066	c.1862G>A	c.(1861-1863)CGC>CAC	p.R621H	ACTN2_uc001hyg.2_Missense_Mutation_p.R413H|ACTN2_uc009xgi.1_Missense_Mutation_p.R621H|ACTN2_uc010pxu.1_Missense_Mutation_p.R310H|ACTN2_uc001hyh.2_Missense_Mutation_p.R309H	NM_001103	NP_001094	P35609	ACTN2_HUMAN	actinin, alpha 2	621	Spectrin 3.				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)															---	---	---	---
RYR2	6262	broad.mit.edu	37	1	237863633	237863633	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:237863633G>A	uc001hyl.1	+	65	9353	c.9233G>A	c.(9232-9234)GGC>GAC	p.G3078D	RYR2_uc010pxz.1_Missense_Mutation_p.G33D	NM_001035	NP_001026	Q92736	RYR2_HUMAN	cardiac muscle ryanodine receptor	3078	Cytoplasmic (By similarity).				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)															---	---	---	---
EXO1	9156	broad.mit.edu	37	1	242013818	242013818	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:242013818A>G	uc001hzh.2	+	4	631	c.91A>G	c.(91-93)ACA>GCA	p.T31A	EXO1_uc001hzi.2_Missense_Mutation_p.T31A|EXO1_uc001hzj.2_Missense_Mutation_p.T31A|EXO1_uc009xgq.2_Missense_Mutation_p.T31A	NM_130398	NP_569082	Q9UQ84	EXO1_HUMAN	exonuclease 1 isoform b	31	N-domain.				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					---	---	---	---
EXO1	9156	broad.mit.edu	37	1	242023820	242023820	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:242023820T>C	uc001hzh.2	+	9	1298	c.758T>C	c.(757-759)GTT>GCT	p.V253A	EXO1_uc001hzi.2_Missense_Mutation_p.V253A|EXO1_uc001hzj.2_Missense_Mutation_p.V253A|EXO1_uc009xgq.2_Missense_Mutation_p.V253A	NM_130398	NP_569082	Q9UQ84	EXO1_HUMAN	exonuclease 1 isoform b	253	Interaction with MSH3.				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					---	---	---	---
CEP170	9859	broad.mit.edu	37	1	243349291	243349291	+	Silent	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:243349291T>C	uc001hzs.2	-	10	1764	c.1356A>G	c.(1354-1356)TCA>TCG	p.S452S	CEP170_uc001hzt.2_Intron|CEP170_uc001hzu.2_Intron	NM_014812	NP_055627	Q5SW79	CE170_HUMAN	centrosomal protein 170kDa isoform alpha	452						centriole|microtubule|spindle				ovary(1)|haematopoietic_and_lymphoid_tissue(1)	2	all_neural(11;0.101)	all_cancers(173;0.003)	all cancers(7;5.81e-06)|GBM - Glioblastoma multiforme(7;0.000443)|OV - Ovarian serous cystadenocarcinoma(106;0.0101)															---	---	---	---
AKT3	10000	broad.mit.edu	37	1	243858918	243858918	+	Silent	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:243858918A>G	uc001iab.1	-	2	228	c.147T>C	c.(145-147)TAT>TAC	p.Y49Y	AKT3_uc001hzz.1_Silent_p.Y49Y	NM_005465	NP_005456	Q9Y243	AKT3_HUMAN	AKT3 kinase isoform 1	49	PH.				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)															---	---	---	---
C1orf101	257044	broad.mit.edu	37	1	244640867	244640867	+	Silent	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:244640867T>C	uc001iam.2	+	3	198	c.139T>C	c.(139-141)TTA>CTA	p.L47L	C1orf101_uc001iak.1_5'UTR|C1orf101_uc001ial.2_Silent_p.L47L|C1orf101_uc010pym.1_5'UTR|C1orf101_uc010pyn.1_Silent_p.L50L	NM_001130957	NP_001124429	Q5SY80	CA101_HUMAN	hypothetical protein LOC257044 isoform 1	47	Extracellular (Potential).					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)															---	---	---	---
HNRNPU	3192	broad.mit.edu	37	1	245019418	245019418	+	Missense_Mutation	SNP	A	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:245019418A>T	uc001iaz.1	-	11	2173	c.1955T>A	c.(1954-1956)ATA>AAA	p.I652K	HNRNPU_uc001iaw.1_RNA|HNRNPU_uc001iax.1_RNA|HNRNPU_uc001iay.1_Missense_Mutation_p.I376K|HNRNPU_uc001iba.1_Missense_Mutation_p.I633K	NM_031844	NP_114032	Q00839	HNRPU_HUMAN	heterogeneous nuclear ribonucleoprotein U	652					CRD-mediated mRNA stabilization	catalytic step 2 spliceosome|cell surface|CRD-mediated mRNA stability complex|heterogeneous nuclear ribonucleoprotein complex|nucleoplasm	ATP binding|DNA binding|protein binding|RNA binding				0	all_cancers(71;6.97e-06)|all_epithelial(71;0.000104)|all_neural(11;0.0269)|Breast(184;0.0545)|Glioma(6;0.0724)|Ovarian(71;0.0761)|all_lung(81;0.0989)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.00868)															---	---	---	---
KIF26B	55083	broad.mit.edu	37	1	245318761	245318761	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:245318761C>T	uc001ibf.1	+	1	475	c.35C>T	c.(34-36)GCG>GTG	p.A12V	KIF26B_uc010pyq.1_Missense_Mutation_p.A12V	NM_018012	NP_060482	Q2KJY2	KI26B_HUMAN	kinesin family member 26B	12					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)															---	---	---	---
TFB2M	64216	broad.mit.edu	37	1	246727684	246727684	+	Silent	SNP	C	T	T	rs145781366	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:246727684C>T	uc001ibn.2	-	2	491	c.366G>A	c.(364-366)GCG>GCA	p.A122A	CNST_uc001ibo.3_5'Flank|CNST_uc001ibp.2_5'Flank|TFB2M_uc010pys.1_RNA	NM_022366	NP_071761	Q9H5Q4	TFB2M_HUMAN	transcription factor B2, mitochondrial	122					positive regulation of transcription, DNA-dependent|transcription initiation from mitochondrial promoter	mitochondrial nucleoid	protein binding|rRNA (adenine-N6,N6-)-dimethyltransferase activity|transcription cofactor activity			ovary(1)	1	all_cancers(71;4.25e-05)|all_epithelial(71;4.92e-06)|Ovarian(71;0.0254)|all_lung(81;0.0272)|Breast(184;0.0318)|Lung NSC(105;0.0376)		OV - Ovarian serous cystadenocarcinoma(106;0.00358)															---	---	---	---
AHCTF1	25909	broad.mit.edu	37	1	247039473	247039473	+	Missense_Mutation	SNP	C	T	T	rs141990857		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:247039473C>T	uc001ibu.1	-	23	2961	c.2954G>A	c.(2953-2955)CGT>CAT	p.R985H	AHCTF1_uc001ibv.1_Missense_Mutation_p.R994H|AHCTF1_uc009xgs.1_5'UTR|AHCTF1_uc001ibw.1_RNA	NM_015446	NP_056261	Q8WYP5	ELYS_HUMAN	transcription factor ELYS	985					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)															---	---	---	---
AHCTF1	25909	broad.mit.edu	37	1	247058004	247058004	+	Silent	SNP	C	T	T	rs61854024	byFrequency;by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:247058004C>T	uc001ibu.1	-	13	1768	c.1761G>A	c.(1759-1761)ACG>ACA	p.T587T	AHCTF1_uc001ibv.1_Silent_p.T596T|AHCTF1_uc009xgs.1_Translation_Start_Site	NM_015446	NP_056261	Q8WYP5	ELYS_HUMAN	transcription factor ELYS	587	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)															---	---	---	---
ZNF669	79862	broad.mit.edu	37	1	247265408	247265408	+	Missense_Mutation	SNP	A	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:247265408A>T	uc001ice.2	-	2	442	c.269T>A	c.(268-270)GTG>GAG	p.V90E	ZNF669_uc001icf.2_Missense_Mutation_p.V4E	NM_024804	NP_079080	Q96BR6	ZN669_HUMAN	zinc finger protein 669 isoform 1	90	KRAB.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0	all_cancers(71;4.09e-05)|all_epithelial(71;6.72e-06)|Breast(184;0.0226)|Ovarian(71;0.0283)|all_lung(81;0.0488)|Lung NSC(105;0.053)		OV - Ovarian serous cystadenocarcinoma(106;0.00427)															---	---	---	---
ZNF496	84838	broad.mit.edu	37	1	247492032	247492032	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:247492032C>T	uc001ico.2	-	4	992	c.527G>A	c.(526-528)TGC>TAC	p.C176Y	ZNF496_uc009xgv.2_Missense_Mutation_p.C176Y|ZNF496_uc001icp.2_Missense_Mutation_p.C176Y|ZNF496_uc010pyv.1_Missense_Mutation_p.C176Y	NM_032752	NP_116141	Q96IT1	ZN496_HUMAN	zinc finger protein 496	176					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)															---	---	---	---
OR2M3	127062	broad.mit.edu	37	1	248366764	248366764	+	Missense_Mutation	SNP	A	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:248366764A>T	uc010pzg.1	+	1	395	c.395A>T	c.(394-396)TAC>TTC	p.Y132F		NM_001004689	NP_001004689	Q8NG83	OR2M3_HUMAN	olfactory receptor, family 2, subfamily M,	132	Cytoplasmic (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)|skin(1)	2	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;0.0245)															---	---	---	---
OR2G6	391211	broad.mit.edu	37	1	248685461	248685461	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:248685461C>T	uc001ien.1	+	1	514	c.514C>T	c.(514-516)CGC>TGC	p.R172C		NM_001013355	NP_001013373	Q5TZ20	OR2G6_HUMAN	olfactory receptor, family 2, subfamily G,	172	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(2)|skin(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)	all_cancers(173;0.0156)	OV - Ovarian serous cystadenocarcinoma(106;0.0265)															---	---	---	---
PGBD2	267002	broad.mit.edu	37	1	249210813	249210813	+	Silent	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:249210813T>C	uc001ifh.2	+	3	177	c.30T>C	c.(28-30)GCT>GCC	p.A10A	PGBD2_uc001ifg.2_Intron|PGBD2_uc009xhd.2_Silent_p.A7A	NM_170725	NP_733843	Q6P3X8	PGBD2_HUMAN	hypothetical protein LOC267002 isoform a	10										ovary(1)	1	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;0.012)	OV - Ovarian serous cystadenocarcinoma(106;0.00989)															---	---	---	---
PXDN	7837	broad.mit.edu	37	2	1652167	1652167	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:1652167G>A	uc002qxa.2	-	17	3449	c.3385C>T	c.(3385-3387)CGT>TGT	p.R1129C		NM_012293	NP_036425	Q92626	PXDN_HUMAN	peroxidasin precursor	1129					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)														---	---	---	---
SOX11	6664	broad.mit.edu	37	2	5833531	5833531	+	Silent	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:5833531C>T	uc002qyj.2	+	1	733	c.678C>T	c.(676-678)GAC>GAT	p.D226D		NM_003108	NP_003099	P35716	SOX11_HUMAN	SRY-box 11	226	Poly-Asp.				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)														---	---	---	---
YWHAQ	10971	broad.mit.edu	37	2	9727541	9727541	+	Splice_Site	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:9727541A>G	uc002qzw.2	-	4	842	c.678_splice	c.e4+1	p.T226_splice	YWHAQ_uc002qzx.2_Splice_Site_p.T226_splice	NM_006826	NP_006817			tyrosine 3/tryptophan 5 -monooxygenase						negative regulation of transcription, DNA-dependent	centrosome|nucleus	protein N-terminus binding			breast(1)	1	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)			Epithelial(75;0.241)														---	---	---	---
ODC1	4953	broad.mit.edu	37	2	10582260	10582260	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:10582260G>A	uc010exg.1	-	9	1225	c.791C>T	c.(790-792)CCG>CTG	p.P264L	ODC1_uc002ran.1_5'Flank|ODC1_uc002rao.1_Missense_Mutation_p.P264L|ODC1_uc010yjd.1_Missense_Mutation_p.P134L	NM_002539	NP_002530	P11926	DCOR_HUMAN	ornithine decarboxylase 1	264					polyamine biosynthetic process|regulation of cellular amino acid metabolic process|response to virus	cytosol	ornithine decarboxylase activity|protein binding			ovary(1)	1	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)			Epithelial(75;0.11)|OV - Ovarian serous cystadenocarcinoma(76;0.161)	Pyridoxal Phosphate(DB00114)|Spermine(DB00127)													---	---	---	---
NOL10	79954	broad.mit.edu	37	2	10803114	10803114	+	Silent	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:10803114G>A	uc002raq.2	-	9	773	c.648C>T	c.(646-648)TGC>TGT	p.C216C	NOL10_uc010yje.1_Silent_p.C190C|NOL10_uc010yjf.1_Silent_p.C166C|NOL10_uc002rap.2_Silent_p.C216C|NOL10_uc002rar.2_Silent_p.C66C	NM_024894	NP_079170	Q9BSC4	NOL10_HUMAN	nucleolar protein 10	216						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	11052979	11052979	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:11052979C>T	uc002rax.2	+	1	917	c.427C>T	c.(427-429)CGC>TGC	p.R143C		NM_002236	NP_002227	Q9H3M0	KCNF1_HUMAN	potassium voltage-gated channel, subfamily F,	143	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)														---	---	---	---
GREB1	9687	broad.mit.edu	37	2	11772107	11772107	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:11772107T>C	uc002rbk.1	+	27	4984	c.4684T>C	c.(4684-4686)TAC>CAC	p.Y1562H	GREB1_uc002rbp.1_Missense_Mutation_p.Y560H	NM_014668	NP_055483	Q4ZG55	GREB1_HUMAN	growth regulation by estrogen in breast cancer 1	1562						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	11964747	11964747	+	Intron	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:11964747T>C	uc010yjn.1	+						LPIN1_uc010yjm.1_Intron|LPIN1_uc002rbt.2_Intron|LPIN1_uc010yjo.1_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)														---	---	---	---
NBAS	51594	broad.mit.edu	37	2	15468328	15468328	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:15468328C>T	uc002rcc.1	-	37	4482	c.4456G>A	c.(4456-4458)GCT>ACT	p.A1486T	NBAS_uc010exl.1_Missense_Mutation_p.A558T|NBAS_uc002rcd.1_RNA	NM_015909	NP_056993	A2RRP1	NBAS_HUMAN	neuroblastoma-amplified protein	1486										ovary(2)|liver(1)|skin(1)	4																		---	---	---	---
FAM49A	81553	broad.mit.edu	37	2	16743390	16743390	+	Silent	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:16743390T>C	uc010exm.1	-	5	466	c.318A>G	c.(316-318)TTA>TTG	p.L106L	FAM49A_uc002rck.1_Silent_p.L106L	NM_030797	NP_110424	Q9H0Q0	FA49A_HUMAN	family with sequence similarity 49, member A	106						intracellular					0	Acute lymphoblastic leukemia(172;0.0734)|all_hematologic(175;0.088)		GBM - Glioblastoma multiforme(3;0.00969)															---	---	---	---
SMC6	79677	broad.mit.edu	37	2	17906610	17906610	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:17906610T>C	uc002rco.2	-	9	936	c.640A>G	c.(640-642)ACG>GCG	p.T214A	SMC6_uc010exo.2_Missense_Mutation_p.T214A|SMC6_uc002rcn.2_Missense_Mutation_p.T214A|SMC6_uc002rcp.1_Missense_Mutation_p.T240A|SMC6_uc002rcq.2_Missense_Mutation_p.T240A|SMC6_uc002rcr.1_Missense_Mutation_p.T214A	NM_001142286	NP_001135758	Q96SB8	SMC6_HUMAN	SMC6 protein	214					DNA recombination|DNA repair	chromosome|nucleus	ATP binding			breast(4)|upper_aerodigestive_tract(1)|kidney(1)	6	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.158)																	---	---	---	---
KCNS3	3790	broad.mit.edu	37	2	18112977	18112977	+	Silent	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:18112977C>T	uc002rcv.2	+	3	1153	c.702C>T	c.(700-702)ACC>ACT	p.T234T	KCNS3_uc002rcw.2_Silent_p.T234T	NM_002252	NP_002243	Q9BQ31	KCNS3_HUMAN	potassium voltage-gated channel	234	Helical; Name=Segment S2; (Potential).				energy reserve metabolic process|regulation of insulin secretion	Golgi apparatus|voltage-gated potassium channel complex	delayed rectifier potassium channel activity|potassium channel regulator activity			ovary(4)	4	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.158)																	---	---	---	---
KCNS3	3790	broad.mit.edu	37	2	18113409	18113409	+	Silent	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:18113409G>A	uc002rcv.2	+	3	1585	c.1134G>A	c.(1132-1134)CCG>CCA	p.P378P	KCNS3_uc002rcw.2_Silent_p.P378P	NM_002252	NP_002243	Q9BQ31	KCNS3_HUMAN	potassium voltage-gated channel	378	Segment H5 (pore-forming) (Potential).				energy reserve metabolic process|regulation of insulin secretion	Golgi apparatus|voltage-gated potassium channel complex	delayed rectifier potassium channel activity|potassium channel regulator activity	p.P378L(1)		ovary(4)	4	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.158)																	---	---	---	---
NT5C1B	93034	broad.mit.edu	37	2	18764195	18764195	+	Silent	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:18764195T>C	uc002rcz.2	-	7	1244	c.1140A>G	c.(1138-1140)GTA>GTG	p.V380V	NT5C1B_uc002rcy.2_Silent_p.V380V|NT5C1B_uc010exr.2_Silent_p.V322V|NT5C1B_uc010yju.1_Silent_p.V320V|NT5C1B_uc002rda.2_Silent_p.V320V|NT5C1B_uc010yjv.1_Silent_p.V397V|NT5C1B_uc010yjw.1_Silent_p.V363V|NT5C1B_uc010exs.2_Silent_p.V382V	NM_001002006	NP_001002006	Q96P26	5NT1B_HUMAN	5' nucleotidase, cytosolic IB isoform 1	380					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)																---	---	---	---
NT5C1B	93034	broad.mit.edu	37	2	18765960	18765960	+	Silent	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:18765960G>A	uc002rcz.2	-	5	827	c.723C>T	c.(721-723)ACC>ACT	p.T241T	NT5C1B_uc002rcy.2_Silent_p.T241T|NT5C1B_uc010exr.2_Silent_p.T183T|NT5C1B_uc010yju.1_Silent_p.T181T|NT5C1B_uc002rda.2_Silent_p.T181T|NT5C1B_uc010yjv.1_Silent_p.T258T|NT5C1B_uc010yjw.1_Silent_p.T224T|NT5C1B_uc010exs.2_Silent_p.T243T|NT5C1B_uc002rdb.1_Silent_p.T33T	NM_001002006	NP_001002006	Q96P26	5NT1B_HUMAN	5' nucleotidase, cytosolic IB isoform 1	241					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	20113965	20113965	+	Silent	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:20113965G>A	uc002rdi.2	-	27	3336	c.3228C>T	c.(3226-3228)TGC>TGT	p.C1076C	WDR35_uc002rdj.2_Silent_p.C1065C|WDR35_uc010ext.2_RNA|WDR35_uc002rdh.2_Intron	NM_001006657	NP_001006658	Q9P2L0	WDR35_HUMAN	WD repeat domain 35 isoform 1	1076										ovary(1)	1	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)																	---	---	---	---
APOB	338	broad.mit.edu	37	2	21229220	21229220	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:21229220C>T	uc002red.2	-	26	10648	c.10520G>A	c.(10519-10521)CGG>CAG	p.R3507Q		NM_000384	NP_000375	P04114	APOB_HUMAN	apolipoprotein B precursor	3507	Heparin-binding.				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	21245755	21245755	+	Silent	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:21245755G>A	uc002red.2	-	18	2892	c.2764C>T	c.(2764-2766)CTG>TTG	p.L922L		NM_000384	NP_000375	P04114	APOB_HUMAN	apolipoprotein B precursor	922	Heparin-binding.				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)													---	---	---	---
C2orf44	80304	broad.mit.edu	37	2	24261474	24261474	+	Silent	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:24261474A>G	uc002rep.2	-	2	1022	c.891T>C	c.(889-891)GGT>GGC	p.G297G	C2orf44_uc010eya.2_Silent_p.G297G	NM_025203	NP_079479	Q9H6R7	CB044_HUMAN	hypothetical protein LOC80304 isoform 1	297							protein binding			ovary(1)|breast(1)	2	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)																	---	---	---	---
NCOA1	8648	broad.mit.edu	37	2	24914466	24914466	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:24914466C>T	uc002rfk.2	+	7	907	c.649C>T	c.(649-651)CGT>TGT	p.R217C	NCOA1_uc010eye.2_Missense_Mutation_p.R217C|NCOA1_uc002rfi.2_Missense_Mutation_p.R66C|NCOA1_uc002rfj.2_Missense_Mutation_p.R217C|NCOA1_uc002rfl.2_Missense_Mutation_p.R217C	NM_003743	NP_003734	Q15788	NCOA1_HUMAN	nuclear receptor coactivator 1 isoform 1	217									PAX3/NCOA1(8)	soft_tissue(8)|ovary(1)|lung(1)|skin(1)	11	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)							T	PAX3	alveolar rhadomyosarcoma								---	---	---	---
POMC	5443	broad.mit.edu	37	2	25383940	25383940	+	3'UTR	SNP	C	T	T	rs35411223		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:25383940C>T	uc002rfy.1	-	4					POMC_uc002rfz.1_3'UTR|POMC_uc002rga.1_3'UTR	NM_001035256	NP_001030333			proopiomelanocortin preproprotein						cell-cell signaling|cellular nitrogen compound metabolic process|cellular pigmentation|generation of precursor metabolites and energy|hormone biosynthetic process|negative regulation of tumor necrosis factor production|neuropeptide signaling pathway|peptide hormone processing|positive regulation of transcription from RNA polymerase II promoter|regulation of appetite|regulation of blood pressure	extracellular space|stored secretory granule	hormone activity|type 1 melanocortin receptor binding|type 3 melanocortin receptor binding|type 4 melanocortin receptor binding			ovary(1)	1	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)				Hydrocortisone(DB00741)|Loperamide(DB00836)|Trilostane(DB01108)													---	---	---	---
ASXL2	55252	broad.mit.edu	37	2	25965106	25965106	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:25965106A>G	uc002rgs.2	-	12	4321	c.4100T>C	c.(4099-4101)ATC>ACC	p.I1367T	ASXL2_uc002rgt.1_Missense_Mutation_p.I850T	NM_018263	NP_060733	Q76L83	ASXL2_HUMAN	additional sex combs like 2	1367					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	26152255	26152255	+	Missense_Mutation	SNP	G	A	A	rs139838043		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:26152255G>A	uc002rgu.2	-	7	2864	c.2207C>T	c.(2206-2208)GCG>GTG	p.A736V	KIF3C_uc010eyj.1_RNA|KIF3C_uc010ykr.1_Missense_Mutation_p.A734V	NM_002254	NP_002245	O14782	KIF3C_HUMAN	kinesin family member 3C	736	Globular (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)																	---	---	---	---
HADHA	3030	broad.mit.edu	37	2	26426928	26426928	+	Intron	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:26426928T>C	uc002rgy.2	-						HADHA_uc010yks.1_Intron	NM_000182	NP_000173			mitochondrial trifunctional protein, alpha						fatty acid beta-oxidation	fatty acid beta-oxidation multienzyme complex|mitochondrial nucleoid|nucleolus	3-hydroxyacyl-CoA dehydrogenase activity|acetyl-CoA C-acetyltransferase activity|coenzyme binding|enoyl-CoA hydratase activity|long-chain-3-hydroxyacyl-CoA dehydrogenase activity|protein binding			ovary(1)	1	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)				NADH(DB00157)													---	---	---	---
CIB4	130106	broad.mit.edu	37	2	26864133	26864133	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:26864133T>C	uc002rhm.2	-	1	79	c.50A>G	c.(49-51)TAC>TGC	p.Y17C		NM_001029881	NP_001025052	A0PJX0	CIB4_HUMAN	calcium and integrin binding family member 4	17							calcium ion binding			ovary(1)	1	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)																	---	---	---	---
C2orf18	54978	broad.mit.edu	37	2	26998046	26998046	+	Silent	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:26998046G>A	uc002rhp.1	+	3	361	c.285G>A	c.(283-285)GCG>GCA	p.A95A	C2orf18_uc002rhq.1_Intron|C2orf18_uc010eyo.1_Silent_p.A42A|C2orf18_uc010ylc.1_Intron	NM_017877	NP_060347	Q8N357	CB018_HUMAN	ANT2-binding protein precursor	95	Helical; (Potential).					integral to membrane|lysosomal membrane					0	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)																	---	---	---	---
C2orf18	54978	broad.mit.edu	37	2	27001354	27001354	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:27001354G>A	uc002rhp.1	+	6	1167	c.1091G>A	c.(1090-1092)CGC>CAC	p.R364H	C2orf18_uc002rhq.1_Missense_Mutation_p.R281H|C2orf18_uc010eyo.1_Missense_Mutation_p.R311H|C2orf18_uc010ylc.1_Missense_Mutation_p.R217H	NM_017877	NP_060347	Q8N357	CB018_HUMAN	ANT2-binding protein precursor	364						integral to membrane|lysosomal membrane					0	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)																	---	---	---	---
KHK	3795	broad.mit.edu	37	2	27317796	27317796	+	Intron	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:27317796A>G	uc002ril.2	+						KHK_uc002rim.2_Missense_Mutation_p.H113R|KHK_uc002rin.2_Intron|KHK_uc002rio.2_Intron	NM_000221	NP_000212			ketohexokinase isoform a						fructose catabolic process	cytosol	ATP binding|ketohexokinase activity|protein binding				0	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)																	---	---	---	---
SLC5A6	8884	broad.mit.edu	37	2	27429781	27429781	+	Silent	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:27429781C>T	uc002rjd.2	-	4	814	c.423G>A	c.(421-423)GTG>GTA	p.V141V	SLC5A6_uc010eyv.1_Silent_p.V141V	NM_021095	NP_066918	Q9Y289	SC5A6_HUMAN	solute carrier family 5 (sodium-dependent	141					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)													---	---	---	---
CAD	790	broad.mit.edu	37	2	27456379	27456379	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:27456379A>G	uc002rji.2	+	20	3353	c.3191A>G	c.(3190-3192)CAG>CGG	p.Q1064R	CAD_uc010eyw.2_Missense_Mutation_p.Q1001R	NM_004341	NP_004332	P27708	PYR1_HUMAN	carbamoylphosphate synthetase 2/aspartate	1064	CPSase B.|ATP-grasp 2.|CPSase (Carbamoyl-phosphate synthase).				'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)													---	---	---	---
GCKR	2646	broad.mit.edu	37	2	27729370	27729370	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:27729370A>G	uc002rky.2	+	11	958	c.892A>G	c.(892-894)ACA>GCA	p.T298A	GCKR_uc010ezd.2_Missense_Mutation_p.T298A|GCKR_uc010ylu.1_Missense_Mutation_p.T108A	NM_001486	NP_001477	Q14397	GCKR_HUMAN	glucokinase regulatory protein	298					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)																	---	---	---	---
GCKR	2646	broad.mit.edu	37	2	27745360	27745360	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:27745360G>A	uc002rky.2	+	18	1672	c.1606G>A	c.(1606-1608)GAG>AAG	p.E536K	GCKR_uc010ezd.2_Missense_Mutation_p.E534K|GCKR_uc010ylu.1_Missense_Mutation_p.E346K	NM_001486	NP_001477	Q14397	GCKR_HUMAN	glucokinase regulatory protein	536					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	27804147	27804147	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:27804147T>C	uc002rkz.3	+	1	4759	c.4708T>C	c.(4708-4710)TCT>CCT	p.S1570P	ZNF512_uc010ylv.1_5'Flank|ZNF512_uc010ylw.1_5'Flank|ZNF512_uc002rlb.2_5'Flank|ZNF512_uc010ylx.1_5'Flank|ZNF512_uc002rlc.2_5'Flank|ZNF512_uc002rla.2_5'Flank|ZNF512_uc010yly.1_5'Flank|ZNF512_uc010ylz.1_5'Flank	NM_032266	NP_115642	Q68DN1	CB016_HUMAN	hypothetical protein LOC84226	1570	Arg-rich.									large_intestine(1)	1	Acute lymphoblastic leukemia(172;0.155)																	---	---	---	---
PLB1	151056	broad.mit.edu	37	2	28775809	28775809	+	Silent	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:28775809G>A	uc002rmb.1	+	17	1098	c.1098G>A	c.(1096-1098)GCG>GCA	p.A366A	PLB1_uc010ezj.1_Silent_p.A377A|PLB1_uc002rmc.2_Silent_p.A54A	NM_153021	NP_694566	Q6P1J6	PLB1_HUMAN	phospholipase B1 precursor	366	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)																	---	---	---	---
PPP1CB	5500	broad.mit.edu	37	2	29022074	29022074	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:29022074C>A	uc002rmg.2	+	9	1049	c.889C>A	c.(889-891)CCA>ACA	p.P297T	PPP1CB_uc010ymj.1_Missense_Mutation_p.P269T|PPP1CB_uc010yml.1_Missense_Mutation_p.P269T|PPP1CB_uc002rmh.2_Missense_Mutation_p.P297T|SPDYA_uc002rmi.2_5'UTR	NM_206876	NP_996759	P62140	PP1B_HUMAN	protein phosphatase 1, catalytic subunit, beta	297					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)																	---	---	---	---
C2orf71	388939	broad.mit.edu	37	2	29295376	29295376	+	Silent	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:29295376G>A	uc002rmt.1	-	1	1752	c.1752C>T	c.(1750-1752)AGC>AGT	p.S584S		NM_001029883	NP_001025054	A6NGG8	CB071_HUMAN	hypothetical protein LOC388939	584					response to stimulus|visual perception	photoreceptor outer segment				skin(1)	1																		---	---	---	---
GALNT14	79623	broad.mit.edu	37	2	31168703	31168703	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:31168703T>C	uc002rnr.2	-	7	1307	c.688A>G	c.(688-690)ATC>GTC	p.I230V	GALNT14_uc002rnq.2_Missense_Mutation_p.I210V|GALNT14_uc002rns.2_Missense_Mutation_p.I235V|GALNT14_uc010ymr.1_Missense_Mutation_p.I195V|GALNT14_uc010ezo.1_Missense_Mutation_p.I197V|GALNT14_uc010ezp.1_Intron	NM_024572	NP_078848	Q96FL9	GLT14_HUMAN	N-acetylgalactosaminyltransferase 14	230	Lumenal (Potential).					Golgi membrane|integral to membrane	polypeptide N-acetylgalactosaminyltransferase activity|sugar binding			upper_aerodigestive_tract(2)|skin(1)	3	Acute lymphoblastic leukemia(172;0.155)																	---	---	---	---
SLC30A6	55676	broad.mit.edu	37	2	32432002	32432002	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:32432002G>T	uc002roe.1	+	12	853	c.816G>T	c.(814-816)GAG>GAT	p.E272D	SLC30A6_uc002rof.1_Missense_Mutation_p.E312D|SLC30A6_uc010ymw.1_Missense_Mutation_p.E243D|SLC30A6_uc010ezr.1_Missense_Mutation_p.E272D|SLC30A6_uc002rog.1_Missense_Mutation_p.E75D|SLC30A6_uc010ezs.1_Missense_Mutation_p.E198D|SLC30A6_uc002roh.1_Missense_Mutation_p.E75D	NM_017964	NP_060434	Q6NXT4	ZNT6_HUMAN	solute carrier family 30 (zinc transporter),	272	Cytoplasmic (Potential).					Golgi membrane|integral to membrane	zinc ion transmembrane transporter activity				0	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.208)																	---	---	---	---
TTC27	55622	broad.mit.edu	37	2	32865443	32865443	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:32865443T>G	uc002rom.2	+	4	734	c.503T>G	c.(502-504)CTA>CGA	p.L168R	TTC27_uc010ymx.1_Missense_Mutation_p.L118R	NM_017735	NP_060205	Q6P3X3	TTC27_HUMAN	tetratricopeptide repeat domain 27	168							protein binding			central_nervous_system(1)	1																		---	---	---	---
LTBP1	4052	broad.mit.edu	37	2	33572512	33572512	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:33572512T>C	uc002ros.2	+	26	3938	c.3938T>C	c.(3937-3939)GTG>GCG	p.V1313A	LTBP1_uc002rot.2_Missense_Mutation_p.V987A|LTBP1_uc002rou.2_Missense_Mutation_p.V986A|LTBP1_uc002rov.2_Missense_Mutation_p.V933A|LTBP1_uc010ymz.1_Missense_Mutation_p.V944A|LTBP1_uc010yna.1_Missense_Mutation_p.V891A|LTBP1_uc010ynb.1_Missense_Mutation_p.V210A	NM_206943	NP_996826	Q14766	LTBP1_HUMAN	latent transforming growth factor beta binding	1312	EGF-like 14; 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	33572556	33572556	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:33572556T>C	uc002ros.2	+	26	3982	c.3982T>C	c.(3982-3984)TGC>CGC	p.C1328R	LTBP1_uc002rot.2_Missense_Mutation_p.C1002R|LTBP1_uc002rou.2_Missense_Mutation_p.C1001R|LTBP1_uc002rov.2_Missense_Mutation_p.C948R|LTBP1_uc010ymz.1_Missense_Mutation_p.C959R|LTBP1_uc010yna.1_Missense_Mutation_p.C906R|LTBP1_uc010ynb.1_Missense_Mutation_p.C225R	NM_206943	NP_996826	Q14766	LTBP1_HUMAN	latent transforming growth factor beta binding	1327	EGF-like 14; 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)																---	---	---	---
FAM98A	25940	broad.mit.edu	37	2	33813399	33813399	+	Intron	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:33813399T>C	uc002rpa.1	-						FAM98A_uc010yne.1_Intron|FAM98A_uc010ynd.1_5'Flank|FAM98A_uc002roz.1_Intron	NM_015475	NP_056290			hypothetical protein LOC25940											ovary(1)	1	all_hematologic(175;0.115)																	---	---	---	---
CRIM1	51232	broad.mit.edu	37	2	36726469	36726469	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:36726469C>T	uc002rpd.2	+	8	1519	c.1480C>T	c.(1480-1482)CGG>TGG	p.R494W		NM_016441	NP_057525	Q9NZV1	CRIM1_HUMAN	cysteine-rich motor neuron 1 precursor	494	Antistasin-like 1.|Extracellular (Potential).				nervous system development|regulation of cell growth	extracellular region|integral to membrane|plasma membrane	insulin-like growth factor binding|insulin-like growth factor receptor activity|serine-type endopeptidase inhibitor activity			ovary(2)|skin(1)	3		all_hematologic(82;0.131)|Acute lymphoblastic leukemia(82;0.154)																---	---	---	---
HEATR5B	54497	broad.mit.edu	37	2	37259778	37259778	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:37259778T>C	uc002rpp.1	-	22	3451	c.3355A>G	c.(3355-3357)AGT>GGT	p.S1119G		NM_019024	NP_061897	Q9P2D3	HTR5B_HUMAN	HEAT repeat containing 5B	1119							binding			ovary(5)|skin(2)|breast(1)	8		all_hematologic(82;0.21)																---	---	---	---
CDC42EP3	10602	broad.mit.edu	37	2	37873428	37873428	+	Silent	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:37873428C>T	uc002rqi.1	-	2	1296	c.303G>A	c.(301-303)CCG>CCA	p.P101P		NM_006449	NP_006440	Q9UKI2	BORG2_HUMAN	Cdc42 effector protein 3	101					regulation of cell shape|signal transduction	actin cytoskeleton|cytoplasm|endomembrane system|membrane	cytoskeletal regulatory protein binding				0		all_hematologic(82;0.172)																---	---	---	---
HNRPLL	92906	broad.mit.edu	37	2	38811056	38811056	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:38811056T>C	uc002rqw.2	-	4	969	c.559A>G	c.(559-561)ACT>GCT	p.T187A	HNRPLL_uc002rqv.2_5'Flank|HNRPLL_uc002rqx.2_Missense_Mutation_p.T182A	NM_138394	NP_612403	Q8WVV9	HNRLL_HUMAN	heterogeneous nuclear ribonucleoprotein L-like	187	RRM 2.				mRNA processing|positive regulation of RNA splicing	nucleus|ribonucleoprotein complex	mRNA binding|nucleotide binding|protein binding			skin(1)	1		all_hematologic(82;0.248)																---	---	---	---
THUMPD2	80745	broad.mit.edu	37	2	39964184	39964184	+	Silent	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:39964184G>A	uc002rru.2	-	10	1240	c.1203C>T	c.(1201-1203)GGC>GGT	p.G401G	THUMPD2_uc002rrv.2_RNA|THUMPD2_uc010ynt.1_Silent_p.G292G	NM_025264	NP_079540	Q9BTF0	THUM2_HUMAN	THUMP domain containing 2	401							methyltransferase activity			skin(1)	1		all_hematologic(82;0.248)																---	---	---	---
C2orf34	79823	broad.mit.edu	37	2	44933427	44933427	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:44933427G>A	uc002rum.2	+	5	543	c.439G>A	c.(439-441)GCC>ACC	p.A147T		NM_024766	NP_079042	Q7Z624	CMKMT_HUMAN	hypothetical protein LOC79823	147						cytoplasm	calmodulin-lysine N-methyltransferase activity				0		all_hematologic(82;0.0892)|Acute lymphoblastic leukemia(82;0.17)																---	---	---	---
SRBD1	55133	broad.mit.edu	37	2	45808835	45808835	+	Silent	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:45808835G>A	uc002rus.2	-	6	1006	c.930C>T	c.(928-930)CAC>CAT	p.H310H		NM_018079	NP_060549	Q8N5C6	SRBD1_HUMAN	S1 RNA binding domain 1	310					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)															---	---	---	---
EPAS1	2034	broad.mit.edu	37	2	46608724	46608724	+	Intron	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:46608724G>A	uc002ruv.2	+						EPAS1_uc002ruw.2_Intron	NM_001430	NP_001421			endothelial PAS domain protein 1						angiogenesis|myoblast cell fate commitment|positive regulation of transcription from RNA polymerase II promoter|response to hypoxia	transcription factor complex	histone acetyltransferase binding|protein heterodimerization activity|sequence-specific enhancer binding RNA polymerase II transcription factor activity|signal transducer activity|transcription coactivator activity|transcription factor binding			ovary(1)|skin(1)	2		all_hematologic(82;0.152)|Acute lymphoblastic leukemia(82;0.18)	LUSC - Lung squamous cell carcinoma(58;0.151)															---	---	---	---
STON1-GTF2A1L	286749	broad.mit.edu	37	2	48873926	48873926	+	Silent	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:48873926T>C	uc010yol.1	+	5	2741	c.2694T>C	c.(2692-2694)TAT>TAC	p.Y898Y	STON1-GTF2A1L_uc002rwp.1_Silent_p.Y945Y|GTF2A1L_uc002rws.1_Silent_p.Y241Y|GTF2A1L_uc010yom.1_Silent_p.Y207Y|GTF2A1L_uc002rwt.2_Silent_p.Y241Y	NM_006873	NP_006864	B7ZL16	B7ZL16_HUMAN	stonin 1	898					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)															---	---	---	---
STON1-GTF2A1L	286749	broad.mit.edu	37	2	48898735	48898735	+	Silent	SNP	T	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:48898735T>G	uc010yol.1	+	7	3263	c.3216T>G	c.(3214-3216)CCT>CCG	p.P1072P	STON1-GTF2A1L_uc002rwp.1_Silent_p.P1119P|GTF2A1L_uc002rws.1_Silent_p.P415P|GTF2A1L_uc010yom.1_Silent_p.P381P|GTF2A1L_uc002rwt.2_Silent_p.P415P	NM_006873	NP_006864	B7ZL16	B7ZL16_HUMAN	stonin 1	1072					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	48925867	48925867	+	Silent	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:48925867C>T	uc002rwu.3	-	9	823	c.753G>A	c.(751-753)ACG>ACA	p.T251T	GTF2A1L_uc002rwt.2_Intron|LHCGR_uc002rwv.2_RNA	NM_000233	NP_000224	P22888	LSHR_HUMAN	luteinizing hormone/choriogonadotropin receptor	251	Extracellular (Potential).				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	49190248	49190248	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:49190248G>A	uc002rww.2	-	10	1786	c.1712C>T	c.(1711-1713)GCC>GTC	p.A571V	FSHR_uc002rwx.2_Missense_Mutation_p.A509V|FSHR_uc010fbn.2_Missense_Mutation_p.A545V	NM_000145	NP_000136	P23945	FSHR_HUMAN	follicle stimulating hormone receptor isoform 1	571	Cytoplasmic (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				---	---	---	---
FSHR	2492	broad.mit.edu	37	2	49190590	49190590	+	Missense_Mutation	SNP	A	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:49190590A>T	uc002rww.2	-	10	1444	c.1370T>A	c.(1369-1371)GTC>GAC	p.V457D	FSHR_uc002rwx.2_Missense_Mutation_p.V395D|FSHR_uc010fbn.2_Missense_Mutation_p.V431D	NM_000145	NP_000136	P23945	FSHR_HUMAN	follicle stimulating hormone receptor isoform 1	457	Helical; Name=3; (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				---	---	---	---
FSHR	2492	broad.mit.edu	37	2	49190974	49190974	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:49190974G>A	uc002rww.2	-	10	1060	c.986C>T	c.(985-987)ACG>ATG	p.T329M	FSHR_uc002rwx.2_Missense_Mutation_p.T267M|FSHR_uc010fbn.2_Missense_Mutation_p.T303M	NM_000145	NP_000136	P23945	FSHR_HUMAN	follicle stimulating hormone receptor isoform 1	329	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				---	---	---	---
GPR75	10936	broad.mit.edu	37	2	54080434	54080434	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:54080434T>C	uc002rxo.3	-	2	1731	c.1460A>G	c.(1459-1461)AAC>AGC	p.N487S	ASB3_uc002rxi.3_Intron	NM_006794	NP_006785	O95800	GPR75_HUMAN	G protein-coupled receptor 75	487	Cytoplasmic (Potential).					integral to plasma membrane	G-protein coupled receptor activity			ovary(1)|skin(1)	2			Lung(47;0.125)|LUSC - Lung squamous cell carcinoma(58;0.181)															---	---	---	---
GPR75	10936	broad.mit.edu	37	2	54081112	54081112	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:54081112C>A	uc002rxo.3	-	2	1053	c.782G>T	c.(781-783)GGA>GTA	p.G261V	ASB3_uc002rxi.3_Intron	NM_006794	NP_006785	O95800	GPR75_HUMAN	G protein-coupled receptor 75	261	Cytoplasmic (Potential).					integral to plasma membrane	G-protein coupled receptor activity			ovary(1)|skin(1)	2			Lung(47;0.125)|LUSC - Lung squamous cell carcinoma(58;0.181)															---	---	---	---
TSPYL6	388951	broad.mit.edu	37	2	54482194	54482194	+	Silent	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:54482194A>G	uc002rxr.2	-	1	1216	c.1095T>C	c.(1093-1095)ATT>ATC	p.I365I	ACYP2_uc002rxq.3_Intron	NM_001003937	NP_001003937	Q8N831	TSYL6_HUMAN	TSPY-like 6	365					nucleosome assembly	nucleus					0																		---	---	---	---
MTIF2	4528	broad.mit.edu	37	2	55470684	55470684	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:55470684G>A	uc002ryn.2	-	13	2169	c.1432C>T	c.(1432-1434)CGT>TGT	p.R478C	MTIF2_uc010yox.1_Missense_Mutation_p.R147C|MTIF2_uc002ryo.2_Missense_Mutation_p.R478C	NM_001005369	NP_001005369	P46199	IF2M_HUMAN	mitochondrial translational initiation factor 2	478					regulation of translational initiation	mitochondrion	GTP binding|GTPase activity|ribosomal small subunit binding|translation initiation factor activity			ovary(1)	1																		---	---	---	---
MTIF2	4528	broad.mit.edu	37	2	55471161	55471161	+	Intron	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:55471161A>G	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	55570914	55570914	+	Silent	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:55570914A>G	uc002ryv.2	-	12	2045	c.1203T>C	c.(1201-1203)GAT>GAC	p.D401D	CCDC88A_uc010yoz.1_Silent_p.D401D|CCDC88A_uc010ypa.1_Silent_p.D401D|CCDC88A_uc010ypb.1_Silent_p.D303D	NM_001135597	NP_001129069	Q3V6T2	GRDN_HUMAN	coiled-coil domain containing 88A isoform 1	401	Potential.				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																		---	---	---	---
BCL11A	53335	broad.mit.edu	37	2	60695904	60695904	+	Silent	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:60695904C>T	uc002sae.1	-	3	678	c.450G>A	c.(448-450)ACG>ACA	p.T150T	BCL11A_uc002sab.2_Silent_p.T150T|BCL11A_uc002sac.2_Silent_p.T150T|BCL11A_uc010ypi.1_5'UTR|BCL11A_uc010ypj.1_Intron|BCL11A_uc002sad.1_5'UTR|BCL11A_uc002saf.1_Intron	NM_022893	NP_075044	Q9H165	BC11A_HUMAN	B-cell CLL/lymphoma 11A isoform 1	150	Required for nuclear body formation and for SUMO1 recruitment (By similarity).				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								---	---	---	---
PEX13	5194	broad.mit.edu	37	2	61258980	61258980	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:61258980A>G	uc002sau.3	+	2	602	c.519A>G	c.(517-519)ATA>ATG	p.I173M		NM_002618	NP_002609	Q92968	PEX13_HUMAN	peroxisomal biogenesis factor 13	173	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)															---	---	---	---
AHSA2	130872	broad.mit.edu	37	2	61412730	61412730	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:61412730T>C	uc002sbc.1	+	4	1755	c.169T>C	c.(169-171)TAT>CAT	p.Y57H	AHSA2_uc002sbb.1_RNA	NM_152392	NP_689605	Q719I0	AHSA2_HUMAN	AHA1, activator of heat shock 90kDa protein	219					response to stress	cytoplasm	ATPase activator activity|chaperone binding			breast(1)	1			Epithelial(17;0.0994)															---	---	---	---
EHBP1	23301	broad.mit.edu	37	2	63175942	63175942	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:63175942T>C	uc002sby.2	+	14	2548	c.2066T>C	c.(2065-2067)CTA>CCA	p.L689P	EHBP1_uc010fcp.2_Missense_Mutation_p.L654P|EHBP1_uc002sbz.2_Missense_Mutation_p.L654P|EHBP1_uc002scb.2_Missense_Mutation_p.L654P	NM_015252	NP_056067	Q8NDI1	EHBP1_HUMAN	EH domain binding protein 1 isoform 1	689						cytoplasm|membrane				ovary(1)|breast(1)	2	Lung NSC(7;0.0951)|all_lung(7;0.169)		LUSC - Lung squamous cell carcinoma(7;7.74e-05)|Epithelial(17;0.189)											Hereditary_Prostate_Cancer				---	---	---	---
VPS54	51542	broad.mit.edu	37	2	64120588	64120588	+	Silent	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:64120588G>A	uc002scq.2	-	23	3073	c.2910C>T	c.(2908-2910)GCC>GCT	p.A970A	VPS54_uc002scp.2_Silent_p.A958A|VPS54_uc002scn.2_Silent_p.A132A|VPS54_uc002sco.2_Silent_p.A455A|VPS54_uc010fct.2_Silent_p.A817A	NM_016516	NP_057600	Q9P1Q0	VPS54_HUMAN	vacuolar protein sorting 54 isoform 1	970					protein transport|retrograde transport, endosome to Golgi						0																		---	---	---	---
PNO1	56902	broad.mit.edu	37	2	68388870	68388870	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:68388870A>G	uc002seh.2	+	3	475	c.413A>G	c.(412-414)AAA>AGA	p.K138R		NM_020143	NP_064528	Q9NRX1	PNO1_HUMAN	partner of NOB1	138						nucleolus	RNA binding				0																		---	---	---	---
FBXO48	554251	broad.mit.edu	37	2	68691336	68691336	+	3'UTR	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:68691336T>C	uc002seo.2	-	4						NM_001024680	NP_001019851			F-box protein 48												0																		---	---	---	---
NAT8	9027	broad.mit.edu	37	2	73868307	73868307	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:73868307C>T	uc002sji.1	-	2	616	c.449G>A	c.(448-450)CGT>CAT	p.R150H		NM_003960	NP_003951	Q9UHE5	NAT8_HUMAN	N-acetyltransferase 8	150	N-acetyltransferase.				gastrulation with mouth forming second|response to drug	integral to membrane	N-acetyltransferase activity			ovary(1)	1																		---	---	---	---
MOGS	7841	broad.mit.edu	37	2	74688883	74688883	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:74688883C>T	uc010ffj.2	-	4	2196	c.2033G>A	c.(2032-2034)CGG>CAG	p.R678Q	MOGS_uc010ffh.2_Missense_Mutation_p.R403Q|MOGS_uc010yrt.1_Missense_Mutation_p.R559Q|MOGS_uc010ffi.2_Missense_Mutation_p.R572Q	NM_006302	NP_006293	Q13724	MOGS_HUMAN	mannosyl-oligosaccharide glucosidase isoform 1	678	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																		---	---	---	---
TLX2	3196	broad.mit.edu	37	2	74742835	74742835	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:74742835A>G	uc002smb.1	+	2	799	c.476A>G	c.(475-477)AAG>AGG	p.K159R	TLX2_uc002sma.1_Silent_p.E29E	NM_016170	NP_057254	O43763	TLX2_HUMAN	T-cell leukemia homeobox 2	159	Homeobox.					nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity				0																		---	---	---	---
LOXL3	84695	broad.mit.edu	37	2	74779513	74779513	+	Silent	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:74779513G>A	uc002smp.1	-	2	321	c.249C>T	c.(247-249)TGC>TGT	p.C83C	LOXL3_uc002smo.1_5'Flank|LOXL3_uc010ffm.1_Silent_p.C83C|LOXL3_uc002smq.1_Silent_p.C83C|LOXL3_uc010ffn.1_Silent_p.C83C|DOK1_uc002smr.2_Intron|DOK1_uc002sms.2_5'Flank|DOK1_uc010ffo.2_5'Flank|DOK1_uc002smt.2_5'Flank|DOK1_uc002smu.2_5'Flank|DOK1_uc010yrz.1_5'Flank|DOK1_uc002smv.2_5'Flank|DOK1_uc002smw.1_5'Flank	NM_032603	NP_115992	P58215	LOXL3_HUMAN	lysyl oxidase-like 3 precursor	83	SRCR 1.					extracellular space|membrane	copper ion binding|protein-lysine 6-oxidase activity|scavenger receptor activity				0																		---	---	---	---
C2orf65	130951	broad.mit.edu	37	2	74834210	74834210	+	Silent	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:74834210C>T	uc002smy.2	-	4	684	c.567G>A	c.(565-567)GCG>GCA	p.A189A	C2orf65_uc010ysa.1_Silent_p.A189A|C2orf65_uc002smz.2_Silent_p.A189A	NM_138804	NP_620159	Q8TC57	CB065_HUMAN	hypothetical protein LOC130951	189					chromatin assembly|female gamete generation|RNA processing|spermatogenesis	integral to membrane				ovary(1)|pancreas(1)	2																		---	---	---	---
LRRTM1	347730	broad.mit.edu	37	2	80530392	80530392	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:80530392G>A	uc002sok.1	-	2	823	c.553C>T	c.(553-555)CGC>TGC	p.R185C	CTNNA2_uc010yse.1_Intron|CTNNA2_uc010ysf.1_Intron|CTNNA2_uc010ysg.1_Intron|CTNNA2_uc010ysh.1_Intron|CTNNA2_uc010ysi.1_5'Flank|LRRTM1_uc002soj.3_RNA	NM_178839	NP_849161	Q86UE6	LRRT1_HUMAN	leucine rich repeat transmembrane neuronal 1	185	Lumenal (Potential).					axon|endoplasmic reticulum membrane|growth cone|integral to membrane				ovary(3)|upper_aerodigestive_tract(1)|skin(1)	5															HNSCC(69;0.2)			---	---	---	---
CTNNA2	1496	broad.mit.edu	37	2	80646713	80646713	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:80646713A>G	uc010ysh.1	+	8	1282	c.1277A>G	c.(1276-1278)AAC>AGC	p.N426S	CTNNA2_uc010yse.1_Missense_Mutation_p.N426S|CTNNA2_uc010ysf.1_Missense_Mutation_p.N426S|CTNNA2_uc010ysg.1_Missense_Mutation_p.N426S|CTNNA2_uc010ysi.1_Missense_Mutation_p.N58S	NM_004389	NP_004380	P26232	CTNA2_HUMAN	catenin, alpha 2 isoform 1	426					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																		---	---	---	---
ELMOD3	84173	broad.mit.edu	37	2	85590275	85590275	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:85590275A>G	uc002spf.3	+	7	850	c.185A>G	c.(184-186)GAA>GGA	p.E62G	ELMOD3_uc010fgg.2_Intron|ELMOD3_uc002spg.3_Missense_Mutation_p.E62G|ELMOD3_uc002sph.3_Missense_Mutation_p.E62G|ELMOD3_uc010ysn.1_Missense_Mutation_p.E62G|ELMOD3_uc010yso.1_RNA|ELMOD3_uc010ysp.1_RNA	NM_001135021	NP_001128493	Q96FG2	ELMD3_HUMAN	ELMO/CED-12 domain containing 3 isoform b	62					phagocytosis	cytoskeleton				ovary(2)	2																		---	---	---	---
VPS24	51652	broad.mit.edu	37	2	86734601	86734601	+	Splice_Site	SNP	C	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:86734601C>G	uc002srj.2	-	5	652	c.523_splice	c.e5+1	p.G175_splice	VPS24_uc002srk.2_Splice_Site_p.G109_splice|VPS24_uc002srl.2_Splice_Site_p.G135_splice|VPS24_uc010ytl.1_Splice_Site_p.G204_splice	NM_016079	NP_057163			vacuolar protein sorting 24 isoform 1						cell cycle|cell division|cellular membrane organization|endosome transport|protein transport	cytosol|late endosome membrane	protein binding			central_nervous_system(1)	1																		---	---	---	---
EIF2AK3	9451	broad.mit.edu	37	2	88874289	88874289	+	Silent	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:88874289A>G	uc002stc.3	-	13	2914	c.2712T>C	c.(2710-2712)TGT>TGC	p.C904C		NM_004836	NP_004827	Q9NZJ5	E2AK3_HUMAN	eukaryotic translation initiation factor 2-alpha	904	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																		---	---	---	---
MRPS5	64969	broad.mit.edu	37	2	95770424	95770424	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:95770424G>A	uc002sub.2	-	7	942	c.724C>T	c.(724-726)CGT>TGT	p.R242C	MRPS5_uc002suc.2_Intron|MRPS5_uc010yud.1_Missense_Mutation_p.R242C	NM_031902	NP_114108	P82675	RT05_HUMAN	mitochondrial ribosomal protein S5	242	S5 DRBM.				translation	mitochondrion|ribosome	protein binding|RNA binding|structural constituent of ribosome			ovary(2)|central_nervous_system(1)	3																		---	---	---	---
ZAP70	7535	broad.mit.edu	37	2	98349474	98349474	+	Missense_Mutation	SNP	C	T	T	rs141613906		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:98349474C>T	uc002syd.1	+	5	899	c.692C>T	c.(691-693)ACG>ATG	p.T231M	ZAP70_uc010yvf.1_Missense_Mutation_p.T231M|ZAP70_uc002sye.1_Missense_Mutation_p.T121M|ZAP70_uc002syf.1_5'Flank	NM_001079	NP_001070	P43403	ZAP70_HUMAN	zeta-chain associated protein kinase 70kDa	231	SH2 2.				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																		---	---	---	---
ZAP70	7535	broad.mit.edu	37	2	98350985	98350985	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:98350985C>T	uc002syd.1	+	9	1099	c.892C>T	c.(892-894)CGC>TGC	p.R298C	ZAP70_uc010yvf.1_3'UTR|ZAP70_uc002sye.1_Missense_Mutation_p.R188C|ZAP70_uc002syf.1_Translation_Start_Site	NM_001079	NP_001070	P43403	ZAP70_HUMAN	zeta-chain associated protein kinase 70kDa	298	Interdomain B.				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	98373619	98373619	+	Silent	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:98373619C>T	uc002syh.3	-	41	5824	c.5595G>A	c.(5593-5595)ACG>ACA	p.T1865T	TMEM131_uc002syg.2_Silent_p.T245T	NM_015348	NP_056163	Q92545	TM131_HUMAN	RW1 protein	1865						integral to membrane				ovary(4)|central_nervous_system(2)	6																		---	---	---	---
INPP4A	3631	broad.mit.edu	37	2	99182162	99182162	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:99182162A>G	uc002syy.2	+	21	2620	c.2227A>G	c.(2227-2229)ACC>GCC	p.T743A	INPP4A_uc010yvj.1_Missense_Mutation_p.T704A|INPP4A_uc010yvk.1_Missense_Mutation_p.T704A|INPP4A_uc002syx.2_Missense_Mutation_p.T738A|INPP4A_uc010fik.2_Intron	NM_001134224	NP_001127696	Q96PE3	INP4A_HUMAN	inositol polyphosphate-4-phosphatase, type 1	743					signal transduction		phosphatidylinositol-3,4-bisphosphate 4-phosphatase activity|phosphatidylinositol-4,5-bisphosphate 4-phosphatase activity			kidney(1)	1																		---	---	---	---
AFF3	3899	broad.mit.edu	37	2	100210297	100210297	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:100210297G>A	uc002tag.2	-	14	2062	c.1826C>T	c.(1825-1827)GCG>GTG	p.A609V	AFF3_uc002taf.2_Missense_Mutation_p.A634V|AFF3_uc010fiq.1_Missense_Mutation_p.A609V|AFF3_uc010yvr.1_Missense_Mutation_p.A762V|AFF3_uc002tah.1_Missense_Mutation_p.A634V	NM_002285	NP_002276	P51826	AFF3_HUMAN	AF4/FMR2 family, member 3 isoform 1	609					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																		---	---	---	---
PDCL3	79031	broad.mit.edu	37	2	101188241	101188241	+	Silent	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:101188241C>T	uc002tao.2	+	5	670	c.558C>T	c.(556-558)GGC>GGT	p.G186G		NM_024065	NP_076970	Q9H2J4	PDCL3_HUMAN	phosducin-like 3	186					apoptosis|interspecies interaction between organisms	cytoplasm	protein binding				0																		---	---	---	---
NPAS2	4862	broad.mit.edu	37	2	101584898	101584898	+	Intron	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:101584898G>A	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																		---	---	---	---
MAP4K4	9448	broad.mit.edu	37	2	102503715	102503715	+	Intron	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:102503715C>T	uc002tbg.2	+						MAP4K4_uc002tbc.2_Intron|MAP4K4_uc002tbd.2_Intron|MAP4K4_uc002tbe.2_Missense_Mutation_p.H1037Y|MAP4K4_uc002tbf.2_Intron|MAP4K4_uc010yvy.1_Intron|MAP4K4_uc002tbh.2_Missense_Mutation_p.H1036Y|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																		---	---	---	---
SLC9A2	6549	broad.mit.edu	37	2	103321035	103321035	+	Silent	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:103321035C>T	uc002tca.2	+	10	2020	c.1878C>T	c.(1876-1878)GCC>GCT	p.A626A		NM_003048	NP_003039	Q9UBY0	SL9A2_HUMAN	solute carrier family 9 (sodium/hydrogen	626	Cytoplasmic (Potential).					integral to membrane|plasma membrane	sodium:hydrogen antiporter activity			central_nervous_system(3)|skin(3)|breast(2)	8																		---	---	---	---
EDAR	10913	broad.mit.edu	37	2	109522796	109522796	+	Missense_Mutation	SNP	T	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:109522796T>A	uc002teq.3	-	11	1423	c.992A>T	c.(991-993)GAT>GTT	p.D331V	EDAR_uc010fjn.2_Missense_Mutation_p.D363V|EDAR_uc010yws.1_Missense_Mutation_p.D363V	NM_022336	NP_071731	Q9UNE0	EDAR_HUMAN	ectodysplasin A receptor precursor	331	Cytoplasmic (Potential).				apoptosis|cell differentiation	integral to membrane	protein binding|transmembrane receptor activity			skin(1)	1																		---	---	---	---
EDAR	10913	broad.mit.edu	37	2	109546647	109546647	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:109546647C>T	uc002teq.3	-	3	534	c.103G>A	c.(103-105)GAG>AAG	p.E35K	EDAR_uc010fjn.2_Missense_Mutation_p.E35K|EDAR_uc010yws.1_Missense_Mutation_p.E35K	NM_022336	NP_071731	Q9UNE0	EDAR_HUMAN	ectodysplasin A receptor precursor	35	TNFR-Cys 1.|Extracellular (Potential).				apoptosis|cell differentiation	integral to membrane	protein binding|transmembrane receptor activity			skin(1)	1																		---	---	---	---
SH3RF3	344558	broad.mit.edu	37	2	110015349	110015349	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:110015349G>A	uc010ywt.1	+	4	1249	c.1249G>A	c.(1249-1251)GCG>ACG	p.A417T		NM_001099289	NP_001092759	Q8TEJ3	SH3R3_HUMAN	SH3 domain containing ring finger 3	417							zinc ion binding			ovary(1)	1																		---	---	---	---
BUB1	699	broad.mit.edu	37	2	111411073	111411073	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:111411073T>C	uc002tgc.2	-	17	2016	c.1904A>G	c.(1903-1905)CAG>CGG	p.Q635R	BUB1_uc010yxh.1_Missense_Mutation_p.Q615R|BUB1_uc010fkb.2_Missense_Mutation_p.Q635R	NM_004336	NP_004327	O43683	BUB1_HUMAN	budding uninhibited by benzimidazoles 1	635					apoptosis|cell division|chromosome segregation|interspecies interaction between organisms|mitotic cell cycle spindle assembly checkpoint|mitotic prometaphase|regulation of sister chromatid cohesion	condensed chromosome kinetochore|cytosol	ATP binding|protein binding|protein serine/threonine kinase activity			lung(2)|breast(2)|stomach(1)|ovary(1)|kidney(1)	7		Ovarian(717;0.0822)		BRCA - Breast invasive adenocarcinoma(221;0.0556)														---	---	---	---
BCL2L11	10018	broad.mit.edu	37	2	111921736	111921736	+	Silent	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:111921736C>T	uc002tgv.1	+	4	813	c.525C>T	c.(523-525)GCC>GCT	p.A175A	BCL2L11_uc002tgu.1_Silent_p.A115A|BCL2L11_uc002tgw.1_RNA|BCL2L11_uc002tgx.1_RNA|BCL2L11_uc010fkd.1_RNA|BCL2L11_uc002tgy.1_RNA|BCL2L11_uc002tgz.1_Silent_p.A85A|BCL2L11_uc010fke.1_RNA|BCL2L11_uc002tha.1_3'UTR|BCL2L11_uc002thb.1_RNA|BCL2L11_uc002thc.1_RNA|BCL2L11_uc002thd.1_3'UTR	NM_138621	NP_619527	O43521	B2L11_HUMAN	BCL2-like 11 isoform 1	175					activation of pro-apoptotic gene products|induction of apoptosis by extracellular signals|induction of apoptosis by intracellular signals|nerve growth factor receptor signaling pathway|positive regulation of protein homooligomerization|positive regulation of release of cytochrome c from mitochondria	cytosol|endomembrane system|mitochondrial outer membrane|plasma membrane	protein binding|protein binding				0																		---	---	---	---
MERTK	10461	broad.mit.edu	37	2	112722803	112722803	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:112722803C>A	uc002thk.1	+	5	915	c.793C>A	c.(793-795)CAC>AAC	p.H265N	MERTK_uc002thl.1_Missense_Mutation_p.H89N	NM_006343	NP_006334	Q12866	MERTK_HUMAN	MER receptor tyrosine kinase precursor	265	Extracellular (Potential).|Ig-like C2-type 2.				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																		---	---	---	---
POLR1B	84172	broad.mit.edu	37	2	113317023	113317023	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:113317023G>A	uc002thw.2	+	9	2064	c.1484G>A	c.(1483-1485)GGC>GAC	p.G495D	POLR1B_uc010fkn.2_Missense_Mutation_p.G439D|POLR1B_uc002thx.2_Missense_Mutation_p.G356D|POLR1B_uc010fko.2_Intron|POLR1B_uc010fkp.2_Intron|POLR1B_uc010yxn.1_Missense_Mutation_p.G533D|POLR1B_uc002thy.2_Missense_Mutation_p.G356D|POLR1B_uc010yxo.1_Missense_Mutation_p.G272D	NM_019014	NP_061887	Q9H9Y6	RPA2_HUMAN	RNA polymerase I polypeptide B isoform 1	495					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|metal ion binding|protein binding|ribonucleoside binding			ovary(1)	1																		---	---	---	---
DDX18	8886	broad.mit.edu	37	2	118575134	118575134	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:118575134A>G	uc002tlh.1	+	2	299	c.200A>G	c.(199-201)GAA>GGA	p.E67G		NM_006773	NP_006764	Q9NVP1	DDX18_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 18	67							ATP binding|ATP-dependent RNA helicase activity|RNA binding			breast(2)|ovary(1)|lung(1)	4																		---	---	---	---
EN1	2019	broad.mit.edu	37	2	119604313	119604313	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:119604313C>T	uc002tlm.2	-	1	1447	c.431G>A	c.(430-432)CGT>CAT	p.R144H		NM_001426	NP_001417	Q05925	HME1_HUMAN	engrailed homeobox 1	144					skeletal system development	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			large_intestine(1)|lung(1)	2																		---	---	---	---
C2orf76	130355	broad.mit.edu	37	2	120097468	120097468	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:120097468G>T	uc002tls.2	-	3	609	c.68C>A	c.(67-69)CCT>CAT	p.P23H	C2orf76_uc010flf.1_Missense_Mutation_p.P23H|C2orf76_uc010yyg.1_RNA|C2orf76_uc002tlt.2_Missense_Mutation_p.P23H|C2orf76_uc002tlu.2_Missense_Mutation_p.P23H	NM_001017927	NP_001017927	Q3KRA6	CB076_HUMAN	hypothetical protein LOC130355	23											0																		---	---	---	---
PTPN4	5775	broad.mit.edu	37	2	120567494	120567494	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:120567494G>A	uc002tmf.1	+	2	836	c.65G>A	c.(64-66)CGA>CAA	p.R22Q		NM_002830	NP_002821	P29074	PTN4_HUMAN	protein tyrosine phosphatase, non-receptor type	22						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	120776669	120776669	+	Silent	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:120776669T>C	uc002tmg.2	+	2	135	c.9T>C	c.(7-9)AGT>AGC	p.S3S	EPB41L5_uc010flk.2_Silent_p.S3S|EPB41L5_uc010fll.2_Silent_p.S3S|EPB41L5_uc002tmh.3_Silent_p.S3S	NM_020909	NP_065960	Q9HCM4	E41L5_HUMAN	erythrocyte membrane protein band 4.1 like 5	3						cytoplasm|cytoskeleton|extrinsic to membrane	cytoskeletal protein binding			ovary(1)	1																		---	---	---	---
INHBB	3625	broad.mit.edu	37	2	121106927	121106927	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:121106927C>T	uc002tmn.2	+	2	747	c.701C>T	c.(700-702)GCC>GTC	p.A234V		NM_002193	NP_002184	P09529	INHBB_HUMAN	inhibin beta B subunit preproprotein	234					activin receptor signaling pathway|cellular response to insulin stimulus|cellular response to starvation|defense response|fat cell differentiation|growth|negative regulation of follicle-stimulating hormone secretion|negative regulation of hepatocyte growth factor biosynthetic process|negative regulation of insulin secretion|ovarian follicle development|positive regulation of follicle-stimulating hormone secretion|positive regulation of ovulation	extracellular region|perinuclear region of cytoplasm	cytokine activity|growth factor activity|hormone activity|host cell surface receptor binding|protein homodimerization activity			pancreas(2)|skin(1)	3		Prostate(154;0.122)																---	---	---	---
INHBB	3625	broad.mit.edu	37	2	121107323	121107323	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:121107323G>A	uc002tmn.2	+	2	1143	c.1097G>A	c.(1096-1098)GGC>GAC	p.G366D		NM_002193	NP_002184	P09529	INHBB_HUMAN	inhibin beta B subunit preproprotein	366					activin receptor signaling pathway|cellular response to insulin stimulus|cellular response to starvation|defense response|fat cell differentiation|growth|negative regulation of follicle-stimulating hormone secretion|negative regulation of hepatocyte growth factor biosynthetic process|negative regulation of insulin secretion|ovarian follicle development|positive regulation of follicle-stimulating hormone secretion|positive regulation of ovulation	extracellular region|perinuclear region of cytoplasm	cytokine activity|growth factor activity|hormone activity|host cell surface receptor binding|protein homodimerization activity			pancreas(2)|skin(1)	3		Prostate(154;0.122)																---	---	---	---
GLI2	2736	broad.mit.edu	37	2	121736119	121736119	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:121736119A>G	uc010flp.2	+	9	1508	c.1478A>G	c.(1477-1479)CAC>CGC	p.H493R	GLI2_uc002tmq.1_Missense_Mutation_p.H165R|GLI2_uc002tmr.1_Missense_Mutation_p.H148R|GLI2_uc002tmt.3_Missense_Mutation_p.H165R|GLI2_uc002tmu.3_Missense_Mutation_p.H148R|GLI2_uc002tmw.1_Missense_Mutation_p.H476R	NM_005270	NP_005261	P10070	GLI2_HUMAN	GLI-Kruppel family member GLI2	493	C2H2-type 2; degenerate.				axon guidance|branching morphogenesis of a tube|cell proliferation|cerebellar cortex morphogenesis|developmental growth|embryonic digestive tract development|epidermal cell differentiation|floor plate formation|heart development|hindgut morphogenesis|kidney development|lung development|negative regulation of transcription from RNA polymerase II promoter|odontogenesis of dentine-containing tooth|osteoblast development|osteoblast differentiation|pituitary gland development|positive regulation of DNA replication|positive regulation of T cell differentiation in thymus|positive regulation of transcription from RNA polymerase II promoter|proximal/distal pattern formation|skeletal system development|smoothened signaling pathway involved in ventral spinal cord interneuron specification|spinal cord ventral commissure morphogenesis	nucleus|nucleus	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(8)|lung(2)|breast(1)|central_nervous_system(1)|pancreas(1)	13	Renal(3;0.0496)	Prostate(154;0.0623)																---	---	---	---
WDR33	55339	broad.mit.edu	37	2	128528470	128528470	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:128528470C>T	uc002tpg.1	-	2	269	c.86G>A	c.(85-87)CGA>CAA	p.R29Q	WDR33_uc002tph.1_Missense_Mutation_p.R29Q|WDR33_uc002tpi.1_Missense_Mutation_p.R29Q	NM_018383	NP_060853	Q9C0J8	WDR33_HUMAN	WD repeat domain 33 isoform 1	29					postreplication repair|spermatogenesis	collagen|nucleus	protein binding				0	Colorectal(110;0.1)			BRCA - Breast invasive adenocarcinoma(221;0.0695)														---	---	---	---
TUBA3E	112714	broad.mit.edu	37	2	130951905	130951905	+	Silent	SNP	G	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:130951905G>T	uc002tqv.2	-	4	611	c.510C>A	c.(508-510)GCC>GCA	p.A170A		NM_207312	NP_997195	Q6PEY2	TBA3E_HUMAN	tubulin, alpha 3e	170					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	131102227	131102227	+	Silent	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:131102227A>G	uc002tra.1	+	3	155	c.138A>G	c.(136-138)TTA>TTG	p.L46L	CCDC115_uc002tqw.1_5'Flank|CCDC115_uc010zaf.1_5'Flank|CCDC115_uc002tqx.2_5'Flank|CCDC115_uc002tqy.1_5'Flank|CCDC115_uc002tqz.1_5'Flank	NM_033416	NP_219484	Q96G21	IMP4_HUMAN	IMP4, U3 small nucleolar ribonucleoprotein,	46	Arg-rich.				rRNA processing|translation	nucleolus|ribonucleoprotein complex	aminoacyl-tRNA ligase activity|ATP binding|protein binding			central_nervous_system(2)	2	Colorectal(110;0.1)																	---	---	---	---
PLEKHB2	55041	broad.mit.edu	37	2	131904319	131904319	+	Silent	SNP	C	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:131904319C>A	uc002tsg.3	+	8	1202	c.642C>A	c.(640-642)GCC>GCA	p.A214A	PLEKHB2_uc002tsh.2_Intron|PLEKHB2_uc002tsj.3_Silent_p.A213A|PLEKHB2_uc002tsf.3_Silent_p.A222A|PLEKHB2_uc010zao.1_Silent_p.A164A|PLEKHB2_uc010zap.1_Missense_Mutation_p.P178H|PLEKHB2_uc010zaq.1_Missense_Mutation_p.P170H|PLEKHB2_uc002tsi.3_Silent_p.A255A	NM_001100623	NP_001094093	Q96CS7	PKHB2_HUMAN	pleckstrin homology domain containing, family B	214						membrane	protein binding			ovary(2)	2				BRCA - Breast invasive adenocarcinoma(221;0.0828)														---	---	---	---
TUBA3D	113457	broad.mit.edu	37	2	132240333	132240333	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:132240333G>A	uc002tsu.3	+	5	1372	c.1265G>A	c.(1264-1266)CGC>CAC	p.R422H		NM_080386	NP_525125	Q13748	TBA3C_HUMAN	tubulin, alpha 3d	422					'de novo' posttranslational protein folding|microtubule-based movement|protein polymerization	cytoplasm|microtubule	GTP binding|GTPase activity|protein binding|structural molecule activity				0				BRCA - Breast invasive adenocarcinoma(221;0.13)														---	---	---	---
CCDC74A	90557	broad.mit.edu	37	2	132290601	132290601	+	Silent	SNP	G	A	A	rs141289181		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:132290601G>A	uc002tta.2	+	7	1018	c.966G>A	c.(964-966)ACG>ACA	p.T322T	CCDC74A_uc002ttb.2_Silent_p.T256T	NM_138770	NP_620125	Q96AQ1	CC74A_HUMAN	coiled-coil domain containing 74A	322										skin(1)	1																		---	---	---	---
MGAT5	4249	broad.mit.edu	37	2	135199475	135199475	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:135199475G>T	uc002ttv.1	+	15	2161	c.2016G>T	c.(2014-2016)AAG>AAT	p.K672N		NM_002410	NP_002401	Q09328	MGT5A_HUMAN	N-acetylglucosaminyltransferase V	672	Lumenal (Potential).				post-translational protein modification|protein N-linked glycosylation via asparagine	Golgi membrane|integral to membrane	alpha-1,6-mannosyl-glycoprotein 6-beta-N-acetylglucosaminyltransferase activity			ovary(2)|skin(1)	3				BRCA - Breast invasive adenocarcinoma(221;0.0964)														---	---	---	---
CCNT2	905	broad.mit.edu	37	2	135711581	135711581	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:135711581G>T	uc002tuc.1	+	9	1588	c.1556G>T	c.(1555-1557)AGT>ATT	p.S519I	CCNT2_uc002tub.1_Missense_Mutation_p.S519I|CCNT2_uc010zbf.1_Missense_Mutation_p.S344I|CCNT2_uc002tud.1_Missense_Mutation_p.S182I	NM_058241	NP_490595	O60583	CCNT2_HUMAN	cyclin T2 isoform b	519					cell cycle|cell division|interspecies interaction between organisms|regulation of cyclin-dependent protein kinase activity|regulation of transcription, DNA-dependent|transcription elongation from RNA polymerase II promoter|viral reproduction	nucleoplasm	protein kinase binding			ovary(2)|lung(1)	3				BRCA - Breast invasive adenocarcinoma(221;0.107)														---	---	---	---
YSK4	80122	broad.mit.edu	37	2	135745792	135745792	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:135745792G>A	uc002tue.1	-	7	681	c.650C>T	c.(649-651)ACG>ATG	p.T217M	YSK4_uc002tuf.1_Intron|YSK4_uc010fnc.1_Intron|YSK4_uc010fnd.1_Missense_Mutation_p.T104M|YSK4_uc010zbg.1_Intron|YSK4_uc002tuh.3_Translation_Start_Site|YSK4_uc002tui.3_Missense_Mutation_p.T234M	NM_025052	NP_079328	Q56UN5	YSK4_HUMAN	Yeast Sps1/Ste20-related kinase 4 isoform 1	217							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	136261973	136261973	+	Silent	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:136261973C>T	uc002tum.2	-	2	204	c.87G>A	c.(85-87)TTG>TTA	p.L29L	ZRANB3_uc002tuk.2_5'UTR|ZRANB3_uc002tul.2_Silent_p.L29L|ZRANB3_uc002tun.1_Intron	NM_032143	NP_115519	Q5FWF4	ZRAB3_HUMAN	zinc finger, RAN-binding domain containing 3	29						intracellular	ATP binding|DNA binding|endonuclease activity|helicase activity|zinc ion binding			lung(2)	2				BRCA - Breast invasive adenocarcinoma(221;0.135)														---	---	---	---
MIR128-1	406915	broad.mit.edu	37	2	136422981	136422981	+	RNA	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:136422981C>T	hsa-mir-128-1|MI0000447	+			c.15C>T			R3HDM1_uc002tuo.2_Intron|R3HDM1_uc010fni.2_Intron|R3HDM1_uc002tup.2_Intron|R3HDM1_uc010zbh.1_Intron|uc010zbi.1_RNA																	0																		---	---	---	---
R3HDM1	23518	broad.mit.edu	37	2	136437855	136437855	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:136437855A>G	uc002tuo.2	+	20	2685	c.2315A>G	c.(2314-2316)TAC>TGC	p.Y772C	R3HDM1_uc010fni.2_Missense_Mutation_p.Y771C|R3HDM1_uc002tup.2_Missense_Mutation_p.Y717C|R3HDM1_uc010zbh.1_Missense_Mutation_p.Y520C	NM_015361	NP_056176	Q15032	R3HD1_HUMAN	R3H domain containing 1	772							nucleic acid binding			skin(1)	1				BRCA - Breast invasive adenocarcinoma(221;0.127)														---	---	---	---
UBXN4	23190	broad.mit.edu	37	2	136527335	136527335	+	Intron	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:136527335A>G	uc002tur.2	+						UBXN4_uc002tus.2_Intron	NM_014607	NP_055422			UBX domain containing 2						response to unfolded protein	endoplasmic reticulum membrane|nuclear envelope	protein binding			skin(2)	2																		---	---	---	---
LCT	3938	broad.mit.edu	37	2	136562354	136562354	+	Missense_Mutation	SNP	C	T	T	rs139591272	byFrequency	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:136562354C>T	uc002tuu.1	-	10	4458	c.4447G>A	c.(4447-4449)GCC>ACC	p.A1483T		NM_002299	NP_002290	P09848	LPH_HUMAN	lactase-phlorizin hydrolase preproprotein	1483	Extracellular (Potential).|4.|4 X approximate repeats.				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)														---	---	---	---
LCT	3938	broad.mit.edu	37	2	136566117	136566117	+	Missense_Mutation	SNP	A	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:136566117A>C	uc002tuu.1	-	8	3811	c.3800T>G	c.(3799-3801)ATC>AGC	p.I1267S		NM_002299	NP_002290	P09848	LPH_HUMAN	lactase-phlorizin hydrolase preproprotein	1267	3.|Extracellular (Potential).|4 X approximate repeats.				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)														---	---	---	---
LCT	3938	broad.mit.edu	37	2	136567033	136567033	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:136567033C>T	uc002tuu.1	-	8	2895	c.2884G>A	c.(2884-2886)GAT>AAT	p.D962N		NM_002299	NP_002290	P09848	LPH_HUMAN	lactase-phlorizin hydrolase preproprotein	962	3.|Extracellular (Potential).|4 X approximate repeats.				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)														---	---	---	---
LCT	3938	broad.mit.edu	37	2	136567211	136567211	+	Silent	SNP	C	T	T	rs138911236	byFrequency;by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:136567211C>T	uc002tuu.1	-	8	2717	c.2706G>A	c.(2704-2706)ACG>ACA	p.T902T		NM_002299	NP_002290	P09848	LPH_HUMAN	lactase-phlorizin hydrolase preproprotein	902	3.|Extracellular (Potential).|4 X approximate repeats.				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)														---	---	---	---
LRP1B	53353	broad.mit.edu	37	2	141081561	141081561	+	Nonsense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:141081561G>A	uc002tvj.1	-	81	13387	c.12415C>T	c.(12415-12417)CGA>TGA	p.R4139*		NM_018557	NP_061027	Q9NZR2	LRP1B_HUMAN	low density lipoprotein-related protein 1B	4139	Extracellular (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)			---	---	---	---
ZEB2	9839	broad.mit.edu	37	2	145161588	145161588	+	Silent	SNP	G	A	A	rs140169964		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:145161588G>A	uc002tvu.2	-	6	1182	c.702C>T	c.(700-702)CAC>CAT	p.H234H	ZEB2_uc002tvv.2_Silent_p.H228H|ZEB2_uc010zbm.1_Silent_p.H205H|ZEB2_uc010fnp.2_Silent_p.H142H|ZEB2_uc010fnq.1_Silent_p.H263H	NM_014795	NP_055610	O60315	ZEB2_HUMAN	zinc finger homeobox 1b	234	C2H2-type 1.					cytoplasm|nucleolus	phosphatase regulator activity|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|SMAD binding|zinc ion binding			ovary(5)|pancreas(2)|upper_aerodigestive_tract(1)|large_intestine(1)	9				BRCA - Breast invasive adenocarcinoma(221;0.112)														---	---	---	---
RBM43	375287	broad.mit.edu	37	2	152112187	152112187	+	Missense_Mutation	SNP	T	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:152112187T>A	uc002txh.2	-	2	222	c.74A>T	c.(73-75)GAC>GTC	p.D25V		NM_198557	NP_940959	Q6ZSC3	RBM43_HUMAN	RNA binding motif protein 43	25	RRM.						nucleotide binding|RNA binding				0				BRCA - Breast invasive adenocarcinoma(221;0.131)														---	---	---	---
RIF1	55183	broad.mit.edu	37	2	152291967	152291967	+	Intron	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:152291967T>C	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	152301958	152301958	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:152301958T>C	uc002txm.2	+	19	2223	c.2093T>C	c.(2092-2094)GTG>GCG	p.V698A	RIF1_uc002txl.2_Missense_Mutation_p.V698A|RIF1_uc010fnv.1_Missense_Mutation_p.V662A|RIF1_uc002txn.2_Missense_Mutation_p.V698A|RIF1_uc002txo.2_Missense_Mutation_p.V698A	NM_018151	NP_060621	Q5UIP0	RIF1_HUMAN	RAP1 interacting factor 1	698					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)														---	---	---	---
UPP2	151531	broad.mit.edu	37	2	158977959	158977959	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:158977959G>A	uc002tzp.2	+	5	687	c.493G>A	c.(493-495)GTA>ATA	p.V165I	UPP2_uc002tzo.2_Missense_Mutation_p.V222I	NM_173355	NP_775491	O95045	UPP2_HUMAN	uridine phosphorylase 2 isoform a	165					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																		---	---	---	---
PKP4	8502	broad.mit.edu	37	2	159481473	159481473	+	Silent	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:159481473C>T	uc002tzv.2	+	7	947	c.687C>T	c.(685-687)GGC>GGT	p.G229G	PKP4_uc002tzt.1_Silent_p.G81G|PKP4_uc002tzu.2_Silent_p.G229G|PKP4_uc002tzw.2_Silent_p.G229G|PKP4_uc002tzx.2_5'UTR|PKP4_uc002tzy.1_5'UTR|PKP4_uc002tzz.1_Silent_p.G227G|PKP4_uc002uaa.2_Silent_p.G81G	NM_003628	NP_003619	Q99569	PKP4_HUMAN	plakophilin 4 isoform a	229					cell adhesion	desmosome	protein binding			ovary(5)|skin(2)	7															HNSCC(62;0.18)			---	---	---	---
MARCH7	64844	broad.mit.edu	37	2	160605264	160605264	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:160605264T>C	uc002uax.2	+	5	1585	c.1463T>C	c.(1462-1464)GTC>GCC	p.V488A	MARCH7_uc010foq.2_Missense_Mutation_p.V488A|MARCH7_uc010zcn.1_Missense_Mutation_p.V432A|MARCH7_uc010for.2_Missense_Mutation_p.V450A|MARCH7_uc002uay.2_RNA	NM_022826	NP_073737	Q9H992	MARH7_HUMAN	axotrophin	488							ligase activity|zinc ion binding				0																		---	---	---	---
RBMS1	5937	broad.mit.edu	37	2	161137828	161137828	+	Silent	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:161137828G>A	uc002ubo.2	-	10	1392	c.948C>T	c.(946-948)CAC>CAT	p.H316H	RBMS1_uc002ubj.2_Silent_p.H296H|RBMS1_uc002ubk.2_Silent_p.H280H|RBMS1_uc002ubl.2_Silent_p.H311H|RBMS1_uc002ubn.2_Silent_p.H313H|RBMS1_uc002ubi.3_Silent_p.H329H|RBMS1_uc002ubm.2_Silent_p.H299H|RBMS1_uc002ubp.2_Silent_p.H332H|RBMS1_uc010fox.2_3'UTR	NM_016836	NP_058520	P29558	RBMS1_HUMAN	RNA binding motif, single stranded interacting	316				QH -> HD (in Ref. 2; CAA54628).	DNA replication|RNA processing	nucleus	double-stranded DNA binding|nucleotide binding|protein binding|RNA binding|single-stranded DNA binding				0																		---	---	---	---
TBR1	10716	broad.mit.edu	37	2	162274271	162274271	+	Silent	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:162274271G>A	uc002ubw.1	+	2	1079	c.777G>A	c.(775-777)GCG>GCA	p.A259A	TBR1_uc010foy.2_5'Flank	NM_006593	NP_006584	Q16650	TBR1_HUMAN	T-box, brain, 1	259	T-box.					nucleus	DNA binding|sequence-specific DNA binding transcription factor activity			ovary(1)|central_nervous_system(1)	2																		---	---	---	---
DPP4	1803	broad.mit.edu	37	2	162891710	162891710	+	Silent	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:162891710C>T	uc002ubz.2	-	9	1299	c.738G>A	c.(736-738)CTG>CTA	p.L246L	DPP4_uc010fpb.2_5'UTR	NM_001935	NP_001926	P27487	DPP4_HUMAN	dipeptidylpeptidase IV	246	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)													---	---	---	---
GRB14	2888	broad.mit.edu	37	2	165350992	165350992	+	Silent	SNP	G	A	A	rs138769540	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:165350992G>A	uc002ucl.2	-	13	1966	c.1425C>T	c.(1423-1425)TTC>TTT	p.F475F	GRB14_uc010zcv.1_Silent_p.F388F|GRB14_uc002ucm.2_RNA	NM_004490	NP_004481	Q14449	GRB14_HUMAN	growth factor receptor-bound protein 14	475	SH2.				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																		---	---	---	---
COBLL1	22837	broad.mit.edu	37	2	165551885	165551885	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:165551885C>T	uc010zcw.1	-	15	2456	c.2332G>A	c.(2332-2334)GTA>ATA	p.V778I	COBLL1_uc002ucp.2_Missense_Mutation_p.V711I|COBLL1_uc002ucq.2_Missense_Mutation_p.V673I|COBLL1_uc010zcx.1_Missense_Mutation_p.V719I|COBLL1_uc002ucn.2_Missense_Mutation_p.V139I|COBLL1_uc002uco.2_Missense_Mutation_p.V442I	NM_014900	NP_055715	Q53SF7	COBL1_HUMAN	COBL-like 1	749										ovary(2)|pancreas(1)	3																		---	---	---	---
SCN3A	6328	broad.mit.edu	37	2	165947843	165947843	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:165947843G>A	uc002ucx.2	-	28	5312	c.4820C>T	c.(4819-4821)GCT>GTT	p.A1607V	SCN3A_uc010zcy.1_Missense_Mutation_p.A90V|SCN3A_uc002ucy.2_Missense_Mutation_p.A1558V|SCN3A_uc002ucz.2_Missense_Mutation_p.A1558V	NM_006922	NP_008853	Q9NY46	SCN3A_HUMAN	sodium channel, voltage-gated, type III, alpha	1607	Helical; Name=S3 of repeat IV; (Potential).					voltage-gated sodium channel complex	voltage-gated sodium channel activity			ovary(4)|breast(3)|skin(2)|central_nervous_system(1)	10					Lamotrigine(DB00555)													---	---	---	---
GALNT3	2591	broad.mit.edu	37	2	166618487	166618487	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:166618487C>A	uc010fph.1	-	4	1153	c.766G>T	c.(766-768)GGT>TGT	p.G256C	GALNT3_uc010fpi.1_Missense_Mutation_p.G256C	NM_004482	NP_004473	Q14435	GALT3_HUMAN	polypeptide N-acetylgalactosaminyltransferase 3	256	Catalytic subdomain A.|Lumenal (Potential).				protein O-linked glycosylation via serine|protein O-linked glycosylation via threonine	Golgi cisterna membrane|integral to membrane|membrane fraction|nucleus|perinuclear region of cytoplasm	calcium ion binding|manganese ion binding|polypeptide N-acetylgalactosaminyltransferase activity|sugar binding			central_nervous_system(2)|ovary(1)	3																		---	---	---	---
SCN1A	6323	broad.mit.edu	37	2	166848872	166848872	+	Missense_Mutation	SNP	A	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:166848872A>T	uc010zcz.1	-	26	4898	c.4880T>A	c.(4879-4881)ATC>AAC	p.I1627N		NM_006920	NP_008851	P35498	SCN1A_HUMAN	sodium channel, voltage-gated, type I, alpha	1638	Helical; Voltage-sensor; Name=S4 of repeat IV; (By similarity).|IV.					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)													---	---	---	---
SCN1A	6323	broad.mit.edu	37	2	166900400	166900400	+	Silent	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:166900400A>G	uc010zcz.1	-	11	1840	c.1822T>C	c.(1822-1824)TTG>CTG	p.L608L	SCN1A_uc002udo.3_Silent_p.L477L|SCN1A_uc010fpk.2_Silent_p.L477L	NM_006920	NP_008851	P35498	SCN1A_HUMAN	sodium channel, voltage-gated, type I, alpha	608						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)													---	---	---	---
SCN7A	6332	broad.mit.edu	37	2	167285738	167285738	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:167285738G>A	uc002udu.1	-	16	2766	c.2639C>T	c.(2638-2640)GCT>GTT	p.A880V	SCN7A_uc010fpm.1_RNA	NM_002976	NP_002967	Q01118	SCN7A_HUMAN	sodium channel, voltage-gated, type VII, alpha	880					muscle contraction	voltage-gated sodium channel complex	voltage-gated sodium channel activity			large_intestine(1)	1																		---	---	---	---
SCN7A	6332	broad.mit.edu	37	2	167318940	167318940	+	Silent	SNP	G	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:167318940G>T	uc002udu.1	-	9	1169	c.1042C>A	c.(1042-1044)CGG>AGG	p.R348R	SCN7A_uc010fpm.1_RNA	NM_002976	NP_002967	Q01118	SCN7A_HUMAN	sodium channel, voltage-gated, type VII, alpha	348					muscle contraction	voltage-gated sodium channel complex	voltage-gated sodium channel activity			large_intestine(1)	1																		---	---	---	---
LRP2	4036	broad.mit.edu	37	2	170092427	170092427	+	Missense_Mutation	SNP	T	C	C	rs146792863		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:170092427T>C	uc002ues.2	-	29	5056	c.4843A>G	c.(4843-4845)ATG>GTG	p.M1615V		NM_004525	NP_004516	P98164	LRP2_HUMAN	low density lipoprotein-related protein 2	1615	LDL-receptor class B 13.|Extracellular (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	170092579	170092579	+	Splice_Site	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:170092579C>T	uc002ues.2	-	29	4905	c.4692_splice	c.e29-1	p.N1564_splice		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)													---	---	---	---
KLHL23	151230	broad.mit.edu	37	2	170592072	170592072	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:170592072T>C	uc002ufh.1	+	4	886	c.548T>C	c.(547-549)TTT>TCT	p.F183S	KLHL23_uc002ufi.1_Missense_Mutation_p.F183S	NM_144711	NP_653312	Q8NBE8	KLH23_HUMAN	kelch-like 23	183	BACK.										0																		---	---	---	---
MAP1D	254042	broad.mit.edu	37	2	172930337	172930337	+	Silent	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:172930337C>T	uc002uhk.2	+	4	427	c.354C>T	c.(352-354)GAC>GAT	p.D118D	MAP1D_uc010zdw.1_5'UTR	NM_199227	NP_954697	Q6UB28	AMP1D_HUMAN	methionine aminopeptidase 1D precursor	118					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)															---	---	---	---
CIR1	9541	broad.mit.edu	37	2	175245452	175245452	+	Intron	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:175245452A>G	uc002uim.2	-						CIR1_uc002uin.2_Intron|CIR1_uc002uio.2_5'UTR|CIR1_uc002uip.2_5'UTR	NM_004882	NP_004873			CBF1 interacting corepressor						mRNA processing|negative regulation of transcription, DNA-dependent|RNA splicing	nuclear speck	protein binding|sequence-specific DNA binding transcription factor activity|transcription corepressor activity			large_intestine(1)	1																		---	---	---	---
CIR1	9541	broad.mit.edu	37	2	175246433	175246433	+	Silent	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:175246433T>C	uc002uim.2	-	3	333	c.240A>G	c.(238-240)AAA>AAG	p.K80K	CIR1_uc002uin.2_5'UTR|CIR1_uc002uio.2_5'UTR|CIR1_uc002uip.2_5'UTR	NM_004882	NP_004873	Q86X95	CIR1_HUMAN	CBF1 interacting corepressor	80	Interaction with RBPJ.				mRNA processing|negative regulation of transcription, DNA-dependent|RNA splicing	nuclear speck	protein binding|sequence-specific DNA binding transcription factor activity|transcription corepressor activity			large_intestine(1)	1																		---	---	---	---
CHN1	1123	broad.mit.edu	37	2	175664955	175664955	+	Silent	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:175664955T>C	uc002uji.2	-	13	1799	c.1269A>G	c.(1267-1269)GGA>GGG	p.G423G	CHN1_uc010zeq.1_Silent_p.G397G|CHN1_uc002ujj.2_Silent_p.G198G|CHN1_uc002ujg.2_Silent_p.G298G	NM_001822	NP_001813	P15882	CHIN_HUMAN	chimerin (chimaerin) 1 isoform a	423	Rho-GAP.				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								---	---	---	---
HOXD12	3238	broad.mit.edu	37	2	176964671	176964671	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:176964671G>A	uc010zev.1	+	1	142	c.142G>A	c.(142-144)GCG>ACG	p.A48T	HOXD12_uc010zew.1_Missense_Mutation_p.A48T	NM_021193	NP_067016	P35452	HXD12_HUMAN	homeobox D12	48						nuclear chromosome	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity				0			OV - Ovarian serous cystadenocarcinoma(117;0.0207)|Epithelial(96;0.18)	Colorectal(32;0.0521)|READ - Rectum adenocarcinoma(9;0.0678)														---	---	---	---
TTN	7273	broad.mit.edu	37	2	179400171	179400171	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:179400171T>C	uc010zfg.1	-	307	93691	c.93467A>G	c.(93466-93468)TAC>TGC	p.Y31156C	uc002umo.2_Intron|uc002ump.1_Intron|TTN_uc010zfh.1_Missense_Mutation_p.Y24851C|TTN_uc010zfi.1_Missense_Mutation_p.Y24784C|TTN_uc010zfj.1_Missense_Mutation_p.Y24659C	NM_133378	NP_596869	Q8WZ42	TITIN_HUMAN	titin isoform N2-A	32083							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)															---	---	---	---
Unknown	0	broad.mit.edu	37	2	179444078	179444078	+	Intron	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:179444078T>C	uc002umo.2	+						uc002ump.1_Intron|TTN_uc010zfg.1_Missense_Mutation_p.Y19992C|TTN_uc010zfh.1_Missense_Mutation_p.Y13687C|TTN_uc010zfi.1_Missense_Mutation_p.Y13620C|TTN_uc010zfj.1_Missense_Mutation_p.Y13495C|uc002umv.1_Nonstop_Mutation_p.*102Q					Homo sapiens cDNA FLJ36414 fis, clone THYMU2010848.																														---	---	---	---
TTN	7273	broad.mit.edu	37	2	179459370	179459370	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:179459370A>G	uc010zfg.1	-	245	50371	c.50147T>C	c.(50146-50148)GTA>GCA	p.V16716A	uc002umo.2_Intron|uc002ump.1_Intron|TTN_uc010zfh.1_Missense_Mutation_p.V10411A|TTN_uc010zfi.1_Missense_Mutation_p.V10344A|TTN_uc010zfj.1_Missense_Mutation_p.V10219A	NM_133378	NP_596869	Q8WZ42	TITIN_HUMAN	titin isoform N2-A	17643							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	179470363	179470363	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:179470363G>A	uc010zfg.1	-	228	46179	c.45955C>T	c.(45955-45957)CGC>TGC	p.R15319C	uc002ump.1_Intron|TTN_uc010zfh.1_Missense_Mutation_p.R9014C|TTN_uc010zfi.1_Missense_Mutation_p.R8947C|TTN_uc010zfj.1_Missense_Mutation_p.R8822C	NM_133378	NP_596869	Q8WZ42	TITIN_HUMAN	titin isoform N2-A	16246							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	179568977	179568977	+	Silent	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:179568977G>A	uc010zfg.1	-	103	26612	c.26388C>T	c.(26386-26388)CAC>CAT	p.H8796H	TTN_uc010zfh.1_Intron|TTN_uc010zfi.1_Intron|TTN_uc010zfj.1_Intron|TTN_uc002umz.1_Silent_p.H5457H	NM_133378	NP_596869	Q8WZ42	TITIN_HUMAN	titin isoform N2-A	9723							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	179587229	179587229	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:179587229C>T	uc010zfg.1	-	74	18777	c.18553G>A	c.(18553-18555)GAA>AAA	p.E6185K	TTN_uc010zfh.1_Intron|TTN_uc010zfi.1_Intron|TTN_uc010zfj.1_Intron|TTN_uc002umz.1_Missense_Mutation_p.E2846K	NM_133378	NP_596869	Q8WZ42	TITIN_HUMAN	titin isoform N2-A	7112							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	179589049	179589049	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:179589049T>C	uc010zfg.1	-	69	17545	c.17321A>G	c.(17320-17322)TAC>TGC	p.Y5774C	TTN_uc010zfh.1_Intron|TTN_uc010zfi.1_Intron|TTN_uc010zfj.1_Intron|TTN_uc002umz.1_Missense_Mutation_p.Y2435C	NM_133378	NP_596869	Q8WZ42	TITIN_HUMAN	titin isoform N2-A	6701							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	179616463	179616463	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:179616463T>C	uc002unb.2	-	46	10888	c.10664A>G	c.(10663-10665)GAG>GGG	p.E3555G	TTN_uc010zfg.1_Intron|TTN_uc010zfh.1_Intron|TTN_uc010zfi.1_Intron|TTN_uc010zfj.1_Intron|TTN_uc002umz.1_Intron	NM_133379	NP_596870	Q8WZ42	TITIN_HUMAN	titin isoform novex-3	Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment							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	179639032	179639032	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:179639032C>T	uc010zfg.1	-	30	7183	c.6959G>A	c.(6958-6960)CGT>CAT	p.R2320H	TTN_uc010zfh.1_Missense_Mutation_p.R2274H|TTN_uc010zfi.1_Missense_Mutation_p.R2274H|TTN_uc010zfj.1_Missense_Mutation_p.R2274H|TTN_uc002unb.2_Missense_Mutation_p.R2320H|uc002unc.1_5'Flank	NM_133378	NP_596869	Q8WZ42	TITIN_HUMAN	titin isoform N2-A	2320							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	179641220	179641220	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:179641220T>C	uc010zfg.1	-	28	5595	c.5371A>G	c.(5371-5373)ACC>GCC	p.T1791A	TTN_uc010zfh.1_Missense_Mutation_p.T1745A|TTN_uc010zfi.1_Missense_Mutation_p.T1745A|TTN_uc010zfj.1_Missense_Mutation_p.T1745A|TTN_uc002unb.2_Missense_Mutation_p.T1791A|uc002unc.1_5'Flank	NM_133378	NP_596869	Q8WZ42	TITIN_HUMAN	titin isoform N2-A	1791							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)															---	---	---	---
ITGA4	3676	broad.mit.edu	37	2	182344996	182344996	+	Intron	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:182344996A>G	uc002unu.2	+						ITGA4_uc010zfl.1_Intron	NM_000885	NP_000876			integrin alpha 4 precursor						blood coagulation|integrin-mediated signaling pathway|leukocyte cell-cell adhesion|leukocyte migration|regulation of immune response	integrin complex	identical protein binding|receptor activity			ovary(3)|lung(1)|central_nervous_system(1)|pancreas(1)	6			OV - Ovarian serous cystadenocarcinoma(117;0.0593)		Natalizumab(DB00108)													---	---	---	---
PPP1R1C	151242	broad.mit.edu	37	2	182928488	182928488	+	Nonsense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:182928488C>T	uc002uoo.2	+	4	498	c.211C>T	c.(211-213)CAG>TAG	p.Q71*	PPP1R1C_uc002uon.2_RNA|PPP1R1C_uc002uop.1_Nonsense_Mutation_p.Q71*|PPP1R1C_uc010frm.1_Nonsense_Mutation_p.Q78*|PPP1R1C_uc010frn.1_RNA	NM_001080545	NP_001074014	Q8WVI7	PPR1C_HUMAN	protein phosphatase 1, regulatory (inhibitor)	71					signal transduction	cytoplasm	protein phosphatase inhibitor activity				0			OV - Ovarian serous cystadenocarcinoma(117;0.0628)															---	---	---	---
Unknown	0	broad.mit.edu	37	2	186671731	186671731	+	Intron	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:186671731C>T	uc002upm.2	+						uc010zfu.1_Missense_Mutation_p.P398S					Homo sapiens cDNA FLJ44048 fis, clone TESTI4030669.																														---	---	---	---
COL3A1	1281	broad.mit.edu	37	2	189872765	189872765	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:189872765C>T	uc002uqj.1	+	47	3539	c.3422C>T	c.(3421-3423)CCT>CTT	p.P1141L		NM_000090	NP_000081	P02461	CO3A1_HUMAN	collagen type III alpha 1 preproprotein	1141	Triple-helical region.				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)													---	---	---	---
COL5A2	1290	broad.mit.edu	37	2	189910558	189910558	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:189910558C>T	uc002uqk.2	-	46	3552	c.3277G>A	c.(3277-3279)GCT>ACT	p.A1093T	COL5A2_uc010frx.2_Missense_Mutation_p.A669T	NM_000393	NP_000384	P05997	CO5A2_HUMAN	alpha 2 type V collagen preproprotein	1093					axon guidance|collagen fibril organization|eye morphogenesis|skin development	collagen type V	extracellular matrix structural constituent			ovary(2)	2			OV - Ovarian serous cystadenocarcinoma(117;0.0106)|Epithelial(96;0.127)															---	---	---	---
ANKAR	150709	broad.mit.edu	37	2	190541718	190541718	+	Nonsense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:190541718C>T	uc002uqw.1	+	1	289	c.289C>T	c.(289-291)CGA>TGA	p.R97*	ANKAR_uc002uqu.2_Intron|ANKAR_uc002uqv.1_Nonsense_Mutation_p.R168*	NM_144708	NP_653309	Q7Z5J8	ANKAR_HUMAN	ankyrin and armadillo repeat containing	168						integral to membrane	binding			ovary(2)|pancreas(1)|skin(1)	4			OV - Ovarian serous cystadenocarcinoma(117;0.00156)|Epithelial(96;0.0256)|all cancers(119;0.0744)															---	---	---	---
STAT1	6772	broad.mit.edu	37	2	191841680	191841680	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:191841680G>A	uc002usj.2	-	22	2333	c.1945C>T	c.(1945-1947)CGC>TGC	p.R649C	STAT1_uc010fse.1_Missense_Mutation_p.R649C|STAT1_uc002usk.2_Missense_Mutation_p.R649C|STAT1_uc002usl.2_Missense_Mutation_p.R651C	NM_007315	NP_009330	P42224	STAT1_HUMAN	signal transducer and activator of transcription	649	SH2.				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)													---	---	---	---
STAT1	6772	broad.mit.edu	37	2	191848416	191848416	+	Silent	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:191848416G>A	uc002usj.2	-	17	1786	c.1398C>T	c.(1396-1398)AGC>AGT	p.S466S	STAT1_uc010fse.1_Silent_p.S466S|STAT1_uc002usk.2_Silent_p.S466S|STAT1_uc002usl.2_Silent_p.S468S|STAT1_uc010fsf.1_Silent_p.S278S	NM_007315	NP_009330	P42224	STAT1_HUMAN	signal transducer and activator of transcription	466					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)													---	---	---	---
TMEFF2	23671	broad.mit.edu	37	2	192815032	192815032	+	3'UTR	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:192815032T>C	uc002utc.2	-	10						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)															---	---	---	---
TMEFF2	23671	broad.mit.edu	37	2	193059073	193059073	+	Intron	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:193059073A>G	uc002utc.2	-						TMEFF2_uc002utd.1_Intron	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)															---	---	---	---
DNAH7	56171	broad.mit.edu	37	2	196722327	196722327	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:196722327T>C	uc002utj.3	-	44	8289	c.8188A>G	c.(8188-8190)AAA>GAA	p.K2730E		NM_018897	NP_061720	Q8WXX0	DYH7_HUMAN	dynein, axonemal, heavy chain 7	2730	Stalk (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	196723249	196723249	+	Silent	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:196723249G>A	uc002utj.3	-	43	8117	c.8016C>T	c.(8014-8016)GCC>GCT	p.A2672A		NM_018897	NP_061720	Q8WXX0	DYH7_HUMAN	dynein, axonemal, heavy chain 7	2672	Stalk (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	196799511	196799511	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:196799511A>G	uc002utj.3	-	21	3376	c.3275T>C	c.(3274-3276)GTG>GCG	p.V1092A		NM_018897	NP_061720	Q8WXX0	DYH7_HUMAN	dynein, axonemal, heavy chain 7	1092	Stem (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	196825228	196825228	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:196825228G>A	uc002utj.3	-	18	2748	c.2647C>T	c.(2647-2649)CCA>TCA	p.P883S		NM_018897	NP_061720	Q8WXX0	DYH7_HUMAN	dynein, axonemal, heavy chain 7	883	Stem (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																		---	---	---	---
GTF3C3	9330	broad.mit.edu	37	2	197643679	197643679	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:197643679A>G	uc002uts.2	-	10	1421	c.1331T>C	c.(1330-1332)CTC>CCC	p.L444P	GTF3C3_uc010zgu.1_Intron|GTF3C3_uc002utt.3_Missense_Mutation_p.L119P	NM_012086	NP_036218	Q9Y5Q9	TF3C3_HUMAN	general transcription factor IIIC, polypeptide	444	TPR 7.					transcription factor TFIIIC complex	DNA binding|protein binding			ovary(3)|breast(3)|pancreas(1)	7																		---	---	---	---
ANKRD44	91526	broad.mit.edu	37	2	197951443	197951443	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:197951443C>T	uc002uua.1	-	13	1279	c.1202G>A	c.(1201-1203)AGC>AAC	p.S401N	ANKRD44_uc002utz.3_Missense_Mutation_p.S133N|ANKRD44_uc002uub.2_Missense_Mutation_p.S426N|ANKRD44_uc010zgw.1_Missense_Mutation_p.S354N	NM_153697	NP_710181	Q8N8A2	ANR44_HUMAN	ankyrin repeat domain 44	426	ANK 13.						protein binding			ovary(4)|skin(1)	5			OV - Ovarian serous cystadenocarcinoma(117;0.246)															---	---	---	---
SATB2	23314	broad.mit.edu	37	2	200173545	200173545	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:200173545A>G	uc002uuy.1	-	10	2495	c.1678T>C	c.(1678-1680)TCA>CCA	p.S560P	SATB2_uc010fsq.1_Missense_Mutation_p.S442P|SATB2_uc002uuz.1_Missense_Mutation_p.S560P|SATB2_uc002uva.1_Missense_Mutation_p.S560P	NM_015265	NP_056080	Q9UPW6	SATB2_HUMAN	SATB homeobox 2	560	CUT 2.					cytoplasm|nuclear matrix	sequence-specific DNA binding transcription factor activity			ovary(1)	1																		---	---	---	---
FZD7	8324	broad.mit.edu	37	2	202900161	202900161	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:202900161G>A	uc002uyw.1	+	1	852	c.791G>A	c.(790-792)TGC>TAC	p.C264Y		NM_003507	NP_003498	O75084	FZD7_HUMAN	frizzled 7 precursor	264	Helical; Name=1; (Potential).				axonogenesis|brain development|canonical Wnt receptor signaling pathway|cellular response to retinoic acid|G-protein signaling, coupled to cGMP nucleotide second messenger|gonad development|mesenchymal to epithelial transition|negative regulation of cell-substrate adhesion|negative regulation of ectodermal cell fate specification|positive regulation of epithelial cell proliferation involved in wound healing|positive regulation of phosphorylation|positive regulation of transcription, DNA-dependent|regulation of catenin import into nucleus|vasculature development|Wnt receptor signaling pathway, calcium modulating pathway	apical part of cell|cytoplasm|integral to membrane|neuron projection membrane	G-protein coupled receptor activity|PDZ domain binding|Wnt receptor activity|Wnt-protein binding			skin(2)|ovary(1)|breast(1)	4																OREG0015146	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
ICA1L	130026	broad.mit.edu	37	2	203679450	203679450	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:203679450C>T	uc002uzh.1	-	9	1005	c.841G>A	c.(841-843)GGT>AGT	p.G281S	ICA1L_uc002uzi.1_Missense_Mutation_p.G281S	NM_138468	NP_612477	Q8NDH6	ICA1L_HUMAN	islet cell autoantigen 1,69kDa-like isoform 1	281											0																		---	---	---	---
CTLA4	1493	broad.mit.edu	37	2	204735463	204735463	+	Silent	SNP	C	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:204735463C>A	uc002vak.1	+	2	421	c.264C>A	c.(262-264)ACC>ACA	p.T88T	CTLA4_uc002val.1_Silent_p.T88T|CTLA4_uc010fty.1_Intron|CTLA4_uc010ftz.1_Intron	NM_005214	NP_005205	P16410	CTLA4_HUMAN	cytotoxic T-lymphocyte-associated protein 4	88	Ig-like V-type.|Extracellular (Potential).				B cell receptor signaling pathway|immune response|negative regulation of B cell proliferation|negative regulation of regulatory T cell differentiation|positive regulation of apoptosis|response to DNA damage stimulus|T cell costimulation	clathrin-coated endocytic vesicle|external side of plasma membrane|Golgi apparatus|integral to plasma membrane|perinuclear region of cytoplasm					0					Abatacept(DB01281)													---	---	---	---
EEF1B2	1933	broad.mit.edu	37	2	207027088	207027088	+	Intron	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:207027088T>C	uc002vbf.1	+						NDUFS1_uc002vbe.2_5'Flank|NDUFS1_uc010zir.1_5'Flank|NDUFS1_uc010zis.1_5'Flank|NDUFS1_uc010zit.1_5'Flank|NDUFS1_uc010ziu.1_5'Flank|EEF1B2_uc002vbg.1_Intron|EEF1B2_uc002vbh.1_Intron	NM_001037663	NP_001032752			eukaryotic translation elongation factor 1 beta							cytosol|eukaryotic translation elongation factor 1 complex	protein binding|translation elongation factor activity				0																		---	---	---	---
ZDBF2	57683	broad.mit.edu	37	2	207170818	207170818	+	Silent	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:207170818G>A	uc002vbp.2	+	5	1816	c.1566G>A	c.(1564-1566)GTG>GTA	p.V522V		NM_020923	NP_065974	Q9HCK1	ZDBF2_HUMAN	zinc finger, DBF-type containing 2	522							nucleic acid binding|zinc ion binding			ovary(3)	3																		---	---	---	---
MAP2	4133	broad.mit.edu	37	2	210560789	210560789	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:210560789A>G	uc002vde.1	+	7	4143	c.3895A>G	c.(3895-3897)ACT>GCT	p.T1299A	MAP2_uc002vdc.1_Missense_Mutation_p.T1299A|MAP2_uc002vdd.1_Intron|MAP2_uc002vdf.1_Intron|MAP2_uc002vdg.1_Intron|MAP2_uc002vdh.1_Intron|MAP2_uc002vdi.1_Missense_Mutation_p.T1295A	NM_002374	NP_002365	P11137	MAP2_HUMAN	microtubule-associated protein 2 isoform 1	1299					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)													---	---	---	---
LANCL1	10314	broad.mit.edu	37	2	211306048	211306048	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:211306048T>C	uc010zjh.1	-	5	602	c.527A>G	c.(526-528)CAA>CGA	p.Q176R	LANCL1_uc002ved.2_Missense_Mutation_p.Q176R|LANCL1_uc010fuq.2_Missense_Mutation_p.Q176R	NM_001136574	NP_001130046	O43813	LANC1_HUMAN	lanthionine synthetase C-like protein 1	176						cytoplasm|integral to plasma membrane|microtubule cytoskeleton|nucleus	catalytic activity|G-protein coupled receptor activity|glutathione binding|low-density lipoprotein particle receptor binding|SH3 domain binding|zinc ion binding				0				Epithelial(149;0.00562)|Lung(261;0.0468)|LUSC - Lung squamous cell carcinoma(261;0.0495)|all cancers(144;0.0569)														---	---	---	---
ABCA12	26154	broad.mit.edu	37	2	215843537	215843537	+	Silent	SNP	G	T	T	rs138215759		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:215843537G>T	uc002vew.2	-	32	5188	c.4968C>A	c.(4966-4968)ACC>ACA	p.T1656T	ABCA12_uc002vev.2_Silent_p.T1338T|ABCA12_uc010zjn.1_Silent_p.T583T	NM_173076	NP_775099	Q86UK0	ABCAC_HUMAN	ATP-binding cassette, sub-family A, member 12	1656					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)														---	---	---	---
FN1	2335	broad.mit.edu	37	2	216285501	216285501	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:216285501T>C	uc002vfa.2	-	11	1836	c.1570A>G	c.(1570-1572)ACT>GCT	p.T524A	FN1_uc002vfb.2_Missense_Mutation_p.T524A|FN1_uc002vfc.2_Missense_Mutation_p.T524A|FN1_uc002vfd.2_Missense_Mutation_p.T524A|FN1_uc002vfe.2_Missense_Mutation_p.T524A|FN1_uc002vff.2_Missense_Mutation_p.T524A|FN1_uc002vfg.2_Missense_Mutation_p.T524A|FN1_uc002vfh.2_Missense_Mutation_p.T524A|FN1_uc002vfi.2_Missense_Mutation_p.T524A|FN1_uc002vfj.2_Missense_Mutation_p.T524A|FN1_uc002vfl.2_Missense_Mutation_p.T524A	NM_212482	NP_997647	P02751	FINC_HUMAN	fibronectin 1 isoform 1 preproprotein	524	Collagen-binding.|Fibronectin type-I 8.				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)													---	---	---	---
XRCC5	7520	broad.mit.edu	37	2	216992403	216992403	+	Intron	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:216992403T>C	uc002vfy.2	+						XRCC5_uc002vfz.2_Intron	NM_021141	NP_066964			ATP-dependent DNA helicase II						double-strand break repair via nonhomologous end joining|initiation of viral infection|negative regulation of transcription, DNA-dependent|provirus integration|telomere maintenance|transcription, DNA-dependent	Ku70:Ku80 complex|nonhomologous end joining complex|nuclear telomere cap complex|nucleoplasm	ATP binding|ATP-dependent DNA helicase activity|double-stranded DNA binding|protein C-terminus binding|telomeric DNA binding|transcription regulatory region DNA binding			lung(1)|kidney(1)	2		Renal(323;0.0328)		Epithelial(149;9.78e-06)|all cancers(144;0.000632)|LUSC - Lung squamous cell carcinoma(224;0.00871)|Lung(261;0.0117)									Direct_reversal_of_damage|NHEJ					---	---	---	---
TNS1	7145	broad.mit.edu	37	2	218673400	218673400	+	Intron	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:218673400G>A	uc002vgt.2	-						TNS1_uc002vgr.2_Intron|TNS1_uc002vgs.2_Intron|TNS1_uc002vgq.2_Intron	NM_022648	NP_072174			tensin							cytoplasm|cytoskeleton|focal adhesion	actin binding			ovary(3)|breast(1)	4		Renal(207;0.0483)|Lung NSC(271;0.213)		Epithelial(149;4.43e-06)|all cancers(144;0.000653)|LUSC - Lung squamous cell carcinoma(224;0.0091)|Lung(261;0.013)														---	---	---	---
CXCR2	3579	broad.mit.edu	37	2	219000447	219000447	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:219000447G>A	uc002vgz.1	+	4	1148	c.923G>A	c.(922-924)TGC>TAC	p.C308Y	CXCR2_uc002vha.1_Missense_Mutation_p.C308Y|CXCR2_uc002vhb.1_Missense_Mutation_p.C308Y	NM_001557	NP_001548	P25025	CXCR2_HUMAN	interleukin 8 receptor beta	308	Helical; Name=7; (Potential).				activation of phospholipase C activity by G-protein coupled receptor protein signaling pathway coupled to IP3 second messenger|cellular defense response|dendritic cell chemotaxis|inflammatory response|neutrophil activation|neutrophil chemotaxis|positive regulation of cell proliferation	cell surface|integral to plasma membrane|mast cell granule	interleukin-8 receptor activity			lung(1)|breast(1)	2																		---	---	---	---
GPBAR1	151306	broad.mit.edu	37	2	219127693	219127693	+	Silent	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:219127693C>T	uc010zjw.1	+	2	493	c.246C>T	c.(244-246)TAC>TAT	p.Y82Y	GPBAR1_uc010zjx.1_Silent_p.Y82Y|GPBAR1_uc010zjy.1_Silent_p.Y82Y	NM_170699	NP_733800	Q8TDU6	GPBAR_HUMAN	G protein-coupled bile acid receptor 1	82	Extracellular (Potential).					integral to membrane|plasma membrane	G-protein coupled receptor activity			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)														---	---	---	---
PNKD	25953	broad.mit.edu	37	2	219144738	219144738	+	Intron	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:219144738G>A	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)														---	---	---	---
RQCD1	9125	broad.mit.edu	37	2	219445442	219445442	+	Silent	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:219445442T>C	uc010zkh.1	+	2	183	c.183T>C	c.(181-183)GGT>GGC	p.G61G	RQCD1_uc002vih.1_Silent_p.G61G|RQCD1_uc010zki.1_Silent_p.G61G	NM_005444	NP_005435	Q92600	RCD1_HUMAN	RCD1 required for cell differentiation1 homolog	61					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)														---	---	---	---
ZNF142	7701	broad.mit.edu	37	2	219507480	219507480	+	Silent	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:219507480T>C	uc002vin.2	-	8	4195	c.3759A>G	c.(3757-3759)AAA>AAG	p.K1253K	ZNF142_uc002vil.2_Silent_p.K1214K|ZNF142_uc010fvt.2_Silent_p.K1090K|ZNF142_uc002vim.2_Silent_p.K1090K	NM_001105537	NP_001099007	P52746	ZN142_HUMAN	zinc finger protein 142	1253					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			breast(2)|ovary(1)|skin(1)	4		Renal(207;0.0474)		Epithelial(149;5.21e-07)|all cancers(144;0.000106)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00948)														---	---	---	---
ZNF142	7701	broad.mit.edu	37	2	219511055	219511055	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:219511055C>A	uc002vin.2	-	7	1726	c.1290G>T	c.(1288-1290)AAG>AAT	p.K430N	ZNF142_uc002vil.2_Missense_Mutation_p.K391N|ZNF142_uc010fvt.2_Missense_Mutation_p.K267N|ZNF142_uc002vim.2_Missense_Mutation_p.K267N	NM_001105537	NP_001099007	P52746	ZN142_HUMAN	zinc finger protein 142	430	C2H2-type 9.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			breast(2)|ovary(1)|skin(1)	4		Renal(207;0.0474)		Epithelial(149;5.21e-07)|all cancers(144;0.000106)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00948)														---	---	---	---
BCS1L	617	broad.mit.edu	37	2	219527232	219527232	+	Splice_Site	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:219527232G>A	uc002vio.2	+	6	1138	c.720_splice	c.e6-1	p.I240_splice	ZNF142_uc002vin.2_5'Flank|ZNF142_uc010fvt.2_5'Flank|ZNF142_uc002vim.2_5'Flank|BCS1L_uc002vip.2_Splice_Site_p.I240_splice|BCS1L_uc002viq.2_Splice_Site_p.I240_splice|BCS1L_uc010fvu.2_Splice_Site_p.I240_splice|BCS1L_uc010fvv.2_Splice_Site_p.I240_splice|BCS1L_uc002vir.2_Splice_Site_p.I240_splice|BCS1L_uc002vis.2_Splice_Site_p.I240_splice	NM_004328	NP_004319			BCS1-like						mitochondrial respiratory chain complex I assembly|mitochondrial respiratory chain complex III assembly|mitochondrial respiratory chain complex IV assembly	integral to membrane|mitochondrial respiratory chain complex III	ATP binding|nucleoside-triphosphatase activity|protein binding				0		Renal(207;0.0474)		Epithelial(149;7.12e-07)|all cancers(144;0.000131)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)														---	---	---	---
TTLL4	9654	broad.mit.edu	37	2	219616515	219616515	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:219616515A>G	uc002viy.2	+	16	3332	c.2962A>G	c.(2962-2964)AAA>GAA	p.K988E	TTLL4_uc010zkl.1_Missense_Mutation_p.K823E|TTLL4_uc010fvx.2_Missense_Mutation_p.K924E|TTLL4_uc010zkm.1_Missense_Mutation_p.K191E	NM_014640	NP_055455	Q14679	TTLL4_HUMAN	tubulin tyrosine ligase-like family, member 4	988					protein polyglutamylation	cilium|microtubule basal body	ATP binding|tubulin binding|tubulin-tyrosine ligase activity			ovary(2)|skin(1)	3		Renal(207;0.0915)		Epithelial(149;5.03e-07)|all cancers(144;0.000106)|LUSC - Lung squamous cell carcinoma(224;0.00829)|Lung(261;0.0101)														---	---	---	---
CYP27A1	1593	broad.mit.edu	37	2	219677360	219677360	+	Silent	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:219677360C>T	uc002viz.3	+	4	1166	c.732C>T	c.(730-732)ATC>ATT	p.I244I		NM_000784	NP_000775	Q02318	CP27A_HUMAN	cytochrome P450, family 27, subfamily A,	244					bile acid biosynthetic process|xenobiotic metabolic process	mitochondrial matrix	cholestanetriol 26-monooxygenase activity|electron carrier activity|heme binding			ovary(1)	1		Renal(207;0.0474)		Epithelial(149;9.48e-07)|all cancers(144;0.000171)|LUSC - Lung squamous cell carcinoma(224;0.00813)|Lung(261;0.00981)	Cholecalciferol(DB00169)													---	---	---	---
PRKAG3	53632	broad.mit.edu	37	2	219694774	219694774	+	Missense_Mutation	SNP	A	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:219694774A>C	uc002vjb.1	-	4	579	c.560T>G	c.(559-561)TTC>TGC	p.F187C	PRKAG3_uc010zkn.1_RNA|PRKAG3_uc010fvy.1_Missense_Mutation_p.F187C|PRKAG3_uc010zko.1_Missense_Mutation_p.F183C	NM_017431	NP_059127	Q9UGI9	AAKG3_HUMAN	AMP-activated protein kinase, non-catalytic	187					cell cycle arrest|fatty acid biosynthetic process|insulin receptor signaling pathway|intracellular protein kinase cascade|regulation of fatty acid oxidation	cytosol	AMP-activated protein kinase activity|protein kinase binding			ovary(1)|lung(1)	2		Renal(207;0.0474)		Epithelial(149;4.35e-07)|all cancers(144;8.96e-05)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)														---	---	---	---
ABCB6	10058	broad.mit.edu	37	2	220081483	220081483	+	Silent	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:220081483C>T	uc002vkc.1	-	3	1036	c.759G>A	c.(757-759)CTG>CTA	p.L253L	ABCB6_uc010fwe.1_Silent_p.L207L|ABCB6_uc010zku.1_Intron	NM_005689	NP_005680	Q9NP58	ABCB6_HUMAN	ATP-binding cassette, sub-family B, member 6	253					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	220087503	220087503	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:220087503C>T	uc002vke.1	-	11	1898	c.1712G>A	c.(1711-1713)CGT>CAT	p.R571H	ABCB6_uc010fwe.1_5'Flank|ABCB6_uc010zku.1_5'Flank|ATG9A_uc002vkd.1_RNA|ATG9A_uc002vkf.1_Missense_Mutation_p.R571H	NM_001077198	NP_001070666	Q7Z3C6	ATG9A_HUMAN	APG9 autophagy 9-like 1	571	Cytoplasmic (By similarity).				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)														---	---	---	---
ACCN4	55515	broad.mit.edu	37	2	220379638	220379638	+	Silent	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:220379638A>G	uc002vma.2	+	1	587	c.573A>G	c.(571-573)GGA>GGG	p.G191G	ACCN4_uc010fwi.1_Silent_p.G191G|ACCN4_uc010fwj.1_Silent_p.G191G|ACCN4_uc002vly.1_Silent_p.G191G|ACCN4_uc002vlz.2_Silent_p.G191G|ACCN4_uc002vmb.2_5'Flank	NM_182847	NP_878267	Q96FT7	ACCN4_HUMAN	amiloride-sensitive cation channel 4 isoform 2	191	Cytoplasmic (Potential).					integral to plasma membrane	sodium channel activity|sodium ion transmembrane transporter activity			ovary(2)	2		Renal(207;0.0183)		Epithelial(149;5.47e-10)|all cancers(144;9e-08)|LUSC - Lung squamous cell carcinoma(224;0.00813)|Lung(261;0.0086)|READ - Rectum adenocarcinoma(5;0.156)														---	---	---	---
SLC4A3	6508	broad.mit.edu	37	2	220495031	220495031	+	Silent	SNP	G	A	A	rs34803760		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:220495031G>A	uc002vmp.3	+	6	1037	c.768G>A	c.(766-768)GCG>GCA	p.A256A	SLC4A3_uc002vmn.2_Silent_p.A283A|SLC4A3_uc002vmo.3_Silent_p.A283A|SLC4A3_uc010fwm.2_5'UTR|SLC4A3_uc010fwn.1_5'Flank	NM_005070	NP_005061	P48751	B3A3_HUMAN	solute carrier family 4, anion exchanger, member	256	Cytoplasmic.				bicarbonate transport	integral to plasma membrane|membrane fraction	inorganic anion exchanger activity			ovary(2)|upper_aerodigestive_tract(1)|breast(1)|skin(1)	5		Renal(207;0.0183)		Epithelial(149;2.53e-07)|all cancers(144;5.57e-05)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)														---	---	---	---
SCG2	7857	broad.mit.edu	37	2	224463892	224463892	+	Nonsense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:224463892G>A	uc002vnm.2	-	2	242	c.109C>T	c.(109-111)CAG>TAG	p.Q37*		NM_003469	NP_003460	P13521	SCG2_HUMAN	secretogranin II precursor	37					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)														---	---	---	---
DOCK10	55619	broad.mit.edu	37	2	225719751	225719751	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:225719751C>A	uc010fwz.1	-	16	2056	c.1817G>T	c.(1816-1818)AGA>ATA	p.R606I	DOCK10_uc002vob.2_Missense_Mutation_p.R600I	NM_014689	NP_055504	Q96BY6	DOC10_HUMAN	dedicator of cytokinesis 10	606							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)														---	---	---	---
KIAA1486	57624	broad.mit.edu	37	2	226516173	226516173	+	Silent	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:226516173C>T	uc002voe.2	+	6	2029	c.1854C>T	c.(1852-1854)GGC>GGT	p.G618G	KIAA1486_uc010fxa.1_3'UTR|KIAA1486_uc002vof.1_Silent_p.G388G	NM_020864	NP_065915	Q9P242	K1486_HUMAN	hypothetical protein LOC57624	618										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)														---	---	---	---
COL4A4	1286	broad.mit.edu	37	2	227915687	227915687	+	Intron	SNP	C	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:227915687C>A	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)														---	---	---	---
COL4A4	1286	broad.mit.edu	37	2	227973577	227973577	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:227973577G>A	uc010zlt.1	-	11	1319	c.665C>T	c.(664-666)CCG>CTG	p.P222L		NM_000092	NP_000083	P53420	CO4A4_HUMAN	alpha 4 type IV collagen precursor	222	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)														---	---	---	---
C2orf83	56918	broad.mit.edu	37	2	228476242	228476242	+	Silent	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:228476242G>A	uc002vph.2	-	3	556	c.321C>T	c.(319-321)GCC>GCT	p.A107A	C2orf83_uc010zlu.1_3'UTR	NM_020161	NP_064546	Q53S99	CB083_HUMAN	hypothetical protein LOC56918 isoform 1	107						membrane	folic acid binding|reduced folate carrier activity				0																		---	---	---	---
SLC19A3	80704	broad.mit.edu	37	2	228564077	228564077	+	Silent	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:228564077G>A	uc002vpi.2	-	3	443	c.354C>T	c.(352-354)GCC>GCT	p.A118A	SLC19A3_uc002vpj.2_RNA|SLC19A3_uc010zlv.1_Silent_p.A114A	NM_025243	NP_079519	Q9BZV2	S19A3_HUMAN	solute carrier family 19, member 3	118	Helical; (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)													---	---	---	---
SP110	3431	broad.mit.edu	37	2	231042261	231042261	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:231042261A>G	uc002vqh.3	-	14	1823	c.1583T>C	c.(1582-1584)CTG>CCG	p.L528P	SP110_uc002vqg.3_Missense_Mutation_p.L528P|SP110_uc002vqi.3_Missense_Mutation_p.L528P|SP110_uc010fxk.2_Missense_Mutation_p.L526P|SP110_uc010fxj.2_Missense_Mutation_p.L171P	NM_004509	NP_004500	Q9HB58	SP110_HUMAN	SP110 nuclear body protein isoform a	528	Nuclear hormone receptor interaction (Potential).|SAND.				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)														---	---	---	---
ALPI	248	broad.mit.edu	37	2	233322297	233322297	+	Missense_Mutation	SNP	A	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:233322297A>C	uc002vst.3	+	6	748	c.671A>C	c.(670-672)AAG>ACG	p.K224T	ALPI_uc002vsu.3_Missense_Mutation_p.K135T	NM_001631	NP_001622	P09923	PPBI_HUMAN	intestinal alkaline phosphatase precursor	224					phosphorylation	anchored to membrane|integral to membrane|plasma membrane	alkaline phosphatase activity|metal ion binding|protein binding			central_nervous_system(1)	1		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;1.64e-16)|Kidney(3;9.71e-08)|KIRC - Kidney renal clear cell carcinoma(3;2.74e-06)|BRCA - Breast invasive adenocarcinoma(100;0.000763)|Lung(119;0.00564)|LUSC - Lung squamous cell carcinoma(224;0.00746)														---	---	---	---
GIGYF2	26058	broad.mit.edu	37	2	233671354	233671354	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:233671354C>T	uc002vti.3	+	17	2130	c.1793C>T	c.(1792-1794)CCC>CTC	p.P598L	GIGYF2_uc010zmj.1_Missense_Mutation_p.P598L|GIGYF2_uc002vtg.2_Missense_Mutation_p.P592L|GIGYF2_uc002vtj.3_Missense_Mutation_p.P619L|GIGYF2_uc002vtk.3_Missense_Mutation_p.P598L|GIGYF2_uc002vth.3_Missense_Mutation_p.P592L|GIGYF2_uc010zmk.1_RNA|GIGYF2_uc010zml.1_Missense_Mutation_p.P429L	NM_015575	NP_056390	Q6Y7W6	PERQ2_HUMAN	GRB10 interacting GYF protein 2 isoform b	598					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)														---	---	---	---
ATG16L1	55054	broad.mit.edu	37	2	234200895	234200895	+	Nonsense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:234200895C>T	uc002vty.2	+	15	1809	c.1552C>T	c.(1552-1554)CGA>TGA	p.R518*	ATG16L1_uc002vtx.1_Nonsense_Mutation_p.R355*|ATG16L1_uc002vua.2_Nonsense_Mutation_p.R499*|ATG16L1_uc002vub.2_Nonsense_Mutation_p.R376*|ATG16L1_uc002vtz.2_Nonsense_Mutation_p.R339*|ATG16L1_uc002vud.3_Nonsense_Mutation_p.R434*	NM_030803	NP_110430	Q676U5	A16L1_HUMAN	APG16 autophagy 16-like isoform 1	518	WD 5.				autophagic vacuole assembly|protein homooligomerization|protein transport	autophagic vacuole|pre-autophagosomal structure membrane	protein binding				0		Breast(86;0.0013)|Renal(207;0.00339)|all_hematologic(139;0.0116)|all_lung(227;0.0179)|Acute lymphoblastic leukemia(138;0.0327)|Lung NSC(271;0.0539)		Epithelial(121;1.53e-17)|BRCA - Breast invasive adenocarcinoma(100;0.000379)|LUSC - Lung squamous cell carcinoma(224;0.00619)|Lung(119;0.00732)|GBM - Glioblastoma multiforme(43;0.11)														---	---	---	---
SAG	6295	broad.mit.edu	37	2	234240330	234240330	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:234240330G>A	uc002vuh.2	+	10	1166	c.778G>A	c.(778-780)GTC>ATC	p.V260I	SAG_uc010zmq.1_Missense_Mutation_p.V126I	NM_000541	NP_000532	P10523	ARRS_HUMAN	S-arrestin	260					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)														---	---	---	---
USP40	55230	broad.mit.edu	37	2	234442370	234442370	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:234442370C>T	uc010zmr.1	-	10	1259	c.1259G>A	c.(1258-1260)CGT>CAT	p.R420H	USP40_uc010zmt.1_Missense_Mutation_p.R64H	NM_018218	NP_060688	Q9NVE5	UBP40_HUMAN	ubiquitin thioesterase 40	408					ubiquitin-dependent protein catabolic process		cysteine-type peptidase activity|ubiquitin thiolesterase activity			ovary(1)|lung(1)|breast(1)	3		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;0.0539)		Epithelial(121;1.71e-17)|BRCA - Breast invasive adenocarcinoma(100;0.000407)|Lung(119;0.00277)|LUSC - Lung squamous cell carcinoma(224;0.00646)														---	---	---	---
SH3BP4	23677	broad.mit.edu	37	2	235943707	235943707	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:235943707G>T	uc002vvp.2	+	3	454	c.61G>T	c.(61-63)GGG>TGG	p.G21W	SH3BP4_uc010fym.2_Missense_Mutation_p.G21W|SH3BP4_uc002vvq.2_Missense_Mutation_p.G21W	NM_014521	NP_055336	Q9P0V3	SH3B4_HUMAN	SH3-domain binding protein 4	21					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	236715932	236715932	+	Missense_Mutation	SNP	G	A	A	rs143715398	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:236715932G>A	uc002vvs.2	+	9	1602	c.1007G>A	c.(1006-1008)CGT>CAT	p.R336H	AGAP1_uc002vvt.2_Missense_Mutation_p.R336H	NM_001037131	NP_001032208	Q9UPQ3	AGAP1_HUMAN	centaurin, gamma 2 isoform 1	336					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																		---	---	---	---
COL6A3	1293	broad.mit.edu	37	2	238259821	238259821	+	Silent	SNP	G	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:238259821G>T	uc002vwl.2	-	27	7053	c.6768C>A	c.(6766-6768)GCC>GCA	p.A2256A	COL6A3_uc002vwo.2_Silent_p.A2050A|COL6A3_uc010znj.1_Silent_p.A1649A|COL6A3_uc002vwp.1_Silent_p.A77A	NM_004369	NP_004360	P12111	CO6A3_HUMAN	alpha 3 type VI collagen isoform 1 precursor	2256	Triple-helical region.|Collagen-like 4.				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)														---	---	---	---
HDAC4	9759	broad.mit.edu	37	2	240085501	240085501	+	Silent	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:240085501G>A	uc002vyk.3	-	6	1401	c.609C>T	c.(607-609)TAC>TAT	p.Y203Y	HDAC4_uc010fyz.1_Silent_p.Y198Y|HDAC4_uc010zoa.1_Silent_p.Y198Y|HDAC4_uc010fza.2_Silent_p.Y203Y|HDAC4_uc010fyy.2_Silent_p.Y155Y|HDAC4_uc010znz.1_Silent_p.Y86Y	NM_006037	NP_006028	P56524	HDAC4_HUMAN	histone deacetylase 4	203	Interaction with MEF2A.				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)														---	---	---	---
GPC1	2817	broad.mit.edu	37	2	241404068	241404068	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:241404068A>G	uc002vyw.3	+	5	1140	c.919A>G	c.(919-921)ACA>GCA	p.T307A		NM_002081	NP_002072	P35052	GPC1_HUMAN	glypican 1 precursor	307					axon guidance	anchored to membrane|extracellular space|integral to plasma membrane|proteinaceous extracellular matrix	heparan sulfate proteoglycan binding			breast(1)	1		all_epithelial(40;2.79e-15)|Breast(86;2.41e-05)|Renal(207;0.00183)|Ovarian(221;0.0228)|all_lung(227;0.0335)|Lung NSC(271;0.106)|all_hematologic(139;0.158)|Melanoma(123;0.16)|Hepatocellular(293;0.244)		Epithelial(32;4.51e-33)|all cancers(36;1.74e-30)|OV - Ovarian serous cystadenocarcinoma(60;4.73e-15)|Kidney(56;2.99e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.23e-08)|BRCA - Breast invasive adenocarcinoma(100;9.1e-06)|Colorectal(34;0.000487)|Lung(119;0.0013)|LUSC - Lung squamous cell carcinoma(224;0.0154)|COAD - Colon adenocarcinoma(134;0.0194)|READ - Rectum adenocarcinoma(96;0.0949)														---	---	---	---
HDLBP	3069	broad.mit.edu	37	2	242179364	242179364	+	Silent	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:242179364G>A	uc002waz.2	-	18	2571	c.2343C>T	c.(2341-2343)GAC>GAT	p.D781D	HDLBP_uc002wba.2_Silent_p.D781D|HDLBP_uc002wbb.2_Silent_p.D733D	NM_203346	NP_976221	Q00341	VIGLN_HUMAN	high density lipoprotein binding protein	781	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	242195709	242195709	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:242195709G>A	uc002waz.2	-	7	991	c.763C>T	c.(763-765)CGC>TGC	p.R255C	HDLBP_uc002wba.2_Missense_Mutation_p.R255C|HDLBP_uc002wbb.2_Missense_Mutation_p.R276C|HDLBP_uc010fzn.1_Missense_Mutation_p.R7C	NM_203346	NP_976221	Q00341	VIGLN_HUMAN	high density lipoprotein binding protein	255	KH 2.				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)														---	---	---	---
DTYMK	1841	broad.mit.edu	37	2	242617982	242617982	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:242617982G>A	uc002wbz.1	-	4	442	c.413C>T	c.(412-414)GCG>GTG	p.A138V	DTYMK_uc010zpa.1_Missense_Mutation_p.A114V|DTYMK_uc010zpb.1_RNA|DTYMK_uc002wca.1_RNA|DTYMK_uc002wcb.1_5'Flank	NM_012145	NP_036277	P23919	KTHY_HUMAN	deoxythymidylate kinase (thymidylate kinase)	138					cell cycle|cell proliferation|nucleobase, nucleoside and nucleotide interconversion	cytosol	ATP binding|nucleoside phosphate kinase activity|thymidylate kinase activity				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;1.6e-33)|all cancers(36;3.57e-31)|OV - Ovarian serous cystadenocarcinoma(60;3.23e-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)														---	---	---	---
ING5	84289	broad.mit.edu	37	2	242662669	242662669	+	Silent	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:242662669G>A	uc002wcd.2	+	7	688	c.663G>A	c.(661-663)ACG>ACA	p.T221T		NM_032329	NP_115705	Q8WYH8	ING5_HUMAN	inhibitor of growth family, member 5	221	PHD-type.				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	431011	431011	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:431011A>G	uc003bou.2	+	19	2547	c.2276A>G	c.(2275-2277)GAG>GGG	p.E759G	CHL1_uc003bot.2_Missense_Mutation_p.E775G|CHL1_uc003bow.1_Missense_Mutation_p.E759G|CHL1_uc011asi.1_Missense_Mutation_p.E775G	NM_006614	NP_006605	O00533	CHL1_HUMAN	cell adhesion molecule with homology to L1CAM	759	Fibronectin type-III 2.|Extracellular (Potential).				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)														---	---	---	---
CRBN	51185	broad.mit.edu	37	3	3196481	3196481	+	Missense_Mutation	SNP	C	T	T	rs150489082		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:3196481C>T	uc003bpq.2	-	7	804	c.785G>A	c.(784-786)CGT>CAT	p.R262H	CRBN_uc003bpr.2_Missense_Mutation_p.R261H|CRBN_uc010hbw.2_Missense_Mutation_p.R262H|CRBN_uc011aso.1_Missense_Mutation_p.R199H	NM_016302	NP_057386	Q96SW2	CRBN_HUMAN	cereblon	262	Lon.				proteasomal ubiquitin-dependent protein catabolic process|protein ubiquitination	Cul4A-RING ubiquitin ligase complex|cytoplasm|membrane|nucleus	ATP-dependent peptidase activity|protein binding			ovary(1)	1				Epithelial(13;0.00244)|OV - Ovarian serous cystadenocarcinoma(96;0.00617)|all cancers(10;0.0079)														---	---	---	---
LRRN1	57633	broad.mit.edu	37	3	3886739	3886739	+	Silent	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:3886739T>C	uc003bpt.3	+	2	1175	c.414T>C	c.(412-414)TGT>TGC	p.C138C	SUMF1_uc003bps.1_Intron	NM_020873	NP_065924	Q6UXK5	LRRN1_HUMAN	leucine rich repeat neuronal 1 precursor	138	LRR 3.|Extracellular (Potential).					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)														---	---	---	---
TTLL3	26140	broad.mit.edu	37	3	9860572	9860572	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:9860572A>G	uc003btg.2	+	6	713	c.497A>G	c.(496-498)TAC>TGC	p.Y166C	ARPC4_uc003btc.1_Intron|TTLL3_uc003btd.3_Intron|TTLL3_uc003btf.3_Translation_Start_Site|TTLL3_uc010hco.1_Missense_Mutation_p.Y102C|TTLL3_uc003bth.3_Translation_Start_Site|TTLL3_uc011atj.1_Missense_Mutation_p.Y102C|TTLL3_uc003btj.3_Translation_Start_Site|TTLL3_uc003bti.3_Translation_Start_Site	NM_001025930	NP_001021100	Q9Y4R7	TTLL3_HUMAN	tubulin tyrosine ligase-like family, member 3	166	TTL.				axoneme assembly|cilium assembly|protein polyglycylation	cilium axoneme|cytoplasm|microtubule	protein-glycine ligase activity, initiating|tubulin-tyrosine ligase activity			large_intestine(2)	2	Medulloblastoma(99;0.227)																	---	---	---	---
IL17RC	84818	broad.mit.edu	37	3	9959399	9959399	+	Silent	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:9959399C>T	uc003bua.2	+	2	557	c.321C>T	c.(319-321)GGC>GGT	p.G107G	CIDEC_uc003bto.2_Intron|IL17RC_uc010hcr.2_RNA|IL17RC_uc011ato.1_RNA|IL17RC_uc010hcs.2_Silent_p.G36G|IL17RC_uc003btz.2_Silent_p.G36G|IL17RC_uc011atp.1_5'UTR|IL17RC_uc003bud.2_5'UTR|IL17RC_uc003bub.2_Silent_p.G36G|IL17RC_uc010hct.2_Silent_p.G36G|IL17RC_uc010hcu.2_Silent_p.G36G|IL17RC_uc010hcv.2_Silent_p.G36G|IL17RC_uc011atq.1_Silent_p.G36G|IL17RC_uc003buc.2_5'UTR	NM_153461	NP_703191	Q8NAC3	I17RC_HUMAN	interleukin 17 receptor C isoform 1 precursor	107	Extracellular (Potential).					integral to membrane|plasma membrane	receptor activity			ovary(1)|pancreas(1)	2																		---	---	---	---
GRIP2	80852	broad.mit.edu	37	3	14559346	14559346	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:14559346T>C	uc011avi.1	-	11	1384	c.1384A>G	c.(1384-1386)AGC>GGC	p.S462G	GRIP2_uc011avh.1_5'UTR	NM_001080423	NP_001073892	Q9C0E4	GRIP2_HUMAN	glutamate receptor interacting protein 2	364					synaptic transmission	cytosol|plasma membrane	protein binding			pancreas(1)	1																		---	---	---	---
EAF1	85403	broad.mit.edu	37	3	15473665	15473665	+	Silent	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:15473665T>C	uc003bzu.2	+	3	493	c.270T>C	c.(268-270)ATT>ATC	p.I90I	EAF1_uc011avq.1_Intron	NM_033083	NP_149074	Q96JC9	EAF1_HUMAN	ELL associated factor 1	90					regulation of transcription, DNA-dependent|transcription, DNA-dependent	Cajal body|nuclear speck	protein binding			central_nervous_system(1)	1																		---	---	---	---
BTD	686	broad.mit.edu	37	3	15686103	15686103	+	Missense_Mutation	SNP	A	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:15686103A>T	uc003cah.2	+	4	843	c.740A>T	c.(739-741)GAT>GTT	p.D247V	BTD_uc011avv.1_Missense_Mutation_p.D249V|BTD_uc011avw.1_Missense_Mutation_p.D249V|BTD_uc011avx.1_Missense_Mutation_p.D227V	NM_000060	NP_000051	P43251	BTD_HUMAN	biotinidase precursor	247	CN hydrolase.				central nervous system development|epidermis development|nitrogen compound metabolic process	extracellular space	biotin carboxylase activity|biotinidase activity				0																		---	---	---	---
RFTN1	23180	broad.mit.edu	37	3	16475450	16475450	+	Silent	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:16475450C>T	uc003cay.2	-	3	522	c.240G>A	c.(238-240)GCG>GCA	p.A80A	RFTN1_uc010hes.2_Silent_p.A44A	NM_015150	NP_055965	Q14699	RFTN1_HUMAN	raft-linking protein	80						plasma membrane				ovary(3)|central_nervous_system(1)	4																		---	---	---	---
TBC1D5	9779	broad.mit.edu	37	3	17226662	17226662	+	Silent	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:17226662C>T	uc003cbf.2	-	19	3456	c.1791G>A	c.(1789-1791)GGG>GGA	p.G597G	TBC1D5_uc010heu.2_Silent_p.G184G|TBC1D5_uc010hev.2_Silent_p.G619G|TBC1D5_uc003cbe.2_Silent_p.G597G|TBC1D5_uc010hew.1_Silent_p.G571G	NM_014744	NP_055559	Q92609	TBCD5_HUMAN	TBC1 domain family, member 5 isoform b	597						intracellular	protein binding|Rab GTPase activator activity			ovary(1)	1																		---	---	---	---
SATB1	6304	broad.mit.edu	37	3	18391011	18391011	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:18391011C>T	uc003cbh.2	-	11	3678	c.1943G>A	c.(1942-1944)CGA>CAA	p.R648Q	SATB1_uc003cbi.2_Missense_Mutation_p.R680Q|SATB1_uc003cbj.2_Missense_Mutation_p.R648Q	NM_002971	NP_002962	Q01826	SATB1_HUMAN	special AT-rich sequence binding protein 1	648	Homeobox.			R->A: Reduced interaction with matrix attachment region (MAR) DNA; when associated with A-646.	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																		---	---	---	---
THRB	7068	broad.mit.edu	37	3	24169080	24169080	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:24169080C>T	uc003ccx.3	-	10	1403	c.1054G>A	c.(1054-1056)GCC>ACC	p.A352T	THRB_uc010hfe.2_Missense_Mutation_p.A352T|THRB_uc003ccy.3_Missense_Mutation_p.A352T|THRB_uc003ccz.3_Missense_Mutation_p.A347T	NM_001128176	NP_001121648	P10828	THB_HUMAN	thyroid hormone receptor, beta	352	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)													---	---	---	---
TOP2B	7155	broad.mit.edu	37	3	25666276	25666276	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:25666276C>T	uc011awn.1	-	19	2286	c.2243G>A	c.(2242-2244)CGG>CAG	p.R748Q	TOP2B_uc003cdj.2_Missense_Mutation_p.R743Q	NM_001068	NP_001059	Q02880	TOP2B_HUMAN	DNA topoisomerase II, beta isozyme	748					DNA topological change|DNA-dependent DNA replication|mitotic cell cycle G2/M transition decatenation checkpoint|mitotic recombination|resolution of meiotic recombination intermediates|sister chromatid segregation	cytosol|DNA topoisomerase complex (ATP-hydrolyzing)|nucleolus|nucleoplasm|synaptonemal complex|WINAC complex	ATP binding|chromatin binding|DNA topoisomerase (ATP-hydrolyzing) activity|DNA-dependent ATPase activity|histone deacetylase binding|protein C-terminus binding|protein heterodimerization activity|protein kinase C binding|sequence-specific DNA binding transcription factor activity			breast(2)|ovary(1)|lung(1)|skin(1)	5																		---	---	---	---
TOP2B	7155	broad.mit.edu	37	3	25668727	25668727	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:25668727C>T	uc011awn.1	-	16	2010	c.1967G>A	c.(1966-1968)CGC>CAC	p.R656H	TOP2B_uc003cdj.2_Missense_Mutation_p.R651H	NM_001068	NP_001059	Q02880	TOP2B_HUMAN	DNA topoisomerase II, beta isozyme	656					DNA topological change|DNA-dependent DNA replication|mitotic cell cycle G2/M transition decatenation checkpoint|mitotic recombination|resolution of meiotic recombination intermediates|sister chromatid segregation	cytosol|DNA topoisomerase complex (ATP-hydrolyzing)|nucleolus|nucleoplasm|synaptonemal complex|WINAC complex	ATP binding|chromatin binding|DNA topoisomerase (ATP-hydrolyzing) activity|DNA-dependent ATPase activity|histone deacetylase binding|protein C-terminus binding|protein heterodimerization activity|protein kinase C binding|sequence-specific DNA binding transcription factor activity			breast(2)|ovary(1)|lung(1)|skin(1)	5																		---	---	---	---
STT3B	201595	broad.mit.edu	37	3	31663664	31663664	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:31663664T>C	uc011axe.1	+	10	1403	c.1403T>C	c.(1402-1404)GTG>GCG	p.V468A		NM_178862	NP_849193	Q8TCJ2	STT3B_HUMAN	source of immunodominant MHC-associated	468	Helical; (Potential).				protein N-linked glycosylation via asparagine	integral to membrane|oligosaccharyltransferase complex	dolichyl-diphosphooligosaccharide-protein glycotransferase activity|protein binding				0																		---	---	---	---
CMTM8	152189	broad.mit.edu	37	3	32411432	32411432	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:32411432A>G	uc003cex.2	+	4	789	c.495A>G	c.(493-495)ATA>ATG	p.I165M	CMTM8_uc010hfu.2_Missense_Mutation_p.I107M	NM_178868	NP_849199	Q8IZV2	CKLF8_HUMAN	CKLF-like MARVEL transmembrane domain containing	165	MARVEL.|Helical; (Potential).				chemotaxis	extracellular space|integral to membrane	cytokine activity				0																		---	---	---	---
GLB1	2720	broad.mit.edu	37	3	33110391	33110391	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:33110391T>C	uc003cfi.1	-	3	434	c.317A>G	c.(316-318)TAT>TGT	p.Y106C	GLB1_uc003cfh.1_Missense_Mutation_p.Y76C|GLB1_uc003cfj.1_Intron|GLB1_uc011axk.1_Missense_Mutation_p.Y154C	NM_000404	NP_000395	P16278	BGAL_HUMAN	galactosidase, beta 1 isoform a preproprotein	106					carbohydrate metabolic process	lysosome|perinuclear region of cytoplasm	beta-galactosidase activity|cation binding|protein binding			large_intestine(1)	1		Melanoma(143;0.104)																---	---	---	---
FBXL2	25827	broad.mit.edu	37	3	33427109	33427109	+	3'UTR	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:33427109G>A	uc003cfp.2	+	15					FBXL2_uc011axm.1_RNA|FBXL2_uc011axn.1_RNA|FBXL2_uc011axo.1_3'UTR|FBXL2_uc011axp.1_3'UTR|FBXL2_uc011axq.1_RNA|FBXL2_uc011axr.1_RNA|FBXL2_uc011axs.1_RNA	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																		---	---	---	---
TRANK1	9881	broad.mit.edu	37	3	36872532	36872532	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:36872532C>T	uc003cgj.2	-	12	7062	c.6760G>A	c.(6760-6762)GCC>ACC	p.A2254T		NM_014831	NP_055646	O15050	TRNK1_HUMAN	lupus brain antigen 1	2804					DNA repair		ATP binding|ATP-dependent DNA helicase activity|DNA binding			ovary(1)|central_nervous_system(1)	2																		---	---	---	---
TRANK1	9881	broad.mit.edu	37	3	36898546	36898546	+	Silent	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:36898546G>A	uc003cgj.2	-	3	1187	c.885C>T	c.(883-885)TTC>TTT	p.F295F		NM_014831	NP_055646	O15050	TRNK1_HUMAN	lupus brain antigen 1	845					DNA repair		ATP binding|ATP-dependent DNA helicase activity|DNA binding			ovary(1)|central_nervous_system(1)	2																		---	---	---	---
LRRFIP2	9209	broad.mit.edu	37	3	37136292	37136292	+	Silent	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:37136292A>G	uc003cgp.2	-	18	1449	c.1026T>C	c.(1024-1026)AGT>AGC	p.S342S	LRRFIP2_uc011ayf.1_Silent_p.S182S|LRRFIP2_uc003cgr.2_Silent_p.S110S|LRRFIP2_uc003cgs.3_Silent_p.S110S|LRRFIP2_uc003cgt.3_Silent_p.S110S	NM_006309	NP_006300	Q9Y608	LRRF2_HUMAN	leucine rich repeat (in FLII) interacting	342	DVL3-binding.|Ser-rich.				Wnt receptor signaling pathway		LRR domain binding			ovary(1)	1																		---	---	---	---
SLC22A13	9390	broad.mit.edu	37	3	38316619	38316619	+	Silent	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:38316619G>A	uc003chz.3	+	4	831	c.777G>A	c.(775-777)GCG>GCA	p.A259A	SLC22A13_uc011aym.1_RNA|SLC22A13_uc011ayn.1_Silent_p.A259A	NM_004256	NP_004247	Q9Y226	S22AD_HUMAN	solute carrier family 22 (organic anion	259	Helical; (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)														---	---	---	---
ACVR2B	93	broad.mit.edu	37	3	38520748	38520748	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:38520748G>A	uc003cif.2	+	6	820	c.796G>A	c.(796-798)GCC>ACC	p.A266T	ACVR2B_uc003cig.2_Missense_Mutation_p.A57T	NM_001106	NP_001097	Q13705	AVR2B_HUMAN	activin A receptor, type IIB precursor	266	Cytoplasmic (Potential).|Protein kinase.				activin receptor signaling pathway|anterior/posterior pattern formation|BMP signaling pathway|positive regulation of activin receptor signaling pathway|positive regulation of bone mineralization|positive regulation of osteoblast differentiation|regulation of transcription, DNA-dependent	cell surface|cytoplasm|integral to plasma membrane	activin receptor activity|ATP binding|growth factor binding|metal ion binding|receptor signaling protein serine/threonine kinase activity|transforming growth factor beta receptor activity			lung(1)	1	Medulloblastoma(35;0.163)			KIRC - Kidney renal clear cell carcinoma(284;0.0565)|Kidney(284;0.071)														---	---	---	---
EXOG	9941	broad.mit.edu	37	3	38565462	38565462	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:38565462T>C	uc003cih.2	+	6	812	c.716T>C	c.(715-717)GTA>GCA	p.V239A	EXOG_uc010hhg.2_RNA|EXOG_uc011ayq.1_Missense_Mutation_p.V189A|EXOG_uc003cij.2_Missense_Mutation_p.V99A|EXOG_uc010hhd.2_Missense_Mutation_p.V99A|EXOG_uc010hhe.2_Missense_Mutation_p.V99A|EXOG_uc003cik.2_Missense_Mutation_p.V99A|EXOG_uc010hhf.2_Missense_Mutation_p.V99A|EXOG_uc003cii.2_Missense_Mutation_p.V99A	NM_005107	NP_005098	Q9Y2C4	EXOG_HUMAN	endo/exonuclease (5'-3'), endonuclease G-like	239						mitochondrial inner membrane	endonuclease activity|metal ion binding|nucleic acid binding				0																		---	---	---	---
SCN5A	6331	broad.mit.edu	37	3	38627442	38627442	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:38627442T>C	uc003cio.2	-	16	2721	c.2527A>G	c.(2527-2529)ACA>GCA	p.T843A	SCN5A_uc003cin.2_Missense_Mutation_p.T843A|SCN5A_uc003cil.3_Missense_Mutation_p.T843A|SCN5A_uc010hhi.2_Missense_Mutation_p.T843A|SCN5A_uc010hhk.2_Missense_Mutation_p.T843A|SCN5A_uc011ayr.1_Missense_Mutation_p.T843A|SCN5A_uc010hhj.1_Missense_Mutation_p.T454A	NM_198056	NP_932173	Q14524	SCN5A_HUMAN	voltage-gated sodium channel type V alpha	843	Helical; Name=S5 of repeat II; (Potential).				blood circulation|cellular response to calcium ion|muscle contraction|regulation of heart contraction	sarcolemma|voltage-gated sodium channel complex	protein binding|voltage-gated sodium channel activity			ovary(4)|pancreas(2)|skin(2)|central_nervous_system(1)	9	Medulloblastoma(35;0.163)			KIRC - Kidney renal clear cell carcinoma(284;0.0822)|Kidney(284;0.1)	Benzonatate(DB00868)|Bepridil(DB01244)|Carbamazepine(DB00564)|Cocaine(DB00907)|Dibucaine(DB00527)|Disopyramide(DB00280)|Encainide(DB01228)|Ethotoin(DB00754)|Flecainide(DB01195)|Fosphenytoin(DB01320)|Hexylcaine(DB00473)|Indecainide(DB00192)|Lamotrigine(DB00555)|Lidocaine(DB00281)|Mephenytoin(DB00532)|Mexiletine(DB00379)|Mibefradil(DB01388)|Moricizine(DB00680)|Oxcarbazepine(DB00776)|Phenytoin(DB00252)|Prilocaine(DB00750)|Procainamide(DB01035)|Propafenone(DB01182)|Quinidine(DB00908)|Riluzole(DB00740)|Tocainide(DB01056)|Verapamil(DB00661)													---	---	---	---
SCN10A	6336	broad.mit.edu	37	3	38798258	38798258	+	Silent	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:38798258C>T	uc003ciq.2	-	9	1197	c.1197G>A	c.(1195-1197)GCG>GCA	p.A399A		NM_006514	NP_006505	Q9Y5Y9	SCNAA_HUMAN	sodium channel, voltage-gated, type X, alpha	399	Helical; Name=S6 of repeat I; (Potential).|I.				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	38888728	38888728	+	Silent	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:38888728A>G	uc011ays.1	-	26	5032	c.4833T>C	c.(4831-4833)ACT>ACC	p.T1611T		NM_014139	NP_054858	Q9UI33	SCNBA_HUMAN	sodium channel, voltage-gated, type XI, alpha	1611					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)													---	---	---	---
TRAK1	22906	broad.mit.edu	37	3	42167092	42167092	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:42167092C>T	uc003cky.2	+	2	488	c.272C>T	c.(271-273)ACG>ATG	p.T91M	TRAK1_uc011azh.1_Missense_Mutation_p.T91M|TRAK1_uc011azi.1_Missense_Mutation_p.T91M	NM_001042646	NP_001036111	Q9UPV9	TRAK1_HUMAN	OGT(O-Glc-NAc transferase)-interacting protein	91	HAP1 N-terminal.				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																		---	---	---	---
LYZL4	131375	broad.mit.edu	37	3	42448466	42448466	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:42448466C>T	uc003cle.2	-	3	413	c.164G>A	c.(163-165)AGC>AAC	p.S55N		NM_144634	NP_653235	Q96KX0	LYZL4_HUMAN	lysozyme-like 4 precursor	55					cell wall macromolecule catabolic process	extracellular region	lysozyme activity			central_nervous_system(1)	1				KIRC - Kidney renal clear cell carcinoma(284;0.222)														---	---	---	---
NKTR	4820	broad.mit.edu	37	3	42674258	42674258	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:42674258G>A	uc003clo.2	+	9	863	c.716G>A	c.(715-717)CGA>CAA	p.R239Q	NKTR_uc003clm.1_5'UTR|NKTR_uc003clp.2_5'UTR|NKTR_uc011azp.1_Missense_Mutation_p.R129Q|NKTR_uc003clq.1_Missense_Mutation_p.R129Q|NKTR_uc003clr.1_5'UTR|NKTR_uc003cls.2_5'UTR	NM_005385	NP_005376	P30414	NKTR_HUMAN	natural killer-tumor recognition sequence	239	Arg/Lys-rich (basic).|Arg/Ser-rich.				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	42728103	42728103	+	Silent	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:42728103C>T	uc003clv.1	+	1	1093	c.993C>T	c.(991-993)TAC>TAT	p.Y331Y		NM_152393	NP_689606	Q2TBA0	KBTB5_HUMAN	kelch repeat and BTB (POZ) domain containing 5	331										ovary(1)	1				KIRC - Kidney renal clear cell carcinoma(284;0.214)														---	---	---	---
HIGD1A	25994	broad.mit.edu	37	3	42845665	42845665	+	Intron	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:42845665C>T	uc003cma.3	-						CCBP2_uc003cmc.1_5'Flank|HIGD1A_uc010hid.2_Missense_Mutation_p.E7K|HIGD1A_uc003cmb.3_Intron	NM_001099669	NP_001093139			HIG1 domain family, member 1A isoform b						response to stress	integral to membrane|protein complex	protein binding				0				KIRC - Kidney renal clear cell carcinoma(284;0.217)														---	---	---	---
ZNF662	389114	broad.mit.edu	37	3	42956390	42956390	+	Silent	SNP	C	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:42956390C>A	uc003cmi.2	+	5	1177	c.825C>A	c.(823-825)CCC>CCA	p.P275P	ZNF662_uc003cmk.2_Silent_p.P301P|ZNF662_uc003cmj.2_Silent_p.P167P	NM_207404	NP_997287	Q6ZS27	ZN662_HUMAN	zinc finger protein 662 isoform 1	275					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0				KIRC - Kidney renal clear cell carcinoma(284;0.217)														---	---	---	---
ZNF197	10168	broad.mit.edu	37	3	44683625	44683625	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:44683625A>G	uc003cnm.2	+	6	1209	c.1003A>G	c.(1003-1005)ACT>GCT	p.T335A	ZNF197_uc003cnn.2_Intron|ZNF197_uc003cno.2_Intron|ZNF197_uc003cnp.2_Intron	NM_006991	NP_008922	O14709	ZN197_HUMAN	zinc finger protein 197 isoform 1	335					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)														---	---	---	---
CCR2	729230	broad.mit.edu	37	3	46399434	46399434	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:46399434A>G	uc003cpn.3	+	2	901	c.416A>G	c.(415-417)TAC>TGC	p.Y139C	CCR2_uc003cpm.3_Missense_Mutation_p.Y139C	NM_001123041	NP_001116513	P41597	CCR2_HUMAN	chemokine (C-C motif) receptor 2 isoform A	139	Cytoplasmic (Potential).				astrocyte cell migration|blood vessel remodeling|cellular defense response|chemokine-mediated signaling pathway|dendritic cell chemotaxis|elevation of cytosolic calcium ion concentration|immune response|inflammatory response|interspecies interaction between organisms|JAK-STAT cascade|monocyte extravasation|negative regulation of adenylate cyclase activity|negative regulation of angiogenesis|negative regulation of eosinophil degranulation|negative regulation of type 2 immune response|positive regulation of alpha-beta T cell proliferation|positive regulation of immune complex clearance by monocytes and macrophages|positive regulation of inflammatory response|positive regulation of interferon-gamma production|positive regulation of interleukin-2 production|positive regulation of monocyte chemotaxis|positive regulation of T cell chemotaxis|positive regulation of T cell extravasation|positive regulation of T-helper 1 type immune response|positive regulation of tumor necrosis factor biosynthetic process|regulation of vascular endothelial growth factor production|T-helper 17 cell chemotaxis	cytosol|dendrite|integral to plasma membrane|perikaryon|perinuclear region of cytoplasm|soluble fraction	C-C chemokine receptor activity|CCR2 chemokine receptor binding|protein homodimerization activity			lung(1)|breast(1)	2				BRCA - Breast invasive adenocarcinoma(193;0.00114)|KIRC - Kidney renal clear cell carcinoma(197;0.0174)|Kidney(197;0.0206)														---	---	---	---
CCR5	1234	broad.mit.edu	37	3	46415392	46415392	+	Silent	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:46415392G>A	uc003cpo.3	+	3	1121	c.999G>A	c.(997-999)GAG>GAA	p.E333E	CCR5_uc010hjd.2_Silent_p.E333E	NM_001100168	NP_001093638	P51681	CCR5_HUMAN	chemokine (C-C motif) receptor 5	333	Cytoplasmic (Potential).		E -> G (in THCCR5-2).		cell-cell signaling|cellular defense response|dendritic cell chemotaxis|elevation of cytosolic calcium ion concentration|entry into host cell|immune response|inflammatory response|initiation of viral infection	endosome|external side of plasma membrane|integral to plasma membrane	actin binding|C-C chemokine receptor activity|coreceptor activity|phosphatidylinositol phospholipase C activity			lung(4)|upper_aerodigestive_tract(1)|central_nervous_system(1)	6				BRCA - Breast invasive adenocarcinoma(193;0.00112)|KIRC - Kidney renal clear cell carcinoma(197;0.017)|Kidney(197;0.02)	Maraviroc(DB04835)													---	---	---	---
LTF	4057	broad.mit.edu	37	3	46479521	46479521	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:46479521C>T	uc003cpq.2	-	16	2046	c.2008G>A	c.(2008-2010)GCC>ACC	p.A670T	LTF_uc003fzr.2_Missense_Mutation_p.A626T|LTF_uc010hjh.2_Missense_Mutation_p.A668T|LTF_uc003cpr.2_Missense_Mutation_p.A657T	NM_002343	NP_002334	P02788	TRFL_HUMAN	lactotransferrin precursor	670	Transferrin-like 2.				cellular iron ion homeostasis|defense response to bacterium|humoral immune response|iron ion transport	extracellular region|stored secretory granule	ferric iron binding|heparin binding|protein binding|serine-type endopeptidase activity			central_nervous_system(2)|ovary(1)|lung(1)	4				all cancers(1;7.55e-14)|GBM - Glioblastoma multiforme(1;2.1e-09)|Epithelial(1;9.25e-07)|Colorectal(1;3.81e-05)|BRCA - Breast invasive adenocarcinoma(193;0.00129)|COAD - Colon adenocarcinoma(1;0.00308)|KIRC - Kidney renal clear cell carcinoma(197;0.0205)|Kidney(197;0.0242)|OV - Ovarian serous cystadenocarcinoma(275;0.089)	Pefloxacin(DB00487)													---	---	---	---
NBEAL2	23218	broad.mit.edu	37	3	47045400	47045400	+	Silent	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:47045400C>T	uc003cqp.2	+	36	5994	c.5815C>T	c.(5815-5817)CTG>TTG	p.L1939L	NBEAL2_uc010hjm.1_Silent_p.L1316L|NBEAL2_uc010hjn.1_Silent_p.L335L|NBEAL2_uc010hjo.1_5'Flank	NM_015175	NP_055990	Q6ZNJ1	NBEL2_HUMAN	neurobeachin-like 2	1939							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)														---	---	---	---
SETD2	29072	broad.mit.edu	37	3	47129749	47129749	+	Intron	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:47129749A>G	uc003cqs.2	-						SETD2_uc003cqv.2_Intron	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								---	---	---	---
KIF9	64147	broad.mit.edu	37	3	47278089	47278089	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:47278089G>T	uc010hjp.2	-	19	2549	c.1945C>A	c.(1945-1947)CTG>ATG	p.L649M	KIF9_uc003cqx.2_Missense_Mutation_p.L649M|KIF9_uc003cqy.2_Missense_Mutation_p.L584M|KIF9_uc011bat.1_RNA|uc003cqw.1_Intron	NM_001134878	NP_001128350	Q9HAQ2	KIF9_HUMAN	kinesin family member 9 isoform 2	649					blood coagulation|microtubule-based movement	cytoplasm|microtubule	ATP binding|microtubule motor activity			skin(1)	1		Acute lymphoblastic leukemia(5;0.164)		BRCA - Breast invasive adenocarcinoma(193;0.000284)|KIRC - Kidney renal clear cell carcinoma(197;0.00609)|Kidney(197;0.007)														---	---	---	---
CSPG5	10675	broad.mit.edu	37	3	47614289	47614289	+	Silent	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:47614289G>A	uc003crp.3	-	3	1445	c.1269C>T	c.(1267-1269)TGC>TGT	p.C423C	CSPG5_uc003crn.2_Silent_p.C285C|CSPG5_uc003cro.3_Silent_p.C423C|CSPG5_uc011bbb.1_Silent_p.C285C	NM_006574	NP_006565	O95196	CSPG5_HUMAN	chondroitin sulfate proteoglycan 5 (neuroglycan	423	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)														---	---	---	---
SMARCC1	6599	broad.mit.edu	37	3	47651575	47651575	+	Silent	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:47651575T>C	uc003crq.2	-	26	3142	c.3024A>G	c.(3022-3024)CCA>CCG	p.P1008P	SMARCC1_uc011bbc.1_RNA|SMARCC1_uc011bbd.1_Silent_p.P899P	NM_003074	NP_003065	Q92922	SMRC1_HUMAN	SWI/SNF-related matrix-associated	1008	Pro-rich.				chromatin remodeling|nervous system development|transcription, DNA-dependent	nBAF complex|npBAF complex|nucleoplasm|SWI/SNF complex|WINAC complex	DNA binding|protein N-terminus binding|transcription coactivator activity			skin(2)|lung(1)	3				BRCA - Breast invasive adenocarcinoma(193;7.47e-05)|KIRC - Kidney renal clear cell carcinoma(197;0.00862)|Kidney(197;0.01)														---	---	---	---
CAMP	820	broad.mit.edu	37	3	48265861	48265861	+	Silent	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:48265861G>A	uc003csj.1	+	2	359	c.219G>A	c.(217-219)ACG>ACA	p.T73T		NM_004345	NP_004336	P49913	CAMP_HUMAN	cathelicidin antimicrobial peptide	73					killing by host of symbiont cells|negative regulation of growth of symbiont on or near host surface	extracellular region				upper_aerodigestive_tract(1)	1				BRCA - Breast invasive adenocarcinoma(193;0.000614)|KIRC - Kidney renal clear cell carcinoma(197;0.00544)|Kidney(197;0.00605)														---	---	---	---
ZNF589	51385	broad.mit.edu	37	3	48310195	48310195	+	Silent	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:48310195G>A	uc003csl.3	+	4	1080	c.1014G>A	c.(1012-1014)GGG>GGA	p.G338G	ZNF589_uc010hjt.1_Silent_p.G335G|ZNF589_uc003csn.2_RNA|ZNF589_uc011bbg.1_Intron|ZNF589_uc003csm.2_Intron	NM_016089	NP_057173	Q86UQ0	ZN589_HUMAN	zinc finger protein 589	338	C2H2-type 4.				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)														---	---	---	---
COL7A1	1294	broad.mit.edu	37	3	48623585	48623585	+	Silent	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:48623585G>A	uc003ctz.2	-	27	3646	c.3645C>T	c.(3643-3645)GCC>GCT	p.A1215A		NM_000094	NP_000085	Q02388	CO7A1_HUMAN	alpha 1 type VII collagen precursor	1215	Nonhelical region (NC1).|VWFA 2.				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)														---	---	---	---
COL7A1	1294	broad.mit.edu	37	3	48626176	48626176	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:48626176G>A	uc003ctz.2	-	19	2487	c.2486C>T	c.(2485-2487)GCA>GTA	p.A829V		NM_000094	NP_000085	Q02388	CO7A1_HUMAN	alpha 1 type VII collagen precursor	829	Nonhelical region (NC1).|Fibronectin type-III 7.				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)														---	---	---	---
ARIH2	10425	broad.mit.edu	37	3	48965066	48965066	+	Silent	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:48965066A>G	uc003cvb.2	+	3	387	c.75A>G	c.(73-75)GAA>GAG	p.E25E	ARIH2_uc003cvc.2_Silent_p.E25E|ARIH2_uc003cvf.2_5'UTR|ARIH2_uc010hkl.2_Silent_p.E25E|ARIH2_uc003cvd.1_Silent_p.E25E|ARIH2_uc003cve.1_Silent_p.E25E	NM_006321	NP_006312	O95376	ARI2_HUMAN	ariadne homolog 2	25	Asp/Glu-rich (acidic).|Poly-Glu.				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)														---	---	---	---
WDR6	11180	broad.mit.edu	37	3	49050500	49050500	+	Silent	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:49050500C>T	uc003cvj.2	+	2	1761	c.1623C>T	c.(1621-1623)CGC>CGT	p.R541R	WDR6_uc011bbx.1_Missense_Mutation_p.A370V|WDR6_uc011bby.1_Intron|WDR6_uc010hkn.2_Silent_p.R485R|WDR6_uc011bbz.1_Silent_p.R460R	NM_018031	NP_060501	Q9NNW5	WDR6_HUMAN	WD repeat domain 6 protein	511	WD 8.				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)														---	---	---	---
USP19	10869	broad.mit.edu	37	3	49153935	49153935	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:49153935G>A	uc003cwd.1	-	7	1090	c.929C>T	c.(928-930)ACC>ATC	p.T310I	USP19_uc003cwa.2_Missense_Mutation_p.T116I|USP19_uc003cvz.3_Missense_Mutation_p.T411I|USP19_uc011bcg.1_Missense_Mutation_p.T401I|USP19_uc003cwb.2_Missense_Mutation_p.T396I|USP19_uc003cwc.1_Missense_Mutation_p.T66I|USP19_uc011bch.1_Missense_Mutation_p.T411I|USP19_uc011bci.1_Missense_Mutation_p.T396I	NM_006677	NP_006668	O94966	UBP19_HUMAN	ubiquitin thioesterase 19	310	CS 2.|Cytoplasmic (Potential).				ER-associated protein catabolic process|positive regulation of cell cycle process|protein deubiquitination|regulation of protein stability|response to endoplasmic reticulum stress|skeletal muscle atrophy	endoplasmic reticulum membrane|integral to membrane	ubiquitin thiolesterase activity|ubiquitin-specific protease activity|zinc ion binding			ovary(4)|breast(2)|lung(1)	7				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	49161384	49161384	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:49161384C>T	uc003cwe.2	-	24	3873	c.3574G>A	c.(3574-3576)GCA>ACA	p.A1192T		NM_002292	NP_002283	P55268	LAMB2_HUMAN	laminin, beta 2 precursor	1192	Domain II.				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)														---	---	---	---
CCDC71	64925	broad.mit.edu	37	3	49200814	49200814	+	Silent	SNP	C	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:49200814C>A	uc003cwg.3	-	2	966	c.828G>T	c.(826-828)CTG>CTT	p.L276L		NM_022903	NP_075054	Q8IV32	CCD71_HUMAN	coiled-coil domain containing 71	276										ovary(1)	1				BRCA - Breast invasive adenocarcinoma(193;8.01e-05)|Kidney(197;0.00217)|KIRC - Kidney renal clear cell carcinoma(197;0.00244)														---	---	---	---
APEH	327	broad.mit.edu	37	3	49720115	49720115	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:49720115G>A	uc003cxf.2	+	19	2229	c.1829G>A	c.(1828-1830)CGG>CAG	p.R610Q	APEH_uc010hkw.1_Missense_Mutation_p.R610Q	NM_001640	NP_001631	P13798	ACPH_HUMAN	N-acylaminoacyl-peptide hydrolase	610					proteolysis	cytoplasm|nuclear membrane	serine-type endopeptidase activity			ovary(1)	1				BRCA - Breast invasive adenocarcinoma(193;4.53e-05)|Kidney(197;0.00218)|KIRC - Kidney renal clear cell carcinoma(197;0.00244)														---	---	---	---
AMIGO3	386724	broad.mit.edu	37	3	49756585	49756585	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:49756585A>G	uc003cxj.2	-	1	654	c.314T>C	c.(313-315)TTC>TCC	p.F105S	RNF123_uc003cxh.2_Intron|RNF123_uc003cxi.2_Intron	NM_198722	NP_942015	Q86WK7	AMGO3_HUMAN	adhesion molecule with Ig-like domain 3	105	Extracellular (Potential).|LRR 2.				heterophilic cell-cell adhesion	integral to membrane				pancreas(1)	1				BRCA - Breast invasive adenocarcinoma(193;4.47e-05)|Kidney(197;0.00216)|KIRC - Kidney renal clear cell carcinoma(197;0.00244)												OREG0015572	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
UBA7	7318	broad.mit.edu	37	3	49848476	49848476	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:49848476C>T	uc003cxr.2	-	10	1342	c.1171G>A	c.(1171-1173)GCC>ACC	p.A391T		NM_003335	NP_003326	P41226	UBA7_HUMAN	ubiquitin-like modifier activating enzyme 7	391	2 approximate repeats.				ISG15-protein conjugation|negative regulation of type I interferon production	cytosol	ATP binding|ISG15 activating enzyme activity|ligase activity			ovary(1)|pancreas(1)	2				BRCA - Breast invasive adenocarcinoma(193;3.58e-06)|KIRC - Kidney renal clear cell carcinoma(197;0.00544)|Kidney(197;0.00607)														---	---	---	---
MST1R	4486	broad.mit.edu	37	3	49924773	49924773	+	Silent	SNP	G	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:49924773G>T	uc003cxy.3	-	20	4434	c.4170C>A	c.(4168-4170)CCC>CCA	p.P1390P	MST1R_uc011bdc.1_Silent_p.P269P	NM_002447	NP_002438	Q04912	RON_HUMAN	macrophage stimulating 1 receptor precursor	1390	Cytoplasmic (Potential).				cellular component movement|defense response|multicellular organismal development|positive regulation of cell proliferation|single fertilization|transmembrane receptor protein tyrosine kinase signaling pathway	integral to plasma membrane	ATP binding|macrophage colony-stimulating factor receptor activity|protein binding			ovary(5)|lung(1)	6				BRCA - Breast invasive adenocarcinoma(193;4.65e-05)|KIRC - Kidney renal clear cell carcinoma(197;0.00553)|Kidney(197;0.00625)														---	---	---	---
RBM5	10181	broad.mit.edu	37	3	50137981	50137981	+	Silent	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:50137981C>T	uc003cyg.2	+	6	574	c.426C>T	c.(424-426)TTC>TTT	p.F142F	RBM5_uc003cyf.2_3'UTR|RBM5_uc011bdj.1_Silent_p.F86F|RBM5_uc011bdk.1_Intron	NM_005778	NP_005769	P52756	RBM5_HUMAN	RNA binding motif protein 5	142	RRM 1.				apoptosis|negative regulation of cell proliferation|positive regulation of apoptosis|regulation of alternative nuclear mRNA splicing, via spliceosome|spliceosome assembly	nucleoplasm|spliceosomal complex	DNA binding|mRNA binding|nucleotide binding|protein binding|zinc ion binding			lung(1)	1				BRCA - Breast invasive adenocarcinoma(193;0.000121)|KIRC - Kidney renal clear cell carcinoma(197;0.00558)|Kidney(197;0.00632)														---	---	---	---
GNAT1	2779	broad.mit.edu	37	3	50232041	50232041	+	Silent	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:50232041G>A	uc003cym.2	+	7	932	c.816G>A	c.(814-816)GAG>GAA	p.E272E	GNAT1_uc003cyl.2_Silent_p.E272E	NM_144499	NP_653082	P11488	GNAT1_HUMAN	rod-type transducin alpha subunit	272					detection of chemical stimulus involved in sensory perception of bitter taste|G-protein signaling, coupled to cAMP nucleotide second messenger|negative regulation of cyclic-nucleotide phosphodiesterase activity|rhodopsin mediated phototransduction|sensory perception of umami taste	heterotrimeric G-protein complex|photoreceptor inner segment|photoreceptor outer segment membrane	acyl binding|G-protein beta/gamma-subunit complex binding|G-protein-coupled receptor binding|GDP binding|GTP binding|GTPase activity|protein kinase binding|signal transducer activity			ovary(1)|central_nervous_system(1)|pancreas(1)	3				BRCA - Breast invasive adenocarcinoma(193;0.000272)|KIRC - Kidney renal clear cell carcinoma(197;0.00544)|Kidney(197;0.00605)												OREG0015580	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
NPRL2	10641	broad.mit.edu	37	3	50385270	50385270	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:50385270C>T	uc003daj.1	-	10	1398	c.995G>A	c.(994-996)CGG>CAG	p.R332Q	ZMYND10_uc003dag.1_5'Flank|ZMYND10_uc010hll.1_5'Flank|ZMYND10_uc003dah.1_5'Flank|ZMYND10_uc010hlm.1_5'Flank|NPRL2_uc003dai.1_Missense_Mutation_p.R212Q	NM_006545	NP_006536	Q8WTW4	NPRL2_HUMAN	tumor suppressor candidate 4	332					negative regulation of kinase activity		protein binding|protein kinase activity			lung(1)	1																		---	---	---	---
MAPKAPK3	7867	broad.mit.edu	37	3	50683642	50683642	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:50683642G>A	uc003day.1	+	10	1372	c.776G>A	c.(775-777)CGC>CAC	p.R259H	MAPKAPK3_uc003daz.1_Missense_Mutation_p.R259H|MAPKAPK3_uc003dba.1_Missense_Mutation_p.R259H|MAPKAPK3_uc010hlr.1_Missense_Mutation_p.R259H	NM_004635	NP_004626	Q16644	MAPK3_HUMAN	mitogen-activated protein kinase-activated	259	Protein kinase.				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			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	51398039	51398039	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:51398039G>A	uc011bds.1	+	47	5005	c.4982G>A	c.(4981-4983)AGC>AAC	p.S1661N		NM_004947	NP_004938	Q8IZD9	DOCK3_HUMAN	dedicator of cytokinesis 3	1661						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)														---	---	---	---
VPRBP	9730	broad.mit.edu	37	3	51454265	51454265	+	Silent	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:51454265G>A	uc003dbe.1	-	17	3747	c.3579C>T	c.(3577-3579)ATC>ATT	p.I1193I	VPRBP_uc003dbf.1_Silent_p.I469I	NM_014703	NP_055518	Q9Y4B6	VPRBP_HUMAN	HIV-1 Vpr binding protein	1193	WD 3.				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)														---	---	---	---
VPRBP	9730	broad.mit.edu	37	3	51458187	51458187	+	Missense_Mutation	SNP	A	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:51458187A>C	uc003dbe.1	-	14	2405	c.2237T>G	c.(2236-2238)ATG>AGG	p.M746R	VPRBP_uc003dbf.1_Missense_Mutation_p.M22R	NM_014703	NP_055518	Q9Y4B6	VPRBP_HUMAN	HIV-1 Vpr binding protein	746					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	51746830	51746830	+	Silent	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:51746830C>T	uc010hlv.2	+	3	1031	c.792C>T	c.(790-792)CGC>CGT	p.R264R	GRM2_uc003dbo.3_Intron|GRM2_uc010hlu.2_RNA	NM_000839	NP_000830	Q14416	GRM2_HUMAN	glutamate receptor, metabotropic 2 isoform a	264	Extracellular (Potential).				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)													---	---	---	---
DNAH1	25981	broad.mit.edu	37	3	52389048	52389048	+	Nonsense_Mutation	SNP	G	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:52389048G>T	uc011bef.1	+	21	3931	c.3670G>T	c.(3670-3672)GAG>TAG	p.E1224*		NM_015512	NP_056327	Q9P2D7	DYH1_HUMAN	dynein, axonemal, heavy chain 1	1224	Stem (By similarity).|Potential.				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)														---	---	---	---
DNAH1	25981	broad.mit.edu	37	3	52420204	52420204	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:52420204G>A	uc011bef.1	+	55	8915	c.8654G>A	c.(8653-8655)CGG>CAG	p.R2885Q	DNAH1_uc003ddv.2_5'UTR	NM_015512	NP_056327	Q9P2D7	DYH1_HUMAN	dynein, axonemal, heavy chain 1	2885	Potential.|Stalk (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)														---	---	---	---
SPCS1	28972	broad.mit.edu	37	3	52740731	52740731	+	Intron	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:52740731T>C	uc011bei.1	+						GLT8D1_uc003dfj.2_5'Flank|GLT8D1_uc003dfk.2_5'Flank|GLT8D1_uc003dfl.2_5'Flank|GLT8D1_uc003dfm.2_5'Flank|GLT8D1_uc003dfn.2_5'Flank|GLT8D1_uc003dfo.1_5'Flank|GLT8D1_uc010hmm.1_5'Flank	NM_014041	NP_054760			signal peptidase complex subunit 1 homolog						energy reserve metabolic process|regulation of insulin secretion|signal peptide processing	integral to endoplasmic reticulum membrane|microsome|signal peptidase complex	peptidase activity				0				BRCA - Breast invasive adenocarcinoma(193;6.51e-05)|Kidney(197;0.000583)|KIRC - Kidney renal clear cell carcinoma(197;0.000751)|OV - Ovarian serous cystadenocarcinoma(275;0.0469)														---	---	---	---
SFMBT1	51460	broad.mit.edu	37	3	52955809	52955809	+	Silent	SNP	G	A	A	rs147500116		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:52955809G>A	uc003dgf.2	-	12	1739	c.1170C>T	c.(1168-1170)CTC>CTT	p.L390L	SFMBT1_uc010hmr.2_Silent_p.L337L|SFMBT1_uc003dgg.2_Silent_p.L390L|SFMBT1_uc003dgh.2_Silent_p.L390L	NM_001005159	NP_001005159	Q9UHJ3	SMBT1_HUMAN	Scm-like with four mbt domains 1	390	MBT 4.				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)														---	---	---	---
DCP1A	55802	broad.mit.edu	37	3	53326412	53326412	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:53326412T>C	uc003dgs.3	-	7	1163	c.1070A>G	c.(1069-1071)AAC>AGC	p.N357S	DCP1A_uc003dgt.3_RNA	NM_018403	NP_060873	Q9NPI6	DCP1A_HUMAN	DCP1 decapping enzyme homolog A	357					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)														---	---	---	---
CHDH	55349	broad.mit.edu	37	3	53851808	53851808	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:53851808C>T	uc003dgz.2	-	9	2221	c.1781G>A	c.(1780-1782)CGC>CAC	p.R594H		NM_018397	NP_060867	Q8NE62	CHDH_HUMAN	choline dehydrogenase precursor	594					alcohol metabolic process		choline dehydrogenase activity|flavin adenine dinucleotide binding			ovary(1)|central_nervous_system(1)	2		Hepatocellular(537;0.152)		BRCA - Breast invasive adenocarcinoma(193;0.000158)|KIRC - Kidney renal clear cell carcinoma(284;0.00588)|Kidney(284;0.00673)|OV - Ovarian serous cystadenocarcinoma(275;0.118)	Choline(DB00122)													---	---	---	---
CACNA2D3	55799	broad.mit.edu	37	3	54922047	54922047	+	Silent	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:54922047G>A	uc003dhf.2	+	24	2166	c.2118G>A	c.(2116-2118)GCG>GCA	p.A706A	CACNA2D3_uc011beu.1_RNA|CACNA2D3_uc003dhg.1_Silent_p.A612A|CACNA2D3_uc003dhh.1_RNA|uc003dhk.1_Intron	NM_018398	NP_060868	Q8IZS8	CA2D3_HUMAN	calcium channel, voltage-dependent, alpha	706	Extracellular (Potential).					integral to membrane	calcium channel activity|metal ion binding|voltage-gated ion channel activity			large_intestine(3)|ovary(1)|breast(1)|central_nervous_system(1)|skin(1)	7				KIRC - Kidney renal clear cell carcinoma(284;0.00287)|Kidney(284;0.00327)														---	---	---	---
ACOX2	8309	broad.mit.edu	37	3	58519163	58519163	+	Intron	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:58519163T>C	uc003dkl.2	-							NM_003500	NP_003491			acyl-Coenzyme A oxidase 2						bile acid biosynthetic process|fatty acid beta-oxidation using acyl-CoA oxidase	peroxisomal matrix	3alpha,7alpha,12alpha-trihydroxy-5beta-cholestanoyl-CoA 24-hydroxylase activity|acyl-CoA dehydrogenase activity|pristanoyl-CoA oxidase activity				0				BRCA - Breast invasive adenocarcinoma(55;0.000194)|Kidney(10;0.00255)|KIRC - Kidney renal clear cell carcinoma(10;0.00268)|OV - Ovarian serous cystadenocarcinoma(275;0.156)												OREG0015638	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
FAM3D	131177	broad.mit.edu	37	3	58639414	58639414	+	Silent	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:58639414C>T	uc003dkq.2	-	3	405	c.108G>A	c.(106-108)CTG>CTA	p.L36L		NM_138805	NP_620160	Q96BQ1	FAM3D_HUMAN	family with sequence similarity 3, member D	36					negative regulation of insulin secretion	extracellular region	cytokine activity				0				BRCA - Breast invasive adenocarcinoma(55;0.000225)|Kidney(10;0.000667)|KIRC - Kidney renal clear cell carcinoma(10;0.000802)|OV - Ovarian serous cystadenocarcinoma(275;0.169)														---	---	---	---
FEZF2	55079	broad.mit.edu	37	3	62355979	62355979	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:62355979T>C	uc003dlh.2	-	4	1366	c.1159A>G	c.(1159-1161)AAG>GAG	p.K387E	FEZF2_uc003dli.2_Missense_Mutation_p.K387E	NM_018008	NP_060478	Q8TBJ5	FEZF2_HUMAN	FEZ family zinc finger 2	387					transcription, DNA-dependent	nucleus	zinc ion binding			lung(1)	1		Lung SC(41;0.0262)		BRCA - Breast invasive adenocarcinoma(55;0.000221)|KIRC - Kidney renal clear cell carcinoma(15;0.00834)|Kidney(15;0.00957)														---	---	---	---
PSMD6	9861	broad.mit.edu	37	3	64004632	64004632	+	Silent	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:64004632A>G	uc003dma.1	-	4	604	c.579T>C	c.(577-579)GAT>GAC	p.D193D	PSMD6_uc003dlz.1_Silent_p.D144D|PSMD6_uc003dmb.1_Silent_p.D246D|PSMD6_uc003dmc.1_Silent_p.D154D|PSMD6_uc003dmd.1_Silent_p.D155D	NM_014814	NP_055629	Q15008	PSMD6_HUMAN	proteasome (prosome, macropain) 26S subunit,	193	PCI.				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 complex	ATPase activity|protein binding			central_nervous_system(1)|skin(1)	2		Lung NSC(201;0.136)		BRCA - Breast invasive adenocarcinoma(55;0.000805)|Kidney(15;0.00188)|KIRC - Kidney renal clear cell carcinoma(15;0.00212)														---	---	---	---
PRICKLE2	166336	broad.mit.edu	37	3	64138867	64138867	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:64138867G>T	uc003dmf.2	-	6	1364	c.778C>A	c.(778-780)CAA>AAA	p.Q260K		NM_198859	NP_942559	Q7Z3G6	PRIC2_HUMAN	prickle-like 2	260	LIM zinc-binding 3.					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)														---	---	---	---
MAGI1	9223	broad.mit.edu	37	3	65342628	65342628	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:65342628A>G	uc003dmn.2	-	23	4340	c.3814T>C	c.(3814-3816)TAT>CAT	p.Y1272H	MAGI1_uc003dmm.2_3'UTR	NM_001033057	NP_001028229	Q96QZ7	MAGI1_HUMAN	membrane associated guanylate kinase, WW and PDZ	1301					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)														---	---	---	---
MAGI1	9223	broad.mit.edu	37	3	65415771	65415771	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:65415771T>C	uc003dmn.2	-	12	2117	c.1591A>G	c.(1591-1593)ACA>GCA	p.T531A	MAGI1_uc003dmm.2_Missense_Mutation_p.T531A|MAGI1_uc003dmo.2_Missense_Mutation_p.T531A|MAGI1_uc003dmp.2_Missense_Mutation_p.T531A|MAGI1_uc010hny.2_Missense_Mutation_p.T416A	NM_001033057	NP_001028229	Q96QZ7	MAGI1_HUMAN	membrane associated guanylate kinase, WW and PDZ	531	PDZ 2.				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)														---	---	---	---
FAM19A1	407738	broad.mit.edu	37	3	68466481	68466481	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:68466481G>A	uc003dnd.2	+	3	386	c.170G>A	c.(169-171)CGC>CAC	p.R57H	FAM19A1_uc003dne.2_Missense_Mutation_p.R57H|FAM19A1_uc003dng.2_Missense_Mutation_p.R57H	NM_213609	NP_998774	Q7Z5A9	F19A1_HUMAN	family with sequence similarity 19 (chemokine	57						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)														---	---	---	---
ARL6IP5	10550	broad.mit.edu	37	3	69134331	69134331	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:69134331A>G	uc003dnr.2	+	1	242	c.133A>G	c.(133-135)ACC>GCC	p.T45A		NM_006407	NP_006398	O75915	PRAF3_HUMAN	ADP-ribosylation-like factor 6 interacting	45	Helical; (Potential).				L-glutamate transport	endoplasmic reticulum membrane|integral to membrane				ovary(1)	1		Lung NSC(201;0.0193)|Prostate(884;0.174)		BRCA - Breast invasive adenocarcinoma(55;7.78e-05)|Epithelial(33;0.000818)|LUSC - Lung squamous cell carcinoma(21;0.0118)|Lung(16;0.0189)|KIRC - Kidney renal clear cell carcinoma(39;0.203)|Kidney(39;0.238)														---	---	---	---
FOXP1	27086	broad.mit.edu	37	3	71064722	71064722	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:71064722C>T	uc003dol.2	-	8	1275	c.952G>A	c.(952-954)GAA>AAA	p.E318K	FOXP1_uc003dom.2_Missense_Mutation_p.E242K|FOXP1_uc003don.2_RNA|FOXP1_uc003doo.2_Missense_Mutation_p.E318K|FOXP1_uc003dop.2_Missense_Mutation_p.E318K|FOXP1_uc003doq.1_Missense_Mutation_p.E317K|FOXP1_uc003doi.2_Missense_Mutation_p.E218K|FOXP1_uc003doj.2_Missense_Mutation_p.E218K|FOXP1_uc003dok.2_Missense_Mutation_p.E131K|FOXP1_uc003dor.1_Missense_Mutation_p.E96K	NM_032682	NP_116071	Q9H334	FOXP1_HUMAN	forkhead box P1 isoform 1	318	C2H2-type.				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	74316488	74316488	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:74316488C>T	uc003dpm.1	-	20	2826	c.2746G>A	c.(2746-2748)GAC>AAC	p.D916N		NM_020872	NP_065923	Q9P232	CNTN3_HUMAN	contactin 3 precursor	916	Fibronectin type-III 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	77693994	77693994	+	Silent	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:77693994C>T	uc003dpy.3	+	25	4717	c.4074C>T	c.(4072-4074)AGC>AGT	p.S1358S	ROBO2_uc003dpz.2_Silent_p.S1423S|ROBO2_uc011bgj.1_RNA|ROBO2_uc011bgk.1_Silent_p.S1362S	NM_002942	NP_002933	Q9HCK4	ROBO2_HUMAN	roundabout, axon guidance receptor, homolog 2	1358	Cytoplasmic (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)														---	---	---	---
EPHA6	285220	broad.mit.edu	37	3	96533600	96533600	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:96533600C>T	uc010how.1	+	1	176	c.133C>T	c.(133-135)CGC>TGC	p.R45C	EPHA6_uc003drp.1_Missense_Mutation_p.R45C	NM_001080448	NP_001073917	Q9UF33	EPHA6_HUMAN	EPH receptor A6 isoform a	Error:Variant_position_missing_in_Q9UF33_after_alignment						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	97510619	97510619	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:97510619A>G	uc003drv.2	+	8	797	c.484A>G	c.(484-486)AGT>GGT	p.S162G	ARL6_uc003drw.2_RNA|ARL6_uc003dru.2_Missense_Mutation_p.S162G|ARL6_uc010hoy.2_Missense_Mutation_p.S162G	NM_177976	NP_816931	Q9H0F7	ARL6_HUMAN	ADP-ribosylation factor-like 6	162					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				---	---	---	---
CRYBG3	131544	broad.mit.edu	37	3	97662119	97662119	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:97662119G>T	uc003drx.2	+	19	3094	c.3030G>T	c.(3028-3030)GAG>GAT	p.E1010D	CRYBG3_uc010hoz.1_RNA|MINA_uc003dry.1_3'UTR|MINA_uc003drz.1_3'UTR|MINA_uc003dsa.1_3'UTR|MINA_uc003dsb.1_3'UTR|MINA_uc003dsc.1_3'UTR	NM_153605	NP_705833			beta-gamma crystallin domain containing 3												0																		---	---	---	---
OR5H2	79310	broad.mit.edu	37	3	98002313	98002313	+	Silent	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:98002313T>C	uc003dsj.1	+	1	582	c.582T>C	c.(580-582)TGT>TGC	p.C194C		NM_001005482	NP_001005482	Q8NGV7	OR5H2_HUMAN	olfactory receptor, family 5, subfamily H,	194	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(3)	3																		---	---	---	---
OR5K3	403277	broad.mit.edu	37	3	98109892	98109892	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:98109892A>G	uc011bgw.1	+	1	383	c.383A>G	c.(382-384)AAC>AGC	p.N128S		NM_001005516	NP_001005516	A6NET4	OR5K3_HUMAN	olfactory receptor, family 5, subfamily K,	128	Cytoplasmic (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity				0																		---	---	---	---
CLDND1	56650	broad.mit.edu	37	3	98240213	98240213	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:98240213G>A	uc003dsp.2	-	2	936	c.56C>T	c.(55-57)TCC>TTC	p.S19F	CLDND1_uc003dso.2_Missense_Mutation_p.S19F|CLDND1_uc003dsq.2_Missense_Mutation_p.S19F|CLDND1_uc003dss.2_Missense_Mutation_p.S19F|CLDND1_uc003dsr.2_Intron|CLDND1_uc003dst.2_Missense_Mutation_p.S42F|CLDND1_uc003dsu.2_Missense_Mutation_p.S19F|CLDND1_uc003dsv.2_Missense_Mutation_p.S19F	NM_019895	NP_063948	Q9NY35	CLDN1_HUMAN	claudin domain containing 1 protein isoform a	19	Helical; (Potential).					integral to membrane				ovary(1)	1																		---	---	---	---
CPOX	1371	broad.mit.edu	37	3	98304495	98304495	+	Missense_Mutation	SNP	T	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:98304495T>A	uc003dsx.2	-	5	1055	c.962A>T	c.(961-963)GAT>GTT	p.D321V		NM_000097	NP_000088	P36551	HEM6_HUMAN	coproporphyrinogen oxidase precursor	321						mitochondrial intermembrane space	coproporphyrinogen oxidase activity|protein homodimerization activity				0																		---	---	---	---
FILIP1L	11259	broad.mit.edu	37	3	99567803	99567803	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:99567803A>G	uc003dtm.2	-	5	3180	c.2717T>C	c.(2716-2718)GTT>GCT	p.V906A	C3orf26_uc003dtk.1_Intron|C3orf26_uc003dtl.2_Intron|FILIP1L_uc003dto.2_Missense_Mutation_p.V906A|FILIP1L_uc010hpf.2_Missense_Mutation_p.V482A|FILIP1L_uc010hpg.2_Missense_Mutation_p.V666A|FILIP1L_uc003dtn.2_Missense_Mutation_p.V666A|FILIP1L_uc003dtp.1_Missense_Mutation_p.V666A	NM_182909	NP_878913	Q4L180	FIL1L_HUMAN	filamin A interacting protein 1-like isoform 1	906						cytoplasm|membrane|myosin complex|nucleus				ovary(1)	1																		---	---	---	---
LNP1	348801	broad.mit.edu	37	3	100170750	100170750	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:100170750T>C	uc003dtx.3	+	3	1624	c.344T>C	c.(343-345)TTT>TCT	p.F115S	LNP1_uc003dty.3_RNA|LNP1_uc011bhb.1_RNA	NM_001085451	NP_001078920	A1A4G5	LNP1_HUMAN	leukemia NUP98 fusion partner 1	115											0																		---	---	---	---
GPR128	84873	broad.mit.edu	37	3	100378603	100378603	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:100378603T>C	uc003duc.2	+	14	2163	c.1895T>C	c.(1894-1896)GTA>GCA	p.V632A	GPR128_uc011bhc.1_Missense_Mutation_p.V333A|GPR128_uc003dud.2_Missense_Mutation_p.V155A	NM_032787	NP_116176	Q96K78	GP128_HUMAN	G protein-coupled receptor 128 precursor	632	Helical; Name=5; (Potential).				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	100451347	100451347	+	Intron	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:100451347T>C	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								---	---	---	---
IMPG2	50939	broad.mit.edu	37	3	100964721	100964721	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:100964721T>C	uc003duq.1	-	12	1671	c.1468A>G	c.(1468-1470)ACC>GCC	p.T490A	IMPG2_uc011bhe.1_Missense_Mutation_p.T353A	NM_016247	NP_057331	Q9BZV3	IMPG2_HUMAN	interphotoreceptor matrix proteoglycan 2	490	Extracellular (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																		---	---	---	---
FAM55C	91775	broad.mit.edu	37	3	101540803	101540803	+	3'UTR	SNP	T	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:101540803T>G	uc003dvn.2	+	8					FAM55C_uc010hpn.2_3'UTR	NM_145037	NP_659474			hypothetical protein LOC91775 precursor							extracellular region				ovary(1)|pancreas(1)|skin(1)	3																		---	---	---	---
ZPLD1	131368	broad.mit.edu	37	3	102189310	102189310	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:102189310G>A	uc003dvs.1	+	16	1888	c.1006G>A	c.(1006-1008)GCG>ACG	p.A336T	ZPLD1_uc003dvt.1_Missense_Mutation_p.A352T|ZPLD1_uc011bhg.1_Missense_Mutation_p.A336T	NM_175056	NP_778226	Q8TCW7	ZPLD1_HUMAN	zona pellucida-like domain containing 1	336	Extracellular (Potential).					integral to membrane				ovary(2)|skin(2)|central_nervous_system(1)	5																		---	---	---	---
ALCAM	214	broad.mit.edu	37	3	105243334	105243334	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:105243334A>G	uc003dvx.2	+	3	916	c.376A>G	c.(376-378)ACA>GCA	p.T126A	ALCAM_uc003dvv.2_Missense_Mutation_p.T126A|ALCAM_uc003dvw.1_Missense_Mutation_p.T126A|ALCAM_uc003dvy.2_Missense_Mutation_p.T126A|ALCAM_uc011bhh.1_Missense_Mutation_p.T75A	NM_001627	NP_001618	Q13740	CD166_HUMAN	activated leukocyte cell adhesion molecule	126	Extracellular (Potential).|Ig-like V-type 2.				cell adhesion|signal transduction	integral to membrane	receptor binding			ovary(2)|breast(1)	3																		---	---	---	---
MYH15	22989	broad.mit.edu	37	3	108117611	108117611	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:108117611C>T	uc003dxa.1	-	36	5123	c.5066G>A	c.(5065-5067)CGC>CAC	p.R1689H		NM_014981	NP_055796	Q9Y2K3	MYH15_HUMAN	myosin, heavy polypeptide 15	1689	Potential.					myofibril|myosin filament	actin binding|ATP binding|calmodulin binding|motor activity			ovary(5)|central_nervous_system(2)	7																		---	---	---	---
KIAA1524	57650	broad.mit.edu	37	3	108271111	108271111	+	Silent	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:108271111T>C	uc003dxb.3	-	20	2786	c.2517A>G	c.(2515-2517)ACA>ACG	p.T839T		NM_020890	NP_065941	Q8TCG1	CIP2A_HUMAN	p90 autoantigen	839	Potential.					cytoplasm|integral to membrane	protein binding			ovary(2)|central_nervous_system(1)	3																		---	---	---	---
TMPRSS7	344805	broad.mit.edu	37	3	111782479	111782479	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:111782479G>A	uc010hqb.2	+	10	1347	c.1177G>A	c.(1177-1179)GTG>ATG	p.V393M	TMPRSS7_uc011bhr.1_Missense_Mutation_p.V248M	NM_001042575	NP_001036040	Q7RTY8	TMPS7_HUMAN	transmembrane protease, serine 7	519	LDL-receptor class A 1.|Extracellular (Potential).|LDL-receptor class A 2.				proteolysis	integral to membrane|plasma membrane	serine-type endopeptidase activity			ovary(1)|kidney(1)	2																		---	---	---	---
CCDC80	151887	broad.mit.edu	37	3	112358259	112358259	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:112358259C>T	uc003dzf.2	-	2	712	c.494G>A	c.(493-495)CGC>CAC	p.R165H	CCDC80_uc011bhv.1_Missense_Mutation_p.R165H|CCDC80_uc003dzg.2_Missense_Mutation_p.R165H|CCDC80_uc003dzh.1_Missense_Mutation_p.R165H	NM_199512	NP_955806	Q76M96	CCD80_HUMAN	steroid-sensitive protein 1 precursor	165										ovary(2)	2																		---	---	---	---
CD200R1L	344807	broad.mit.edu	37	3	112538718	112538718	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:112538718G>A	uc003dzi.1	-	5	930	c.704C>T	c.(703-705)GCG>GTG	p.A235V	CD200R1L_uc011bhw.1_Missense_Mutation_p.A214V|CD200R1L_uc010hqf.1_Missense_Mutation_p.A214V	NM_001008784	NP_001008784	Q6Q8B3	MO2R2_HUMAN	CD200 cell surface glycoprotein receptor 2	235	Extracellular (Potential).					integral to membrane	receptor activity			ovary(1)	1																		---	---	---	---
SIDT1	54847	broad.mit.edu	37	3	113329980	113329980	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:113329980G>A	uc003eak.2	+	18	2497	c.1846G>A	c.(1846-1848)GTC>ATC	p.V616I	SIDT1_uc011bif.1_RNA|SIDT1_uc003eaj.1_Missense_Mutation_p.V616I|SIDT1_uc011big.1_Missense_Mutation_p.V369I|SIDT1_uc011bih.1_RNA|SIDT1_uc011bii.1_Missense_Mutation_p.V69I	NM_017699	NP_060169	Q9NXL6	SIDT1_HUMAN	SID1 transmembrane family, member 1 precursor	616	Helical; (Potential).					integral to membrane				ovary(3)|pancreas(1)|skin(1)	5																		---	---	---	---
KIAA2018	205717	broad.mit.edu	37	3	113378594	113378594	+	Silent	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:113378594C>T	uc003eam.2	-	7	2346	c.1935G>A	c.(1933-1935)GCG>GCA	p.A645A	KIAA2018_uc003eal.2_Silent_p.A589A	NM_001009899	NP_001009899	Q68DE3	K2018_HUMAN	hypothetical protein LOC205717	645					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	113563488	113563488	+	Missense_Mutation	SNP	A	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:113563488A>T	uc003eaq.3	+	2	242	c.166A>T	c.(166-168)AGC>TGC	p.S56C	GRAMD1C_uc011bil.1_RNA|GRAMD1C_uc011bim.1_RNA	NM_017577	NP_060047	Q8IYS0	GRM1C_HUMAN	GRAM domain containing 1C	56						integral to membrane				ovary(2)|skin(1)	3																		---	---	---	---
IGSF11	152404	broad.mit.edu	37	3	118621497	118621497	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:118621497T>C	uc003ebw.2	-	7	1413	c.1166A>G	c.(1165-1167)AAT>AGT	p.N389S	IGSF11_uc011biv.1_Missense_Mutation_p.N361S|IGSF11_uc003ebx.2_Missense_Mutation_p.N365S|IGSF11_uc003eby.2_Missense_Mutation_p.N388S|IGSF11_uc003ebz.2_Missense_Mutation_p.N364S|IGSF11_uc010hqs.2_Missense_Mutation_p.N388S	NM_001015887	NP_001015887	Q5DX21	IGS11_HUMAN	immunoglobulin superfamily, member 11 isoform b	389	Cytoplasmic (Potential).				cell adhesion|regulation of growth	integral to membrane|plasma membrane	receptor activity				0																		---	---	---	---
C3orf15	89876	broad.mit.edu	37	3	119452209	119452209	+	Splice_Site	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:119452209A>G	uc003ede.3	+	10	1279	c.1202_splice	c.e10-2	p.G401_splice	C3orf15_uc010hqy.1_Splice_Site_p.G401_splice|C3orf15_uc010hqz.2_Splice_Site_p.G339_splice|C3orf15_uc011bjd.1_Splice_Site_p.G275_splice|C3orf15_uc011bje.1_Splice_Site_p.G381_splice|C3orf15_uc010hra.1_Splice_Site_p.G162_splice	NM_033364	NP_203528			AAT1-alpha							mitochondrion	protein binding			ovary(2)|pancreas(1)	3				GBM - Glioblastoma multiforme(114;0.186)														---	---	---	---
GTF2E1	2960	broad.mit.edu	37	3	120489647	120489647	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:120489647G>A	uc003edz.3	+	3	635	c.521G>A	c.(520-522)CGC>CAC	p.R174H		NM_005513	NP_005504	P29083	T2EA_HUMAN	general transcription factor IIE, polypeptide 1,	174					interspecies interaction between organisms|regulation of transcription, DNA-dependent|transcription elongation from RNA polymerase II promoter|transcription initiation from RNA polymerase II promoter|viral reproduction	nucleoplasm	protein binding|zinc ion binding	p.R174C(1)		ovary(1)	1				GBM - Glioblastoma multiforme(114;0.159)														---	---	---	---
STXBP5L	9515	broad.mit.edu	37	3	120941962	120941962	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:120941962A>G	uc003eec.3	+	11	1209	c.1069A>G	c.(1069-1071)ATT>GTT	p.I357V	STXBP5L_uc011bji.1_Missense_Mutation_p.I357V	NM_014980	NP_055795	Q9Y2K9	STB5L_HUMAN	syntaxin binding protein 5-like	357	WD 7.				exocytosis|protein transport	cytoplasm|integral to membrane|plasma membrane		p.I357I(1)		ovary(7)|skin(2)	9				GBM - Glioblastoma multiforme(114;0.0694)														---	---	---	---
POLQ	10721	broad.mit.edu	37	3	121206244	121206244	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:121206244C>T	uc003eee.3	-	16	5663	c.5534G>A	c.(5533-5535)CGG>CAG	p.R1845Q	POLQ_uc003eed.2_Missense_Mutation_p.R1017Q	NM_199420	NP_955452	O75417	DPOLQ_HUMAN	DNA polymerase theta	1845					DNA repair|DNA replication	nucleoplasm	ATP binding|ATP-dependent helicase activity|damaged DNA binding|DNA-directed DNA polymerase activity|single-stranded DNA-dependent ATPase activity			ovary(4)|breast(3)|lung(2)|upper_aerodigestive_tract(1)|skin(1)	11				GBM - Glioblastoma multiforme(114;0.0915)									DNA_polymerases_(catalytic_subunits)					---	---	---	---
ARGFX	503582	broad.mit.edu	37	3	121289638	121289638	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:121289638A>G	uc003eef.2	+	2	173	c.78A>G	c.(76-78)ATA>ATG	p.I26M		NM_001012659	NP_001012677	A6NJG6	ARGFX_HUMAN	arginine-fifty homeobox	26						nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			skin(2)|ovary(1)	3				GBM - Glioblastoma multiforme(114;0.152)														---	---	---	---
GOLGB1	2804	broad.mit.edu	37	3	121396151	121396151	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:121396151T>C	uc003eei.3	-	16	9131	c.9005A>G	c.(9004-9006)AAA>AGA	p.K3002R	GOLGB1_uc010hrc.2_Missense_Mutation_p.K3007R|GOLGB1_uc003eej.3_Missense_Mutation_p.K2968R	NM_004487	NP_004478	Q14789	GOGB1_HUMAN	golgi autoantigen, golgin subfamily b,	3002	Cytoplasmic (Potential).|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	121414055	121414055	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:121414055A>G	uc003eei.3	-	13	5426	c.5300T>C	c.(5299-5301)GTA>GCA	p.V1767A	GOLGB1_uc010hrc.2_Missense_Mutation_p.V1772A|GOLGB1_uc003eej.3_Missense_Mutation_p.V1733A|GOLGB1_uc011bjm.1_Missense_Mutation_p.V1653A|GOLGB1_uc010hrd.1_Missense_Mutation_p.V1731A	NM_004487	NP_004478	Q14789	GOGB1_HUMAN	golgi autoantigen, golgin subfamily b,	1767	Cytoplasmic (Potential).|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	121416218	121416218	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:121416218T>C	uc003eei.3	-	13	3263	c.3137A>G	c.(3136-3138)TAC>TGC	p.Y1046C	GOLGB1_uc010hrc.2_Missense_Mutation_p.Y1051C|GOLGB1_uc003eej.3_Missense_Mutation_p.Y1012C|GOLGB1_uc011bjm.1_Missense_Mutation_p.Y932C|GOLGB1_uc010hrd.1_Missense_Mutation_p.Y1010C	NM_004487	NP_004478	Q14789	GOGB1_HUMAN	golgi autoantigen, golgin subfamily b,	1046	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)														---	---	---	---
SLC15A2	6565	broad.mit.edu	37	3	121647285	121647285	+	Silent	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:121647285G>A	uc003eep.2	+	15	1377	c.1224G>A	c.(1222-1224)CAG>CAA	p.Q408Q	SLC15A2_uc011bjn.1_Silent_p.Q377Q	NM_021082	NP_066568	Q16348	S15A2_HUMAN	peptide transporter 2 isoform a	408					protein transport	integral to plasma membrane	peptide:hydrogen symporter activity|protein binding			skin(1)	1				GBM - Glioblastoma multiforme(114;0.0967)	Cefadroxil(DB01140)													---	---	---	---
SLC15A2	6565	broad.mit.edu	37	3	121647385	121647385	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:121647385T>C	uc003eep.2	+	15	1477	c.1324T>C	c.(1324-1326)TCC>CCC	p.S442P	SLC15A2_uc011bjn.1_Missense_Mutation_p.S411P	NM_021082	NP_066568	Q16348	S15A2_HUMAN	peptide transporter 2 isoform a	442					protein transport	integral to plasma membrane	peptide:hydrogen symporter activity|protein binding			skin(1)	1				GBM - Glioblastoma multiforme(114;0.0967)	Cefadroxil(DB01140)													---	---	---	---
CD86	942	broad.mit.edu	37	3	121825098	121825098	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:121825098T>C	uc003eet.2	+	4	570	c.454T>C	c.(454-456)TAC>CAC	p.Y152H	CD86_uc011bjo.1_Missense_Mutation_p.Y70H|CD86_uc011bjp.1_Missense_Mutation_p.Y40H|CD86_uc003eeu.2_Missense_Mutation_p.Y146H	NM_175862	NP_787058	P42081	CD86_HUMAN	CD86 antigen isoform 1	152	Ig-like C2-type.|Extracellular (Potential).				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	121973072	121973072	+	Silent	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:121973072A>G	uc003eev.3	+	2	408	c.36A>G	c.(34-36)GCA>GCG	p.A12A	CASR_uc003eew.3_Silent_p.A12A	NM_000388	NP_000379	P41180	CASR_HUMAN	calcium-sensing receptor precursor	12					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)													---	---	---	---
CASR	846	broad.mit.edu	37	3	121981025	121981025	+	Silent	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:121981025C>T	uc003eev.3	+	4	1515	c.1143C>T	c.(1141-1143)GGC>GGT	p.G381G	CASR_uc003eew.3_Silent_p.G381G	NM_000388	NP_000379	P41180	CASR_HUMAN	calcium-sensing receptor precursor	381	Extracellular (Potential).				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)													---	---	---	---
SEMA5B	54437	broad.mit.edu	37	3	122628986	122628986	+	3'UTR	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:122628986G>A	uc003efz.1	-	23					SEMA5B_uc011bju.1_3'UTR|SEMA5B_uc003ega.1_RNA|SEMA5B_uc003efy.1_3'UTR	NM_001031702	NP_001026872			semaphorin 5B isoform 1						cell differentiation|nervous system development	integral to membrane	receptor activity			ovary(2)|breast(2)|pancreas(2)|central_nervous_system(1)	7				GBM - Glioblastoma multiforme(114;0.0367)														---	---	---	---
SEC22A	26984	broad.mit.edu	37	3	122944071	122944071	+	Silent	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:122944071C>T	uc003ege.2	+	4	547	c.468C>T	c.(466-468)TGC>TGT	p.C156C	SEC22A_uc003egf.2_Silent_p.C156C	NM_012430	NP_036562	Q96IW7	SC22A_HUMAN	SEC22 vesicle trafficking protein homolog A	156	Cytoplasmic (Potential).				ER to Golgi vesicle-mediated transport|protein transport	endoplasmic reticulum membrane|integral to membrane	transporter activity			ovary(1)	1				GBM - Glioblastoma multiforme(114;0.0548)														---	---	---	---
ADCY5	111	broad.mit.edu	37	3	123047573	123047573	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:123047573G>A	uc003egh.1	-	6	1723	c.1723C>T	c.(1723-1725)CTT>TTT	p.L575F	ADCY5_uc003egg.1_Missense_Mutation_p.L208F|ADCY5_uc003egi.1_Missense_Mutation_p.L134F	NM_183357	NP_899200	O95622	ADCY5_HUMAN	adenylate cyclase 5	575	Guanylate cyclase 1.|Cytoplasmic (Potential).				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)												OREG0015742	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
MYLK	4638	broad.mit.edu	37	3	123458802	123458802	+	Silent	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:123458802T>C	uc003ego.2	-	6	702	c.420A>G	c.(418-420)TTA>TTG	p.L140L	MYLK_uc011bjw.1_Silent_p.L140L|MYLK_uc003egp.2_Silent_p.L140L|MYLK_uc003egq.2_Silent_p.L140L|MYLK_uc003egr.2_Silent_p.L140L|MYLK_uc003egs.2_5'UTR|MYLK_uc010hrs.1_Silent_p.L140L	NM_053025	NP_444253	Q15746	MYLK_HUMAN	myosin light chain kinase isoform 1	140					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)														---	---	---	---
CCDC14	64770	broad.mit.edu	37	3	123634155	123634155	+	Missense_Mutation	SNP	A	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:123634155A>T	uc011bjx.1	-	13	2424	c.2333T>A	c.(2332-2334)ATT>AAT	p.I778N	CCDC14_uc003egv.3_Missense_Mutation_p.I419N|CCDC14_uc003egx.3_Missense_Mutation_p.I578N|CCDC14_uc010hrt.2_Missense_Mutation_p.I737N|CCDC14_uc003egy.3_Missense_Mutation_p.I578N|CCDC14_uc003egz.2_Intron	NM_022757	NP_073594	Q49A88	CCD14_HUMAN	coiled-coil domain containing 14	778						centrosome					0		Lung NSC(201;0.0371)|Prostate(884;0.0405)|Myeloproliferative disorder(1037;0.205)		Lung(219;0.00942)|GBM - Glioblastoma multiforme(114;0.159)														---	---	---	---
KALRN	8997	broad.mit.edu	37	3	124352784	124352784	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:124352784C>A	uc003ehg.2	+	36	5676	c.5549C>A	c.(5548-5550)CCT>CAT	p.P1850H	KALRN_uc003ehi.2_Missense_Mutation_p.P223H|KALRN_uc003ehk.2_Missense_Mutation_p.P153H|KALRN_uc003ehj.2_Missense_Mutation_p.P153H	NM_001024660	NP_001019831	O60229	KALRN_HUMAN	kalirin, RhoGEF kinase isoform 1	1850					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	124438241	124438241	+	Missense_Mutation	SNP	G	A	A	rs144099513		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:124438241G>A	uc003ehg.2	+	60	9012	c.8885G>A	c.(8884-8886)CGC>CAC	p.R2962H	KALRN_uc003ehk.2_Missense_Mutation_p.R1265H	NM_001024660	NP_001019831	O60229	KALRN_HUMAN	kalirin, RhoGEF kinase isoform 1	2961					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	124485174	124485174	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:124485174G>A	uc003eho.2	-	13	2333	c.2036C>T	c.(2035-2037)GCT>GTT	p.A679V	ITGB5_uc010hrx.2_RNA	NM_002213	NP_002204	P18084	ITB5_HUMAN	integrin, beta 5 precursor	679	Extracellular (Potential).				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)														---	---	---	---
MUC13	56667	broad.mit.edu	37	3	124646412	124646412	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:124646412C>T	uc003ehq.1	-	2	502	c.478G>A	c.(478-480)GCT>ACT	p.A160T		NM_033049	NP_149038	Q9H3R2	MUC13_HUMAN	mucin 13, epithelial transmembrane	160	Thr-rich.|Extracellular (Potential).					extracellular region|integral to membrane|plasma membrane					0																		---	---	---	---
MUC13	56667	broad.mit.edu	37	3	124646492	124646492	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:124646492A>G	uc003ehq.1	-	2	422	c.398T>C	c.(397-399)GTT>GCT	p.V133A		NM_033049	NP_149038	Q9H3R2	MUC13_HUMAN	mucin 13, epithelial transmembrane	133	Thr-rich.|Extracellular (Potential).					extracellular region|integral to membrane|plasma membrane					0																		---	---	---	---
HEG1	57493	broad.mit.edu	37	3	124721136	124721136	+	Silent	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:124721136T>C	uc003ehs.3	-	10	3389	c.3321A>G	c.(3319-3321)TTA>TTG	p.L1107L	HEG1_uc003ehr.3_5'Flank|HEG1_uc011bke.1_Silent_p.L1207L	NM_020733	NP_065784	Q9ULI3	HEG1_HUMAN	HEG homolog 1 precursor	1107	Extracellular (Potential).					extracellular region|integral to membrane	calcium ion binding			ovary(2)	2																		---	---	---	---
SLC12A8	84561	broad.mit.edu	37	3	124837663	124837663	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:124837663C>T	uc003ehv.3	-	8	973	c.862G>A	c.(862-864)GCC>ACC	p.A288T	SLC12A8_uc003ehw.3_Missense_Mutation_p.A317T|SLC12A8_uc010hrz.1_Silent_p.A161A|SLC12A8_uc003eht.3_Missense_Mutation_p.A89T|SLC12A8_uc003ehu.3_Missense_Mutation_p.A41T|SLC12A8_uc010hry.2_Missense_Mutation_p.A41T	NM_024628	NP_078904	A0AV02	S12A8_HUMAN	solute carrier family 12, member 8	288	Helical; (Potential).				potassium ion transport	integral to membrane	symporter activity				0																		---	---	---	---
SLC41A3	54946	broad.mit.edu	37	3	125725854	125725854	+	Intron	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:125725854C>T	uc003eij.2	-						SLC41A3_uc003eii.2_3'UTR|SLC41A3_uc003eil.2_3'UTR|SLC41A3_uc003eik.2_Intron|SLC41A3_uc011bkh.1_3'UTR	NM_001008485	NP_001008485			solute carrier family 41, member 3 isoform 1							integral to membrane|plasma membrane	cation transmembrane transporter activity				0				GBM - Glioblastoma multiforme(114;0.167)														---	---	---	---
ALDH1L1	10840	broad.mit.edu	37	3	125877431	125877431	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:125877431C>T	uc003eim.1	-	3	369	c.179G>A	c.(178-180)CGT>CAT	p.R60H	ALDH1L1_uc010hse.1_RNA|ALDH1L1_uc011bki.1_Missense_Mutation_p.R60H|ALDH1L1_uc003eio.2_5'Flank|ALDH1L1_uc010hsf.1_Missense_Mutation_p.R86H|ALDH1L1_uc003eip.1_Translation_Start_Site|ALDH1L1_uc011bkj.1_Intron	NM_012190	NP_036322	O75891	AL1L1_HUMAN	aldehyde dehydrogenase 1 family, member L1	60	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)													---	---	---	---
UROC1	131669	broad.mit.edu	37	3	126219696	126219696	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:126219696C>A	uc003eiz.1	-	11	1019	c.987G>T	c.(985-987)TTG>TTT	p.L329F	UROC1_uc010hsi.1_Missense_Mutation_p.L389F	NM_144639	NP_653240	Q96N76	HUTU_HUMAN	urocanase domain containing 1 isoform 1	329					histidine catabolic process	cytosol	urocanate hydratase activity			ovary(1)	1				GBM - Glioblastoma multiforme(114;0.17)														---	---	---	---
SEC61A1	29927	broad.mit.edu	37	3	127786816	127786816	+	Intron	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:127786816C>T	uc003ekb.2	+						RUVBL1_uc003eke.2_Intron|RUVBL1_uc003ekf.2_Intron|SEC61A1_uc003ekc.2_Intron|SEC61A1_uc003ekd.2_Intron|SEC61A1_uc003ekg.2_Intron	NM_013336	NP_037468			Sec61 alpha 1 subunit						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																OREG0015775	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
KIAA1257	57501	broad.mit.edu	37	3	128696951	128696951	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:128696951A>G	uc003elj.3	-	5	941	c.745T>C	c.(745-747)TCG>CCG	p.S249P	KIAA1257_uc003elg.1_Missense_Mutation_p.S249P|KIAA1257_uc003eli.3_Missense_Mutation_p.S137P	NM_020741	NP_065792	Q9ULG3	K1257_HUMAN	hypothetical protein LOC57501	249											0																		---	---	---	---
RAB43	339122	broad.mit.edu	37	3	128813951	128813951	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:128813951C>T	uc003eln.1	-	2	553	c.266G>A	c.(265-267)CGC>CAC	p.R89H	RAB43_uc003elo.1_Missense_Mutation_p.A305T|RAB43_uc010hsy.1_Missense_Mutation_p.R89H	NM_198490	NP_940892	Q86YS6	RAB43_HUMAN	RAB43 protein	89					protein transport|small GTPase mediated signal transduction	plasma membrane	GTP binding			lung(1)	1																		---	---	---	---
ACPP	55	broad.mit.edu	37	3	132056328	132056328	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:132056328C>A	uc010htp.2	+	5	575	c.485C>A	c.(484-486)CCT>CAT	p.P162H	ACPP_uc003eon.3_Intron|ACPP_uc003eop.3_Missense_Mutation_p.P162H	NM_001099	NP_001090	P15309	PPAP_HUMAN	acid phosphatase, prostate short isoform	162						extracellular region|lysosomal membrane	5'-nucleotidase activity|acid phosphatase activity			ovary(1)	1																		---	---	---	---
DNAJC13	23317	broad.mit.edu	37	3	132203480	132203480	+	Silent	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:132203480G>A	uc003eor.2	+	29	3296	c.3231G>A	c.(3229-3231)CTG>CTA	p.L1077L		NM_015268	NP_056083	O75165	DJC13_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 13	1077							heat shock protein binding			ovary(1)|breast(1)	2																		---	---	---	---
DNAJC13	23317	broad.mit.edu	37	3	132213104	132213104	+	Splice_Site	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:132213104G>A	uc003eor.2	+	34	4006	c.3941_splice	c.e34+1	p.P1314_splice		NM_015268	NP_056083			DnaJ (Hsp40) homolog, subfamily C, member 13								heat shock protein binding			ovary(1)|breast(1)	2																		---	---	---	---
UBA5	79876	broad.mit.edu	37	3	132384847	132384847	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:132384847T>C	uc003epa.3	+	3	469	c.227T>C	c.(226-228)GTA>GCA	p.V76A	NPHP3_uc003eoz.1_Intron|UBA5_uc010htr.2_Missense_Mutation_p.V20A|UBA5_uc010htt.2_Missense_Mutation_p.V76A|UBA5_uc003epb.3_Missense_Mutation_p.V20A	NM_024818	NP_079094	Q9GZZ9	UBA5_HUMAN	ubiquitin-activating enzyme 5 isoform 1	76					protein ufmylation	aggresome|cytoplasm|cytoplasm|nucleus	ATP binding|cofactor binding|metal ion binding|oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor|protein binding|UFM1 activating enzyme activity			kidney(1)	1																		---	---	---	---
ANAPC13	25847	broad.mit.edu	37	3	134197508	134197508	+	Missense_Mutation	SNP	A	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:134197508A>T	uc003eqi.2	-	3	246	c.149T>A	c.(148-150)GTC>GAC	p.V50D	ANAPC13_uc003eqj.2_RNA|ANAPC13_uc003eqk.3_RNA	NM_015391	NP_056206	Q9BS18	APC13_HUMAN	anaphase promoting complex subunit 13	50					cell division|mitosis|protein K11-linked ubiquitination	anaphase-promoting complex				skin(1)	1																		---	---	---	---
KY	339855	broad.mit.edu	37	3	134337985	134337985	+	Intron	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:134337985C>T	uc010hty.2	-						KY_uc011blw.1_Intron|KY_uc011blx.1_Intron|KY_uc003eqr.1_Intron	NM_178554	NP_848649			kyphoscoliosis peptidase							cytoskeleton|Z disc	peptidase activity			ovary(2)	2																		---	---	---	---
STAG1	10274	broad.mit.edu	37	3	136323299	136323299	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:136323299G>T	uc003era.1	-	4	441	c.149C>A	c.(148-150)CCT>CAT	p.P50H	STAG1_uc003erb.1_Missense_Mutation_p.P50H|STAG1_uc003erc.1_5'UTR|STAG1_uc010hua.1_5'UTR|STAG1_uc003erd.2_5'UTR|STAG1_uc003ere.2_Missense_Mutation_p.P50H	NM_005862	NP_005853	Q8WVM7	STAG1_HUMAN	stromal antigen 1	50					cell division|chromosome segregation|mitotic metaphase/anaphase transition|mitotic prometaphase	cell junction|chromatin|chromosome, centromeric region|nucleoplasm	protein binding			ovary(2)	2																		---	---	---	---
A4GNT	51146	broad.mit.edu	37	3	137843567	137843567	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:137843567G>A	uc003ers.2	-	3	764	c.562C>T	c.(562-564)CGG>TGG	p.R188W		NM_016161	NP_057245	Q9UNA3	A4GCT_HUMAN	alpha-1,4-N-acetylglucosaminyltransferase	188	Lumenal (Potential).				protein O-linked glycosylation	Golgi membrane|Golgi stack|integral to membrane|membrane fraction	acetylglucosaminyltransferase activity|galactosyltransferase activity			central_nervous_system(1)	1																		---	---	---	---
DBR1	51163	broad.mit.edu	37	3	137885983	137885983	+	Silent	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:137885983T>C	uc003erv.2	-	5	790	c.654A>G	c.(652-654)AAA>AAG	p.K218K	DBR1_uc003eru.2_Silent_p.K167K|DBR1_uc003ert.2_5'Flank	NM_016216	NP_057300	Q9UK59	DBR1_HUMAN	debranching enzyme homolog 1	218						nucleus	metal ion binding|RNA lariat debranching enzyme activity				0																		---	---	---	---
PIK3CB	5291	broad.mit.edu	37	3	138461473	138461473	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:138461473G>A	uc011bmq.1	-	3	548	c.548C>T	c.(547-549)TCC>TTC	p.S183F		NM_006219	NP_006210	P42338	PK3CB_HUMAN	catalytic phosphatidylinositol 3-kinase beta	183	PI3K-RBD.				activation of MAPK activity|chemotaxis|fibroblast growth factor receptor signaling pathway|G-protein coupled receptor protein signaling pathway|insulin receptor signaling pathway|leukocyte migration|nerve growth factor receptor signaling pathway|phosphatidylinositol-mediated signaling|platelet activation|T cell receptor signaling pathway	phosphatidylinositol 3-kinase complex	1-phosphatidylinositol-3-kinase activity|ATP binding|phosphatidylinositol-4,5-bisphosphate 3-kinase activity			breast(2)|ovary(1)|lung(1)|skin(1)	5																		---	---	---	---
FOXL2	668	broad.mit.edu	37	3	138664449	138664449	+	Silent	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:138664449C>T	uc003esw.2	-	1	1534	c.1116G>A	c.(1114-1116)TCG>TCA	p.S372S	uc003esv.1_5'Flank|C3orf72_uc003esx.1_5'Flank|C3orf72_uc011bmr.1_5'Flank	NM_023067	NP_075555	P58012	FOXL2_HUMAN	forkhead box L2	372					convergent extension|DNA fragmentation involved in apoptotic nuclear change|embryonic eye morphogenesis|extraocular skeletal muscle development|female somatic sex determination|induction of apoptosis|menstruation|negative regulation of transcription, DNA-dependent|ovarian follicle development|pattern specification process|positive regulation of caspase activity|positive regulation of transcription from RNA polymerase II promoter|regulation of sequence-specific DNA binding transcription factor activity	transcription factor complex	caspase regulator activity|DNA bending activity|double-stranded DNA binding|estrogen receptor 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|ubiquitin conjugating enzyme binding			ovary(266)|large_intestine(1)|skin(1)	268								Mis		granulosa-cell tumour of the ovary		Blepharophimosis|ptosis and epicanthus inversus Types I|II; Premature ovarian failure type III						---	---	---	---
CLSTN2	64084	broad.mit.edu	37	3	140122666	140122666	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:140122666A>G	uc003etn.2	+	3	618	c.428A>G	c.(427-429)AAG>AGG	p.K143R	CLSTN2_uc003etm.2_Missense_Mutation_p.K143R	NM_022131	NP_071414	Q9H4D0	CSTN2_HUMAN	calsyntenin 2 precursor	143	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)			---	---	---	---
CLSTN2	64084	broad.mit.edu	37	3	140167389	140167389	+	Silent	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:140167389T>C	uc003etn.2	+	6	1006	c.816T>C	c.(814-816)CCT>CCC	p.P272P	CLSTN2_uc003etm.2_Silent_p.P272P	NM_022131	NP_071414	Q9H4D0	CSTN2_HUMAN	calsyntenin 2 precursor	272	Extracellular (Potential).|Cadherin 2.				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	140401892	140401892	+	Silent	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:140401892C>T	uc003eto.1	+	2	1121	c.930C>T	c.(928-930)TGC>TGT	p.C310C		NM_152616	NP_689829	Q8IWZ5	TRI42_HUMAN	tripartite motif-containing 42	310	B box-type 2.					intracellular	zinc ion binding			lung(2)|skin(2)|upper_aerodigestive_tract(1)|breast(1)|central_nervous_system(1)	7																		---	---	---	---
ZBTB38	253461	broad.mit.edu	37	3	141161756	141161756	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:141161756A>G	uc003etw.2	+	8	1508	c.526A>G	c.(526-528)AGT>GGT	p.S176G	ZBTB38_uc010hun.2_Missense_Mutation_p.S173G|ZBTB38_uc010huo.2_Missense_Mutation_p.S176G|ZBTB38_uc003ety.2_Missense_Mutation_p.S176G|ZBTB38_uc010hup.2_Missense_Mutation_p.S177G	NM_001080412	NP_001073881	Q8NAP3	ZBT38_HUMAN	zinc finger and BTB domain containing 38	176					positive regulation of transcription from RNA polymerase II promoter	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(3)	3																		---	---	---	---
ZBTB38	253461	broad.mit.edu	37	3	141163339	141163339	+	Silent	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:141163339C>T	uc003etw.2	+	8	3091	c.2109C>T	c.(2107-2109)GCC>GCT	p.A703A	ZBTB38_uc010hun.2_Silent_p.A700A|ZBTB38_uc010huo.2_Silent_p.A703A|ZBTB38_uc003ety.2_Silent_p.A703A|ZBTB38_uc010hup.2_Silent_p.A704A	NM_001080412	NP_001073881	Q8NAP3	ZBT38_HUMAN	zinc finger and BTB domain containing 38	703					positive regulation of transcription from RNA polymerase II promoter	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(3)	3																		---	---	---	---
RASA2	5922	broad.mit.edu	37	3	141291473	141291473	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:141291473G>A	uc003etz.1	+	12	1192	c.1192G>A	c.(1192-1194)GGA>AGA	p.G398R	RASA2_uc010huq.1_Missense_Mutation_p.G398R|RASA2_uc003eua.1_Missense_Mutation_p.G398R|RASA2_uc011bnc.1_5'UTR	NM_006506	NP_006497	Q15283	RASA2_HUMAN	RAS p21 protein activator 2	398	Ras-GAP.				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																		---	---	---	---
RASA2	5922	broad.mit.edu	37	3	141305516	141305516	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:141305516A>G	uc003etz.1	+	19	1855	c.1855A>G	c.(1855-1857)ACT>GCT	p.T619A	RASA2_uc010huq.1_Missense_Mutation_p.T619A|RASA2_uc003eua.1_Missense_Mutation_p.T619A|RASA2_uc011bnc.1_Missense_Mutation_p.T211A	NM_006506	NP_006497	Q15283	RASA2_HUMAN	RAS p21 protein activator 2	619	PH.				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																		---	---	---	---
GRK7	131890	broad.mit.edu	37	3	141497263	141497263	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:141497263C>T	uc011bnd.1	+	1	221	c.137C>T	c.(136-138)GCG>GTG	p.A46V		NM_139209	NP_631948	Q8WTQ7	GRK7_HUMAN	G-protein-coupled receptor kinase 7 precursor	46					visual perception	membrane	ATP binding|G-protein coupled receptor kinase activity|signal transducer activity			lung(2)|stomach(1)|ovary(1)|skin(1)	5																		---	---	---	---
TFDP2	7029	broad.mit.edu	37	3	141697420	141697420	+	Missense_Mutation	SNP	A	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:141697420A>T	uc003eun.3	-	7	840	c.461T>A	c.(460-462)GTC>GAC	p.V154D	TFDP2_uc003euk.3_Missense_Mutation_p.V67D|TFDP2_uc010hur.2_Missense_Mutation_p.V93D|TFDP2_uc003eul.3_Missense_Mutation_p.V93D|TFDP2_uc011bnf.1_Missense_Mutation_p.V57D|TFDP2_uc011bng.1_Missense_Mutation_p.V18D|TFDP2_uc003eum.3_Missense_Mutation_p.V93D	NM_006286	NP_006277	Q14188	TFDP2_HUMAN	transcription factor Dp-2 (E2F dimerization	154	Potential.				cell cycle	transcription factor complex	DNA binding|protein domain specific binding|sequence-specific DNA binding transcription factor activity|transcription cofactor activity|transcription factor binding			kidney(1)	1																		---	---	---	---
TRPC1	7220	broad.mit.edu	37	3	142510002	142510002	+	Splice_Site	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:142510002T>C	uc003evc.2	+	8	1573	c.1437_splice	c.e8+2	p.K479_splice	TRPC1_uc003evb.2_Splice_Site_p.K445_splice|TRPC1_uc011bni.1_Splice_Site_p.K46_splice	NM_003304	NP_003295			transient receptor potential cation channel,						axon guidance|cytosolic calcium ion homeostasis|positive regulation of release of sequestered calcium ion into cytosol|response to calcium ion	cytosol|integral to plasma membrane	protein binding|store-operated calcium channel activity			ovary(2)	2																		---	---	---	---
PCOLCE2	26577	broad.mit.edu	37	3	142606618	142606618	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:142606618G>A	uc003evd.2	-	2	281	c.85C>T	c.(85-87)CCT>TCT	p.P29S		NM_013363	NP_037495	Q9UKZ9	PCOC2_HUMAN	procollagen C-endopeptidase enhancer 2	29						extracellular region	collagen binding|heparin binding|peptidase activator activity			ovary(2)|skin(1)	3																		---	---	---	---
PAQR9	344838	broad.mit.edu	37	3	142681976	142681976	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:142681976C>T	uc003evg.2	-	1	203	c.203G>A	c.(202-204)TGC>TAC	p.C68Y	PAQR9_uc003evf.1_5'Flank	NM_198504	NP_940906	Q6ZVX9	PAQR9_HUMAN	progestin and adipoQ receptor family member IX	68	Cytoplasmic (Potential).					integral to membrane	receptor activity				0																		---	---	---	---
CHST2	9435	broad.mit.edu	37	3	142840114	142840114	+	Silent	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:142840114T>C	uc003evm.2	+	2	1345	c.456T>C	c.(454-456)AAT>AAC	p.N152N		NM_004267	NP_004258	Q9Y4C5	CHST2_HUMAN	carbohydrate (N-acetylglucosamine-6-O)	152	Lumenal (Potential).				inflammatory response|multicellular organismal development|N-acetylglucosamine metabolic process|sulfur compound metabolic process	integral to membrane|intrinsic to Golgi membrane|trans-Golgi network	N-acetylglucosamine 6-O-sulfotransferase activity			ovary(3)	3																		---	---	---	---
ZIC1	7545	broad.mit.edu	37	3	147130363	147130363	+	Silent	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:147130363C>T	uc003ewe.2	+	2	1760	c.1041C>T	c.(1039-1041)AGC>AGT	p.S347S		NM_003412	NP_003403	Q15915	ZIC1_HUMAN	zinc finger protein of the cerebellum 1	347	C2H2-type 4.				behavior|brain development|cell differentiation|inner ear morphogenesis|pattern specification process|positive regulation of protein import into nucleus|positive regulation of transcription, DNA-dependent|regulation of smoothened signaling pathway	cytoplasm|nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(1)|central_nervous_system(1)	2																		---	---	---	---
CP	1356	broad.mit.edu	37	3	148896196	148896196	+	Intron	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:148896196A>G	uc003ewy.3	-						CP_uc011bnr.1_Intron|CP_uc003eww.3_Intron|CP_uc003ewx.3_Intron|CP_uc003ewz.2_Intron	NM_000096	NP_000087			ceruloplasmin precursor						cellular iron ion homeostasis|copper ion transport|transmembrane transport	extracellular space	chaperone binding|ferroxidase activity			ovary(1)	1		Prostate(884;0.00217)|Hepatocellular(537;0.00826)|Myeloproliferative disorder(1037;0.0122)|all_neural(597;0.0189)|Melanoma(1037;0.152)	LUSC - Lung squamous cell carcinoma(72;0.0473)|Lung(72;0.0607)		Drotrecogin alfa(DB00055)													---	---	---	---
CP	1356	broad.mit.edu	37	3	148903188	148903188	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:148903188C>T	uc003ewy.3	-	12	2376	c.2123G>A	c.(2122-2124)GGC>GAC	p.G708D	CP_uc011bnr.1_RNA|CP_uc003ewx.3_Missense_Mutation_p.G489D|CP_uc003ewz.2_Missense_Mutation_p.G708D	NM_000096	NP_000087	P00450	CERU_HUMAN	ceruloplasmin precursor	708	Plastocyanin-like 4.|F5/8 type A 2.				cellular iron ion homeostasis|copper ion transport|transmembrane transport	extracellular space	chaperone binding|ferroxidase activity			ovary(1)	1		Prostate(884;0.00217)|Hepatocellular(537;0.00826)|Myeloproliferative disorder(1037;0.0122)|all_neural(597;0.0189)|Melanoma(1037;0.152)	LUSC - Lung squamous cell carcinoma(72;0.0473)|Lung(72;0.0607)		Drotrecogin alfa(DB00055)													---	---	---	---
CP	1356	broad.mit.edu	37	3	148919881	148919881	+	Intron	SNP	G	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:148919881G>T	uc003ewy.3	-						CP_uc011bnr.1_Intron|CP_uc003ewx.3_Intron|CP_uc003ewz.2_Intron|CP_uc010hvf.1_Intron	NM_000096	NP_000087			ceruloplasmin precursor						cellular iron ion homeostasis|copper ion transport|transmembrane transport	extracellular space	chaperone binding|ferroxidase activity			ovary(1)	1		Prostate(884;0.00217)|Hepatocellular(537;0.00826)|Myeloproliferative disorder(1037;0.0122)|all_neural(597;0.0189)|Melanoma(1037;0.152)	LUSC - Lung squamous cell carcinoma(72;0.0473)|Lung(72;0.0607)		Drotrecogin alfa(DB00055)													---	---	---	---
EIF2A	83939	broad.mit.edu	37	3	150289883	150289883	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:150289883G>A	uc003eya.2	+	10	966	c.950G>A	c.(949-951)CGT>CAT	p.R317H	SERP1_uc003exz.2_Intron|EIF2A_uc003eyb.2_Missense_Mutation_p.R190H|EIF2A_uc003eyc.2_Missense_Mutation_p.R190H|EIF2A_uc011bnv.1_Missense_Mutation_p.R292H|EIF2A_uc011bnw.1_Missense_Mutation_p.R256H|EIF2A_uc003eyd.2_Missense_Mutation_p.R92H|uc003eye.1_Intron	NM_032025	NP_114414	Q9BY44	EIF2A_HUMAN	eukaryotic translation initiation factor 2A	317					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)															---	---	---	---
MED12L	116931	broad.mit.edu	37	3	151095937	151095937	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:151095937A>G	uc003eyp.2	+	29	4387	c.4349A>G	c.(4348-4350)GAA>GGA	p.E1450G	MED12L_uc011bnz.1_Missense_Mutation_p.E1310G|P2RY12_uc011boa.1_Intron|P2RY12_uc003eyx.1_Intron|MED12L_uc003eyy.1_Missense_Mutation_p.E613G	NM_053002	NP_443728	Q86YW9	MD12L_HUMAN	mediator of RNA polymerase II transcription,	1450					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	151101590	151101590	+	Silent	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:151101590G>A	uc003eyp.2	+	32	4637	c.4599G>A	c.(4597-4599)GTG>GTA	p.V1533V	MED12L_uc011bnz.1_Silent_p.V1393V|P2RY12_uc011boa.1_Intron|P2RY12_uc003eyx.1_Intron|MED12L_uc003eyy.1_Silent_p.V696V	NM_053002	NP_443728	Q86YW9	MD12L_HUMAN	mediator of RNA polymerase II transcription,	1533					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	151154891	151154891	+	Silent	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:151154891A>G	uc011bod.1	-	6	7458	c.7458T>C	c.(7456-7458)CAT>CAC	p.H2486H	IGSF10_uc011bob.1_Silent_p.H513H|IGSF10_uc011boc.1_Silent_p.H465H	NM_178822	NP_849144	Q6WRI0	IGS10_HUMAN	immunoglobulin superfamily, member 10 precursor	2486	Ig-like C2-type 11.				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	151165887	151165887	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:151165887C>A	uc011bod.1	-	4	1882	c.1882G>T	c.(1882-1884)GGC>TGC	p.G628C		NM_178822	NP_849144	Q6WRI0	IGS10_HUMAN	immunoglobulin superfamily, member 10 precursor	628	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)															---	---	---	---
P2RY1	5028	broad.mit.edu	37	3	152554087	152554087	+	Silent	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:152554087C>T	uc003ezq.2	+	1	1352	c.516C>T	c.(514-516)AGC>AGT	p.S172S		NM_002563	NP_002554	P47900	P2RY1_HUMAN	purinergic receptor P2Y1	172	Helical; Name=4; (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)															---	---	---	---
DHX36	170506	broad.mit.edu	37	3	154021206	154021206	+	Intron	SNP	C	T	T	rs116333841	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:154021206C>T	uc003ezy.3	-						DHX36_uc010hvq.2_Intron|DHX36_uc003ezz.3_Intron	NM_020865	NP_065916			DEAH (Asp-Glu-Ala-His) box polypeptide 36							cytoplasm|nucleus	ATP binding|ATP-dependent helicase activity|nucleic acid binding|protein binding			skin(1)	1			LUSC - Lung squamous cell carcinoma(72;0.114)|Lung(72;0.173)															---	---	---	---
PLCH1	23007	broad.mit.edu	37	3	155222357	155222357	+	Missense_Mutation	SNP	A	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:155222357A>C	uc011bok.1	-	12	1932	c.1655T>G	c.(1654-1656)TTT>TGT	p.F552C	PLCH1_uc011boj.1_Missense_Mutation_p.F552C|PLCH1_uc011bol.1_Missense_Mutation_p.F534C	NM_001130960	NP_001124432	Q4KWH8	PLCH1_HUMAN	phospholipase C eta 1 isoform a	552					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	155222370	155222370	+	Missense_Mutation	SNP	G	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:155222370G>C	uc011bok.1	-	12	1919	c.1642C>G	c.(1642-1644)CTC>GTC	p.L548V	PLCH1_uc011boj.1_Missense_Mutation_p.L548V|PLCH1_uc011bol.1_Missense_Mutation_p.L530V	NM_001130960	NP_001124432	Q4KWH8	PLCH1_HUMAN	phospholipase C eta 1 isoform a	548					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)															---	---	---	---
GMPS	8833	broad.mit.edu	37	3	155628609	155628609	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:155628609G>A	uc003faq.2	+	6	990	c.655G>A	c.(655-657)GTG>ATG	p.V219M	GMPS_uc011bom.1_Missense_Mutation_p.V120M	NM_003875	NP_003866	P49915	GUAA_HUMAN	guanine monophosphate synthetase	219					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								---	---	---	---
SHOX2	6474	broad.mit.edu	37	3	157817706	157817706	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:157817706T>G	uc003fbr.2	-	4	784	c.645A>C	c.(643-645)GAA>GAC	p.E215D	SHOX2_uc003fbs.2_Missense_Mutation_p.E239D|SHOX2_uc010hvw.2_Missense_Mutation_p.E215D	NM_006884	NP_006875	O60902	SHOX2_HUMAN	short stature homeobox 2 isoform a	215					nervous system development	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity				0			Lung(72;0.00318)|LUSC - Lung squamous cell carcinoma(72;0.0043)															---	---	---	---
IFT80	57560	broad.mit.edu	37	3	159995363	159995363	+	Intron	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:159995363A>G	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)															---	---	---	---
KPNA4	3840	broad.mit.edu	37	3	160253484	160253484	+	Intron	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:160253484A>G	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)															---	---	---	---
B3GALNT1	8706	broad.mit.edu	37	3	160804389	160804389	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:160804389A>G	uc003fdv.2	-	5	573	c.154T>C	c.(154-156)TTC>CTC	p.F52L	B3GALNT1_uc003fdw.2_Missense_Mutation_p.F52L|B3GALNT1_uc003fdx.2_Missense_Mutation_p.F52L|B3GALNT1_uc003fdy.2_Missense_Mutation_p.F52L|B3GALNT1_uc003fdz.2_Missense_Mutation_p.F52L|B3GALNT1_uc003fea.2_Missense_Mutation_p.F52L|B3GALNT1_uc011bpa.1_Missense_Mutation_p.F52L	NM_033169	NP_149359	O75752	B3GL1_HUMAN	UDP-Gal:betaGlcNAc beta	52	Lumenal (Potential).				protein glycosylation	Golgi membrane|integral to membrane	galactosylgalactosylglucosylceramide beta-D-acetylgalactosaminyltransferase activity|UDP-galactose:beta-N-acetylglucosamine beta-1,3-galactosyltransferase activity			skin(1)	1			LUSC - Lung squamous cell carcinoma(72;4.41e-05)|Lung(72;4.61e-05)															---	---	---	---
NMD3	51068	broad.mit.edu	37	3	160952621	160952621	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:160952621C>T	uc003feb.1	+	6	583	c.464C>T	c.(463-465)GCT>GTT	p.A155V	NMD3_uc003fec.2_Missense_Mutation_p.A155V|NMD3_uc003fed.1_Missense_Mutation_p.A155V|NMD3_uc010hwh.2_5'Flank	NM_015938	NP_057022	Q96D46	NMD3_HUMAN	NMD3 homolog	155					protein transport	cytoplasm|nucleolus|nucleoplasm				ovary(1)	1			Lung(72;0.00111)|LUSC - Lung squamous cell carcinoma(72;0.00156)															---	---	---	---
SLITRK3	22865	broad.mit.edu	37	3	164908341	164908341	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:164908341T>C	uc003fej.3	-	2	722	c.278A>G	c.(277-279)TAT>TGT	p.Y93C	SLITRK3_uc003fek.2_Missense_Mutation_p.Y93C	NM_014926	NP_055741	O94933	SLIK3_HUMAN	slit and trk like 3 protein precursor	93	LRR 1.|Extracellular (Potential).					integral to membrane				ovary(6)|skin(3)|pancreas(1)	10															HNSCC(40;0.11)			---	---	---	---
ZBBX	79740	broad.mit.edu	37	3	167086373	167086373	+	Intron	SNP	A	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:167086373A>T	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																		---	---	---	---
WDR49	151790	broad.mit.edu	37	3	167319997	167319997	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:167319997A>G	uc003fev.1	-	3	476	c.170T>C	c.(169-171)GTC>GCC	p.V57A	WDR49_uc011bpd.1_Missense_Mutation_p.V110A|WDR49_uc003few.1_Missense_Mutation_p.V398A	NM_178824	NP_849146	Q8IV35	WDR49_HUMAN	WD repeat domain 49	57										large_intestine(1)|ovary(1)|skin(1)	3																		---	---	---	---
SERPINI1	5274	broad.mit.edu	37	3	167542333	167542333	+	Missense_Mutation	SNP	T	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:167542333T>A	uc003ffa.3	+	8	1337	c.1139T>A	c.(1138-1140)ATC>AAC	p.I380N	SERPINI1_uc003ffb.3_Missense_Mutation_p.I380N	NM_001122752	NP_001116224	Q99574	NEUS_HUMAN	neuroserpin precursor	380					central nervous system development|peripheral nervous system development|regulation of proteolysis	extracellular region	serine-type endopeptidase inhibitor activity			skin(1)	1																		---	---	---	---
MECOM	2122	broad.mit.edu	37	3	168834246	168834246	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:168834246C>T	uc003ffi.3	-	7	1119	c.850G>A	c.(850-852)GCC>ACC	p.A284T	MECOM_uc010hwk.1_Missense_Mutation_p.A307T|MECOM_uc003ffj.3_Missense_Mutation_p.A349T|MECOM_uc011bpi.1_Missense_Mutation_p.A285T|MECOM_uc003ffn.3_Missense_Mutation_p.A284T|MECOM_uc003ffk.2_Missense_Mutation_p.A284T|MECOM_uc003ffl.2_Missense_Mutation_p.A444T|MECOM_uc011bpj.1_Missense_Mutation_p.A472T|MECOM_uc011bpk.1_Missense_Mutation_p.A274T|MECOM_uc010hwn.2_Missense_Mutation_p.A472T	NM_005241	NP_005232	Q03112	EVI1_HUMAN	MDS1 and EVI1 complex locus isoform b	284					apoptosis|cell differentiation|hemopoietic stem cell proliferation|negative regulation of JNK cascade|negative regulation of programmed cell death|negative regulation of transcription, DNA-dependent|regulation of cell cycle	nuclear speck	DNA binding|protein binding|protein homodimerization activity|sequence-specific DNA binding transcription factor activity|zinc ion binding			lung(5)|skin(5)|upper_aerodigestive_tract(1)|central_nervous_system(1)|ovary(1)|pancreas(1)	14																		---	---	---	---
MYNN	55892	broad.mit.edu	37	3	169497126	169497126	+	Silent	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:169497126C>T	uc003fft.2	+	3	1266	c.837C>T	c.(835-837)AGC>AGT	p.S279S	MYNN_uc011bpm.1_Silent_p.S165S|MYNN_uc003ffu.2_Silent_p.S279S|MYNN_uc003ffv.2_Silent_p.S6S|MYNN_uc010hwo.2_Silent_p.S279S|MYNN_uc003ffw.1_RNA	NM_018657	NP_061127	Q9NPC7	MYNN_HUMAN	myoneurin	279						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)															---	---	---	---
LRRC31	79782	broad.mit.edu	37	3	169558031	169558031	+	Silent	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:169558031A>G	uc003fgc.1	-	9	1475	c.1398T>C	c.(1396-1398)TGT>TGC	p.C466C	LRRC31_uc010hwp.1_Silent_p.C410C	NM_024727	NP_079003	Q6UY01	LRC31_HUMAN	leucine rich repeat containing 31	466	LRR 9.									ovary(2)|skin(1)	3	all_cancers(22;2.76e-22)|all_epithelial(15;4.73e-27)|all_lung(20;9.24e-17)|Lung NSC(18;3.85e-16)|Ovarian(172;0.000223)|Breast(254;0.197)		Lung(28;2.71e-13)|STAD - Stomach adenocarcinoma(35;0.00943)															---	---	---	---
PHC3	80012	broad.mit.edu	37	3	169840404	169840404	+	Silent	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:169840404A>G	uc010hws.1	-	9	1945	c.1881T>C	c.(1879-1881)GAT>GAC	p.D627D	PHC3_uc003fgl.2_Silent_p.D639D|PHC3_uc011bpq.1_Silent_p.D586D	NM_024947	NP_079223	Q8NDX5	PHC3_HUMAN	polyhomeotic like 3	627	Pro-rich.				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)															---	---	---	---
SKIL	6498	broad.mit.edu	37	3	170099139	170099139	+	Intron	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:170099139T>C	uc003fgu.2	+						SKIL_uc011bps.1_Intron|SKIL_uc003fgv.2_Intron|SKIL_uc003fgw.2_Intron	NM_005414	NP_005405			SKI-like isoform 1						cell cycle arrest|negative regulation of cell differentiation|negative regulation of transcription from RNA polymerase II promoter|negative regulation of transforming growth factor beta receptor signaling pathway|positive regulation of axonogenesis|protein heterotrimerization|protein homotrimerization|regulation of apoptosis|regulation of apoptosis|response to antibiotic|response to growth factor stimulus|skeletal muscle tissue development	cytoplasm|PML body	chromatin binding|nucleotide binding|protein complex binding|protein domain specific binding|SMAD binding|transcription corepressor activity|transcription repressor activity			ovary(2)|skin(1)	3	all_cancers(22;7.13e-23)|all_epithelial(15;9.95e-28)|all_lung(20;1.23e-16)|Lung NSC(18;5.15e-16)|Ovarian(172;0.000337)|Breast(254;0.137)		Lung(28;2.71e-13)|STAD - Stomach adenocarcinoma(35;0.197)															---	---	---	---
SLC7A14	57709	broad.mit.edu	37	3	170204106	170204106	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:170204106T>C	uc003fgz.2	-	5	1127	c.811A>G	c.(811-813)ATC>GTC	p.I271V	CLDN11_uc011bpt.1_Intron|uc003fha.1_Intron	NM_020949	NP_066000	Q8TBB6	S7A14_HUMAN	solute carrier family 7 (cationic amino acid	271	Helical; (Potential).					integral to membrane	amino acid transmembrane transporter activity			ovary(2)|upper_aerodigestive_tract(1)|liver(1)|central_nervous_system(1)	5	all_cancers(22;2.41e-22)|all_epithelial(15;4.2e-27)|all_lung(20;1.17e-16)|Lung NSC(18;4.91e-16)|Ovarian(172;0.000902)|Breast(254;0.137)		Lung(28;6.23e-13)|LUSC - Lung squamous cell carcinoma(14;1.48e-12)															---	---	---	---
FNDC3B	64778	broad.mit.edu	37	3	172096128	172096128	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:172096128A>G	uc003fhy.2	+	24	3249	c.3077A>G	c.(3076-3078)TAC>TGC	p.Y1026C	FNDC3B_uc003fhz.3_Missense_Mutation_p.Y1026C	NM_022763	NP_073600	Q53EP0	FND3B_HUMAN	fibronectin type III domain containing 3B	1026	Fibronectin type-III 8.					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)														---	---	---	---
FNDC3B	64778	broad.mit.edu	37	3	172115031	172115031	+	Silent	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:172115031G>A	uc003fhy.2	+	26	3553	c.3381G>A	c.(3379-3381)GCG>GCA	p.A1127A	FNDC3B_uc003fhz.3_Silent_p.A1127A	NM_022763	NP_073600	Q53EP0	FND3B_HUMAN	fibronectin type III domain containing 3B	1127	Fibronectin type-III 9.					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)														---	---	---	---
FXR1	8087	broad.mit.edu	37	3	180669126	180669126	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:180669126T>C	uc003fkq.2	+	8	693	c.671T>C	c.(670-672)GTT>GCT	p.V224A	FXR1_uc003fkp.2_Missense_Mutation_p.V139A|FXR1_uc003fkr.2_Missense_Mutation_p.V224A|FXR1_uc011bqj.1_Missense_Mutation_p.V138A|FXR1_uc003fks.2_Missense_Mutation_p.V138A|FXR1_uc011bqk.1_Missense_Mutation_p.V175A|FXR1_uc011bql.1_Missense_Mutation_p.V211A	NM_005087	NP_005078	P51114	FXR1_HUMAN	fragile X mental retardation-related protein 1	224	KH 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)															---	---	---	---
SOX2	6657	broad.mit.edu	37	3	181430501	181430501	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:181430501C>T	uc003fkx.2	+	1	780	c.353C>T	c.(352-354)ACG>ATG	p.T118M	SOX2OT_uc003fkv.2_Intron|SOX2OT_uc003fkw.3_Intron	NM_003106	NP_003097	P48431	SOX2_HUMAN	sex-determining region Y-box 2	118					cell cycle arrest|chromatin organization|eye development|glial cell fate commitment|inner ear development|negative regulation of canonical Wnt receptor signaling pathway|negative regulation of epithelial cell proliferation|negative regulation of neuron differentiation|osteoblast differentiation|pituitary gland development|positive regulation of MAPKKK cascade|positive regulation of transcription from RNA polymerase II promoter|regulation of caspase activity|response to growth factor stimulus|response to wounding|somatic stem cell maintenance	cytosol|transcription factor complex	miRNA binding|protein binding|sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding				0	all_cancers(143;1.22e-16)|Ovarian(172;0.0283)		all cancers(12;1.82e-48)|Epithelial(37;9.85e-40)|OV - Ovarian serous cystadenocarcinoma(80;7.37e-23)|Lung(8;2.01e-21)|GBM - Glioblastoma multiforme(1;2.13e-08)					A		NSCLC|oesophageal squamous carcinoma		MICROPHTHALMIA AND ESOPHAGEAL ATRESIA SYNDROME						---	---	---	---
SOX2	6657	broad.mit.edu	37	3	181430809	181430809	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:181430809C>T	uc003fkx.2	+	1	1088	c.661C>T	c.(661-663)CCC>TCC	p.P221S	SOX2OT_uc003fkv.2_Intron|SOX2OT_uc003fkw.3_Intron	NM_003106	NP_003097	P48431	SOX2_HUMAN	sex-determining region Y-box 2	221					cell cycle arrest|chromatin organization|eye development|glial cell fate commitment|inner ear development|negative regulation of canonical Wnt receptor signaling pathway|negative regulation of epithelial cell proliferation|negative regulation of neuron differentiation|osteoblast differentiation|pituitary gland development|positive regulation of MAPKKK cascade|positive regulation of transcription from RNA polymerase II promoter|regulation of caspase activity|response to growth factor stimulus|response to wounding|somatic stem cell maintenance	cytosol|transcription factor complex	miRNA binding|protein binding|sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding				0	all_cancers(143;1.22e-16)|Ovarian(172;0.0283)		all cancers(12;1.82e-48)|Epithelial(37;9.85e-40)|OV - Ovarian serous cystadenocarcinoma(80;7.37e-23)|Lung(8;2.01e-21)|GBM - Glioblastoma multiforme(1;2.13e-08)					A		NSCLC|oesophageal squamous carcinoma		MICROPHTHALMIA AND ESOPHAGEAL ATRESIA SYNDROME						---	---	---	---
DCUN1D1	54165	broad.mit.edu	37	3	182681793	182681793	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:182681793A>G	uc003fld.1	-	3	314	c.265T>C	c.(265-267)TTC>CTC	p.F89L	DCUN1D1_uc011bqn.1_5'UTR	NM_020640	NP_065691	Q96GG9	DCNL1_HUMAN	RP42 homolog	89	DCUN1.					ubiquitin ligase complex	protein binding			ovary(1)	1	all_cancers(143;9.04e-15)|Ovarian(172;0.0355)		all cancers(12;2.54e-44)|Epithelial(37;4.71e-38)|LUSC - Lung squamous cell carcinoma(7;5.04e-25)|Lung(8;5.03e-23)|OV - Ovarian serous cystadenocarcinoma(80;7.41e-21)															---	---	---	---
MCF2L2	23101	broad.mit.edu	37	3	183028817	183028817	+	Missense_Mutation	SNP	C	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:183028817C>G	uc003fli.1	-	9	969	c.879G>C	c.(877-879)AGG>AGC	p.R293S	MCF2L2_uc003flj.1_Missense_Mutation_p.R293S|MCF2L2_uc003flp.1_Missense_Mutation_p.R328S|MCF2L2_uc011bqs.1_RNA	NM_015078	NP_055893	Q86YR7	MF2L2_HUMAN	Rho family guanine-nucleotide exchange factor	293					regulation of Rho protein signal transduction	intracellular	Rho guanyl-nucleotide exchange factor activity			ovary(2)|large_intestine(2)|breast(1)	5	all_cancers(143;1.26e-12)|Ovarian(172;0.0355)		all cancers(12;3.35e-44)|Epithelial(37;6.48e-38)|LUSC - Lung squamous cell carcinoma(7;7.12e-25)|Lung(8;6.39e-23)|OV - Ovarian serous cystadenocarcinoma(80;6.75e-21)															---	---	---	---
KLHL24	54800	broad.mit.edu	37	3	183390163	183390163	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:183390163T>C	uc003flv.2	+	7	1788	c.1493T>C	c.(1492-1494)GTA>GCA	p.V498A	KLHL24_uc003flw.2_Missense_Mutation_p.V498A|KLHL24_uc003flx.2_Missense_Mutation_p.V498A	NM_017644	NP_060114	Q6TFL4	KLH24_HUMAN	DRE1 protein	498	Kelch 4.					axon|cytoplasm|perikaryon				ovary(1)	1	all_cancers(143;2.88e-10)|Ovarian(172;0.0303)		all cancers(12;1.43e-42)|Epithelial(37;1.73e-36)|OV - Ovarian serous cystadenocarcinoma(80;8.75e-22)															---	---	---	---
YEATS2	55689	broad.mit.edu	37	3	183436325	183436325	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:183436325G>A	uc003fly.2	+	4	431	c.236G>A	c.(235-237)CGT>CAT	p.R79H		NM_018023	NP_060493	Q9ULM3	YETS2_HUMAN	YEATS domain containing 2	79	Potential.				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)															---	---	---	---
ABCC5	10057	broad.mit.edu	37	3	183639180	183639180	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:183639180A>G	uc003fmg.2	-	30	4387	c.4222T>C	c.(4222-4224)TTT>CTT	p.F1408L	ABCC5_uc011bqt.1_Missense_Mutation_p.F936L|ABCC5_uc010hxl.2_Missense_Mutation_p.F1365L	NM_005688	NP_005679	O15440	MRP5_HUMAN	ATP-binding cassette, sub-family C, member 5	1408	ABC transporter 2.					integral to plasma membrane|membrane fraction	ATP binding|ATPase activity, coupled to transmembrane movement of substances|organic anion transmembrane transporter activity			ovary(2)|large_intestine(1)|central_nervous_system(1)	4	all_cancers(143;1.85e-10)|Ovarian(172;0.0303)		Epithelial(37;1.74e-35)|OV - Ovarian serous cystadenocarcinoma(80;6.48e-22)															---	---	---	---
ABCC5	10057	broad.mit.edu	37	3	183705709	183705709	+	Intron	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:183705709A>G	uc003fmg.2	-						ABCC5_uc011bqt.1_Intron|ABCC5_uc010hxl.2_Intron|ABCC5_uc003fmh.2_Intron|ABCC5_uc010hxm.2_Intron|ABCC5_uc010hxn.2_Intron|ABCC5_uc010hxo.2_Intron	NM_005688	NP_005679			ATP-binding cassette, sub-family C, member 5							integral to plasma membrane|membrane fraction	ATP binding|ATPase activity, coupled to transmembrane movement of substances|organic anion transmembrane transporter activity			ovary(2)|large_intestine(1)|central_nervous_system(1)	4	all_cancers(143;1.85e-10)|Ovarian(172;0.0303)		Epithelial(37;1.74e-35)|OV - Ovarian serous cystadenocarcinoma(80;6.48e-22)															---	---	---	---
HTR3E	285242	broad.mit.edu	37	3	183824455	183824455	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:183824455A>G	uc010hxq.2	+	9	1811	c.1345A>G	c.(1345-1347)ACC>GCC	p.T449A	HTR3E_uc003fml.3_Missense_Mutation_p.T434A|HTR3E_uc003fmm.2_Missense_Mutation_p.T464A|HTR3E_uc010hxr.2_Missense_Mutation_p.T475A|HTR3E_uc003fmn.2_Missense_Mutation_p.T449A	NM_182589	NP_872395	A5X5Y0	5HT3E_HUMAN	5-hydroxytryptamine receptor 3 subunit E	449	Helical; Name=4; (Potential).					integral to membrane|plasma membrane|postsynaptic membrane	extracellular ligand-gated ion channel activity|receptor activity			ovary(1)|central_nervous_system(1)|skin(1)	3	all_cancers(143;1.46e-10)|Ovarian(172;0.0303)		Epithelial(37;7.06e-36)|OV - Ovarian serous cystadenocarcinoma(80;3.11e-22)															---	---	---	---
EIF2B5	8893	broad.mit.edu	37	3	183855771	183855771	+	Missense_Mutation	SNP	G	A	A	rs2971410		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:183855771G>A	uc003fmp.2	+	4	956	c.592G>A	c.(592-594)GAA>AAA	p.E198K	EIF2B5_uc003fmq.2_5'UTR	NM_003907	NP_003898	Q13144	EI2BE_HUMAN	eukaryotic translation initiation factor 2B,	198					astrocyte development|myelination|negative regulation of translational initiation in response to stress|oligodendrocyte development|ovarian follicle development|positive regulation of translational initiation|response to glucose stimulus|response to heat|response to peptide hormone stimulus|RNA metabolic process	cytosol|eukaryotic translation initiation factor 2B complex|nucleus	guanyl-nucleotide exchange factor activity|transferase activity|translation initiation factor activity|translation initiation factor binding			ovary(5)	5	all_cancers(143;7.59e-11)|Ovarian(172;0.0303)		Epithelial(37;7.06e-36)|OV - Ovarian serous cystadenocarcinoma(80;3.11e-22)															---	---	---	---
EIF2B5	8893	broad.mit.edu	37	3	183858478	183858478	+	Silent	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:183858478C>T	uc003fmp.2	+	7	1480	c.1116C>T	c.(1114-1116)TGC>TGT	p.C372C	EIF2B5_uc003fmq.2_Silent_p.C93C|EIF2B5_uc003fmr.2_5'Flank	NM_003907	NP_003898	Q13144	EI2BE_HUMAN	eukaryotic translation initiation factor 2B,	372					astrocyte development|myelination|negative regulation of translational initiation in response to stress|oligodendrocyte development|ovarian follicle development|positive regulation of translational initiation|response to glucose stimulus|response to heat|response to peptide hormone stimulus|RNA metabolic process	cytosol|eukaryotic translation initiation factor 2B complex|nucleus	guanyl-nucleotide exchange factor activity|transferase activity|translation initiation factor activity|translation initiation factor binding			ovary(5)	5	all_cancers(143;7.59e-11)|Ovarian(172;0.0303)		Epithelial(37;7.06e-36)|OV - Ovarian serous cystadenocarcinoma(80;3.11e-22)															---	---	---	---
ABCF3	55324	broad.mit.edu	37	3	183904349	183904349	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:183904349C>T	uc003fmz.2	+	2	261	c.128C>T	c.(127-129)GCT>GTT	p.A43V	ABCF3_uc003fna.2_Missense_Mutation_p.A43V|ABCF3_uc003fnb.2_5'Flank	NM_018358	NP_060828	Q9NUQ8	ABCF3_HUMAN	ATP-binding cassette, sub-family F (GCN20),	43							ATP binding|ATPase activity			ovary(3)|lung(1)	4	all_cancers(143;1.12e-10)|Ovarian(172;0.0339)		Epithelial(37;2.35e-34)|OV - Ovarian serous cystadenocarcinoma(80;2.72e-22)															---	---	---	---
ALG3	10195	broad.mit.edu	37	3	183960697	183960697	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:183960697C>T	uc003fne.2	-	8	1089	c.1058G>A	c.(1057-1059)AGC>AAC	p.S353N	ALG3_uc011brc.1_Missense_Mutation_p.S318N|ALG3_uc011brd.1_Missense_Mutation_p.S297N|ALG3_uc011bre.1_Missense_Mutation_p.S305N	NM_005787	NP_005778	Q92685	ALG3_HUMAN	alpha-1,3-mannosyltransferase ALG3 isoform a	353					dolichol-linked oligosaccharide biosynthetic process|post-translational protein modification|protein N-linked glycosylation via asparagine	endoplasmic reticulum membrane|integral to membrane	alpha-1,3-mannosyltransferase activity				0	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	184008902	184008902	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:184008902A>G	uc003fni.3	+	17	2301	c.2263A>G	c.(2263-2265)ACG>GCG	p.T755A	ECE2_uc011brh.1_Missense_Mutation_p.T608A|ECE2_uc003fnl.3_Missense_Mutation_p.T683A|ECE2_uc003fnm.3_Missense_Mutation_p.T637A|ECE2_uc003fnk.3_Missense_Mutation_p.T608A|ECE2_uc011bri.1_Missense_Mutation_p.T670A|ECE2_uc010hxv.2_3'UTR	NM_014693	NP_055508	O60344	ECE2_HUMAN	endothelin converting enzyme 2 isoform A	755	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)															---	---	---	---
EIF4G1	1981	broad.mit.edu	37	3	184039839	184039839	+	Silent	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:184039839C>T	uc003fnp.2	+	10	1665	c.1467C>T	c.(1465-1467)ACC>ACT	p.T489T	EIF4G1_uc003fno.1_Silent_p.T430T|EIF4G1_uc010hxw.1_Silent_p.T325T|EIF4G1_uc003fnt.2_Silent_p.T200T|EIF4G1_uc003fnq.2_Silent_p.T402T|EIF4G1_uc003fnr.2_Silent_p.T325T|EIF4G1_uc010hxx.2_Silent_p.T496T|EIF4G1_uc003fns.2_Silent_p.T449T|EIF4G1_uc010hxy.2_Silent_p.T496T|EIF4G1_uc003fnv.3_Silent_p.T489T|EIF4G1_uc003fnu.3_Silent_p.T489T|EIF4G1_uc003fnw.2_Silent_p.T496T|EIF4G1_uc003fnx.2_Silent_p.T293T|EIF4G1_uc003fny.3_Silent_p.T293T	NM_198241	NP_937884	Q04637	IF4G1_HUMAN	eukaryotic translation initiation factor 4	489					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)															---	---	---	---
EIF4G1	1981	broad.mit.edu	37	3	184041645	184041645	+	Silent	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:184041645G>A	uc003fnp.2	+	16	2550	c.2352G>A	c.(2350-2352)ACG>ACA	p.T784T	EIF4G1_uc003fno.1_Silent_p.T725T|EIF4G1_uc010hxw.1_Silent_p.T620T|EIF4G1_uc003fnt.2_Silent_p.T495T|EIF4G1_uc003fnq.2_Silent_p.T697T|EIF4G1_uc003fnr.2_Silent_p.T620T|EIF4G1_uc010hxx.2_Silent_p.T791T|EIF4G1_uc003fns.2_Silent_p.T744T|EIF4G1_uc010hxy.2_Silent_p.T791T|EIF4G1_uc003fnv.3_Silent_p.T785T|EIF4G1_uc003fnu.3_Silent_p.T784T|EIF4G1_uc003fnw.2_Silent_p.T791T|EIF4G1_uc003fnx.2_Silent_p.T589T|EIF4G1_uc003fny.3_Silent_p.T588T|SNORD66_uc003fnz.2_5'Flank	NM_198241	NP_937884	Q04637	IF4G1_HUMAN	eukaryotic translation initiation factor 4	784	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)															---	---	---	---
EIF4G1	1981	broad.mit.edu	37	3	184049131	184049131	+	Silent	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:184049131T>C	uc003fnp.2	+	29	4437	c.4239T>C	c.(4237-4239)ATT>ATC	p.I1413I	EIF4G1_uc003fnt.2_Silent_p.I1124I|EIF4G1_uc003fnq.2_Silent_p.I1326I|EIF4G1_uc003fnr.2_Silent_p.I1249I|EIF4G1_uc010hxx.2_Silent_p.I1420I|EIF4G1_uc003fns.2_Silent_p.I1373I|EIF4G1_uc010hxy.2_Silent_p.I1420I|EIF4G1_uc003fnv.3_Silent_p.I1414I|EIF4G1_uc003fnu.3_Silent_p.I1413I|EIF4G1_uc003fnw.2_Silent_p.I1420I|EIF4G1_uc003fnx.2_Silent_p.I1218I|EIF4G1_uc003fny.3_Silent_p.I1217I|EIF4G1_uc003foa.2_Silent_p.I85I	NM_198241	NP_937884	Q04637	IF4G1_HUMAN	eukaryotic translation initiation factor 4	1413					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)															---	---	---	---
MAP3K13	9175	broad.mit.edu	37	3	185183594	185183594	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:185183594A>G	uc010hyf.2	+	10	1714	c.1448A>G	c.(1447-1449)TAC>TGC	p.Y483C	MAP3K13_uc011brt.1_Missense_Mutation_p.Y276C|MAP3K13_uc011bru.1_Missense_Mutation_p.Y339C|MAP3K13_uc003fpi.2_Missense_Mutation_p.Y483C|MAP3K13_uc010hyg.2_Missense_Mutation_p.Y173C	NM_004721	NP_004712	O43283	M3K13_HUMAN	mitogen-activated protein kinase kinase kinase	483					activation of MAPKK activity|JNK cascade|positive regulation of NF-kappaB transcription factor activity|protein autophosphorylation	cytoplasm|membrane|membrane fraction	ATP binding|magnesium ion binding|MAP kinase kinase kinase activity|protein homodimerization activity|protein kinase binding			ovary(2)|skin(1)	3	all_cancers(143;7.21e-11)|Ovarian(172;0.0339)		OV - Ovarian serous cystadenocarcinoma(80;1.93e-20)															---	---	---	---
ETV5	2119	broad.mit.edu	37	3	185774899	185774899	+	Nonsense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:185774899G>A	uc003fpz.2	-	11	1421	c.1174C>T	c.(1174-1176)CGA>TGA	p.R392*	ETV5_uc003fpy.2_Nonsense_Mutation_p.R434*	NM_004454	NP_004445	P41161	ETV5_HUMAN	ets variant gene 5 (ets-related molecule)	392	ETS.				cellular response to oxidative stress	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding			ovary(2)|skin(2)|breast(1)	5	all_cancers(143;4.06e-12)|Ovarian(172;0.0386)|Breast(254;0.247)		OV - Ovarian serous cystadenocarcinoma(80;1.62e-24)					T	TMPRSS2|SCL45A3	Prostate 								---	---	---	---
RTP1	132112	broad.mit.edu	37	3	186917726	186917726	+	Silent	SNP	G	A	A	rs145720156		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:186917726G>A	uc003frg.2	+	2	690	c.660G>A	c.(658-660)GCG>GCA	p.A220A		NM_153708	NP_714919	P59025	RTP1_HUMAN	receptor transporting protein 1	220	Cytoplasmic (Potential).				protein insertion into membrane	cell surface|integral to membrane|plasma membrane	olfactory receptor binding	p.A220V(1)		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)														---	---	---	---
TP63	8626	broad.mit.edu	37	3	189608624	189608624	+	Missense_Mutation	SNP	A	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:189608624A>T	uc003fry.2	+	13	1788	c.1699A>T	c.(1699-1701)ACC>TCC	p.T567S	TP63_uc003frz.2_Intron|TP63_uc010hzc.1_Intron|TP63_uc003fsc.2_Missense_Mutation_p.T473S|TP63_uc003fsd.2_Intron|TP63_uc010hzd.1_Missense_Mutation_p.T388S	NM_003722	NP_003713	Q9H3D4	P63_HUMAN	tumor protein p63 isoform 1	567	SAM.				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)			---	---	---	---
LEPREL1	55214	broad.mit.edu	37	3	189713108	189713108	+	Missense_Mutation	SNP	A	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:189713108A>T	uc011bsk.1	-	2	992	c.604T>A	c.(604-606)TTG>ATG	p.L202M	LEPREL1_uc003fsg.2_Missense_Mutation_p.L21M	NM_018192	NP_060662	Q8IVL5	P3H2_HUMAN	leprecan-like 1 isoform a	202					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)													---	---	---	---
OSTN	344901	broad.mit.edu	37	3	190936652	190936652	+	Silent	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:190936652T>C	uc011bsn.1	+	2	219	c.219T>C	c.(217-219)AAT>AAC	p.N73N		NM_198184	NP_937827	P61366	OSTN_HUMAN	osteocrin precursor	73					cell differentiation|multicellular organismal development|ossification		hormone activity			pancreas(1)|skin(1)	2	all_cancers(143;6.79e-09)|Ovarian(172;0.103)		LUSC - Lung squamous cell carcinoma(58;2.42e-06)|Lung(62;2.86e-06)	GBM - Glioblastoma multiforme(46;0.000254)														---	---	---	---
C3orf59	151963	broad.mit.edu	37	3	192516171	192516171	+	3'UTR	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:192516171A>G	uc011bsp.1	-	2						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)														---	---	---	---
C3orf59	151963	broad.mit.edu	37	3	192517067	192517067	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:192517067A>G	uc011bsp.1	-	2	905	c.584T>C	c.(583-585)GTC>GCC	p.V195A		NM_178496	NP_848591	Q8IYB1	M21D2_HUMAN	hypothetical protein LOC151963	195											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)														---	---	---	---
FAM43A	131583	broad.mit.edu	37	3	194407803	194407803	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:194407803C>T	uc003fuj.2	+	1	1182	c.248C>T	c.(247-249)GCG>GTG	p.A83V		NM_153690	NP_710157	Q8N2R8	FA43A_HUMAN	hypothetical protein LOC131583	83										central_nervous_system(1)	1	all_cancers(143;2.04e-08)|Ovarian(172;0.0634)	Lung NSC(153;0.147)	OV - Ovarian serous cystadenocarcinoma(49;8.37e-18)|LUSC - Lung squamous cell carcinoma(58;3.55e-06)|Lung(62;4.19e-06)	GBM - Glioblastoma multiforme(46;1.78e-05)														---	---	---	---
ACAP2	23527	broad.mit.edu	37	3	195012470	195012470	+	Silent	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:195012470T>C	uc003fun.3	-	20	2269	c.2028A>G	c.(2026-2028)GGA>GGG	p.G676G		NM_012287	NP_036419	Q15057	ACAP2_HUMAN	centaurin, beta 2	676	ANK 2.				regulation of ARF GTPase activity		ARF GTPase activator activity|zinc ion binding			large_intestine(1)|ovary(1)	2																		---	---	---	---
TFRC	7037	broad.mit.edu	37	3	195782099	195782099	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:195782099T>C	uc003fvz.3	-	17	2034	c.1751A>G	c.(1750-1752)AAC>AGC	p.N584S	TFRC_uc003fwa.3_Missense_Mutation_p.N584S|TFRC_uc010hzy.2_Missense_Mutation_p.N503S|TFRC_uc011btr.1_Missense_Mutation_p.N302S	NM_003234	NP_003225	P02786	TFR1_HUMAN	transferrin receptor	584	Extracellular (Potential).|Ligand-binding.				cellular iron ion homeostasis|endocytosis|interspecies interaction between organisms|proteolysis|transferrin transport|transmembrane transport	coated pit|endosome|integral to plasma membrane|melanosome	peptidase activity|transferrin receptor activity			ovary(3)	3	all_cancers(143;1.94e-08)|Ovarian(172;0.0634)|Breast(254;0.206)		Epithelial(36;1.36e-24)|all cancers(36;3.34e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.17e-18)|LUSC - Lung squamous cell carcinoma(58;1.51e-06)|Lung(62;1.95e-06)	GBM - Glioblastoma multiforme(46;0.00233)				T	BCL6	NHL								---	---	---	---
UBXN7	26043	broad.mit.edu	37	3	196089236	196089236	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:196089236G>T	uc003fwm.3	-	9	1232	c.1157C>A	c.(1156-1158)GCT>GAT	p.A386D	UBXN7_uc003fwn.3_Missense_Mutation_p.A238D|UBXN7_uc010iae.2_Missense_Mutation_p.A224D	NM_015562	NP_056377	O94888	UBXN7_HUMAN	UBX domain containing 7	386							protein binding			ovary(2)|pancreas(1)	3																		---	---	---	---
BDH1	622	broad.mit.edu	37	3	197239231	197239231	+	Silent	SNP	G	A	A	rs143508627	byFrequency	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:197239231G>A	uc003fxr.2	-	8	969	c.567C>T	c.(565-567)CGC>CGT	p.R189R	BDH1_uc003fxs.2_Silent_p.R189R|BDH1_uc003fxt.2_Silent_p.R102R|BDH1_uc003fxu.2_Silent_p.R189R	NM_203314	NP_976059	Q02338	BDH_HUMAN	3-hydroxybutyrate dehydrogenase, type 1	189					cellular lipid metabolic process|ketone body biosynthetic process|ketone body catabolic process	mitochondrial matrix	3-hydroxybutyrate dehydrogenase activity			ovary(1)	1	all_cancers(143;3.35e-10)|Ovarian(172;0.0418)|Breast(254;0.0437)	Lung NSC(153;0.118)	Epithelial(36;3.52e-24)|all cancers(36;1.79e-22)|OV - Ovarian serous cystadenocarcinoma(49;2.32e-19)|LUSC - Lung squamous cell carcinoma(58;1.02e-06)|Lung(62;1.34e-06)	GBM - Glioblastoma multiforme(93;0.0977)	NADH(DB00157)													---	---	---	---
LRCH3	84859	broad.mit.edu	37	3	197544087	197544087	+	Silent	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:197544087T>C	uc011bul.1	+	3	453	c.448T>C	c.(448-450)TTG>CTG	p.L150L	LRCH3_uc003fyj.1_Silent_p.L150L|LRCH3_uc011bum.1_Silent_p.L150L|LRCH3_uc011bun.1_Intron	NM_032773	NP_116162	Q96II8	LRCH3_HUMAN	leucine-rich repeats and calponin homology (CH)	150	LRR 3.					extracellular region				ovary(1)	1	all_cancers(143;1.15e-09)|Ovarian(172;0.0418)|Breast(254;0.0976)		Epithelial(36;4.82e-24)|all cancers(36;3.61e-22)|OV - Ovarian serous cystadenocarcinoma(49;7.08e-19)|LUSC - Lung squamous cell carcinoma(58;6.94e-07)|Lung(62;9.92e-07)	GBM - Glioblastoma multiforme(93;0.119)														---	---	---	---
ZNF721	170960	broad.mit.edu	37	4	436180	436180	+	Silent	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:436180A>G	uc003gag.2	-	3	2767	c.2076T>C	c.(2074-2076)ACT>ACC	p.T692T	ABCA11P_uc003gac.2_Intron|ABCA11P_uc003gad.2_Intron|ABCA11P_uc011buv.1_Intron|ABCA11P_uc003gae.2_Intron|ABCA11P_uc010ibd.1_Intron|ZNF721_uc003gaf.3_Silent_p.T724T|ZNF721_uc010ibe.2_Silent_p.T680T	NM_133474	NP_597731	D9N162	D9N162_HUMAN	zinc finger protein 721	692						intracellular	nucleic acid binding|zinc ion binding			ovary(1)	1																		---	---	---	---
CRIPAK	285464	broad.mit.edu	37	4	1388368	1388368	+	Silent	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:1388368C>T	uc003gdf.2	+	1	3029	c.69C>T	c.(67-69)CCC>CCT	p.P23P		NM_175918	NP_787114	Q8N1N5	CRPAK_HUMAN	cysteine-rich PAK1 inhibitor	23					ER-nucleus signaling pathway|negative regulation of protein kinase activity|regulation of cytoskeleton organization|response to estrogen stimulus	endoplasmic reticulum|nucleus|plasma membrane	protein binding				0			OV - Ovarian serous cystadenocarcinoma(23;0.0106)															---	---	---	---
POLN	353497	broad.mit.edu	37	4	2159639	2159639	+	Splice_Site	SNP	C	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:2159639C>A	uc003ger.2	-	13	1612	c.1612_splice	c.e13-1	p.V538_splice	POLN_uc010icg.1_Splice_Site|POLN_uc010ich.1_Intron|POLN_uc011bvi.1_Splice_Site_p.V538_splice	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	2181067	2181067	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:2181067T>C	uc003ger.2	-	6	1147	c.1147A>G	c.(1147-1149)AGC>GGC	p.S383G	POLN_uc010ich.1_Intron|POLN_uc011bvi.1_Missense_Mutation_p.S383G	NM_181808	NP_861524	Q7Z5Q5	DPOLN_HUMAN	DNA-directed DNA polymerase nu	383					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					---	---	---	---
SH3BP2	6452	broad.mit.edu	37	4	2831298	2831298	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:2831298G>A	uc003gfi.3	+	8	785	c.665G>A	c.(664-666)CGG>CAG	p.R222Q	SH3BP2_uc011bvp.1_Missense_Mutation_p.R250Q|SH3BP2_uc003gfj.3_Missense_Mutation_p.R279Q|SH3BP2_uc003gfk.3_Missense_Mutation_p.R222Q|SH3BP2_uc003gfl.3_Missense_Mutation_p.R155Q|SH3BP2_uc003gfm.3_Missense_Mutation_p.R197Q	NM_001122681	NP_001116153	P78314	3BP2_HUMAN	SH3-domain binding protein 2 isoform a	222					signal transduction		SH3 domain binding|SH3/SH2 adaptor activity			central_nervous_system(1)	1				UCEC - Uterine corpus endometrioid carcinoma (64;0.164)										Cherubism				---	---	---	---
HTT	3064	broad.mit.edu	37	4	3132095	3132095	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:3132095T>C	uc011bvq.1	+	15	2082	c.1937T>C	c.(1936-1938)GTT>GCT	p.V646A		NM_002111	NP_002102	P42858	HD_HUMAN	huntingtin	644					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)														---	---	---	---
LYAR	55646	broad.mit.edu	37	4	4285455	4285455	+	Silent	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:4285455T>C	uc011bvy.1	-	3	158	c.15A>G	c.(13-15)ACA>ACG	p.T5T	LYAR_uc003ght.2_Silent_p.T5T	NM_001145725	NP_001139197	Q9NX58	LYAR_HUMAN	Ly1 antibody reactive homolog	5						nucleolus	metal ion binding|protein binding				0				UCEC - Uterine corpus endometrioid carcinoma (64;0.168)														---	---	---	---
EVC	2121	broad.mit.edu	37	4	5746978	5746978	+	Silent	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:5746978A>G	uc003gil.1	+	7	1033	c.849A>G	c.(847-849)ACA>ACG	p.T283T	EVC_uc003gim.1_RNA	NM_153717	NP_714928	P57679	EVC_HUMAN	Ellis van Creveld syndrome protein	283					muscle organ development	integral to membrane				ovary(1)|skin(1)	2		Myeloproliferative disorder(84;0.117)																---	---	---	---
JAKMIP1	152789	broad.mit.edu	37	4	6043898	6043898	+	Silent	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:6043898C>T	uc010idb.1	-	17	2571	c.2085G>A	c.(2083-2085)CTG>CTA	p.L695L	JAKMIP1_uc010idc.1_Silent_p.L510L|JAKMIP1_uc010idd.1_Intron	NM_001099433	NP_001092903	Q96N16	JKIP1_HUMAN	janus kinase and microtubule interacting protein	Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment					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																		---	---	---	---
JAKMIP1	152789	broad.mit.edu	37	4	6114524	6114524	+	Silent	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:6114524C>T	uc003giu.3	-	2	330	c.54G>A	c.(52-54)GCG>GCA	p.A18A	JAKMIP1_uc010idb.1_Silent_p.A18A|JAKMIP1_uc010idc.1_Silent_p.A18A|JAKMIP1_uc010idd.1_Silent_p.A18A|JAKMIP1_uc011bwc.1_Silent_p.A18A|JAKMIP1_uc003giv.3_Silent_p.A18A|JAKMIP1_uc010ide.2_Silent_p.A18A	NM_144720	NP_653321	Q96N16	JKIP1_HUMAN	janus kinase and microtubule interacting protein	18	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																		---	---	---	---
MAN2B2	23324	broad.mit.edu	37	4	6598902	6598902	+	Nonsense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:6598902C>T	uc003gjf.1	+	8	1156	c.1120C>T	c.(1120-1122)CGA>TGA	p.R374*	MAN2B2_uc003gje.1_Nonsense_Mutation_p.R374*|MAN2B2_uc011bwf.1_Nonsense_Mutation_p.R323*	NM_015274	NP_056089	Q9Y2E5	MA2B2_HUMAN	mannosidase, alpha, class 2B, member 2	374					mannose metabolic process	extracellular region	alpha-mannosidase activity|carbohydrate binding|zinc ion binding			ovary(2)	2																		---	---	---	---
AFAP1	60312	broad.mit.edu	37	4	7817770	7817770	+	Silent	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:7817770A>G	uc003gkg.1	-	8	1152	c.879T>C	c.(877-879)ATT>ATC	p.I293I	AFAP1_uc011bwk.1_Silent_p.I293I	NM_198595	NP_940997	Q8N556	AFAP1_HUMAN	actin filament associated protein 1	293						actin cytoskeleton|cytoplasm|focal adhesion	actin binding				0																		---	---	---	---
NKX3-2	579	broad.mit.edu	37	4	13544146	13544146	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:13544146C>T	uc003gmx.2	-	2	549	c.473G>A	c.(472-474)CGC>CAC	p.R158H		NM_001189	NP_001180	P78367	NKX32_HUMAN	NK3 homeobox 2	158					negative regulation of chondrocyte differentiation|transcription from RNA polymerase II promoter	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity				0																		---	---	---	---
SLIT2	9353	broad.mit.edu	37	4	20544179	20544179	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:20544179A>G	uc003gpr.1	+	21	2410	c.2206A>G	c.(2206-2208)ACA>GCA	p.T736A	SLIT2_uc003gps.1_Missense_Mutation_p.T728A	NM_004787	NP_004778	O94813	SLIT2_HUMAN	slit homolog 2 precursor	736	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																		---	---	---	---
GPR125	166647	broad.mit.edu	37	4	22390767	22390767	+	Silent	SNP	G	A	A	rs138178541	byFrequency	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:22390767G>A	uc003gqm.1	-	18	2932	c.2667C>T	c.(2665-2667)TGC>TGT	p.C889C	GPR125_uc010ieo.1_Silent_p.C745C|GPR125_uc003gql.1_Silent_p.C16C	NM_145290	NP_660333	Q8IWK6	GP125_HUMAN	G protein-coupled receptor 125 precursor	889	Helical; Name=4; (Potential).				neuropeptide signaling pathway	integral to membrane	G-protein coupled receptor activity			skin(1)	1		Breast(46;0.198)																---	---	---	---
ARAP2	116984	broad.mit.edu	37	4	36214103	36214103	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:36214103A>G	uc003gsq.1	-	5	1386	c.1048T>C	c.(1048-1050)TCT>CCT	p.S350P	ARAP2_uc003gsr.1_Missense_Mutation_p.S350P	NM_015230	NP_056045	Q8WZ64	ARAP2_HUMAN	ArfGAP with RhoGAP domain, ankyrin repeat and PH	350					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																		---	---	---	---
C4orf19	55286	broad.mit.edu	37	4	37591867	37591867	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:37591867A>G	uc003gsw.3	+	4	373	c.190A>G	c.(190-192)ACT>GCT	p.T64A	C4orf19_uc003gsy.3_Missense_Mutation_p.T64A	NM_001104629	NP_001098099	Q8IY42	CD019_HUMAN	hypothetical protein LOC55286	64											0																		---	---	---	---
PGM2	55276	broad.mit.edu	37	4	37836308	37836308	+	Silent	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:37836308C>T	uc011byb.1	+	3	391	c.318C>T	c.(316-318)GAC>GAT	p.D106D	PGM2_uc011bya.1_Translation_Start_Site|PGM2_uc011byc.1_Intron	NM_018290	NP_060760	Q96G03	PGM2_HUMAN	phosphoglucomutase 2	106					glucose 1-phosphate metabolic process|glycogen biosynthetic process|glycogen catabolic process	cytosol	magnesium ion binding|phosphoglucomutase activity|phosphopentomutase activity			ovary(1)	1																		---	---	---	---
PGM2	55276	broad.mit.edu	37	4	37863208	37863208	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:37863208A>G	uc011byb.1	+	14	1887	c.1814A>G	c.(1813-1815)TAC>TGC	p.Y605C	PGM2_uc011byc.1_Missense_Mutation_p.Y445C	NM_018290	NP_060760	Q96G03	PGM2_HUMAN	phosphoglucomutase 2	605					glucose 1-phosphate metabolic process|glycogen biosynthetic process|glycogen catabolic process	cytosol	magnesium ion binding|phosphoglucomutase activity|phosphopentomutase activity			ovary(1)	1																		---	---	---	---
TMEM156	80008	broad.mit.edu	37	4	38972765	38972765	+	Intron	SNP	A	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:38972765A>T	uc003gto.2	-						TMEM156_uc010ifj.2_Intron	NM_024943	NP_079219			transmembrane protein 156							integral to membrane				skin(1)	1																		---	---	---	---
KLHL5	51088	broad.mit.edu	37	4	39088208	39088208	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:39088208C>A	uc003gts.2	+	5	1187	c.1112C>A	c.(1111-1113)GCT>GAT	p.A371D	KLHL5_uc003gtp.2_Missense_Mutation_p.A325D|KLHL5_uc003gtq.2_Missense_Mutation_p.A184D|KLHL5_uc003gtr.1_Missense_Mutation_p.A371D|KLHL5_uc003gtt.2_Missense_Mutation_p.A310D	NM_015990	NP_057074	Q96PQ7	KLHL5_HUMAN	kelch-like 5 isoform 1	371						cytoplasm|cytoskeleton	actin binding			ovary(1)	1																		---	---	---	---
PDS5A	23244	broad.mit.edu	37	4	39891900	39891900	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:39891900C>T	uc003guv.3	-	17	2395	c.1855G>A	c.(1855-1857)GCA>ACA	p.A619T	PDS5A_uc010ifo.2_Missense_Mutation_p.A579T	NM_001100399	NP_001093869	Q29RF7	PDS5A_HUMAN	PDS5, regulator of cohesion maintenance, homolog	619					cell division|mitosis|negative regulation of DNA replication	chromatin|nucleus	identical protein binding				0																		---	---	---	---
ATP8A1	10396	broad.mit.edu	37	4	42424888	42424888	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:42424888C>T	uc003gwr.2	-	35	3473	c.3241G>A	c.(3241-3243)GTC>ATC	p.V1081I	ATP8A1_uc003gwq.2_Missense_Mutation_p.V307I|ATP8A1_uc003gws.2_Missense_Mutation_p.V1066I	NM_006095	NP_006086	Q9Y2Q0	AT8A1_HUMAN	ATPase, aminophospholipid transporter (APLT),	1081	Cytoplasmic (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)													---	---	---	---
KCTD8	386617	broad.mit.edu	37	4	44177024	44177024	+	Missense_Mutation	SNP	G	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:44177024G>C	uc003gwu.2	-	2	1489	c.1205C>G	c.(1204-1206)CCC>CGC	p.P402R		NM_198353	NP_938167	Q6ZWB6	KCTD8_HUMAN	potassium channel tetramerisation domain	402						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	44450180	44450180	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:44450180G>A	uc003gwu.2	-	1	645	c.361C>T	c.(361-363)CCG>TCG	p.P121S		NM_198353	NP_938167	Q6ZWB6	KCTD8_HUMAN	potassium channel tetramerisation domain	121	BTB.					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)			---	---	---	---
CNGA1	1259	broad.mit.edu	37	4	47938965	47938965	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:47938965T>C	uc003gxt.3	-	11	1812	c.1546A>G	c.(1546-1548)ATG>GTG	p.M516V	uc003gxr.1_Intron|CNGA1_uc003gxu.2_Missense_Mutation_p.M585V	NM_000087	NP_000078	P29973	CNGA1_HUMAN	cyclic nucleotide gated channel alpha 1 isoform	516	cGMP (Potential).|Cytoplasmic (Potential).				response to stimulus|visual perception	integral to plasma membrane	cGMP binding|ion channel activity			ovary(2)	2																		---	---	---	---
CNGA1	1259	broad.mit.edu	37	4	47939106	47939106	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:47939106C>T	uc003gxt.3	-	11	1671	c.1405G>A	c.(1405-1407)GTT>ATT	p.V469I	uc003gxr.1_Intron|CNGA1_uc003gxu.2_Missense_Mutation_p.V538I	NM_000087	NP_000078	P29973	CNGA1_HUMAN	cyclic nucleotide gated channel alpha 1 isoform	469	Extracellular (Potential).				response to stimulus|visual perception	integral to plasma membrane	cGMP binding|ion channel activity			ovary(2)	2																		---	---	---	---
CNGA1	1259	broad.mit.edu	37	4	47939513	47939513	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:47939513A>G	uc003gxt.3	-	11	1264	c.998T>C	c.(997-999)GTC>GCC	p.V333A	uc003gxr.1_Intron|CNGA1_uc003gxu.2_Missense_Mutation_p.V402A	NM_000087	NP_000078	P29973	CNGA1_HUMAN	cyclic nucleotide gated channel alpha 1 isoform	333	Cytoplasmic (Potential).				response to stimulus|visual perception	integral to plasma membrane	cGMP binding|ion channel activity			ovary(2)	2																		---	---	---	---
SLAIN2	57606	broad.mit.edu	37	4	48379905	48379905	+	Intron	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:48379905T>C	uc003gya.3	+							NM_020846	NP_065897			SLAIN motif family, member 2							centrosome					0																		---	---	---	---
SLC10A4	201780	broad.mit.edu	37	4	48487107	48487107	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:48487107T>C	uc003gyc.2	+	2	968	c.749T>C	c.(748-750)TTG>TCG	p.L250S		NM_152679	NP_689892	Q96EP9	NTCP4_HUMAN	solute carrier family 10, member 4	250	Helical; (Potential).					integral to membrane	bile acid:sodium symporter activity			central_nervous_system(1)	1																		---	---	---	---
FRYL	285527	broad.mit.edu	37	4	48563516	48563516	+	Silent	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:48563516C>T	uc003gyh.1	-	33	4439	c.3834G>A	c.(3832-3834)GCG>GCA	p.A1278A	FRYL_uc003gyk.2_Silent_p.A1278A|FRYL_uc003gyi.1_Silent_p.A167A	NM_015030	NP_055845	O94915	FRYL_HUMAN	furry-like	1278					regulation of transcription, DNA-dependent|transcription, DNA-dependent		protein binding			skin(1)	1																		---	---	---	---
USP46	64854	broad.mit.edu	37	4	53492364	53492364	+	Silent	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:53492364A>G	uc003gzn.2	-	4	567	c.382T>C	c.(382-384)TTG>CTG	p.L128L	USP46_uc003gzm.3_Silent_p.L121L|USP46_uc011bzr.1_Silent_p.L105L|USP46_uc011bzs.1_Silent_p.L12L	NM_022832	NP_073743	P62068	UBP46_HUMAN	ubiquitin specific peptidase 46 isoform 1	128					behavior|protein deubiquitination|regulation of synaptic transmission, GABAergic|ubiquitin-dependent protein catabolic process		protein binding|ubiquitin thiolesterase activity|ubiquitin-specific protease activity			ovary(1)	1			LUSC - Lung squamous cell carcinoma(32;0.0295)															---	---	---	---
PDGFRA	5156	broad.mit.edu	37	4	54256051	54256051	+	Intron	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:54256051T>C	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	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)			---	---	---	---
CLOCK	9575	broad.mit.edu	37	4	56301577	56301577	+	3'UTR	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:56301577G>A	uc003haz.1	-	24					CLOCK_uc003hba.1_3'UTR|CLOCK_uc010igu.1_RNA	NM_004898	NP_004889			clock						circadian rhythm|photoperiodism|positive regulation of transcription from RNA polymerase II promoter	cytoplasm|transcription factor complex	DNA binding|histone acetyltransferase activity|sequence-specific DNA binding transcription factor activity|signal transducer activity			central_nervous_system(2)|ovary(1)	3	Lung NSC(11;0.00335)|Glioma(25;0.08)|all_epithelial(27;0.0992)|all_neural(26;0.101)		LUSC - Lung squamous cell carcinoma(4;1.62e-07)|Lung(4;1.34e-06)|Epithelial(7;0.0107)															---	---	---	---
CEP135	9662	broad.mit.edu	37	4	56875941	56875941	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:56875941A>G	uc003hbi.2	+	19	2611	c.2377A>G	c.(2377-2379)AAC>GAC	p.N793D	CEP135_uc003hbj.2_Missense_Mutation_p.N499D	NM_025009	NP_079285	Q66GS9	CP135_HUMAN	centrosome protein 4	793	Potential.				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)																	---	---	---	---
AASDH	132949	broad.mit.edu	37	4	57219728	57219728	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:57219728G>A	uc003hbn.2	-	9	1571	c.1418C>T	c.(1417-1419)GCA>GTA	p.A473V	AASDH_uc010ihb.2_5'UTR|AASDH_uc011caa.1_Missense_Mutation_p.A320V|AASDH_uc003hbo.2_Missense_Mutation_p.A373V|AASDH_uc011cab.1_5'UTR|AASDH_uc010ihc.2_Missense_Mutation_p.A473V|AASDH_uc003hbp.2_Missense_Mutation_p.A473V	NM_181806	NP_861522	Q4L235	ACSF4_HUMAN	aminoadipate-semialdehyde dehydrogenase	473					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)																---	---	---	---
LPHN3	23284	broad.mit.edu	37	4	62599141	62599141	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:62599141T>C	uc010ihh.2	+	5	1237	c.1064T>C	c.(1063-1065)GTA>GCA	p.V355A	LPHN3_uc003hcq.3_Missense_Mutation_p.V355A|LPHN3_uc010ihg.1_Missense_Mutation_p.V423A|LPHN3_uc003hcs.1_Missense_Mutation_p.V184A	NM_015236	NP_056051	Q9HAR2	LPHN3_HUMAN	latrophilin 3 precursor	355	Extracellular (Potential).|Olfactomedin-like.				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	69100313	69100313	+	Silent	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:69100313A>G	uc003hdw.3	-	5	473	c.337T>C	c.(337-339)TTA>CTA	p.L113L		NM_182502	NP_872308	Q86T26	TM11B_HUMAN	transmembrane protease, serine 11B	113	SEA.|Extracellular (Potential).				proteolysis	extracellular region|integral to plasma membrane	serine-type endopeptidase activity			ovary(1)	1																		---	---	---	---
UGT2A3	79799	broad.mit.edu	37	4	69795691	69795691	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:69795691C>T	uc003hef.2	-	6	1455	c.1424G>A	c.(1423-1425)CGA>CAA	p.R475Q	UGT2A3_uc010ihp.1_RNA	NM_024743	NP_079019	Q6UWM9	UD2A3_HUMAN	UDP glucuronosyltransferase 2 family,	475	Extracellular (Potential).					integral to membrane	glucuronosyltransferase activity			ovary(1)|skin(1)	2																		---	---	---	---
UGT2B11	10720	broad.mit.edu	37	4	70074105	70074105	+	Silent	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:70074105A>G	uc003heh.2	-	3	975	c.966T>C	c.(964-966)AAT>AAC	p.N322N	uc003hei.1_Intron	NM_001073	NP_001064	O75310	UDB11_HUMAN	UDP glucuronosyltransferase 2 family,	322					estrogen metabolic process|xenobiotic metabolic process	endoplasmic reticulum membrane|integral to membrane|microsome	glucuronosyltransferase activity			ovary(1)|haematopoietic_and_lymphoid_tissue(1)|skin(1)	3																		---	---	---	---
UGT2B11	10720	broad.mit.edu	37	4	70079850	70079850	+	Silent	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:70079850A>G	uc003heh.2	-	1	600	c.591T>C	c.(589-591)GTT>GTC	p.V197V	uc003hei.1_Intron	NM_001073	NP_001064	O75310	UDB11_HUMAN	UDP glucuronosyltransferase 2 family,	197					estrogen metabolic process|xenobiotic metabolic process	endoplasmic reticulum membrane|integral to membrane|microsome	glucuronosyltransferase activity			ovary(1)|haematopoietic_and_lymphoid_tissue(1)|skin(1)	3																		---	---	---	---
ANKRD17	26057	broad.mit.edu	37	4	73943073	73943073	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:73943073C>A	uc003hgp.2	-	32	7703	c.7586G>T	c.(7585-7587)GGG>GTG	p.G2529V	ANKRD17_uc003hgo.2_Missense_Mutation_p.G2416V|ANKRD17_uc003hgq.2_Missense_Mutation_p.G2278V|ANKRD17_uc003hgr.2_Missense_Mutation_p.G2528V	NM_032217	NP_115593	O75179	ANR17_HUMAN	ankyrin repeat domain protein 17 isoform a	2529					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	73986681	73986681	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:73986681G>T	uc003hgp.2	-	20	3883	c.3766C>A	c.(3766-3768)CTT>ATT	p.L1256I	ANKRD17_uc003hgo.2_Missense_Mutation_p.L1143I|ANKRD17_uc003hgq.2_Missense_Mutation_p.L1005I|ANKRD17_uc003hgr.2_Missense_Mutation_p.L1255I|ANKRD17_uc011cbd.1_Missense_Mutation_p.L821I	NM_032217	NP_115593	O75179	ANR17_HUMAN	ankyrin repeat domain protein 17 isoform a	1256	ANK 21.				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	74021830	74021830	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:74021830A>G	uc003hgp.2	-	4	875	c.758T>C	c.(757-759)TTA>TCA	p.L253S	ANKRD17_uc003hgo.2_Missense_Mutation_p.L140S|ANKRD17_uc003hgq.2_Missense_Mutation_p.L253S|ANKRD17_uc003hgr.2_Missense_Mutation_p.L253S|ANKRD17_uc011cbd.1_5'Flank	NM_032217	NP_115593	O75179	ANR17_HUMAN	ankyrin repeat domain protein 17 isoform a	253	ANK 1.				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)															---	---	---	---
G3BP2	9908	broad.mit.edu	37	4	76582175	76582175	+	Silent	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:76582175A>G	uc003hir.2	-	5	540	c.375T>C	c.(373-375)TAT>TAC	p.Y125Y	G3BP2_uc003his.2_Silent_p.Y125Y|G3BP2_uc003hit.2_Silent_p.Y125Y	NM_012297	NP_036429	Q9UN86	G3BP2_HUMAN	Ras-GTPase activating protein SH3 domain-binding	125	NTF2.				cytoplasmic sequestering of NF-kappaB|mRNA transport|Ras protein signal transduction|regulation of small GTPase mediated signal transduction	cytosol	GTPase activator activity|nucleotide binding|receptor signaling complex scaffold activity|RNA binding			breast(2)|central_nervous_system(1)	3			Lung(101;0.0973)|LUSC - Lung squamous cell carcinoma(112;0.122)															---	---	---	---
SDAD1	55153	broad.mit.edu	37	4	76898920	76898920	+	Intron	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:76898920A>G	uc003hje.3	-						SDAD1_uc003hjf.3_Intron|SDAD1_uc011cbr.1_Intron	NM_018115	NP_060585			SDA1 domain containing 1						protein transport|ribosomal large subunit biogenesis	nucleolus	protein binding			ovary(1)	1			Lung(101;0.0809)|LUSC - Lung squamous cell carcinoma(112;0.0934)															---	---	---	---
PRDM8	56978	broad.mit.edu	37	4	81123223	81123223	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:81123223G>A	uc010ijo.2	+	8	1446	c.607G>A	c.(607-609)GGG>AGG	p.G203R	PRDM8_uc003hmb.3_Missense_Mutation_p.G203R|PRDM8_uc003hmc.3_Missense_Mutation_p.G203R	NM_020226	NP_064611	Q9NQV8	PRDM8_HUMAN	PR domain containing 8	203	Gly-rich.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			skin(1)	1																OREG0016246	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
RASGEF1B	153020	broad.mit.edu	37	4	82366688	82366688	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:82366688G>A	uc003hmi.1	-	8	1064	c.920C>T	c.(919-921)GCG>GTG	p.A307V	RASGEF1B_uc003hmj.1_Missense_Mutation_p.A306V|RASGEF1B_uc010ijq.1_Missense_Mutation_p.A265V	NM_152545	NP_689758	Q0VAM2	RGF1B_HUMAN	RasGEF domain family, member 1B	307	Ras-GEF.				regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	intracellular	Ras guanyl-nucleotide exchange factor activity				0																		---	---	---	---
SEC31A	22872	broad.mit.edu	37	4	83763417	83763417	+	Silent	SNP	G	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:83763417G>T	uc003hnf.2	-	22	3008	c.2844C>A	c.(2842-2844)TCC>TCA	p.S948S	SEC31A_uc003hnd.2_Silent_p.S104S|SEC31A_uc003hne.2_Silent_p.S712S|SEC31A_uc011ccl.1_Silent_p.S909S|SEC31A_uc003hnl.2_Intron|SEC31A_uc003hng.2_Silent_p.S948S|SEC31A_uc003hnh.2_Silent_p.S948S|SEC31A_uc003hni.2_Intron|SEC31A_uc003hnj.2_Silent_p.S909S|SEC31A_uc011ccm.1_Silent_p.S943S|SEC31A_uc011ccn.1_Silent_p.S948S|SEC31A_uc003hnk.2_Silent_p.S909S|SEC31A_uc003hnm.2_Silent_p.S948S	NM_001077207	NP_001070675	O94979	SC31A_HUMAN	SEC31 homolog A isoform 1	948	Interaction with PDCD6.|Pro-rich.				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)																---	---	---	---
COQ2	27235	broad.mit.edu	37	4	84200153	84200153	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:84200153C>T	uc003hog.2	-	2	415	c.407G>A	c.(406-408)CGT>CAT	p.R136H	COQ2_uc011ccp.1_RNA|COQ2_uc003hof.2_RNA|COQ2_uc003hoh.1_Missense_Mutation_p.R136H	NM_015697	NP_056512	Q96H96	COQ2_HUMAN	para-hydroxybenzoate-polyprenyltransferase,	123	Helical; (Potential).				glycerol metabolic process|isoprenoid biosynthetic process|ubiquinone biosynthetic process	mitochondrial membrane	4-hydroxybenzoate decaprenyltransferase activity|4-hydroxybenzoate nonaprenyltransferase activity			ovary(1)|central_nervous_system(1)	2		Hepatocellular(203;0.114)																---	---	---	---
CDS1	1040	broad.mit.edu	37	4	85562005	85562005	+	Missense_Mutation	SNP	A	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:85562005A>T	uc011ccv.1	+	10	1392	c.894A>T	c.(892-894)TTA>TTT	p.L298F	CDS1_uc010ike.1_Missense_Mutation_p.L102F	NM_001263	NP_001254	Q92903	CDS1_HUMAN	CDP-diacylglycerol synthase 1	298	Helical; (Potential).				signal transduction|visual perception	endoplasmic reticulum membrane|integral to membrane	diacylglycerol cholinephosphotransferase activity|phosphatidate cytidylyltransferase activity			large_intestine(2)|ovary(1)|breast(1)	4		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;0.00101)														---	---	---	---
WDFY3	23001	broad.mit.edu	37	4	85638111	85638111	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:85638111T>C	uc003hpd.2	-	49	8221	c.7813A>G	c.(7813-7815)ACA>GCA	p.T2605A	WDFY3_uc003hpe.1_Missense_Mutation_p.T216A	NM_014991	NP_055806	Q8IZQ1	WDFY3_HUMAN	WD repeat and FYVE domain containing 3 isoform	2605						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)														---	---	---	---
WDFY3	23001	broad.mit.edu	37	4	85657414	85657414	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:85657414C>T	uc003hpd.2	-	42	7232	c.6824G>A	c.(6823-6825)CGT>CAT	p.R2275H	WDFY3_uc003hpe.1_5'Flank	NM_014991	NP_055806	Q8IZQ1	WDFY3_HUMAN	WD repeat and FYVE domain containing 3 isoform	2275						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)														---	---	---	---
ARHGAP24	83478	broad.mit.edu	37	4	86863420	86863420	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:86863420T>C	uc003hpk.2	+	5	1042	c.593T>C	c.(592-594)TTT>TCT	p.F198S	ARHGAP24_uc003hpj.2_Missense_Mutation_p.F198S|ARHGAP24_uc003hpl.2_Missense_Mutation_p.F103S|ARHGAP24_uc010ikf.2_Missense_Mutation_p.F113S|ARHGAP24_uc003hpm.2_Missense_Mutation_p.F105S	NM_001025616	NP_001020787	Q8N264	RHG24_HUMAN	Rho GTPase activating protein 24 isoform 1	198	Rho-GAP.				angiogenesis|cell differentiation|regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cell projection|cytoskeleton|cytosol|focal adhesion	GTPase activator activity|protein binding				0		Hepatocellular(203;0.114)|all_hematologic(202;0.21)|Acute lymphoblastic leukemia(40;0.242)		OV - Ovarian serous cystadenocarcinoma(123;0.000571)														---	---	---	---
SPARCL1	8404	broad.mit.edu	37	4	88411972	88411972	+	Silent	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:88411972T>C	uc010ikm.2	-	7	1922	c.1350A>G	c.(1348-1350)GGA>GGG	p.G450G	SPARCL1_uc011cdc.1_Silent_p.G325G|SPARCL1_uc003hqs.3_Silent_p.G450G|SPARCL1_uc011cdd.1_Silent_p.G325G	NM_001128310	NP_001121782	Q14515	SPRL1_HUMAN	SPARC-like 1 precursor	450	Kazal-like.|Follistatin-like.				signal transduction	extracellular space|proteinaceous extracellular matrix	calcium ion binding			ovary(1)	1				OV - Ovarian serous cystadenocarcinoma(123;0.00118)														---	---	---	---
PKD2	5311	broad.mit.edu	37	4	88964577	88964577	+	Silent	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:88964577C>T	uc003hre.2	+	5	1353	c.1287C>T	c.(1285-1287)TAC>TAT	p.Y429Y	PKD2_uc011cdf.1_5'UTR	NM_000297	NP_000288	Q13563	PKD2_HUMAN	polycystin 2	429	Extracellular (Potential).					basal cortex|basal plasma membrane|endoplasmic reticulum|integral to membrane|lamellipodium|microtubule basal body	calcium ion binding|cytoskeletal protein binding|voltage-gated chloride channel activity|voltage-gated sodium channel activity			skin(1)	1		Hepatocellular(203;0.114)|Acute lymphoblastic leukemia(40;0.221)		OV - Ovarian serous cystadenocarcinoma(123;9.98e-10)|COAD - Colon adenocarcinoma(81;0.0237)														---	---	---	---
FAM190A	401145	broad.mit.edu	37	4	91229956	91229956	+	Missense_Mutation	SNP	A	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:91229956A>T	uc003hsv.3	+	2	861	c.521A>T	c.(520-522)AAG>ATG	p.K174M	FAM190A_uc003hsu.3_Missense_Mutation_p.K174M|FAM190A_uc010ikv.2_RNA|FAM190A_uc003hsw.2_Missense_Mutation_p.K174M	NM_001145065	NP_001138537	Q9C0I3	F190A_HUMAN	KIAA1680 protein isoform 1	174										large_intestine(1)|ovary(1)	2																		---	---	---	---
UNC5C	8633	broad.mit.edu	37	4	96140172	96140172	+	Silent	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:96140172G>A	uc003htp.1	-	9	1747	c.1593C>T	c.(1591-1593)ACC>ACT	p.T531T	UNC5C_uc010ilc.1_Silent_p.T550T|UNC5C_uc003htq.2_Silent_p.T550T	NM_003728	NP_003719	O95185	UNC5C_HUMAN	unc5C precursor	531	Cytoplasmic (Potential).|ZU5.				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)														---	---	---	---
RAP1GDS1	5910	broad.mit.edu	37	4	99325693	99325693	+	Missense_Mutation	SNP	C	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:99325693C>G	uc003htx.3	+	7	893	c.703C>G	c.(703-705)CAA>GAA	p.Q235E	RAP1GDS1_uc003htw.3_Missense_Mutation_p.Q236E|RAP1GDS1_uc003htv.3_Missense_Mutation_p.Q236E|RAP1GDS1_uc003htz.3_Missense_Mutation_p.Q186E|RAP1GDS1_uc003hty.3_Missense_Mutation_p.Q187E|RAP1GDS1_uc003hua.3_Missense_Mutation_p.Q144E	NM_001100427	NP_001093897	P52306	GDS1_HUMAN	RAP1, GTP-GDP dissociation stimulator 1 isoform	235							binding|GTPase activator activity			ovary(1)|lung(1)|breast(1)	3				OV - Ovarian serous cystadenocarcinoma(123;2.9e-07)|LUSC - Lung squamous cell carcinoma(1;0.0253)|Lung(1;0.0576)				T	NUP98	T-ALL								---	---	---	---
EIF4E	1977	broad.mit.edu	37	4	99812382	99812382	+	Intron	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:99812382A>G	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)														---	---	---	---
ADH6	130	broad.mit.edu	37	4	100131451	100131451	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:100131451A>G	uc003hup.3	-	5	449	c.355T>C	c.(355-357)TCA>CCA	p.S119P	uc003hum.1_Intron|ADH6_uc003huo.2_Missense_Mutation_p.S119P|ADH6_uc011cef.1_Intron|ADH6_uc010ile.2_Missense_Mutation_p.S119P	NM_000672	NP_000663	P28332	ADH6_HUMAN	class V alcohol dehydrogenase isoform 2	119					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)													---	---	---	---
DNAJB14	79982	broad.mit.edu	37	4	100829995	100829995	+	Silent	SNP	G	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:100829995G>C	uc003hvl.2	-	4	661	c.510C>G	c.(508-510)CTC>CTG	p.L170L	DNAJB14_uc003hvk.2_Silent_p.L85L|DNAJB14_uc010ili.2_Silent_p.L103L	NM_001031723	NP_001026893	Q8TBM8	DJB14_HUMAN	DnaJ (Hsp40) homolog, subfamily B, member 14	170	J.				protein folding	integral to membrane	heat shock protein binding|unfolded protein binding				0				OV - Ovarian serous cystadenocarcinoma(123;4.59e-09)														---	---	---	---
NFKB1	4790	broad.mit.edu	37	4	103459047	103459047	+	Silent	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:103459047C>T	uc011ceq.1	+	5	656	c.189C>T	c.(187-189)GGC>GGT	p.G63G	NFKB1_uc011cep.1_Silent_p.G64G	NM_003998	NP_003989	P19838	NFKB1_HUMAN	nuclear factor kappa-B, subunit 1 isoform 1	63	RHD.				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)													---	---	---	---
NFKB1	4790	broad.mit.edu	37	4	103505828	103505828	+	Intron	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:103505828G>A	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)													---	---	---	---
TBCK	93627	broad.mit.edu	37	4	107154207	107154207	+	Silent	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:107154207A>G	uc010ilv.2	-	17	1892	c.1527T>C	c.(1525-1527)ATT>ATC	p.I509I	TBCK_uc003hyb.2_Silent_p.I252I|TBCK_uc003hye.2_Silent_p.I470I|TBCK_uc003hyc.2_Silent_p.I446I|TBCK_uc003hyd.2_Silent_p.I337I|TBCK_uc003hyf.2_Silent_p.I509I	NM_001163435	NP_001156907	Q8TEA7	TBCK_HUMAN	TBC domain-containing protein kinase-like	509	Rab-GAP TBC.					intracellular	Rab GTPase activator activity			large_intestine(2)|upper_aerodigestive_tract(1)|stomach(1)|ovary(1)	5																		---	---	---	---
PAPSS1	9061	broad.mit.edu	37	4	108581180	108581180	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:108581180G>A	uc003hyk.2	-	6	802	c.718C>T	c.(718-720)CCA>TCA	p.P240S	PAPSS1_uc011cfh.1_RNA	NM_005443	NP_005434	O43252	PAPS1_HUMAN	3'-phosphoadenosine 5'-phosphosulfate synthase	240	Adenylyl-sulfate kinase.				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)														---	---	---	---
AGXT2L1	64850	broad.mit.edu	37	4	109681040	109681040	+	Missense_Mutation	SNP	A	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:109681040A>T	uc003hzc.2	-	3	381	c.200T>A	c.(199-201)GTC>GAC	p.V67D	AGXT2L1_uc010imc.2_Missense_Mutation_p.V61D|AGXT2L1_uc011cfm.1_Missense_Mutation_p.V27D|AGXT2L1_uc011cfn.1_5'UTR|AGXT2L1_uc011cfo.1_Missense_Mutation_p.V9D	NM_031279	NP_112569	Q8TBG4	AT2L1_HUMAN	alanine-glyoxylate aminotransferase 2-like 1	67					cellular amino acid metabolic process	mitochondrion	alanine-glyoxylate transaminase activity|pyridoxal phosphate binding			ovary(1)	1				OV - Ovarian serous cystadenocarcinoma(123;0.000281)														---	---	---	---
CCDC109B	55013	broad.mit.edu	37	4	110608694	110608694	+	Silent	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:110608694G>A	uc011cfs.1	+	8	1096	c.957G>A	c.(955-957)GCG>GCA	p.A319A		NM_017918	NP_060388	Q9NWR8	C109B_HUMAN	coiled-coil domain containing 109B	319	Potential.					integral to membrane					0				OV - Ovarian serous cystadenocarcinoma(123;6.65e-06)														---	---	---	---
NEUROG2	63973	broad.mit.edu	37	4	113436168	113436168	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:113436168C>T	uc003ias.2	-	2	791	c.464G>A	c.(463-465)CGC>CAC	p.R155H		NM_024019	NP_076924	Q9H2A3	NGN2_HUMAN	neurogenin 2	155	Helix-loop-helix motif.				positive regulation of sequence-specific DNA binding transcription factor activity|transcription, DNA-dependent	nucleus	E-box binding			skin(2)|central_nervous_system(1)	3		Ovarian(17;0.156)		OV - Ovarian serous cystadenocarcinoma(123;0.00168)														---	---	---	---
C4orf21	55345	broad.mit.edu	37	4	113540017	113540017	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:113540017T>C	uc003iau.2	-	6	1392	c.1181A>G	c.(1180-1182)AAT>AGT	p.N394S	C4orf21_uc003iaw.2_Missense_Mutation_p.N394S	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)														---	---	---	---
LARP7	51574	broad.mit.edu	37	4	113575231	113575231	+	Silent	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:113575231C>T	uc003iay.2	+	12	1862	c.1584C>T	c.(1582-1584)CAC>CAT	p.H528H	LARP7_uc003iaz.2_Silent_p.H535H|LARP7_uc003iba.2_Silent_p.H449H|LARP7_uc003ibb.2_Silent_p.H528H	NM_016648	NP_057732	Q4G0J3	LARP7_HUMAN	La ribonucleoprotein domain family, member 7	528					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)														---	---	---	---
ANK2	287	broad.mit.edu	37	4	114262943	114262943	+	Silent	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:114262943A>G	uc003ibe.3	+	33	4093	c.3993A>G	c.(3991-3993)GTA>GTG	p.V1331V	ANK2_uc003ibd.3_Silent_p.V1322V|ANK2_uc003ibf.3_Silent_p.V1331V|ANK2_uc011cgc.1_Silent_p.V507V|ANK2_uc003ibg.3_Silent_p.V326V|ANK2_uc003ibh.3_Silent_p.V5V|ANK2_uc011cgb.1_Silent_p.V1346V	NM_001148	NP_001139	Q01484	ANK2_HUMAN	ankyrin 2 isoform 1	1298					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)														---	---	---	---
NDST3	9348	broad.mit.edu	37	4	118975822	118975822	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:118975822T>C	uc003ibx.2	+	2	1160	c.757T>C	c.(757-759)TTT>CTT	p.F253L	NDST3_uc011cgf.1_Missense_Mutation_p.F253L|NDST3_uc003ibw.2_Missense_Mutation_p.F253L	NM_004784	NP_004775	O95803	NDST3_HUMAN	N-deacetylase/N-sulfotransferase (heparan	253	Lumenal (Potential).|Heparan sulfate N-deacetylase 3.					Golgi membrane|integral to membrane	[heparan sulfate]-glucosamine N-sulfotransferase activity|hydrolase activity			large_intestine(1)	1																		---	---	---	---
SYNPO2	171024	broad.mit.edu	37	4	119948054	119948054	+	Missense_Mutation	SNP	G	A	A	rs150550402		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:119948054G>A	uc003icm.3	+	3	726	c.530G>A	c.(529-531)CGC>CAC	p.R177H	SYNPO2_uc010ina.2_Missense_Mutation_p.R177H|SYNPO2_uc010inb.2_Missense_Mutation_p.R177H|SYNPO2_uc011cgh.1_Intron|SYNPO2_uc010inc.2_Missense_Mutation_p.R105H	NM_001128933	NP_001122405	Q9UMS6	SYNP2_HUMAN	synaptopodin 2 isoform b	177						nucleus|Z disc	14-3-3 protein binding|actin binding|muscle alpha-actinin binding			ovary(2)	2																		---	---	---	---
USP53	54532	broad.mit.edu	37	4	120182885	120182885	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:120182885A>G	uc003ics.3	+	11	1904	c.838A>G	c.(838-840)ACT>GCT	p.T280A	USP53_uc003icr.3_Missense_Mutation_p.T280A|USP53_uc003icu.3_5'UTR	NM_019050	NP_061923	Q70EK8	UBP53_HUMAN	ubiquitin specific protease 53	280					ubiquitin-dependent protein catabolic process		ubiquitin thiolesterase activity			ovary(1)|breast(1)|kidney(1)|skin(1)	4																		---	---	---	---
TRPC3	7222	broad.mit.edu	37	4	122824136	122824136	+	Silent	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:122824136T>C	uc003ieg.2	-	9	2408	c.2334A>G	c.(2332-2334)CCA>CCG	p.P778P	TRPC3_uc010inr.2_Silent_p.P650P|TRPC3_uc003ief.2_Silent_p.P705P|TRPC3_uc011cgl.1_Silent_p.P442P	NM_001130698	NP_001124170	Q13507	TRPC3_HUMAN	transient receptor potential cation channel,	693	Cytoplasmic (Potential).				axon guidance|phototransduction|platelet activation	integral to plasma membrane	protein binding|store-operated calcium channel activity			ovary(2)	2																		---	---	---	---
KIAA1109	84162	broad.mit.edu	37	4	123165109	123165109	+	Missense_Mutation	SNP	A	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:123165109A>T	uc003ieh.2	+	29	4888	c.4843A>T	c.(4843-4845)ACA>TCA	p.T1615S	KIAA1109_uc003iek.2_Missense_Mutation_p.T234S	NM_015312	NP_056127	Q2LD37	K1109_HUMAN	fragile site-associated protein	1615					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	123171596	123171596	+	Silent	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:123171596G>A	uc003ieh.2	+	35	5835	c.5790G>A	c.(5788-5790)GTG>GTA	p.V1930V	KIAA1109_uc003iek.2_Silent_p.V549V	NM_015312	NP_056127	Q2LD37	K1109_HUMAN	fragile site-associated protein	1930					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	123184131	123184131	+	Silent	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:123184131G>A	uc003ieh.2	+	41	7020	c.6975G>A	c.(6973-6975)ACG>ACA	p.T2325T	KIAA1109_uc003iel.1_Silent_p.T260T|KIAA1109_uc003iek.2_Silent_p.T944T	NM_015312	NP_056127	Q2LD37	K1109_HUMAN	fragile site-associated protein	2325					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	123268937	123268937	+	Intron	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:123268937A>G	uc003ieh.2	+						KIAA1109_uc003iem.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																		---	---	---	---
IL2	3558	broad.mit.edu	37	4	123374884	123374884	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:123374884A>G	uc003ier.2	-	3	387	c.332T>C	c.(331-333)GTA>GCA	p.V111A		NM_000586	NP_000577	P60568	IL2_HUMAN	interleukin 2 precursor	111					anti-apoptosis|cell adhesion|cell-cell signaling|immune response|natural killer cell activation|negative regulation of B cell apoptosis|positive regulation of activated T cell proliferation|positive regulation of B cell proliferation|positive regulation of cell growth|positive regulation of interleukin-17 production|positive regulation of tyrosine phosphorylation of Stat5 protein|T cell differentiation	extracellular space	cytokine activity|growth factor activity|interleukin-2 receptor binding|kinase activator activity			skin(1)	1				LUSC - Lung squamous cell carcinoma(721;0.185)				T	TNFRSF17	intestinal T-cell lymphoma								---	---	---	---
FGF2	2247	broad.mit.edu	37	4	123813400	123813400	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:123813400G>A	uc003iev.1	+	3	784	c.716G>A	c.(715-717)CGA>CAA	p.R239Q		NM_002006	NP_001997	P09038	FGF2_HUMAN	fibroblast growth factor 2	239					activation of MAPK activity|branching involved in ureteric bud morphogenesis|cell migration involved in sprouting angiogenesis|chemotaxis|chondroblast differentiation|embryonic morphogenesis|fibroblast growth factor receptor signaling pathway|inositol phosphate biosynthetic process|insulin receptor signaling pathway|negative regulation of blood vessel endothelial cell migration|negative regulation of cell death|organ morphogenesis|phosphatidylinositol biosynthetic process|positive regulation of angiogenesis|positive regulation of blood vessel endothelial cell migration|positive regulation of cardiac muscle cell proliferation|positive regulation of cell division|positive regulation of cell fate specification|positive regulation of ERK1 and ERK2 cascade|positive regulation of phosphatidylinositol 3-kinase activity|positive regulation of phospholipase C activity|Ras protein signal transduction|release of sequestered calcium ion into cytosol|wound healing	extracellular space	fibroblast growth factor receptor binding|growth factor activity|heparin binding|ligand-dependent nuclear receptor transcription coactivator activity			ovary(1)|lung(1)|central_nervous_system(1)	3					Pentosan Polysulfate(DB00686)													---	---	---	---
FAT4	79633	broad.mit.edu	37	4	126238423	126238423	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:126238423G>A	uc003ifj.3	+	1	857	c.857G>A	c.(856-858)CGC>CAC	p.R286H		NM_024582	NP_078858	Q6V0I7	FAT4_HUMAN	FAT tumor suppressor homolog 4 precursor	286	Cadherin 3.|Extracellular (Potential).				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(9)|skin(5)|upper_aerodigestive_tract(2)|pancreas(2)	18																OREG0016317	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
HSPA4L	22824	broad.mit.edu	37	4	128741587	128741587	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:128741587C>T	uc003ifm.2	+	14	1932	c.1679C>T	c.(1678-1680)GCT>GTT	p.A560V	HSPA4L_uc010iny.1_Missense_Mutation_p.A519V|HSPA4L_uc011cgr.1_Missense_Mutation_p.A527V	NM_014278	NP_055093	O95757	HS74L_HUMAN	heat shock 70kDa protein 4-like	560					protein folding|response to unfolded protein	cytoplasm|nucleus	ATP binding|protein binding			ovary(2)|central_nervous_system(1)|skin(1)	4																		---	---	---	---
PCDH18	54510	broad.mit.edu	37	4	138452628	138452628	+	Missense_Mutation	SNP	A	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:138452628A>T	uc003ihe.3	-	1	1002	c.615T>A	c.(613-615)GAT>GAA	p.D205E	PCDH18_uc003ihf.3_Missense_Mutation_p.D198E|PCDH18_uc011cgz.1_Intron|PCDH18_uc003ihg.3_5'UTR|PCDH18_uc011cha.1_Intron	NM_019035	NP_061908	Q9HCL0	PCD18_HUMAN	protocadherin 18 precursor	205	Extracellular (Potential).|Cadherin 2.				brain development|homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			pancreas(3)|skin(2)	5	all_hematologic(180;0.24)																	---	---	---	---
SETD7	80854	broad.mit.edu	37	4	140439110	140439110	+	Silent	SNP	G	A	A	rs141692129		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:140439110G>A	uc003ihw.2	-	7	1135	c.849C>T	c.(847-849)CAC>CAT	p.H283H		NM_030648	NP_085151	Q8WTS6	SETD7_HUMAN	SET domain-containing protein 7	283	SET.				peptidyl-lysine dimethylation|peptidyl-lysine monomethylation|regulation of transcription, DNA-dependent|transcription, DNA-dependent	chromosome|nucleus	histone-lysine N-methyltransferase activity|p53 binding			ovary(1)|central_nervous_system(1)	2	all_hematologic(180;0.156)																	---	---	---	---
ZNF330	27309	broad.mit.edu	37	4	142145777	142145777	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:142145777G>A	uc003iiq.3	+	4	377	c.157G>A	c.(157-159)GCA>ACA	p.A53T	ZNF330_uc011chl.1_Intron	NM_014487	NP_055302	Q9Y3S2	ZN330_HUMAN	zinc finger protein 330	53	C4-type 1 (Potential).					chromosome, centromeric region|midbody|nucleolus	protein binding|zinc ion binding				0	all_hematologic(180;0.162)																	---	---	---	---
USP38	84640	broad.mit.edu	37	4	144124659	144124659	+	Silent	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:144124659T>C	uc003ijb.2	+	5	1683	c.1149T>C	c.(1147-1149)TGT>TGC	p.C383C	USP38_uc003ija.3_Silent_p.C383C|USP38_uc003ijc.2_RNA	NM_032557	NP_115946	Q8NB14	UBP38_HUMAN	ubiquitin specific peptidase 38	383					ubiquitin-dependent protein catabolic process		cysteine-type peptidase activity|ubiquitin thiolesterase activity			lung(2)|ovary(1)|breast(1)|pancreas(1)	5	all_hematologic(180;0.158)																	---	---	---	---
ABCE1	6059	broad.mit.edu	37	4	146044706	146044706	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:146044706G>A	uc003ijx.2	+	16	2034	c.1594G>A	c.(1594-1596)GTC>ATC	p.V532I	ABCE1_uc003ijy.2_Missense_Mutation_p.V532I|ABCE1_uc010iot.2_RNA	NM_001040876	NP_001035809	P61221	ABCE1_HUMAN	ATP-binding cassette, sub-family E, member 1	532	ABC transporter 2.				interspecies interaction between organisms|response to virus|RNA catabolic process	mitochondrion	ATP binding|ATPase activity|electron carrier activity|iron-sulfur cluster binding|ribonuclease inhibitor activity			skin(1)	1	all_hematologic(180;0.151)																	---	---	---	---
ZNF827	152485	broad.mit.edu	37	4	146806856	146806856	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:146806856G>A	uc003ikn.2	-	4	1769	c.1721C>T	c.(1720-1722)GCG>GTG	p.A574V	ZNF827_uc003ikm.2_Missense_Mutation_p.A574V|ZNF827_uc010iox.2_Missense_Mutation_p.A224V	NM_178835	NP_849157	Q17R98	ZN827_HUMAN	zinc finger protein 827	574					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0	all_hematologic(180;0.151)																	---	---	---	---
ZNF827	152485	broad.mit.edu	37	4	146806895	146806895	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:146806895G>A	uc003ikn.2	-	4	1730	c.1682C>T	c.(1681-1683)GCG>GTG	p.A561V	ZNF827_uc003ikm.2_Missense_Mutation_p.A561V|ZNF827_uc010iox.2_Missense_Mutation_p.A211V	NM_178835	NP_849157	Q17R98	ZN827_HUMAN	zinc finger protein 827	561					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0	all_hematologic(180;0.151)																	---	---	---	---
LRBA	987	broad.mit.edu	37	4	151408995	151408995	+	Intron	SNP	G	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:151408995G>C	uc010ipj.2	-						LRBA_uc003ils.3_Intron|LRBA_uc003ilt.3_Intron|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	151814280	151814280	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:151814280G>T	uc010ipj.2	-	17	2563	c.2089C>A	c.(2089-2091)CTA>ATA	p.L697I	LRBA_uc003ilu.3_Missense_Mutation_p.L697I|LRBA_uc010ipk.1_3'UTR	NM_006726	NP_006717	P50851	LRBA_HUMAN	LPS-responsive vesicle trafficking, beach and	697						endoplasmic reticulum|Golgi apparatus|integral to membrane|lysosome|plasma membrane	protein binding			ovary(3)|breast(3)|skin(1)	7	all_hematologic(180;0.151)																	---	---	---	---
FBXW7	55294	broad.mit.edu	37	4	153251965	153251965	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:153251965T>C	uc003ims.2	-	7	1190	c.1041A>G	c.(1039-1041)ATA>ATG	p.I347M	FBXW7_uc011cii.1_Missense_Mutation_p.I347M|FBXW7_uc003imt.2_Missense_Mutation_p.I347M|FBXW7_uc011cih.1_Missense_Mutation_p.I171M|FBXW7_uc003imq.2_Missense_Mutation_p.I267M|FBXW7_uc003imr.2_Missense_Mutation_p.I229M	NM_033632	NP_361014	Q969H0	FBXW7_HUMAN	F-box and WD repeat domain containing 7 isoform	347					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								---	---	---	---
KIAA0922	23240	broad.mit.edu	37	4	154506693	154506693	+	Missense_Mutation	SNP	G	A	A	rs143387402		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:154506693G>A	uc003inm.3	+	13	1290	c.1238G>A	c.(1237-1239)CGC>CAC	p.R413H	KIAA0922_uc010ipp.2_Missense_Mutation_p.R414H|KIAA0922_uc010ipq.2_Missense_Mutation_p.R266H|KIAA0922_uc010ips.1_Missense_Mutation_p.R25H	NM_015196	NP_056011	A2VDJ0	T131L_HUMAN	hypothetical protein LOC23240 isoform 2	413	Extracellular (Potential).					integral to membrane				upper_aerodigestive_tract(1)|ovary(1)	2	all_hematologic(180;0.093)	Renal(120;0.118)																---	---	---	---
KIAA0922	23240	broad.mit.edu	37	4	154517412	154517412	+	Silent	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:154517412T>C	uc003inm.3	+	20	2047	c.1995T>C	c.(1993-1995)GGT>GGC	p.G665G	KIAA0922_uc010ipp.2_Silent_p.G666G|KIAA0922_uc010ipq.2_Silent_p.G434G	NM_015196	NP_056011	A2VDJ0	T131L_HUMAN	hypothetical protein LOC23240 isoform 2	665	Extracellular (Potential).					integral to membrane				upper_aerodigestive_tract(1)|ovary(1)	2	all_hematologic(180;0.093)	Renal(120;0.118)																---	---	---	---
KIAA0922	23240	broad.mit.edu	37	4	154557555	154557555	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:154557555C>A	uc003inm.3	+	35	4709	c.4657C>A	c.(4657-4659)CCC>ACC	p.P1553T	KIAA0922_uc010ipp.2_Missense_Mutation_p.P1554T|KIAA0922_uc010ipq.2_Missense_Mutation_p.P1322T	NM_015196	NP_056011	A2VDJ0	T131L_HUMAN	hypothetical protein LOC23240 isoform 2	1553	Cytoplasmic (Potential).					integral to membrane				upper_aerodigestive_tract(1)|ovary(1)	2	all_hematologic(180;0.093)	Renal(120;0.118)																---	---	---	---
FGB	2244	broad.mit.edu	37	4	155491641	155491641	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:155491641G>A	uc003ioa.3	+	8	1354	c.1315G>A	c.(1315-1317)GCA>ACA	p.A439T	FGB_uc003iob.3_3'UTR|FGB_uc010ipv.2_Missense_Mutation_p.A377T|FGB_uc010ipw.2_3'UTR|FGB_uc003ioc.3_Missense_Mutation_p.A220T	NM_005141	NP_005132	P02675	FIBB_HUMAN	fibrinogen, beta chain preproprotein	439	Fibrinogen C-terminal.				platelet activation|platelet degranulation|protein polymerization|response to calcium ion|signal transduction	external side of plasma membrane|fibrinogen complex|platelet alpha granule lumen|soluble fraction	chaperone binding|eukaryotic cell surface binding|protein binding, bridging|receptor binding			ovary(2)|upper_aerodigestive_tract(1)	3	all_hematologic(180;0.215)	Renal(120;0.0458)			Sucralfate(DB00364)													---	---	---	---
FAM198B	51313	broad.mit.edu	37	4	159091500	159091500	+	Intron	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:159091500C>T	uc003ipp.3	-						uc003ipu.1_5'Flank|FAM198B_uc003ipq.3_Splice_Site_p.A304_splice|FAM198B_uc003ipr.3_Intron|FAM198B_uc003ips.2_3'UTR|uc003ipt.1_5'Flank	NM_016613	NP_057697			hypothetical protein LOC51313 isoform 2							Golgi membrane|integral to membrane					0																		---	---	---	---
ETFDH	2110	broad.mit.edu	37	4	159603466	159603466	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:159603466C>T	uc003iqb.2	+	3	627	c.295C>T	c.(295-297)CGT>TGT	p.R99C	ETFDH_uc011cjg.1_Missense_Mutation_p.R52C|ETFDH_uc010iqr.2_Intron|ETFDH_uc011cjh.1_Missense_Mutation_p.R38C|ETFDH_uc010iqs.2_Missense_Mutation_p.R38C	NM_004453	NP_004444	Q16134	ETFD_HUMAN	electron-transferring-flavoprotein dehydrogenase	99					fatty acid beta-oxidation using acyl-CoA dehydrogenase|respiratory electron transport chain|response to oxidative stress|transport	integral to mitochondrial inner membrane|mitochondrial matrix	4 iron, 4 sulfur cluster binding|electron carrier activity|electron-transferring-flavoprotein dehydrogenase activity|flavin adenine dinucleotide binding|metal ion binding|oxidoreductase activity, oxidizing metal ions with flavin as acceptor|ubiquinone binding			large_intestine(2)|skin(1)	3	all_hematologic(180;0.24)	Renal(120;0.0458)		COAD - Colon adenocarcinoma(41;0.0172)														---	---	---	---
C4orf45	152940	broad.mit.edu	37	4	159836465	159836465	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:159836465C>T	uc003iqf.1	-	4	488	c.403G>A	c.(403-405)GCT>ACT	p.A135T	C4orf45_uc010iqt.1_RNA	NM_152543	NP_689756	Q96LM5	CD045_HUMAN	hypothetical protein LOC152940	135											0																		---	---	---	---
NPY5R	4889	broad.mit.edu	37	4	164271515	164271515	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:164271515G>T	uc003iqn.2	+	4	272	c.90G>T	c.(88-90)TGG>TGT	p.W30C		NM_006174	NP_006165	Q15761	NPY5R_HUMAN	neuropeptide Y receptor Y5	30	Extracellular (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	164394872	164394872	+	Silent	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:164394872G>A	uc003iqp.3	-	1	176	c.15C>T	c.(13-15)GAC>GAT	p.D5D		NM_032136	NP_115512	Q9H0I9	TKTL2_HUMAN	transketolase-like 2	5						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)																---	---	---	---
C4orf43	55319	broad.mit.edu	37	4	164436573	164436573	+	Silent	SNP	G	A	A	rs140046746	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:164436573G>A	uc003iqq.3	+	5	629	c.348G>A	c.(346-348)ACG>ACA	p.T116T		NM_018352	NP_060822	Q96EY4	CD043_HUMAN	hypothetical protein LOC55319	116											0																		---	---	---	---
MARCH1	55016	broad.mit.edu	37	4	164466843	164466843	+	Missense_Mutation	SNP	A	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:164466843A>T	uc003iqs.1	-	7	1453	c.476T>A	c.(475-477)GTC>GAC	p.V159D	MARCH1_uc003iqr.1_Missense_Mutation_p.V142D	NM_017923	NP_060393	Q8TCQ1	MARH1_HUMAN	membrane-associated RING-CH protein I	159	Helical; (Potential).				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)																---	---	---	---
TRIM61	391712	broad.mit.edu	37	4	165891139	165891139	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:165891139C>T	uc003iqw.2	-	3	627	c.16G>A	c.(16-18)GCC>ACC	p.A6T		NM_001012414	NP_001012414	Q5EBN2	TRI61_HUMAN	tripartite motif-containing 61	6						intracellular	zinc ion binding			skin(1)	1	all_hematologic(180;0.221)	Prostate(90;0.109)		GBM - Glioblastoma multiforme(119;0.155)														---	---	---	---
KLHL2	11275	broad.mit.edu	37	4	166226827	166226827	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:166226827A>G	uc003irb.2	+	9	1248	c.989A>G	c.(988-990)GAA>GGA	p.E330G	KLHL2_uc011cjm.1_Missense_Mutation_p.E334G|KLHL2_uc003irc.2_Missense_Mutation_p.E242G|KLHL2_uc010ira.2_Intron	NM_007246	NP_009177	O95198	KLHL2_HUMAN	kelch-like 2, Mayven isoform 1	330	Kelch 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)														---	---	---	---
TLL1	7092	broad.mit.edu	37	4	166981285	166981285	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:166981285C>A	uc003irh.1	+	15	2599	c.1952C>A	c.(1951-1953)CCA>CAA	p.P651Q	TLL1_uc011cjn.1_Missense_Mutation_p.P674Q|TLL1_uc011cjo.1_Missense_Mutation_p.P475Q	NM_012464	NP_036596	O43897	TLL1_HUMAN	tolloid-like 1 precursor	651	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)														---	---	---	---
CLCN3	1182	broad.mit.edu	37	4	170638961	170638961	+	Intron	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:170638961C>T	uc003isi.2	+						CLCN3_uc003ish.2_Silent_p.I795I|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)														---	---	---	---
WDR17	116966	broad.mit.edu	37	4	177017687	177017687	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:177017687A>G	uc003iuj.2	+	2	173	c.17A>G	c.(16-18)TAC>TGC	p.Y6C	WDR17_uc003iuk.2_Intron|WDR17_uc003ium.3_Intron|WDR17_uc003iul.1_Intron	NM_170710	NP_733828	Q8IZU2	WDR17_HUMAN	WD repeat domain 17 isoform 1	6										ovary(2)|skin(2)|pancreas(1)|central_nervous_system(1)	6		Breast(14;0.00015)|Melanoma(52;0.00886)|Prostate(90;0.00996)|Renal(120;0.0183)|all_hematologic(60;0.107)|all_neural(102;0.164)		all cancers(43;2.21e-20)|Epithelial(43;9.71e-18)|OV - Ovarian serous cystadenocarcinoma(60;2.38e-09)|GBM - Glioblastoma multiforme(59;0.000295)|STAD - Stomach adenocarcinoma(60;0.000703)|LUSC - Lung squamous cell carcinoma(193;0.0232)														---	---	---	---
ASB5	140458	broad.mit.edu	37	4	177190205	177190205	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:177190205A>G	uc003iuq.1	-	1	71	c.55T>C	c.(55-57)TTT>CTT	p.F19L		NM_080874	NP_543150	Q8WWX0	ASB5_HUMAN	ankyrin repeat and SOCS box-containing protein	19					intracellular signal transduction					skin(2)	2		Breast(14;0.00015)|Melanoma(52;0.00886)|Prostate(90;0.00996)|Renal(120;0.0183)|all_hematologic(60;0.107)|all_neural(102;0.164)		all cancers(43;2.13e-20)|Epithelial(43;9.94e-18)|OV - Ovarian serous cystadenocarcinoma(60;2e-09)|GBM - Glioblastoma multiforme(59;0.000254)|STAD - Stomach adenocarcinoma(60;0.000653)|LUSC - Lung squamous cell carcinoma(193;0.0393)														---	---	---	---
SORBS2	8470	broad.mit.edu	37	4	186544058	186544058	+	Intron	SNP	G	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:186544058G>T	uc003iyl.2	-						SORBS2_uc003iyh.2_Intron|SORBS2_uc011ckw.1_Intron|SORBS2_uc003iyi.2_Intron|SORBS2_uc011ckx.1_Intron|SORBS2_uc003iyk.2_Intron|SORBS2_uc003iym.2_Intron|SORBS2_uc003iyn.1_Intron|SORBS2_uc011cku.1_Intron|SORBS2_uc011ckv.1_Intron|SORBS2_uc003iyd.2_Intron|SORBS2_uc003iye.2_Intron|SORBS2_uc003iya.2_Intron|SORBS2_uc003iyb.2_Intron|SORBS2_uc003iyc.2_Intron|SORBS2_uc003iyg.2_Intron|SORBS2_uc003iyf.2_Intron|SORBS2_uc003iyo.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)														---	---	---	---
SORBS2	8470	broad.mit.edu	37	4	186545626	186545626	+	Silent	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:186545626A>G	uc003iyl.2	-	13	1803	c.945T>C	c.(943-945)TGT>TGC	p.C315C	SORBS2_uc003iyh.2_Intron|SORBS2_uc011ckw.1_Intron|SORBS2_uc003iyi.2_Intron|SORBS2_uc011ckx.1_Intron|SORBS2_uc003iyk.2_Intron|SORBS2_uc003iym.2_Silent_p.C415C|SORBS2_uc003iyn.1_Intron|SORBS2_uc011cku.1_Intron|SORBS2_uc011ckv.1_Silent_p.C219C|SORBS2_uc003iyd.2_Intron|SORBS2_uc003iye.2_Intron|SORBS2_uc003iya.2_Intron|SORBS2_uc003iyb.2_Intron|SORBS2_uc003iyc.2_Intron|SORBS2_uc003iyg.2_Silent_p.C429C|SORBS2_uc003iyf.2_Intron|SORBS2_uc003iyo.1_Intron	NM_021069	NP_066547	O94875	SRBS2_HUMAN	sorbin and SH3 domain containing 2 isoform 2	315						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)														---	---	---	---
SORBS2	8470	broad.mit.edu	37	4	186551699	186551699	+	Intron	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:186551699T>C	uc003iyl.2	-						SORBS2_uc003iyh.2_Intron|SORBS2_uc011ckw.1_Intron|SORBS2_uc003iyi.2_Intron|SORBS2_uc011ckx.1_Intron|SORBS2_uc003iyk.2_Intron|SORBS2_uc003iym.2_Intron|SORBS2_uc003iyn.1_Intron|SORBS2_uc011cky.1_Intron|SORBS2_uc011cku.1_Intron|SORBS2_uc011ckv.1_Intron|SORBS2_uc003iyd.2_Intron|SORBS2_uc003iye.2_Intron|SORBS2_uc003iya.2_Intron|SORBS2_uc003iyb.2_Intron|SORBS2_uc003iyc.2_Intron|SORBS2_uc003iyg.2_Intron|SORBS2_uc003iyf.2_Intron|SORBS2_uc003iyo.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)														---	---	---	---
SORBS2	8470	broad.mit.edu	37	4	186578679	186578679	+	Nonsense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:186578679G>A	uc003iyl.2	-	6	1024	c.166C>T	c.(166-168)CGA>TGA	p.R56*	SORBS2_uc003iyh.2_Nonsense_Mutation_p.R235*|SORBS2_uc011ckw.1_Nonsense_Mutation_p.R125*|SORBS2_uc003iyi.2_Nonsense_Mutation_p.R142*|SORBS2_uc011ckx.1_Nonsense_Mutation_p.R102*|SORBS2_uc003iyk.2_Nonsense_Mutation_p.R142*|SORBS2_uc003iym.2_Nonsense_Mutation_p.R156*|SORBS2_uc003iyn.1_Nonsense_Mutation_p.R102*|SORBS2_uc011cky.1_Nonsense_Mutation_p.R119*|SORBS2_uc003iyp.2_Nonsense_Mutation_p.R156*|SORBS2_uc011cku.1_5'Flank|SORBS2_uc011ckv.1_5'Flank|SORBS2_uc003iyd.2_Nonsense_Mutation_p.R235*|SORBS2_uc003iye.2_Nonsense_Mutation_p.R56*|SORBS2_uc003iya.2_Nonsense_Mutation_p.R56*|SORBS2_uc003iyb.2_Nonsense_Mutation_p.R56*|SORBS2_uc003iyc.2_Nonsense_Mutation_p.R56*|SORBS2_uc003iyg.2_Nonsense_Mutation_p.R142*|SORBS2_uc003iyf.2_Nonsense_Mutation_p.R119*|SORBS2_uc003iyo.1_5'Flank	NM_021069	NP_066547	O94875	SRBS2_HUMAN	sorbin and SH3 domain containing 2 isoform 2	56						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)														---	---	---	---
MTNR1A	4543	broad.mit.edu	37	4	187455087	187455087	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:187455087G>T	uc003izd.1	-	2	827	c.809C>A	c.(808-810)CCT>CAT	p.P270H		NM_005958	NP_005949	P48039	MTR1A_HUMAN	melatonin receptor 1A	270	Extracellular (Potential).				circadian rhythm|G-protein signaling, coupled to cyclic nucleotide second messenger|mating behavior	integral to plasma membrane	melatonin receptor activity			ovary(1)|skin(1)|breast(1)|central_nervous_system(1)|pancreas(1)	5		all_cancers(14;6.39e-56)|all_epithelial(14;1.48e-41)|all_lung(41;2.45e-15)|Lung NSC(41;7.26e-15)|Melanoma(20;1.91e-06)|Hepatocellular(41;0.00335)|Prostate(90;0.00996)|all_hematologic(60;0.014)|Colorectal(36;0.0161)|Renal(120;0.0183)|all_neural(102;0.202)		OV - Ovarian serous cystadenocarcinoma(60;7.63e-12)|BRCA - Breast invasive adenocarcinoma(30;6.68e-07)|GBM - Glioblastoma multiforme(59;3.44e-05)|LUSC - Lung squamous cell carcinoma(40;0.000106)|STAD - Stomach adenocarcinoma(60;0.000279)|READ - Rectum adenocarcinoma(43;0.159)	Melatonin(DB01065)|Ramelteon(DB00980)													---	---	---	---
FAT1	2195	broad.mit.edu	37	4	187510240	187510240	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:187510240A>G	uc003izf.2	-	27	13461	c.13273T>C	c.(13273-13275)TAC>CAC	p.Y4425H	FAT1_uc010isn.2_Missense_Mutation_p.Y72H|FAT1_uc003ize.2_Missense_Mutation_p.Y316H	NM_005245	NP_005236	Q14517	FAT1_HUMAN	FAT tumor suppressor 1 precursor	4425	Cytoplasmic (Potential).				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)			---	---	---	---
FAT1	2195	broad.mit.edu	37	4	187522416	187522416	+	Intron	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:187522416A>G	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)			---	---	---	---
FAT1	2195	broad.mit.edu	37	4	187538179	187538179	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:187538179T>C	uc003izf.2	-	11	9243	c.9055A>G	c.(9055-9057)AAC>GAC	p.N3019D		NM_005245	NP_005236	Q14517	FAT1_HUMAN	FAT tumor suppressor 1 precursor	3019	Extracellular (Potential).|Cadherin 27.				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)			---	---	---	---
FAT1	2195	broad.mit.edu	37	4	187557262	187557262	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:187557262A>G	uc003izf.2	-	6	4288	c.4100T>C	c.(4099-4101)GTG>GCG	p.V1367A		NM_005245	NP_005236	Q14517	FAT1_HUMAN	FAT tumor suppressor 1 precursor	1367	Extracellular (Potential).|Cadherin 12.				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)			---	---	---	---
FAT1	2195	broad.mit.edu	37	4	187557818	187557818	+	Missense_Mutation	SNP	C	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:187557818C>G	uc003izf.2	-	5	4081	c.3893G>C	c.(3892-3894)GGC>GCC	p.G1298A		NM_005245	NP_005236	Q14517	FAT1_HUMAN	FAT tumor suppressor 1 precursor	1298	Extracellular (Potential).|Cadherin 11.				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)			---	---	---	---
BRD9	65980	broad.mit.edu	37	5	878574	878574	+	Silent	SNP	C	T	T	rs150581830		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:878574C>T	uc003jbq.2	-	11	1334	c.1167G>A	c.(1165-1167)GCG>GCA	p.A389A	BRD9_uc003jbl.2_Silent_p.A273A|BRD9_uc003jbm.2_RNA|BRD9_uc003jbn.2_RNA|BRD9_uc011cmb.1_Silent_p.A336A|BRD9_uc003jbo.2_Silent_p.A293A|BRD9_uc003jbp.2_Silent_p.A50A|BRD9_uc011cmc.1_RNA	NM_023924	NP_076413	Q9H8M2	BRD9_HUMAN	bromodomain containing 9 isoform 1	389							nucleic acid binding				0			Epithelial(17;0.00202)|OV - Ovarian serous cystadenocarcinoma(19;0.00353)|all cancers(22;0.00815)|Lung(60;0.185)															---	---	---	---
SLC12A7	10723	broad.mit.edu	37	5	1076344	1076344	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:1076344G>T	uc003jbu.2	-	14	1822	c.1756C>A	c.(1756-1758)CTC>ATC	p.L586I		NM_006598	NP_006589	Q9Y666	S12A7_HUMAN	solute carrier family 12 (potassium/chloride	586	Helical; (Potential).				potassium ion transport|sodium ion transport	integral to plasma membrane	potassium:chloride symporter activity			skin(2)|large_intestine(1)|ovary(1)	4	Lung NSC(6;2.47e-13)|all_lung(6;1.67e-12)|all_epithelial(6;5.44e-09)		Epithelial(17;0.000497)|OV - Ovarian serous cystadenocarcinoma(19;0.00239)|all cancers(22;0.00241)|Lung(60;0.165)		Potassium Chloride(DB00761)													---	---	---	---
ADCY2	108	broad.mit.edu	37	5	7804716	7804716	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:7804716T>C	uc003jdz.1	+	22	2861	c.2794T>C	c.(2794-2796)TTC>CTC	p.F932L	ADCY2_uc011cmo.1_Missense_Mutation_p.F752L|ADCY2_uc010itm.1_Missense_Mutation_p.F128L	NM_020546	NP_065433	Q08462	ADCY2_HUMAN	adenylate cyclase 2	932	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																		---	---	---	---
TAS2R1	50834	broad.mit.edu	37	5	9630122	9630122	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:9630122A>G	uc003jem.1	-	1	342	c.23T>C	c.(22-24)ATC>ACC	p.I8T		NM_019599	NP_062545	Q9NYW7	TA2R1_HUMAN	taste receptor T2R1	8	Extracellular (Potential).				chemosensory behavior|sensory perception of taste	integral to membrane	taste receptor activity			ovary(3)	3																		---	---	---	---
CCT5	22948	broad.mit.edu	37	5	10256094	10256094	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:10256094C>T	uc003jeq.2	+	4	530	c.359C>T	c.(358-360)GCG>GTG	p.A120V	CCT5_uc011cmq.1_Intron|CCT5_uc003jer.2_Missense_Mutation_p.A120V|CCT5_uc010its.2_Missense_Mutation_p.A120V|CCT5_uc011cmr.1_Missense_Mutation_p.A65V|CCT5_uc011cms.1_Missense_Mutation_p.A82V|CCT5_uc011cmt.1_Missense_Mutation_p.A27V	NM_012073	NP_036205	P48643	TCPE_HUMAN	chaperonin containing TCP1, subunit 5 (epsilon)	120					'de novo' posttranslational protein folding|response to virus	microtubule organizing center|nucleolus	ATP binding|unfolded protein binding			ovary(2)	2																		---	---	---	---
CTNND2	1501	broad.mit.edu	37	5	11159774	11159774	+	Silent	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:11159774T>C	uc003jfa.1	-	12	2218	c.2073A>G	c.(2071-2073)TCA>TCG	p.S691S	CTNND2_uc010itt.2_Silent_p.S600S|CTNND2_uc011cmy.1_Silent_p.S354S|CTNND2_uc011cmz.1_Silent_p.S258S|CTNND2_uc010itu.1_RNA|CTNND2_uc011cmx.1_Silent_p.S258S	NM_001332	NP_001323	Q9UQB3	CTND2_HUMAN	catenin (cadherin-associated protein), delta 2	691	ARM 5.				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	11199643	11199643	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:11199643G>A	uc003jfa.1	-	11	2037	c.1892C>T	c.(1891-1893)GCC>GTC	p.A631V	CTNND2_uc010itt.2_Missense_Mutation_p.A540V|CTNND2_uc011cmy.1_Missense_Mutation_p.A294V|CTNND2_uc011cmz.1_Missense_Mutation_p.A198V|CTNND2_uc010itu.1_RNA|CTNND2_uc011cmx.1_Missense_Mutation_p.A198V	NM_001332	NP_001323	Q9UQB3	CTND2_HUMAN	catenin (cadherin-associated protein), delta 2	631	ARM 4.				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	13753574	13753574	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:13753574C>T	uc003jfd.2	-	63	10682	c.10640G>A	c.(10639-10641)CGG>CAG	p.R3547Q	DNAH5_uc003jfc.2_5'UTR	NM_001369	NP_001360	Q8TE73	DYH5_HUMAN	dynein, axonemal, heavy chain 5	3547					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	13769145	13769145	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:13769145G>A	uc003jfd.2	-	58	9863	c.9821C>T	c.(9820-9822)TCT>TTT	p.S3274F	DNAH5_uc003jfc.2_5'UTR	NM_001369	NP_001360	Q8TE73	DYH5_HUMAN	dynein, axonemal, heavy chain 5	3274	Stalk (By similarity).|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	13830217	13830217	+	Missense_Mutation	SNP	T	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:13830217T>A	uc003jfd.2	-	37	6209	c.6167A>T	c.(6166-6168)AAA>ATA	p.K2056I		NM_001369	NP_001360	Q8TE73	DYH5_HUMAN	dynein, axonemal, heavy chain 5	2056	AAA 1 (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	13867899	13867899	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:13867899T>C	uc003jfd.2	-	25	4079	c.4037A>G	c.(4036-4038)TAT>TGT	p.Y1346C		NM_001369	NP_001360	Q8TE73	DYH5_HUMAN	dynein, axonemal, heavy chain 5	1346	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				---	---	---	---
FBXL7	23194	broad.mit.edu	37	5	15937163	15937163	+	Silent	SNP	C	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:15937163C>A	uc003jfn.1	+	4	1825	c.1344C>A	c.(1342-1344)ATC>ATA	p.I448I		NM_012304	NP_036436	Q9UJT9	FBXL7_HUMAN	F-box and leucine-rich repeat protein 7	448	LRR 11.				ubiquitin-dependent protein catabolic process	ubiquitin ligase complex	protein binding|ubiquitin-protein ligase activity			ovary(2)|lung(1)	3																		---	---	---	---
MARCH11	441061	broad.mit.edu	37	5	16091065	16091065	+	Nonsense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:16091065C>T	uc003jfo.2	-	3	1032	c.819G>A	c.(817-819)TGG>TGA	p.W273*	MARCH11_uc010itw.1_Nonsense_Mutation_p.W29*	NM_001102562	NP_001096032	A6NNE9	MARHB_HUMAN	membrane-associated ring finger (C3HC4) 11	273						cytoplasmic vesicle membrane|integral to membrane	ligase activity|zinc ion binding				0																		---	---	---	---
CDH10	1008	broad.mit.edu	37	5	24491828	24491828	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:24491828C>A	uc003jgr.1	-	11	2065	c.1733G>T	c.(1732-1734)AGC>ATC	p.S578I	CDH10_uc011cnu.1_RNA	NM_006727	NP_006718	Q9Y6N8	CAD10_HUMAN	cadherin 10, type 2 preproprotein	578	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	24492973	24492973	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:24492973A>G	uc003jgr.1	-	10	1909	c.1577T>C	c.(1576-1578)TTC>TCC	p.F526S	CDH10_uc011cnu.1_RNA	NM_006727	NP_006718	Q9Y6N8	CAD10_HUMAN	cadherin 10, type 2 preproprotein	526	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)			---	---	---	---
CDH9	1007	broad.mit.edu	37	5	26881658	26881658	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:26881658G>A	uc003jgs.1	-	12	2126	c.1957C>T	c.(1957-1959)CGG>TGG	p.R653W	CDH9_uc011cnv.1_Missense_Mutation_p.R246W	NM_016279	NP_057363	Q9ULB4	CADH9_HUMAN	cadherin 9, type 2 preproprotein	653	Cytoplasmic (Potential).				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	26885752	26885752	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:26885752G>A	uc003jgs.1	-	11	2022	c.1853C>T	c.(1852-1854)GCG>GTG	p.A618V	CDH9_uc011cnv.1_Missense_Mutation_p.A211V	NM_016279	NP_057363	Q9ULB4	CADH9_HUMAN	cadherin 9, type 2 preproprotein	618	Helical; (Potential).				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																		---	---	---	---
C5orf22	55322	broad.mit.edu	37	5	31551400	31551400	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:31551400G>A	uc003jhj.3	+	8	1187	c.1060G>A	c.(1060-1062)GTT>ATT	p.V354I	C5orf22_uc011cnw.1_RNA|C5orf22_uc003jhk.3_Missense_Mutation_p.V89I|C5orf22_uc010iuj.2_Missense_Mutation_p.V89I	NM_018356	NP_060826	Q49AR2	CE022_HUMAN	hypothetical protein LOC55322	354										ovary(2)	2																		---	---	---	---
MTMR12	54545	broad.mit.edu	37	5	32230093	32230093	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:32230093C>T	uc003jhq.2	-	16	2205	c.2035G>A	c.(2035-2037)GAC>AAC	p.D679N	MTMR12_uc010iuk.2_Missense_Mutation_p.D625N|MTMR12_uc010iul.2_Missense_Mutation_p.D569N	NM_001040446	NP_001035536	Q9C0I1	MTMRC_HUMAN	myotubularin related protein 12	679						cytoplasm	phosphatase activity			ovary(1)	1																		---	---	---	---
ADAMTS12	81792	broad.mit.edu	37	5	33588787	33588787	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:33588787G>A	uc003jia.1	-	18	2945	c.2782C>T	c.(2782-2784)CAC>TAC	p.H928Y	ADAMTS12_uc010iuq.1_Missense_Mutation_p.H843Y	NM_030955	NP_112217	P58397	ATS12_HUMAN	ADAM metallopeptidase with thrombospondin type 1	928	TSP type-1 3.				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	33997486	33997486	+	Intron	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:33997486C>T	uc003jig.2	-						AMACR_uc003jih.2_Intron|AMACR_uc003jii.2_Intron|AMACR_uc003jij.2_Intron|AMACR_uc003jil.1_3'UTR|AMACR_uc003jik.1_Missense_Mutation_p.G239D	NM_014324	NP_055139			alpha-methylacyl-CoA racemase isoform 1						bile acid biosynthetic process|fatty acid beta-oxidation using acyl-CoA oxidase	mitochondrion|peroxisomal matrix	alpha-methylacyl-CoA racemase activity				0																OREG0016555	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
UGT3A1	133688	broad.mit.edu	37	5	35955837	35955837	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:35955837A>G	uc003jjv.1	-	6	1362	c.1205T>C	c.(1204-1206)GTA>GCA	p.V402A	UGT3A1_uc003jjw.1_RNA|UGT3A1_uc011coq.1_Missense_Mutation_p.V402A|UGT3A1_uc011cor.1_Missense_Mutation_p.V368A	NM_152404	NP_689617	Q6NUS8	UD3A1_HUMAN	UDP glycosyltransferase 3 family, polypeptide A1	402	Extracellular (Potential).					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)															---	---	---	---
NIPBL	25836	broad.mit.edu	37	5	36986318	36986318	+	Silent	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:36986318T>C	uc003jkl.3	+	10	3535	c.3036T>C	c.(3034-3036)GAT>GAC	p.D1012D	NIPBL_uc003jkk.3_Silent_p.D1012D|NIPBL_uc003jkm.1_Silent_p.D891D	NM_133433	NP_597677	Q6KC79	NIPBL_HUMAN	delangin isoform A	1012					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	37044481	37044481	+	Silent	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:37044481T>C	uc003jkl.3	+	35	6640	c.6141T>C	c.(6139-6141)GTT>GTC	p.V2047V	NIPBL_uc003jkk.3_Silent_p.V2047V	NM_133433	NP_597677	Q6KC79	NIPBL_HUMAN	delangin isoform A	2047					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	37122575	37122575	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:37122575T>C	uc011cpa.1	-	47	9043	c.8812A>G	c.(8812-8814)AGG>GGG	p.R2938G	C5orf42_uc003jko.1_5'Flank|C5orf42_uc003jkp.1_RNA|C5orf42_uc011coy.1_Missense_Mutation_p.R1456G|C5orf42_uc003jks.2_RNA|C5orf42_uc011coz.1_Missense_Mutation_p.R2031G	NM_023073	NP_075561	E9PH94	E9PH94_HUMAN	hypothetical protein LOC65250	2938										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	37351344	37351344	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:37351344C>T	uc003jku.1	-	6	789	c.671G>A	c.(670-672)GGC>GAC	p.G224D	NUP155_uc003jkt.1_Missense_Mutation_p.G165D|NUP155_uc010iuz.1_Missense_Mutation_p.G224D	NM_153485	NP_705618	O75694	NU155_HUMAN	nucleoporin 155kDa isoform 1	224					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)															---	---	---	---
LIFR	3977	broad.mit.edu	37	5	38496581	38496581	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:38496581T>C	uc010ive.1	-	13	2120	c.1788A>G	c.(1786-1788)ATA>ATG	p.I596M	LIFR_uc003jli.2_Missense_Mutation_p.I596M	NM_001127671	NP_001121143	P42702	LIFR_HUMAN	leukemia inhibitory factor receptor precursor	596	Extracellular (Potential).|Fibronectin type-III 4.				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								---	---	---	---
OSMR	9180	broad.mit.edu	37	5	38884113	38884113	+	Silent	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:38884113T>C	uc003jln.1	+	5	970	c.603T>C	c.(601-603)AAT>AAC	p.N201N	OSMR_uc003jlm.1_Silent_p.N201N	NM_003999	NP_003990	Q99650	OSMR_HUMAN	oncostatin M receptor precursor	201	Extracellular (Potential).				cell proliferation|positive regulation of cell proliferation	oncostatin-M receptor complex	growth factor binding|oncostatin-M receptor activity			ovary(2)|pancreas(1)|central_nervous_system(1)|skin(1)	5	all_lung(31;0.000365)																	---	---	---	---
RICTOR	253260	broad.mit.edu	37	5	38950533	38950533	+	Silent	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:38950533A>G	uc003jlp.2	-	31	3441	c.3417T>C	c.(3415-3417)GTT>GTC	p.V1139V	RICTOR_uc003jlo.2_Silent_p.V1139V|RICTOR_uc010ivf.2_Silent_p.V854V	NM_152756	NP_689969	Q6R327	RICTR_HUMAN	rapamycin-insensitive companion of mTOR	1139					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)																	---	---	---	---
CARD6	84674	broad.mit.edu	37	5	40853603	40853603	+	Silent	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:40853603A>G	uc003jmg.2	+	3	2244	c.2169A>G	c.(2167-2169)GTA>GTG	p.V723V		NM_032587	NP_115976	Q9BX69	CARD6_HUMAN	caspase recruitment domain family, member 6	723					apoptosis|regulation of apoptosis	intracellular				ovary(2)|skin(2)|lung(1)	5																		---	---	---	---
C7	730	broad.mit.edu	37	5	40937702	40937702	+	Silent	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:40937702A>G	uc003jmh.2	+	6	591	c.477A>G	c.(475-477)AAA>AAG	p.K159K	C7_uc011cpn.1_Intron	NM_000587	NP_000578	P10643	CO7_HUMAN	complement component 7 precursor	159	MACPF.				complement activation, alternative pathway|complement activation, classical pathway|cytolysis	extracellular region|membrane attack complex					0		Ovarian(839;0.0112)																---	---	---	---
HEATR7B2	133558	broad.mit.edu	37	5	41057271	41057271	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:41057271C>T	uc003jmj.3	-	9	1349	c.859G>A	c.(859-861)GCT>ACT	p.A287T	HEATR7B2_uc003jmi.3_Intron	NM_173489	NP_775760	Q7Z745	HTRB2_HUMAN	HEAT repeat family member 7B2	287	HEAT 3.						binding			ovary(6)|central_nervous_system(2)	8																		---	---	---	---
C6	729	broad.mit.edu	37	5	41150028	41150028	+	Intron	SNP	A	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:41150028A>T	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)																---	---	---	---
OXCT1	5019	broad.mit.edu	37	5	41807501	41807501	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:41807501C>T	uc003jmn.2	-	8	1103	c.772G>A	c.(772-774)GAC>AAC	p.D258N		NM_000436	NP_000427	P55809	SCOT1_HUMAN	3-oxoacid CoA transferase 1 precursor	258					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)													---	---	---	---
GHR	2690	broad.mit.edu	37	5	42695165	42695165	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:42695165A>G	uc003jmt.2	+	5	456	c.413A>G	c.(412-414)GAA>GGA	p.E138G	GHR_uc011cpq.1_5'UTR	NM_000163	NP_000154	P10912	GHR_HUMAN	growth hormone receptor precursor	138	Extracellular (Potential).				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	42719197	42719197	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:42719197A>G	uc003jmt.2	+	10	1631	c.1588A>G	c.(1588-1590)ATG>GTG	p.M530V	GHR_uc011cpq.1_Missense_Mutation_p.M343V	NM_000163	NP_000154	P10912	GHR_HUMAN	growth hormone receptor precursor	530	Cytoplasmic (Potential).				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)													---	---	---	---
HCN1	348980	broad.mit.edu	37	5	45262042	45262042	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:45262042C>T	uc003jok.2	-	8	2679	c.2654G>A	c.(2653-2655)CGA>CAA	p.R885Q		NM_021072	NP_066550	O60741	HCN1_HUMAN	hyperpolarization activated cyclic	885	Cytoplasmic (Potential).					integral to membrane	cAMP binding|sodium channel activity|voltage-gated potassium channel activity			ovary(1)	1																		---	---	---	---
ITGA1	3672	broad.mit.edu	37	5	52211415	52211415	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:52211415C>T	uc003jou.2	+	15	2031	c.1979C>T	c.(1978-1980)GCC>GTC	p.A660V	ITGA1_uc003jov.2_RNA|ITGA1_uc003jow.2_Missense_Mutation_p.A191V	NM_181501	NP_852478	P56199	ITA1_HUMAN	integrin, alpha 1 precursor	660	Extracellular (Potential).|FG-GAP 7.				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)																---	---	---	---
FST	10468	broad.mit.edu	37	5	52779374	52779374	+	Silent	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:52779374C>T	uc003jpd.2	+	3	345	c.318C>T	c.(316-318)TGC>TGT	p.C106C	FST_uc003jpc.2_Silent_p.C106C	NM_013409	NP_037541	P19883	FST_HUMAN	follistatin isoform FST344 precursor	106	Follistatin-like 1.				hemopoietic progenitor cell differentiation|negative regulation of activin receptor signaling pathway|negative regulation of follicle-stimulating hormone secretion|negative regulation of transcription from RNA polymerase II promoter|positive regulation of hair follicle development	extracellular region	activin binding|protein binding|signal transducer activity				0		Ovarian(174;1.78e-06)|Lung NSC(810;3.55e-06)|Breast(144;4.08e-05)																---	---	---	---
SLC38A9	153129	broad.mit.edu	37	5	54952562	54952562	+	Silent	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:54952562A>G	uc003jqf.2	-	9	939	c.738T>C	c.(736-738)AGT>AGC	p.S246S	SLC38A9_uc003jqd.2_Silent_p.S183S|SLC38A9_uc010ivx.2_Silent_p.S219S|SLC38A9_uc003jqe.2_RNA|SLC38A9_uc010ivy.2_Silent_p.S117S	NM_173514	NP_775785	Q8NBW4	S38A9_HUMAN	solute carrier family 38, member 9	246					amino acid transport|sodium ion transport	integral to membrane					0		Lung NSC(810;0.00122)|Prostate(74;0.0376)|Breast(144;0.181)																---	---	---	---
IL6ST	3572	broad.mit.edu	37	5	55237126	55237126	+	Silent	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:55237126T>C	uc003jqq.2	-	17	2796	c.2541A>G	c.(2539-2541)AGA>AGG	p.R847R	uc003jqp.2_5'Flank|IL6ST_uc010iwb.2_Silent_p.R786R|IL6ST_uc010iwc.2_3'UTR|IL6ST_uc010iwd.2_Silent_p.R166R|IL6ST_uc011cqk.1_Silent_p.R558R|IL6ST_uc003jqr.2_3'UTR	NM_002184	NP_002175	P40189	IL6RB_HUMAN	interleukin 6 signal transducer isoform 1	847	Cytoplasmic (Potential).				interleukin-6-mediated signaling pathway|leukemia inhibitory factor signaling pathway|negative regulation of interleukin-6-mediated signaling pathway|positive regulation of anti-apoptosis|positive regulation of cardiac muscle hypertrophy|positive regulation of osteoblast differentiation|positive regulation of T cell proliferation|positive regulation of tyrosine phosphorylation of Stat1 protein|positive regulation of tyrosine phosphorylation of Stat3 protein|positive regulation vascular endothelial growth factor production	ciliary neurotrophic factor receptor complex|extracellular region|extracellular space|interleukin-6 receptor complex|oncostatin-M receptor complex	ciliary neurotrophic factor receptor activity|ciliary neurotrophic factor receptor binding|growth factor binding|protein homodimerization activity			large_intestine(1)|ovary(1)	2		Lung NSC(810;8.69e-05)|Prostate(74;0.00308)|Breast(144;0.0544)|Ovarian(174;0.223)						O		hepatocellular ca								---	---	---	---
HTR1A	3350	broad.mit.edu	37	5	63256400	63256400	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:63256400C>T	uc011cqt.1	-	1	1147	c.1147G>A	c.(1147-1149)GCC>ACC	p.A383T		NM_000524	NP_000515	P08908	5HT1A_HUMAN	5-hydroxytryptamine (serotonin) receptor 1A	383	Helical; Name=7; (By similarity).				behavior|positive regulation of cell proliferation	integral to plasma membrane	serotonin receptor activity			ovary(2)|pancreas(2)	4		Lung NSC(810;3.55e-06)|Prostate(74;0.0352)|Ovarian(174;0.0545)|Breast(144;0.0575)|Colorectal(97;0.234)		Lung(70;0.105)	Alprenolol(DB00866)|Aripiprazole(DB01238)|Buspirone(DB00490)|Clozapine(DB00363)|Eletriptan(DB00216)|Ergoloid mesylate(DB01049)|Fluvoxamine(DB00176)|Lisuride(DB00589)|Methysergide(DB00247)|Mirtazapine(DB00370)|Pindolol(DB00960)|Propranolol(DB00571)|Quetiapine(DB01224)|Sertraline(DB01104)|Tegaserod(DB01079)|Trazodone(DB00656)|Venlafaxine(DB00285)|Ziprasidone(DB00246)													---	---	---	---
HTR1A	3350	broad.mit.edu	37	5	63257030	63257030	+	Silent	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:63257030G>A	uc011cqt.1	-	1	517	c.517C>T	c.(517-519)CTG>TTG	p.L173L		NM_000524	NP_000515	P08908	5HT1A_HUMAN	5-hydroxytryptamine (serotonin) receptor 1A	173	Helical; Name=4; (By similarity).				behavior|positive regulation of cell proliferation	integral to plasma membrane	serotonin receptor activity			ovary(2)|pancreas(2)	4		Lung NSC(810;3.55e-06)|Prostate(74;0.0352)|Ovarian(174;0.0545)|Breast(144;0.0575)|Colorectal(97;0.234)		Lung(70;0.105)	Alprenolol(DB00866)|Aripiprazole(DB01238)|Buspirone(DB00490)|Clozapine(DB00363)|Eletriptan(DB00216)|Ergoloid mesylate(DB01049)|Fluvoxamine(DB00176)|Lisuride(DB00589)|Methysergide(DB00247)|Mirtazapine(DB00370)|Pindolol(DB00960)|Propranolol(DB00571)|Quetiapine(DB01224)|Sertraline(DB01104)|Tegaserod(DB01079)|Trazodone(DB00656)|Venlafaxine(DB00285)|Ziprasidone(DB00246)													---	---	---	---
C5orf44	80006	broad.mit.edu	37	5	64931791	64931791	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:64931791A>G	uc003jtz.3	+	3	466	c.136A>G	c.(136-138)ATG>GTG	p.M46V	C5orf44_uc003jua.3_Missense_Mutation_p.M46V|C5orf44_uc003juc.3_Missense_Mutation_p.M46V|C5orf44_uc010iwv.2_Missense_Mutation_p.M46V	NM_024941	NP_079217	A5PLN9	CE044_HUMAN	hypothetical protein LOC80006 isoform 2	46										ovary(1)	1																		---	---	---	---
MAST4	375449	broad.mit.edu	37	5	66448635	66448635	+	Nonsense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:66448635C>T	uc003jut.1	+	24	2967	c.2899C>T	c.(2899-2901)CGA>TGA	p.R967*	MAST4_uc003juw.2_Nonsense_Mutation_p.R895*	NM_015183	NP_055998	O15021	MAST4_HUMAN	microtubule associated serine/threonine kinase	1159	PDZ.					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)														---	---	---	---
PIK3R1	5295	broad.mit.edu	37	5	67591097	67591097	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:67591097A>G	uc003jva.2	+	13	2250	c.1690A>G	c.(1690-1692)AAC>GAC	p.N564D	PIK3R1_uc003jvb.2_Missense_Mutation_p.N564D|PIK3R1_uc003jvc.2_Missense_Mutation_p.N264D|PIK3R1_uc003jvd.2_Missense_Mutation_p.N294D|PIK3R1_uc003jve.2_Missense_Mutation_p.N243D|PIK3R1_uc011crb.1_Missense_Mutation_p.N234D	NM_181523	NP_852664	P27986	P85A_HUMAN	phosphoinositide-3-kinase, regulatory subunit 1	564					epidermal growth factor receptor signaling pathway|fibroblast growth factor receptor signaling pathway|growth hormone receptor signaling pathway|insulin receptor signaling pathway|insulin-like growth factor receptor signaling pathway|interspecies interaction between organisms|leukocyte migration|nerve growth factor receptor signaling pathway|phosphatidylinositol 3-kinase cascade|phosphatidylinositol phosphorylation|phosphatidylinositol-mediated signaling|platelet activation|positive regulation of establishment of protein localization in plasma membrane|positive regulation of glucose import|T cell costimulation|T cell receptor signaling pathway	1-phosphatidylinositol-4-phosphate 3-kinase, class IA complex	1-phosphatidylinositol binding|ErbB-3 class receptor binding|insulin binding|insulin receptor binding|insulin receptor substrate binding|insulin-like growth factor receptor binding|phosphatidylinositol 3-kinase regulator activity|protein phosphatase binding	p.N564D(3)|p.D560_S565del(1)|p.N564K(1)|p.?(1)		endometrium(34)|central_nervous_system(27)|large_intestine(20)|breast(7)|ovary(5)|haematopoietic_and_lymphoid_tissue(3)|lung(2)|urinary_tract(1)|skin(1)|pancreas(1)	101		Lung NSC(167;1.99e-05)|Prostate(74;0.00308)|Ovarian(174;0.00473)|Colorectal(97;0.0176)		OV - Ovarian serous cystadenocarcinoma(47;3.76e-51)|Lung(70;0.0211)	Isoproterenol(DB01064)			Mis|F|O		gliobastoma|ovarian|colorectal					TCGA GBM(4;<1E-08)			---	---	---	---
RAD17	5884	broad.mit.edu	37	5	68709854	68709854	+	Intron	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:68709854A>G	uc003jwo.2	+						RAD17_uc003jwg.2_Intron|RAD17_uc003jwh.2_Intron|RAD17_uc003jwi.2_Intron|RAD17_uc003jwj.2_Intron|RAD17_uc003jwk.2_Intron|RAD17_uc003jwl.2_Intron|RAD17_uc003jwm.2_Intron|RAD17_uc003jwn.2_Intron|RAD17_uc003jwp.2_Intron|MARVELD2_uc010ixf.2_5'Flank|MARVELD2_uc003jwr.1_5'Flank|MARVELD2_uc003jwq.2_5'Flank	NM_133339	NP_579917			RAD17 homolog isoform 2						cell cycle|DNA damage checkpoint|DNA repair|DNA replication|DNA replication checkpoint|mitotic cell cycle checkpoint|negative regulation of DNA replication|regulation of phosphorylation	nucleoplasm	ATP binding|nucleoside-triphosphatase activity|protein binding				0		Lung NSC(167;5.19e-05)|Prostate(74;0.0143)|Ovarian(174;0.0448)|Breast(144;0.198)		OV - Ovarian serous cystadenocarcinoma(47;9.36e-57)|Epithelial(20;1.21e-52)|all cancers(19;3.34e-48)|Lung(70;0.0183)									Direct_reversal_of_damage|Other_conserved_DNA_damage_response_genes					---	---	---	---
MARVELD2	153562	broad.mit.edu	37	5	68715651	68715651	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:68715651C>T	uc003jwq.2	+	2	498	c.439C>T	c.(439-441)CGG>TGG	p.R147W	MARVELD2_uc010ixf.2_Missense_Mutation_p.R147W|MARVELD2_uc003jwr.1_Missense_Mutation_p.R147W|MARVELD2_uc003jws.1_RNA	NM_001038603	NP_001033692	Q8N4S9	MALD2_HUMAN	MARVEL domain containing 2 isoform 1	147	Cytoplasmic (Potential).				sensory perception of sound	integral to membrane|tight junction					0		Lung NSC(167;0.000937)|Prostate(74;0.0187)|Ovarian(174;0.16)		OV - Ovarian serous cystadenocarcinoma(47;7.31e-57)|Epithelial(20;1.05e-52)|all cancers(19;2.63e-48)|Lung(70;0.0183)														---	---	---	---
MARVELD2	153562	broad.mit.edu	37	5	68737385	68737385	+	Silent	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:68737385A>G	uc003jwq.2	+	7	1640	c.1581A>G	c.(1579-1581)GAA>GAG	p.E527E	MARVELD2_uc010ixf.2_Silent_p.E515E|MARVELD2_uc003jwr.1_Intron|MARVELD2_uc003jws.1_RNA	NM_001038603	NP_001033692	Q8N4S9	MALD2_HUMAN	MARVEL domain containing 2 isoform 1	527	Potential.|Cytoplasmic (Potential).				sensory perception of sound	integral to membrane|tight junction					0		Lung NSC(167;0.000937)|Prostate(74;0.0187)|Ovarian(174;0.16)		OV - Ovarian serous cystadenocarcinoma(47;7.31e-57)|Epithelial(20;1.05e-52)|all cancers(19;2.63e-48)|Lung(70;0.0183)														---	---	---	---
MCCC2	64087	broad.mit.edu	37	5	70895565	70895565	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:70895565A>G	uc003kbs.3	+	4	499	c.361A>G	c.(361-363)ACA>GCA	p.T121A	MCCC2_uc010iyv.1_Missense_Mutation_p.T121A|MCCC2_uc003kbt.3_RNA|MCCC2_uc003kbu.1_5'Flank	NM_022132	NP_071415	Q9HCC0	MCCB_HUMAN	methylcrotonoyl-Coenzyme A carboxylase 2 (beta)	121	Carboxyltransferase.				leucine catabolic process	mitochondrial inner membrane|mitochondrial matrix	ATP binding|methylcrotonoyl-CoA carboxylase activity			ovary(1)	1		Lung NSC(167;0.000697)|Prostate(74;0.0107)|Ovarian(174;0.0175)|Breast(144;0.198)		OV - Ovarian serous cystadenocarcinoma(47;2.04e-54)	Biotin(DB00121)													---	---	---	---
MAP1B	4131	broad.mit.edu	37	5	71495360	71495360	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:71495360G>A	uc003kbw.3	+	5	6419	c.6178G>A	c.(6178-6180)GAG>AAG	p.E2060K	MAP1B_uc010iyw.1_Missense_Mutation_p.E2077K|MAP1B_uc010iyx.1_Missense_Mutation_p.E1934K|MAP1B_uc010iyy.1_Missense_Mutation_p.E1934K	NM_005909	NP_005900	P46821	MAP1B_HUMAN	microtubule-associated protein 1B	2060	MAP1B 10.					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)														---	---	---	---
TNPO1	3842	broad.mit.edu	37	5	72183988	72183988	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:72183988C>T	uc003kck.3	+	13	1534	c.1387C>T	c.(1387-1389)CGT>TGT	p.R463C	TNPO1_uc011csj.1_Missense_Mutation_p.R413C|TNPO1_uc003kch.2_Missense_Mutation_p.R455C|TNPO1_uc003kci.3_Missense_Mutation_p.R455C|TNPO1_uc003kcg.3_Missense_Mutation_p.R455C	NM_002270	NP_002261	Q92973	TNPO1_HUMAN	transportin 1 isoform 1	463	HEAT 5.				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)														---	---	---	---
TNPO1	3842	broad.mit.edu	37	5	72185781	72185781	+	Silent	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:72185781A>G	uc003kck.3	+	14	1845	c.1698A>G	c.(1696-1698)AAA>AAG	p.K566K	TNPO1_uc011csj.1_Silent_p.K516K|TNPO1_uc003kch.2_Silent_p.K558K|TNPO1_uc003kci.3_Silent_p.K558K|TNPO1_uc003kcg.3_Silent_p.K558K	NM_002270	NP_002261	Q92973	TNPO1_HUMAN	transportin 1 isoform 1	566					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)														---	---	---	---
TNPO1	3842	broad.mit.edu	37	5	72195900	72195900	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:72195900A>G	uc003kck.3	+	21	2553	c.2406A>G	c.(2404-2406)ATA>ATG	p.I802M	TNPO1_uc011csj.1_Missense_Mutation_p.I752M|TNPO1_uc003kch.2_Missense_Mutation_p.I794M|TNPO1_uc003kci.3_Missense_Mutation_p.I794M|TNPO1_uc003kcg.3_Missense_Mutation_p.I794M	NM_002270	NP_002261	Q92973	TNPO1_HUMAN	transportin 1 isoform 1	802					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)														---	---	---	---
FOXD1	2297	broad.mit.edu	37	5	72743785	72743785	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:72743785T>C	uc003kcp.2	-	1	568	c.403A>G	c.(403-405)ACT>GCT	p.T135A		NM_004472	NP_004463	Q16676	FOXD1_HUMAN	forkhead box D1	135	Fork-head.				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|metanephric capsule specification|negative regulation of transcription, DNA-dependent|neural crest cell migration|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		Lung NSC(167;0.00327)|Ovarian(174;0.0175)|Prostate(461;0.151)		OV - Ovarian serous cystadenocarcinoma(47;1.07e-54)														---	---	---	---
RGNEF	64283	broad.mit.edu	37	5	73148496	73148496	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:73148496C>T	uc011csq.1	+	13	1780	c.1769C>T	c.(1768-1770)TCG>TTG	p.S590L	RGNEF_uc003kcx.2_Missense_Mutation_p.S590L|RGNEF_uc003kcy.1_3'UTR|RGNEF_uc010izf.2_Missense_Mutation_p.S590L|RGNEF_uc011csr.1_Missense_Mutation_p.S277L	NM_001080479	NP_001073948	Q8N1W1	RGNEF_HUMAN	Rho-guanine nucleotide exchange factor	590					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)														---	---	---	---
HEXB	3074	broad.mit.edu	37	5	74009401	74009401	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:74009401G>A	uc003kdf.3	+	7	959	c.842G>A	c.(841-843)CGA>CAA	p.R281Q	HEXB_uc003kdd.2_Missense_Mutation_p.R56Q|HEXB_uc010izh.2_RNA	NM_000521	NP_000512	P07686	HEXB_HUMAN	hexosaminidase B preproprotein	281					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)														---	---	---	---
POLK	51426	broad.mit.edu	37	5	74877123	74877123	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:74877123C>T	uc003kdw.2	+	7	880	c.784C>T	c.(784-786)CCC>TCC	p.P262S	POLK_uc003kdx.2_RNA|POLK_uc003kdy.2_RNA|POLK_uc003kea.2_Missense_Mutation_p.P262S|POLK_uc003keb.2_Missense_Mutation_p.P262S|POLK_uc010izq.2_Missense_Mutation_p.P262S|POLK_uc003kec.2_Missense_Mutation_p.P172S|POLK_uc010izr.2_RNA|POLK_uc010izs.2_RNA|POLK_uc003ked.2_Missense_Mutation_p.P172S|POLK_uc003kee.2_Missense_Mutation_p.P262S|POLK_uc003kef.2_Missense_Mutation_p.P172S	NM_016218	NP_057302	Q9UBT6	POLK_HUMAN	DNA-directed DNA polymerase kappa	262	UmuC.				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	75906983	75906983	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:75906983A>G	uc003kek.2	+	13	1718	c.1496A>G	c.(1495-1497)TAC>TGC	p.Y499C	IQGAP2_uc010izv.2_Missense_Mutation_p.Y52C|IQGAP2_uc011csv.1_Missense_Mutation_p.Y52C|IQGAP2_uc003kel.2_Missense_Mutation_p.Y52C	NM_006633	NP_006624	Q13576	IQGA2_HUMAN	IQ motif containing GTPase activating protein 2	499					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)														---	---	---	---
F2RL1	2150	broad.mit.edu	37	5	76115061	76115061	+	Silent	SNP	C	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:76115061C>A	uc003keo.2	+	1	229	c.54C>A	c.(52-54)GCC>GCA	p.A18A		NM_005242	NP_005233	P55085	PAR2_HUMAN	coagulation factor II (thrombin) receptor-like 1	18					blood coagulation|elevation of cytosolic calcium ion concentration|positive regulation of leukocyte chemotaxis|positive regulation of positive chemotaxis|regulation of blood coagulation	Golgi apparatus|integral to plasma membrane	receptor binding|thrombin receptor activity			central_nervous_system(1)	1		all_lung(232;0.000414)|Lung NSC(167;0.0011)|Ovarian(174;0.0129)|Prostate(461;0.11)		OV - Ovarian serous cystadenocarcinoma(54;7.7e-51)|Epithelial(54;2.77e-45)|all cancers(79;3.47e-41)														---	---	---	---
BHMT	635	broad.mit.edu	37	5	78423699	78423699	+	Silent	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:78423699T>C	uc003kfu.3	+	7	1035	c.930T>C	c.(928-930)ATT>ATC	p.I310I	BHMT_uc011cti.1_Silent_p.I157I	NM_001713	NP_001704	Q93088	BHMT1_HUMAN	betaine-homocysteine methyltransferase	310	Hcy-binding.				protein methylation|regulation of homocysteine metabolic process	cytoplasm	betaine-homocysteine S-methyltransferase activity|homocysteine S-methyltransferase activity|zinc ion binding			ovary(1)	1		all_lung(232;0.00051)|Lung NSC(167;0.00131)|Ovarian(174;0.0261)|Prostate(461;0.191)		OV - Ovarian serous cystadenocarcinoma(54;1.88e-45)|Epithelial(54;8.07e-41)|all cancers(79;3.51e-36)	L-Methionine(DB00134)													---	---	---	---
CMYA5	202333	broad.mit.edu	37	5	79025260	79025260	+	Silent	SNP	A	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:79025260A>C	uc003kgc.2	+	2	744	c.672A>C	c.(670-672)ACA>ACC	p.T224T		NM_153610	NP_705838	Q8N3K9	CMYA5_HUMAN	cardiomyopathy associated 5	224						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)														---	---	---	---
THBS4	7060	broad.mit.edu	37	5	79378294	79378294	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:79378294G>A	uc003kgh.2	+	22	3073	c.2750G>A	c.(2749-2751)CGT>CAT	p.R917H	uc003kgi.3_RNA	NM_003248	NP_003239	P35443	TSP4_HUMAN	thrombospondin 4 precursor	917	TSP C-terminal.				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)														---	---	---	---
ZFYVE16	9765	broad.mit.edu	37	5	79732954	79732954	+	Silent	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:79732954G>A	uc003kgr.3	+	4	752	c.450G>A	c.(448-450)TTG>TTA	p.L150L	ZFYVE16_uc010jak.1_Silent_p.L150L|ZFYVE16_uc003kgp.2_Silent_p.L150L|ZFYVE16_uc003kgq.3_Silent_p.L150L|ZFYVE16_uc003kgs.3_Silent_p.L150L	NM_001105251	NP_001098721	Q7Z3T8	ZFY16_HUMAN	zinc finger, FYVE domain containing 16	150					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)														---	---	---	---
RASGRF2	5924	broad.mit.edu	37	5	80382676	80382676	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:80382676G>A	uc003kha.1	+	9	1294	c.1294G>A	c.(1294-1296)GAC>AAC	p.D432N	RASGRF2_uc011ctn.1_RNA|RASGRF2_uc003khb.1_Missense_Mutation_p.D260N	NM_006909	NP_008840	O14827	RGRF2_HUMAN	Ras protein-specific guanine	432					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)														---	---	---	---
VCAN	1462	broad.mit.edu	37	5	82836624	82836624	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:82836624T>C	uc003kii.3	+	8	8158	c.7802T>C	c.(7801-7803)GTA>GCA	p.V2601A	VCAN_uc003kij.3_Missense_Mutation_p.V1614A|VCAN_uc010jau.2_Intron|VCAN_uc003kik.3_Intron|VCAN_uc003kil.3_Missense_Mutation_p.V1265A	NM_004385	NP_004376	P13611	CSPG2_HUMAN	versican isoform 1 precursor	2601	GAG-beta.				cell adhesion|cell recognition|glial cell migration	extracellular space|proteinaceous extracellular matrix	calcium ion binding|hyaluronic acid binding|sugar binding	p.V2601V(1)		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)														---	---	---	---
EDIL3	10085	broad.mit.edu	37	5	83360521	83360521	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:83360521G>A	uc003kio.1	-	8	1369	c.950C>T	c.(949-951)TCG>TTG	p.S317L	EDIL3_uc003kip.1_Missense_Mutation_p.S307L|EDIL3_uc011ctt.1_Missense_Mutation_p.S94L	NM_005711	NP_005702	O43854	EDIL3_HUMAN	EGF-like repeats and discoidin I-like	317					cell adhesion|multicellular organismal development	extracellular region	calcium ion binding|integrin binding			skin(2)	2		Lung NSC(167;0.000121)|all_lung(232;0.000154)|Ovarian(174;0.0425)		OV - Ovarian serous cystadenocarcinoma(54;4.3e-40)|Epithelial(54;4.79e-32)|all cancers(79;1.54e-26)														---	---	---	---
GPR98	84059	broad.mit.edu	37	5	89948233	89948233	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:89948233T>G	uc003kju.2	+	19	3583	c.3487T>G	c.(3487-3489)TTG>GTG	p.L1163V	GPR98_uc003kjt.2_5'UTR	NM_032119	NP_115495	Q8WXG9	GPR98_HUMAN	G protein-coupled receptor 98 precursor	1163	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	92929408	92929408	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:92929408C>T	uc003kkj.2	+	3	2819	c.1132C>T	c.(1132-1134)CGC>TGC	p.R378C		NM_005654	NP_005645	P10589	COT1_HUMAN	nuclear receptor subfamily 2, group F, member 1	378					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)														---	---	---	---
TTC37	9652	broad.mit.edu	37	5	94852700	94852700	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:94852700A>G	uc003klb.2	-	22	2626	c.2356T>C	c.(2356-2358)TAT>CAT	p.Y786H		NM_014639	NP_055454	Q6PGP7	TTC37_HUMAN	tetratricopeptide repeat domain 37	786							binding			ovary(3)|pancreas(1)	4																		---	---	---	---
ARSK	153642	broad.mit.edu	37	5	94939204	94939204	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:94939204A>G	uc003kld.2	+	8	1743	c.1585A>G	c.(1585-1587)ACC>GCC	p.T529A	ARSK_uc010jbg.2_Missense_Mutation_p.T370A|ARSK_uc011cum.1_RNA	NM_198150	NP_937793	Q6UWY0	ARSK_HUMAN	arylsulfatase K precursor	529						extracellular region	arylsulfatase activity|metal ion binding			pancreas(1)	1		all_cancers(142;3.38e-06)|all_epithelial(76;6.57e-09)|all_lung(232;0.00307)|Lung NSC(167;0.00452)|Ovarian(225;0.00473)		all cancers(79;6.5e-16)														---	---	---	---
RFESD	317671	broad.mit.edu	37	5	94989851	94989851	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:94989851C>T	uc003klf.2	+	3	1478	c.86C>T	c.(85-87)TCT>TTT	p.S29F	RFESD_uc003klg.2_Missense_Mutation_p.S82F|RFESD_uc011cun.1_Missense_Mutation_p.S82F|SPATA9_uc010jbh.1_Intron|SPATA9_uc003klh.1_Intron|SPATA9_uc003kli.1_Intron	NM_173362	NP_775498	Q8TAC1	RFESD_HUMAN	Rieske (Fe-S) domain containing isoform 2	29	Rieske 2.|Rieske 1.						2 iron, 2 sulfur cluster binding|metal ion binding|oxidoreductase activity				0		all_cancers(142;0.000215)|all_epithelial(76;7.43e-07)|all_lung(232;0.0318)|Lung NSC(167;0.041)|Ovarian(225;0.051)|Colorectal(57;0.162)		all cancers(79;5.94e-17)														---	---	---	---
ERAP1	51752	broad.mit.edu	37	5	96126301	96126301	+	Missense_Mutation	SNP	C	T	T	rs150674566		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:96126301C>T	uc003kmm.2	-	9	1713	c.1366G>A	c.(1366-1368)GCA>ACA	p.A456T	ERAP1_uc003kml.2_Missense_Mutation_p.A456T|ERAP1_uc010jbm.1_Missense_Mutation_p.A268T|ERAP1_uc003kmn.2_Missense_Mutation_p.A456T	NM_001040458	NP_001035548	Q9NZ08	ERAP1_HUMAN	type 1 tumor necrosis factor receptor shedding	456	Lumenal (Potential).				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)														---	---	---	---
RGMB	285704	broad.mit.edu	37	5	98129354	98129354	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:98129354G>A	uc003knc.2	+	5	1736	c.1334G>A	c.(1333-1335)CGC>CAC	p.R445H		NM_001012761	NP_001012779	Q6NW40	RGMB_HUMAN	RGM domain family, member B	404					axon guidance|BMP signaling pathway|cell adhesion|positive regulation of transcription, DNA-dependent	anchored to plasma membrane|ER-Golgi intermediate compartment|membrane raft	identical protein binding				0		all_cancers(142;2.76e-08)|all_epithelial(76;2.98e-11)|all_lung(232;0.000485)|Lung NSC(167;0.000693)|Prostate(80;0.000986)|Ovarian(225;0.024)|Colorectal(57;0.117)		COAD - Colon adenocarcinoma(37;0.0587)														---	---	---	---
ST8SIA4	7903	broad.mit.edu	37	5	100222135	100222135	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:100222135A>G	uc003knk.2	-	3	743	c.415T>C	c.(415-417)TTT>CTT	p.F139L	ST8SIA4_uc003knl.2_Missense_Mutation_p.F139L	NM_005668	NP_005659	Q92187	SIA8D_HUMAN	ST8 alpha-N-acetyl-neuraminide	139	Lumenal (Potential).				axon guidance|N-glycan processing	integral to Golgi membrane	alpha-N-acetylneuraminate alpha-2,8-sialyltransferase activity			large_intestine(1)|central_nervous_system(1)	2		all_cancers(142;1.5e-07)|all_epithelial(76;1.43e-10)|Prostate(80;0.000644)|Lung NSC(167;0.0059)|all_lung(232;0.00914)|Ovarian(225;0.024)|Colorectal(57;0.09)|Breast(839;0.203)		COAD - Colon adenocarcinoma(37;0.00402)														---	---	---	---
FER	2241	broad.mit.edu	37	5	108523138	108523138	+	Silent	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:108523138C>T	uc003kop.1	+	20	2715	c.2331C>T	c.(2329-2331)TAC>TAT	p.Y777Y	FER_uc011cvg.1_Silent_p.Y602Y	NM_005246	NP_005237	P16591	FER_HUMAN	fer (fps/fes related) tyrosine kinase	777	Protein 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)														---	---	---	---
MAN2A1	4124	broad.mit.edu	37	5	109049311	109049311	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:109049311G>A	uc003kou.1	+	2	1189	c.226G>A	c.(226-228)GTC>ATC	p.V76I		NM_002372	NP_002363	Q16706	MA2A1_HUMAN	mannosidase, alpha, class 2A, member 1	76	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	109183494	109183494	+	Intron	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:109183494A>G	uc003kou.1	+							NM_002372	NP_002363			mannosidase, alpha, class 2A, member 1						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)														---	---	---	---
TSLP	85480	broad.mit.edu	37	5	110409263	110409263	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:110409263G>A	uc003kpb.2	+	3	470	c.271G>A	c.(271-273)GCG>ACG	p.A91T	TSLP_uc003kpa.2_RNA|TSLP_uc010jbt.1_5'UTR	NM_033035	NP_149024	Q969D9	TSLP_HUMAN	thymic stromal lymphopoietin isoform 1	91						extracellular space	cytokine activity				0		all_cancers(142;2.72e-05)|all_epithelial(76;4.39e-07)|Prostate(80;0.00955)|Lung NSC(167;0.0417)|Ovarian(225;0.0443)|Colorectal(57;0.0464)|all_lung(232;0.0507)|Breast(839;0.244)		OV - Ovarian serous cystadenocarcinoma(64;1.24e-08)|Epithelial(69;1.54e-07)|all cancers(49;1.73e-05)|COAD - Colon adenocarcinoma(37;0.109)														---	---	---	---
KCNN2	3781	broad.mit.edu	37	5	113831822	113831822	+	Silent	SNP	G	A	A	rs145963927		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:113831822G>A	uc003kqo.2	+	8	2140	c.1683G>A	c.(1681-1683)TCG>TCA	p.S561S	KCNN2_uc003kqp.2_Silent_p.S213S|KCNN2_uc010jcg.2_RNA|uc003kqr.1_RNA	NM_021614	NP_067627	Q9H2S1	KCNN2_HUMAN	small conductance calcium-activated potassium	561						integral to membrane	calmodulin binding|small conductance calcium-activated potassium channel activity			ovary(2)	2		all_cancers(142;2.86e-05)|all_epithelial(76;9.33e-06)|Prostate(80;0.00955)|Ovarian(225;0.0444)|Breast(839;0.159)|Lung NSC(810;0.174)|all_lung(232;0.206)		OV - Ovarian serous cystadenocarcinoma(64;1.89e-08)|Epithelial(69;2.04e-08)|all cancers(49;3.74e-06)|COAD - Colon adenocarcinoma(37;0.142)|Colorectal(14;0.195)														---	---	---	---
TRIM36	55521	broad.mit.edu	37	5	114469612	114469612	+	Silent	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:114469612A>G	uc003kqs.2	-	8	1988	c.1479T>C	c.(1477-1479)GGT>GGC	p.G493G	TRIM36_uc011cwc.1_Silent_p.G481G|TRIM36_uc003kqt.2_Silent_p.G338G	NM_018700	NP_061170	Q9NQ86	TRI36_HUMAN	tripartite motif-containing 36 isoform 1	493	Fibronectin type-III.					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)														---	---	---	---
DMXL1	1657	broad.mit.edu	37	5	118507670	118507670	+	Intron	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:118507670T>C	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)														---	---	---	---
HSD17B4	3295	broad.mit.edu	37	5	118844893	118844893	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:118844893T>C	uc003ksj.2	+	16	1514	c.1391T>C	c.(1390-1392)GTT>GCT	p.V464A	HSD17B4_uc011cwg.1_Missense_Mutation_p.V440A|HSD17B4_uc011cwh.1_Missense_Mutation_p.V446A|HSD17B4_uc011cwi.1_Missense_Mutation_p.V489A|HSD17B4_uc003ksk.3_Missense_Mutation_p.V317A|HSD17B4_uc011cwj.1_Missense_Mutation_p.V317A|HSD17B4_uc010jcn.1_Missense_Mutation_p.V202A	NM_000414	NP_000405	P51659	DHB4_HUMAN	hydroxysteroid (17-beta) dehydrogenase 4	464	Enoyl-CoA hydratase 2.				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)													---	---	---	---
PRR16	51334	broad.mit.edu	37	5	120022069	120022069	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:120022069G>T	uc003ksq.2	+	2	743	c.580G>T	c.(580-582)GAC>TAC	p.D194Y	PRR16_uc003ksp.2_Missense_Mutation_p.D171Y|PRR16_uc003ksr.2_Missense_Mutation_p.D124Y	NM_016644	NP_057728	Q569H4	PRR16_HUMAN	proline rich 16	194	Pro-rich.									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)														---	---	---	---
C5orf48	389320	broad.mit.edu	37	5	125971720	125971720	+	Intron	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:125971720T>C	uc003kub.1	+							NM_207408	NP_997291			hypothetical protein LOC389320											ovary(1)	1																		---	---	---	---
FBN2	2201	broad.mit.edu	37	5	127681104	127681104	+	Silent	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:127681104G>A	uc003kuu.2	-	24	3601	c.3162C>T	c.(3160-3162)CGC>CGT	p.R1054R	FBN2_uc003kuv.2_Silent_p.R1021R	NM_001999	NP_001990	P35556	FBN2_HUMAN	fibrillin 2 precursor	1054					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)														---	---	---	---
SLC27A6	28965	broad.mit.edu	37	5	128368875	128368875	+	Missense_Mutation	SNP	T	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:128368875T>A	uc003kuy.2	+	11	2156	c.1760T>A	c.(1759-1761)ATT>AAT	p.I587N	SLC27A6_uc003kuz.2_Missense_Mutation_p.I587N	NM_014031	NP_054750	Q9Y2P4	S27A6_HUMAN	solute carrier family 27 (fatty acid	587					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)														---	---	---	---
RAPGEF6	51735	broad.mit.edu	37	5	131080261	131080261	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:131080261A>G	uc003kvp.1	-	2	357	c.215T>C	c.(214-216)GTA>GCA	p.V72A	FNIP1_uc003kvs.1_Missense_Mutation_p.V72A|FNIP1_uc003kvt.1_Missense_Mutation_p.V72A|FNIP1_uc010jdm.1_Missense_Mutation_p.V72A|FNIP1_uc003kvu.2_Missense_Mutation_p.V72A	NM_016340	NP_057424	Q8TEU7	RPGF6_HUMAN	PDZ domain-containing guanine nucleotide	Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment					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)														---	---	---	---
KIF3A	11127	broad.mit.edu	37	5	132061815	132061815	+	Intron	SNP	C	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:132061815C>A	uc003kxo.2	-						KIF3A_uc003kxn.2_Intron|KIF3A_uc011cxf.1_Intron|KIF3A_uc003kxp.2_Intron	NM_007054	NP_008985			kinesin family member 3A						blood coagulation|organelle organization|plus-end-directed vesicle transport along microtubule	centrosome|cytosol|kinesin II complex|spindle microtubule	ATP binding|plus-end-directed microtubule motor activity|protein binding			pancreas(1)	1		all_cancers(142;0.0751)|Breast(839;0.198)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)															---	---	---	---
SEPT8	23176	broad.mit.edu	37	5	132099950	132099950	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:132099950C>T	uc003kxr.2	-	3	551	c.313G>A	c.(313-315)GTG>ATG	p.V105M	SEPT8_uc003kxs.1_Missense_Mutation_p.V105M|SEPT8_uc003kxu.2_Missense_Mutation_p.V105M|SEPT8_uc011cxi.1_Missense_Mutation_p.V105M|SEPT8_uc003kxv.2_Missense_Mutation_p.V105M|SEPT8_uc003kxt.2_Missense_Mutation_p.V45M	NM_001098811	NP_001092281	Q92599	SEPT8_HUMAN	septin 8 isoform a	105					cell cycle	septin complex	GTP binding|protein binding			ovary(2)	2		all_cancers(142;0.0751)|Breast(839;0.198)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)															---	---	---	---
AFF4	27125	broad.mit.edu	37	5	132224790	132224790	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:132224790T>C	uc003kyd.2	-	14	3121	c.2713A>G	c.(2713-2715)AAG>GAG	p.K905E	AFF4_uc011cxk.1_Missense_Mutation_p.K583E	NM_014423	NP_055238	Q9UHB7	AFF4_HUMAN	ALL1 fused gene from 5q31	905					transcription from RNA polymerase II promoter	mitochondrion|nucleolus	protein binding|sequence-specific DNA binding transcription factor activity			ovary(2)|kidney(2)|skin(1)	5		all_cancers(142;0.145)|Breast(839;0.198)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)															---	---	---	---
HSPA4	3308	broad.mit.edu	37	5	132412369	132412369	+	Silent	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:132412369G>A	uc003kyj.2	+	7	968	c.687G>A	c.(685-687)ACG>ACA	p.T229T		NM_002154	NP_002145	P34932	HSP74_HUMAN	heat shock 70kDa protein 4	229					cellular chaperone-mediated protein complex assembly|protein import into mitochondrial outer membrane|response to unfolded protein	cytoplasm|nucleus	ATP binding			lung(1)|breast(1)	2			KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)															---	---	---	---
UBE2B	7320	broad.mit.edu	37	5	133716461	133716461	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:133716461C>A	uc003kzh.2	+	4	620	c.203C>A	c.(202-204)CCA>CAA	p.P68Q		NM_003337	NP_003328	P63146	UBE2B_HUMAN	ubiquitin-conjugating enzyme E2B	68					canonical Wnt receptor signaling pathway|histone H2A ubiquitination|negative regulation of cAMP-mediated signaling|postreplication repair|proteasomal ubiquitin-dependent protein catabolic process|protein autoubiquitination|protein K11-linked ubiquitination|protein K48-linked ubiquitination|protein K63-linked ubiquitination|protein monoubiquitination|protein stabilization|response to drug|response to UV	cytoplasm|plasma membrane|replication fork	ATP binding|ubiquitin protein ligase binding|ubiquitin-protein ligase activity			lung(1)	1			KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)										Direct_reversal_of_damage|Rad6_pathway					---	---	---	---
PHF15	23338	broad.mit.edu	37	5	133914210	133914210	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:133914210G>A	uc003kzo.1	+	11	1755	c.1576G>A	c.(1576-1578)GAT>AAT	p.D526N	PHF15_uc011cxt.1_Missense_Mutation_p.D570N|PHF15_uc003kzk.2_Missense_Mutation_p.D586N|PHF15_uc003kzl.2_3'UTR|PHF15_uc003kzm.2_Missense_Mutation_p.D527N|PHF15_uc003kzn.2_3'UTR	NM_015288	NP_056103	Q9NQC1	JADE2_HUMAN	PHD finger protein 15	526					histone H3 acetylation|histone H4-K12 acetylation|histone H4-K5 acetylation|histone H4-K8 acetylation	histone acetyltransferase complex	zinc ion binding				0			KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)															---	---	---	---
LECT2	3950	broad.mit.edu	37	5	135290478	135290478	+	Silent	SNP	G	A	A	rs148112810	byFrequency;by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:135290478G>A	uc003lbe.1	-	1	246	c.45C>T	c.(43-45)ACC>ACT	p.T15T		NM_002302	NP_002293	O14960	LECT2_HUMAN	leukocyte cell-derived chemotaxin 2 precursor	15					chemotaxis|skeletal system development	cytoplasm|extracellular space				ovary(1)	1			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0233)															---	---	---	---
KLHL3	26249	broad.mit.edu	37	5	137028011	137028011	+	Silent	SNP	G	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:137028011G>T	uc010jek.2	-	5	933	c.489C>A	c.(487-489)ACC>ACA	p.T163T	KLHL3_uc003lbr.3_Silent_p.T81T|KLHL3_uc011cyd.1_RNA|MYOT_uc011cye.1_Intron|KLHL3_uc010jem.1_Silent_p.T123T|KLHL3_uc010jen.1_RNA|KLHL3_uc003lbs.1_Silent_p.T31T	NM_017415	NP_059111	Q9UH77	KLHL3_HUMAN	kelch-like 3	163						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)														---	---	---	---
FAM13B	51306	broad.mit.edu	37	5	137289987	137289987	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:137289987A>G	uc003lbz.2	-	14	2054	c.1520T>C	c.(1519-1521)ATG>ACG	p.M507T	FAM13B_uc003lcb.2_Missense_Mutation_p.M411T|FAM13B_uc003lca.2_Missense_Mutation_p.M507T	NM_016603	NP_057687	Q9NYF5	FA13B_HUMAN	hypothetical protein LOC51306 isoform 1	507					regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol	GTPase activator activity				0																		---	---	---	---
BRD8	10902	broad.mit.edu	37	5	137503624	137503624	+	Silent	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:137503624T>C	uc003lcf.1	-	9	841	c.786A>G	c.(784-786)TCA>TCG	p.S262S	BRD8_uc003lcc.1_RNA|BRD8_uc011cyl.1_5'Flank|BRD8_uc003lcg.2_Silent_p.S335S|BRD8_uc003lci.2_Silent_p.S335S|BRD8_uc003lch.2_Silent_p.S195S|BRD8_uc011cym.1_Silent_p.S246S|BRD8_uc010jer.1_Silent_p.S301S|BRD8_uc011cyn.1_Silent_p.S221S|BRD8_uc010jes.1_Silent_p.S129S	NM_139199	NP_631938	Q9H0E9	BRD8_HUMAN	bromodomain containing 8 isoform 2	262					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)															---	---	---	---
BRD8	10902	broad.mit.edu	37	5	137506159	137506159	+	Intron	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:137506159A>G	uc003lcf.1	-						BRD8_uc003lcc.1_Intron|BRD8_uc003lcg.2_Intron|BRD8_uc003lci.2_Intron|BRD8_uc003lch.2_Intron|BRD8_uc011cym.1_Intron|BRD8_uc010jer.1_Intron|BRD8_uc011cyn.1_Intron|BRD8_uc010jes.1_Intron	NM_139199	NP_631938			bromodomain containing 8 isoform 2						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)															---	---	---	---
CTNNA1	1495	broad.mit.edu	37	5	138260235	138260235	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:138260235T>C	uc003ldh.2	+	12	1678	c.1583T>C	c.(1582-1584)ATT>ACT	p.I528T	CTNNA1_uc011cyx.1_Missense_Mutation_p.I425T|CTNNA1_uc011cyy.1_Missense_Mutation_p.I405T|CTNNA1_uc003ldi.2_Missense_Mutation_p.I226T|CTNNA1_uc003ldj.2_Missense_Mutation_p.I528T|CTNNA1_uc003ldl.2_Missense_Mutation_p.I158T	NM_001903	NP_001894	P35221	CTNA1_HUMAN	catenin, alpha 1	528					adherens junction organization|apical junction assembly|cell adhesion|cellular response to indole-3-methanol|muscle cell differentiation|positive regulation of muscle cell differentiation	actin cytoskeleton|catenin complex|cytosol	beta-catenin binding|cadherin binding|gamma-catenin binding|structural molecule activity|vinculin binding			breast(6)|ovary(2)|large_intestine(2)|kidney(1)	11			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00325)															---	---	---	---
SLC35A4	113829	broad.mit.edu	37	5	139947360	139947360	+	Silent	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:139947360G>A	uc003lgg.1	+	3	1334	c.606G>A	c.(604-606)TCG>TCA	p.S202S	SLC35A4_uc003lgh.1_Silent_p.S202S	NM_080670	NP_542401	Q96G79	S35A4_HUMAN	solute carrier family 35, member A4	202	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)															---	---	---	---
HARS	3035	broad.mit.edu	37	5	140054699	140054699	+	Missense_Mutation	SNP	C	T	T	rs147185134		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140054699C>T	uc003lgv.2	-	11	1296	c.1214G>A	c.(1213-1215)CGG>CAG	p.R405Q	DND1_uc003lgt.2_5'Flank|HARS_uc003lgu.2_Missense_Mutation_p.R336Q|HARS_uc011czm.1_Missense_Mutation_p.R365Q|HARS_uc003lgw.2_Missense_Mutation_p.R385Q|HARS_uc011czn.1_Missense_Mutation_p.R345Q|HARS_uc010jfu.2_Intron|HARS_uc011czo.1_Missense_Mutation_p.R331Q|HARS_uc011czp.1_Missense_Mutation_p.R291Q	NM_002109	NP_002100	P12081	SYHC_HUMAN	histidyl-tRNA synthetase	405					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)													---	---	---	---
PCDHA4	56144	broad.mit.edu	37	5	140187214	140187214	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140187214C>A	uc003lhi.2	+	1	543	c.442C>A	c.(442-444)CTT>ATT	p.L148I	PCDHA1_uc003lha.2_Intron|PCDHA1_uc003lhb.2_Intron|PCDHA2_uc003lhd.2_Intron|PCDHA3_uc003lhf.2_Intron|PCDHA4_uc003lhh.1_Missense_Mutation_p.L148I|PCDHA4_uc011daa.1_Missense_Mutation_p.L148I	NM_018907	NP_061730	Q9UN74	PCDA4_HUMAN	protocadherin alpha 4 isoform 1 precursor	148	Extracellular (Potential).|Cadherin 2.				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	140188623	140188623	+	Silent	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140188623C>T	uc003lhi.2	+	1	1952	c.1851C>T	c.(1849-1851)GGC>GGT	p.G617G	PCDHA1_uc003lha.2_Intron|PCDHA1_uc003lhb.2_Intron|PCDHA2_uc003lhd.2_Intron|PCDHA3_uc003lhf.2_Intron|PCDHA4_uc003lhh.1_Silent_p.G617G|PCDHA4_uc011daa.1_Silent_p.G617G	NM_018907	NP_061730	Q9UN74	PCDA4_HUMAN	protocadherin alpha 4 isoform 1 precursor	617	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)															---	---	---	---
PCDHA4	56144	broad.mit.edu	37	5	140188965	140188965	+	Silent	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140188965G>A	uc003lhi.2	+	1	2294	c.2193G>A	c.(2191-2193)GCG>GCA	p.A731A	PCDHA1_uc003lha.2_Intron|PCDHA1_uc003lhb.2_Intron|PCDHA2_uc003lhd.2_Intron|PCDHA3_uc003lhf.2_Intron|PCDHA4_uc003lhh.1_Silent_p.A731A|PCDHA4_uc011daa.1_Silent_p.A731A	NM_018907	NP_061730	Q9UN74	PCDA4_HUMAN	protocadherin alpha 4 isoform 1 precursor	731	Cytoplasmic (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)															---	---	---	---
PCDHA5	56143	broad.mit.edu	37	5	140203225	140203225	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140203225G>A	uc003lhl.2	+	1	1865	c.1865G>A	c.(1864-1866)CGC>CAC	p.R622H	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_Missense_Mutation_p.R622H|PCDHA5_uc003lhj.1_Missense_Mutation_p.R622H	NM_018908	NP_061731	Q9Y5H7	PCDA5_HUMAN	protocadherin alpha 5 isoform 1 precursor	622	Extracellular (Potential).|Cadherin 6.				homophilic cell adhesion|nervous system development	integral to plasma membrane	calcium ion binding|protein binding			ovary(1)|breast(1)|skin(1)	3			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)															---	---	---	---
PCDHA6	56142	broad.mit.edu	37	5	140209847	140209847	+	Missense_Mutation	SNP	C	T	T	rs151257683		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140209847C>T	uc003lho.2	+	1	2198	c.2171C>T	c.(2170-2172)TCG>TTG	p.S724L	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_uc011dab.1_Missense_Mutation_p.S724L	NM_018909	NP_061732	Q9UN73	PCDA6_HUMAN	protocadherin alpha 6 isoform 1 precursor	724	Cytoplasmic (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	140214165	140214165	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140214165C>T	uc003lhq.2	+	1	197	c.197C>T	c.(196-198)GCG>GTG	p.A66V	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.A66V	NM_018910	NP_061733	Q9UN72	PCDA7_HUMAN	protocadherin alpha 7 isoform 1 precursor	66	Cadherin 1.|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)															---	---	---	---
PCDHA9	9752	broad.mit.edu	37	5	140229528	140229528	+	Missense_Mutation	SNP	A	G	G	rs34848125		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140229528A>G	uc003lhu.2	+	1	2172	c.1448A>G	c.(1447-1449)GAC>GGC	p.D483G	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.D483G	NM_031857	NP_114063	Q9Y5H5	PCDA9_HUMAN	protocadherin alpha 9 isoform 1 precursor	483	Cadherin 5.|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)															---	---	---	---
PCDHA13	56136	broad.mit.edu	37	5	140264049	140264049	+	Silent	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140264049C>T	uc003lif.2	+	1	2196	c.2196C>T	c.(2194-2196)TGC>TGT	p.C732C	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.C732C|PCDHA13_uc003lid.2_Silent_p.C732C	NM_018904	NP_061727	Q9Y5I0	PCDAD_HUMAN	protocadherin alpha 13 isoform 1 precursor	732	Cytoplasmic (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)															---	---	---	---
PCDHAC2	56134	broad.mit.edu	37	5	140347813	140347813	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140347813C>T	uc003lii.2	+	1	1702	c.1462C>T	c.(1462-1464)CTC>TTC	p.L488F	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|PCDHAC2_uc011dag.1_Missense_Mutation_p.L488F	NM_018899	NP_061722	Q9Y5I4	PCDC2_HUMAN	protocadherin alpha subfamily C, 2 isoform 1	488	Cadherin 5.|Extracellular (Potential).				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)															---	---	---	---
PCDHB2	56133	broad.mit.edu	37	5	140474815	140474815	+	Silent	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140474815T>C	uc003lil.2	+	1	579	c.441T>C	c.(439-441)AGT>AGC	p.S147S	PCDHB2_uc003lim.1_Intron	NM_018936	NP_061759	Q9Y5E7	PCDB2_HUMAN	protocadherin beta 2 precursor	147	Extracellular (Potential).|Cadherin 2.				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	140481969	140481969	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140481969C>T	uc003lio.2	+	1	1736	c.1736C>T	c.(1735-1737)GCG>GTG	p.A579V	uc003lin.2_5'Flank	NM_018937	NP_061760	Q9Y5E6	PCDB3_HUMAN	protocadherin beta 3 precursor	579	Extracellular (Potential).|Cadherin 6.				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)															---	---	---	---
PCDHB7	56129	broad.mit.edu	37	5	140554024	140554024	+	Silent	SNP	C	T	T	rs13185413		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140554024C>T	uc003lit.2	+	1	1782	c.1608C>T	c.(1606-1608)CGC>CGT	p.R536R		NM_018940	NP_061763	Q9Y5E2	PCDB7_HUMAN	protocadherin beta 7 precursor	536	Extracellular (Potential).|Cadherin 5.				calcium-dependent cell-cell adhesion|homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(4)|central_nervous_system(1)|skin(1)	6			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)															---	---	---	---
PCDHB8	56128	broad.mit.edu	37	5	140559226	140559226	+	Silent	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140559226C>T	uc011dai.1	+	1	1797	c.1611C>T	c.(1609-1611)CGC>CGT	p.R537R	PCDHB16_uc003liv.2_5'Flank|PCDHB16_uc010jfw.1_5'Flank	NM_019120	NP_061993	Q9UN66	PCDB8_HUMAN	protocadherin beta 8 precursor	537	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)															---	---	---	---
PCDHB16	57717	broad.mit.edu	37	5	140563446	140563446	+	Missense_Mutation	SNP	A	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140563446A>T	uc003liv.2	+	1	2467	c.1312A>T	c.(1312-1314)ACA>TCA	p.T438S	PCDHB16_uc010jfw.1_Missense_Mutation_p.T110S	NM_020957	NP_066008	Q9NRJ7	PCDBG_HUMAN	protocadherin beta 16 precursor	438	Extracellular (Potential).|Cadherin 4.				calcium-dependent cell-cell adhesion|homophilic cell adhesion|synapse assembly|synaptic transmission	integral to membrane|plasma membrane	calcium ion binding			ovary(1)|pancreas(1)	2			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)															---	---	---	---
PCDHB12	56124	broad.mit.edu	37	5	140589745	140589745	+	Silent	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140589745C>T	uc003liz.2	+	1	1455	c.1266C>T	c.(1264-1266)ACC>ACT	p.T422T	PCDHB12_uc011dak.1_Silent_p.T85T	NM_018932	NP_061755	Q9Y5F1	PCDBC_HUMAN	protocadherin beta 12 precursor	422	Extracellular (Potential).|Cadherin 4.				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)															---	---	---	---
PCDHB12	56124	broad.mit.edu	37	5	140589802	140589802	+	Silent	SNP	C	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140589802C>G	uc003liz.2	+	1	1512	c.1323C>G	c.(1321-1323)GTC>GTG	p.V441V	PCDHB12_uc011dak.1_Silent_p.V104V	NM_018932	NP_061755	Q9Y5F1	PCDBC_HUMAN	protocadherin beta 12 precursor	441	Extracellular (Potential).|Cadherin 4.				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)															---	---	---	---
PCDHB15	56121	broad.mit.edu	37	5	140626370	140626370	+	Silent	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140626370G>A	uc003lje.2	+	1	1224	c.1224G>A	c.(1222-1224)GCG>GCA	p.A408A		NM_018935	NP_061758	Q9Y5E8	PCDBF_HUMAN	protocadherin beta 15 precursor	408	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)															---	---	---	---
SLC25A2	83884	broad.mit.edu	37	5	140682587	140682587	+	Silent	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140682587T>C	uc003ljf.2	-	1	1026	c.846A>G	c.(844-846)GCA>GCG	p.A282A		NM_031947	NP_114153	Q9BXI2	ORNT2_HUMAN	solute carrier family 25 member 2	282	Solcar 3.				mitochondrial ornithine transport|urea cycle	integral to membrane|mitochondrial inner membrane	L-ornithine transmembrane transporter activity			ovary(1)	1		all_lung(500;0.000249)|Lung NSC(810;0.0011)|Ovarian(839;0.00556)|Breast(839;0.0173)|all_hematologic(541;0.152)	KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)	GBM - Glioblastoma multiforme(465;0.00204)	L-Ornithine(DB00129)													---	---	---	---
PCDHGA3	56112	broad.mit.edu	37	5	140723736	140723736	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140723736G>T	uc003ljm.1	+	1	136	c.136G>T	c.(136-138)GGC>TGC	p.G46C	PCDHGA1_uc003lji.1_Intron|PCDHGA2_uc003ljk.1_Intron|PCDHGA3_uc010jfx.1_5'UTR|PCDHGA3_uc011dap.1_Missense_Mutation_p.G46C	NM_018916	NP_061739	Q9Y5H0	PCDG3_HUMAN	protocadherin gamma subfamily A, 3 isoform 1	46	Cadherin 1.|Extracellular (Potential).				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			breast(1)	1			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)													OREG0016855	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
PCDHGA3	56112	broad.mit.edu	37	5	140723858	140723858	+	Silent	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140723858C>T	uc003ljm.1	+	1	258	c.258C>T	c.(256-258)ACC>ACT	p.T86T	PCDHGA1_uc003lji.1_Intron|PCDHGA2_uc003ljk.1_Intron|PCDHGA3_uc010jfx.1_5'UTR|PCDHGA3_uc011dap.1_Silent_p.T86T	NM_018916	NP_061739	Q9Y5H0	PCDG3_HUMAN	protocadherin gamma subfamily A, 3 isoform 1	86	Cadherin 1.|Extracellular (Potential).				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			breast(1)	1			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)															---	---	---	---
PCDHGB1	56104	broad.mit.edu	37	5	140730008	140730008	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140730008A>G	uc003ljo.1	+	1	181	c.181A>G	c.(181-183)ACT>GCT	p.T61A	PCDHGA1_uc003lji.1_Intron|PCDHGA2_uc003ljk.1_Intron|PCDHGA3_uc003ljm.1_Intron|PCDHGA3_uc010jfx.1_Intron|PCDHGB1_uc011daq.1_Missense_Mutation_p.T61A	NM_018922	NP_061745	Q9Y5G3	PCDGD_HUMAN	protocadherin gamma subfamily B, 1 isoform 1	61	Cadherin 1.|Extracellular (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)													OREG0016856	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
PCDHGB1	56104	broad.mit.edu	37	5	140731755	140731755	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140731755G>A	uc003ljo.1	+	1	1928	c.1928G>A	c.(1927-1929)CGT>CAT	p.R643H	PCDHGA1_uc003lji.1_Intron|PCDHGA2_uc003ljk.1_Intron|PCDHGA3_uc003ljm.1_Intron|PCDHGA3_uc010jfx.1_Intron|PCDHGB1_uc011daq.1_Missense_Mutation_p.R643H	NM_018922	NP_061745	Q9Y5G3	PCDGD_HUMAN	protocadherin gamma subfamily B, 1 isoform 1	643	Extracellular (Potential).|Cadherin 6.				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)															---	---	---	---
PCDHGA4	56111	broad.mit.edu	37	5	140736994	140736994	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140736994G>A	uc003ljq.1	+	1	2227	c.2227G>A	c.(2227-2229)GTG>ATG	p.V743M	PCDHGA1_uc003lji.1_Intron|PCDHGA2_uc003ljk.1_Intron|PCDHGA3_uc003ljm.1_Intron|PCDHGA3_uc010jfx.1_Intron|PCDHGB1_uc003ljo.1_Intron|PCDHGB2_uc003ljs.1_5'Flank|PCDHGA4_uc003ljp.1_Missense_Mutation_p.V743M|PCDHGB2_uc011dar.1_5'Flank	NM_018917	NP_061740	Q9Y5G9	PCDG4_HUMAN	protocadherin gamma subfamily A, 4 isoform 1	743	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)															---	---	---	---
PCDHGA6	56109	broad.mit.edu	37	5	140755814	140755814	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140755814T>C	uc003ljy.1	+	1	2164	c.2164T>C	c.(2164-2166)TCA>CCA	p.S722P	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_uc011dau.1_Missense_Mutation_p.S722P	NM_018919	NP_061742	Q9Y5G7	PCDG6_HUMAN	protocadherin gamma subfamily A, 6 isoform 1	722	Cytoplasmic (Potential).				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			breast(1)	1			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)															---	---	---	---
PCDHGA7	56108	broad.mit.edu	37	5	140764011	140764011	+	Silent	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140764011C>T	uc003lka.1	+	1	1545	c.1545C>T	c.(1543-1545)TAC>TAT	p.Y515Y	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_uc003ljz.1_Silent_p.Y515Y	NM_018920	NP_061743	Q9Y5G6	PCDG7_HUMAN	protocadherin gamma subfamily A, 7 isoform 1	515	Extracellular (Potential).|Cadherin 5.				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)															---	---	---	---
PCDHGA8	9708	broad.mit.edu	37	5	140772761	140772761	+	Silent	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140772761C>T	uc003lkd.1	+	1	1279	c.381C>T	c.(379-381)AAC>AAT	p.N127N	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_uc003lkb.3_Silent_p.N127N	NM_032088	NP_114477	Q9Y5G5	PCDG8_HUMAN	protocadherin gamma subfamily A, 8 isoform 1	127	Cadherin 1.|Extracellular (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)															---	---	---	---
PCDHGC4	56098	broad.mit.edu	37	5	140864983	140864983	+	Silent	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140864983C>T	uc003lky.1	+	1	243	c.243C>T	c.(241-243)AGC>AGT	p.S81S	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_uc011dbb.1_Silent_p.S81S	NM_018928	NP_061751	Q9Y5F7	PCDGL_HUMAN	protocadherin gamma subfamily C, 4 isoform 1	81	Cadherin 1.|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)															---	---	---	---
PCDHGC5	56097	broad.mit.edu	37	5	140870270	140870270	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140870270G>A	uc003lla.1	+	1	1463	c.1463G>A	c.(1462-1464)CGC>CAC	p.R488H	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.R488H	NM_018929	NP_061752	Q9Y5F6	PCDGM_HUMAN	protocadherin gamma subfamily C, 5 isoform 1	488	Extracellular (Potential).|Cadherin 5.				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)															---	---	---	---
FCHSD1	89848	broad.mit.edu	37	5	141028852	141028852	+	Silent	SNP	C	T	T	rs112390736		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:141028852C>T	uc003llk.2	-	6	450	c.399G>A	c.(397-399)GCG>GCA	p.A133A	FCHSD1_uc010jgg.2_5'Flank|FCHSD1_uc003llj.2_RNA	NM_033449	NP_258260	Q86WN1	FCSD1_HUMAN	FCH and double SH3 domains 1	133	Potential.								FCHSD1/BRAF(2)	skin(2)|ovary(1)|central_nervous_system(1)	4			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)															---	---	---	---
ARHGAP26	23092	broad.mit.edu	37	5	142437260	142437260	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:142437260C>A	uc011dbj.1	+	17	1521	c.1486C>A	c.(1486-1488)CTC>ATC	p.L496I	ARHGAP26_uc003lmt.2_Missense_Mutation_p.L496I|ARHGAP26_uc003lmw.2_Missense_Mutation_p.L496I	NM_015071	NP_055886	Q9UNA1	RHG26_HUMAN	GTPase regulator associated with the focal	496	Rho-GAP.				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	142661544	142661544	+	Silent	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:142661544T>C	uc003lmz.2	-	9	2736	c.2244A>G	c.(2242-2244)GAA>GAG	p.E748E	NR3C1_uc003lmy.2_Silent_p.E749E|NR3C1_uc003lna.2_Intron|NR3C1_uc003lnb.2_Silent_p.E748E|NR3C1_uc011dbk.1_Silent_p.E351E|NR3C1_uc003lnc.2_Silent_p.E748E|NR3C1_uc003lnd.2_Silent_p.E748E|NR3C1_uc003lne.2_Silent_p.E748E|NR3C1_uc003lnf.2_Silent_p.E749E	NM_000176	NP_000167	P04150	GCR_HUMAN	glucocorticoid receptor isoform alpha	748	Steroid-binding.				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)													---	---	---	---
KCTD16	57528	broad.mit.edu	37	5	143853274	143853274	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:143853274G>A	uc003lnm.1	+	4	1513	c.884G>A	c.(883-885)GGC>GAC	p.G295D	KCTD16_uc003lnn.1_Missense_Mutation_p.G295D	NM_020768	NP_065819	Q68DU8	KCD16_HUMAN	potassium channel tetramerisation domain	295						cell junction|postsynaptic membrane|presynaptic membrane|voltage-gated potassium channel complex	voltage-gated potassium channel activity			large_intestine(2)|ovary(1)|skin(1)	4		all_hematologic(541;0.118)	KIRC - Kidney renal clear cell carcinoma(527;0.00111)|Kidney(363;0.00176)															---	---	---	---
SPINK5	11005	broad.mit.edu	37	5	147486711	147486711	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:147486711A>G	uc003lox.2	+	17	1664	c.1591A>G	c.(1591-1593)ATG>GTG	p.M531V	SPINK5_uc010jgs.1_Missense_Mutation_p.M503V|SPINK5_uc010jgr.2_Missense_Mutation_p.M512V|SPINK5_uc003low.2_Missense_Mutation_p.M531V|SPINK5_uc003loy.2_Missense_Mutation_p.M531V	NM_006846	NP_006837	Q9NQ38	ISK5_HUMAN	serine peptidase inhibitor, Kazal type 5 isoform	531	Kazal-like 8.				anagen|epithelial cell differentiation|extracellular matrix organization|hair cell differentiation|negative regulation of angiogenesis|negative regulation of immune response|regulation of T cell differentiation	cell cortex|cytosol|endoplasmic reticulum membrane|extracellular region|lamellar body|perinuclear region of cytoplasm	serine-type endopeptidase inhibitor activity			skin(2)|ovary(1)|breast(1)	4			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)															---	---	---	---
ADRB2	154	broad.mit.edu	37	5	148207533	148207533	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:148207533A>G	uc003lpr.1	+	1	1378	c.1139A>G	c.(1138-1140)GAC>GGC	p.D380G	SH3TC2_uc003lpp.1_Intron	NM_000024	NP_000015	P07550	ADRB2_HUMAN	adrenergic, beta-2-, receptor, surface	380	Cytoplasmic.				activation of transmembrane receptor protein tyrosine kinase activity|desensitization of G-protein coupled receptor protein signaling pathway by arrestin|endosome to lysosome transport|positive regulation of MAPKKK cascade|receptor-mediated endocytosis	endosome|integral to plasma membrane|lysosome|receptor complex	beta2-adrenergic receptor activity|norepinephrine binding|potassium channel regulator activity|protein homodimerization activity			ovary(1)	1			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)		Alprenolol(DB00866)|Arformoterol(DB01274)|Bambuterol(DB01408)|Bisoprolol(DB00612)|Bitolterol(DB00901)|Bretylium(DB01158)|Carteolol(DB00521)|Carvedilol(DB01136)|Clenbuterol(DB01407)|Desipramine(DB01151)|Epinephrine(DB00668)|Fenoterol(DB01288)|Formoterol(DB00983)|Isoproterenol(DB01064)|Labetalol(DB00598)|Levobunolol(DB01210)|Metipranolol(DB01214)|Nadolol(DB01203)|Norepinephrine(DB00368)|Orciprenaline(DB00816)|Oxprenolol(DB01580)|Penbutolol(DB01359)|Pindolol(DB00960)|Pirbuterol(DB01291)|Procaterol(DB01366)|Propranolol(DB00571)|Pseudoephedrine(DB00852)|Ritodrine(DB00867)|Salbutamol(DB01001)|Salmeterol(DB00938)|Terbutaline(DB00871)|Timolol(DB00373)													---	---	---	---
ABLIM3	22885	broad.mit.edu	37	5	148579916	148579916	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:148579916G>A	uc003lpy.2	+	5	624	c.373G>A	c.(373-375)GGT>AGT	p.G125S	ABLIM3_uc003lpz.1_Missense_Mutation_p.G125S|ABLIM3_uc003lqa.1_Missense_Mutation_p.G133S|ABLIM3_uc003lqb.2_Missense_Mutation_p.G125S|ABLIM3_uc003lqc.1_Missense_Mutation_p.G125S|ABLIM3_uc003lqd.1_Missense_Mutation_p.G125S|ABLIM3_uc003lqf.2_Missense_Mutation_p.G125S|ABLIM3_uc003lqe.1_Missense_Mutation_p.G125S	NM_014945	NP_055760	O94929	ABLM3_HUMAN	actin binding LIM protein family, member 3	125	LIM zinc-binding 2.				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)															---	---	---	---
PPARGC1B	133522	broad.mit.edu	37	5	149216187	149216187	+	Silent	SNP	C	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:149216187C>A	uc003lrc.2	+	8	2211	c.2169C>A	c.(2167-2169)CCC>CCA	p.P723P	PPARGC1B_uc003lrb.1_Silent_p.P723P|PPARGC1B_uc003lrd.2_Silent_p.P684P|PPARGC1B_uc003lrf.2_Silent_p.P702P|PPARGC1B_uc003lre.1_Silent_p.P702P	NM_133263	NP_573570	Q86YN6	PRGC2_HUMAN	peroxisome proliferator-activated receptor	723					estrogen receptor signaling pathway|positive regulation of transcription from RNA polymerase II promoter	mediator complex	AF-2 domain binding|estrogen receptor binding|ligand-dependent nuclear receptor transcription coactivator activity|nucleotide binding|receptor activator activity|RNA binding|RNA polymerase II transcription cofactor activity				0			KIRC - Kidney renal clear cell carcinoma(527;0.000962)|Kidney(363;0.00147)															---	---	---	---
PPARGC1B	133522	broad.mit.edu	37	5	149216302	149216302	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:149216302G>A	uc003lrc.2	+	8	2326	c.2284G>A	c.(2284-2286)GCT>ACT	p.A762T	PPARGC1B_uc003lrb.1_Missense_Mutation_p.A762T|PPARGC1B_uc003lrd.2_Missense_Mutation_p.A723T|PPARGC1B_uc003lrf.2_Missense_Mutation_p.A741T|PPARGC1B_uc003lre.1_Missense_Mutation_p.A741T	NM_133263	NP_573570	Q86YN6	PRGC2_HUMAN	peroxisome proliferator-activated receptor	762					estrogen receptor signaling pathway|positive regulation of transcription from RNA polymerase II promoter	mediator complex	AF-2 domain binding|estrogen receptor binding|ligand-dependent nuclear receptor transcription coactivator activity|nucleotide binding|receptor activator activity|RNA binding|RNA polymerase II transcription cofactor activity				0			KIRC - Kidney renal clear cell carcinoma(527;0.000962)|Kidney(363;0.00147)															---	---	---	---
PDE6A	5145	broad.mit.edu	37	5	149310678	149310678	+	Silent	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:149310678T>C	uc003lrg.3	-	4	891	c.771A>G	c.(769-771)CGA>CGG	p.R257R		NM_000440	NP_000431	P16499	PDE6A_HUMAN	phosphodiesterase 6A	257	GAF 2.				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	149440430	149440430	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:149440430T>C	uc003lrl.2	-	13	2159	c.1964A>G	c.(1963-1965)CAT>CGT	p.H655R	CSF1R_uc011dcd.1_Intron|CSF1R_uc010jhc.2_RNA|CSF1R_uc003lrm.2_Missense_Mutation_p.H655R	NM_005211	NP_005202	P07333	CSF1R_HUMAN	colony stimulating factor 1 receptor precursor	655	Protein kinase.|Cytoplasmic (Potential).				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	149924907	149924907	+	Silent	SNP	C	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:149924907C>A	uc003lsk.3	+	11	2506	c.2004C>A	c.(2002-2004)ACC>ACA	p.T668T	NDST1_uc011dcj.1_Silent_p.T668T	NM_001543	NP_001534	P52848	NDST1_HUMAN	N-deacetylase/N-sulfotransferase (heparan	668	Heparan sulfate N-sulfotransferase 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)													OREG0016935	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
SYNPO	11346	broad.mit.edu	37	5	150029796	150029796	+	Silent	SNP	G	A	A	rs145586254	byFrequency	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:150029796G>A	uc003lsn.2	+	3	3065	c.2691G>A	c.(2689-2691)GCG>GCA	p.A897A	SYNPO_uc003lso.3_Silent_p.A653A|SYNPO_uc003lsp.2_Silent_p.A653A	NM_001109974	NP_001103444	Q8N3V7	SYNPO_HUMAN	synaptopodin isoform B	897	Pro-rich.				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)															---	---	---	---
CCDC69	26112	broad.mit.edu	37	5	150563944	150563944	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:150563944T>C	uc003ltq.2	-	8	797	c.674A>G	c.(673-675)GAC>GGC	p.D225G	CCDC69_uc010jhu.2_Missense_Mutation_p.D78G|CCDC69_uc011dcq.1_RNA	NM_015621	NP_056436	A6NI79	CCD69_HUMAN	coiled-coil domain containing 69	225	Potential.									ovary(2)	2		Medulloblastoma(196;0.091)|all_hematologic(541;0.207)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)															---	---	---	---
FAT2	2196	broad.mit.edu	37	5	150885441	150885441	+	Silent	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:150885441G>A	uc003lue.3	-	23	12748	c.12735C>T	c.(12733-12735)AAC>AAT	p.N4245N	GM2A_uc011dcs.1_Intron|FAT2_uc003lud.3_Silent_p.N852N	NM_001447	NP_001438	Q9NYQ8	FAT2_HUMAN	FAT tumor suppressor 2 precursor	4245	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	150906823	150906823	+	Missense_Mutation	SNP	A	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:150906823A>T	uc003lue.3	-	16	10293	c.10280T>A	c.(10279-10281)TTC>TAC	p.F3427Y	GM2A_uc011dcs.1_Intron|FAT2_uc003lud.3_Missense_Mutation_p.F120Y	NM_001447	NP_001438	Q9NYQ8	FAT2_HUMAN	FAT tumor suppressor 2 precursor	3427	Extracellular (Potential).|Cadherin 31.				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)															---	---	---	---
GEMIN5	25929	broad.mit.edu	37	5	154287187	154287187	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:154287187G>A	uc003lvx.3	-	16	2442	c.2359C>T	c.(2359-2361)CGG>TGG	p.R787W	GEMIN5_uc011ddk.1_Missense_Mutation_p.R786W	NM_015465	NP_056280	Q8TEQ6	GEMI5_HUMAN	gemin 5	787					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)															---	---	---	---
ITK	3702	broad.mit.edu	37	5	156665172	156665172	+	Silent	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:156665172C>T	uc003lwo.1	+	9	904	c.822C>T	c.(820-822)ACC>ACT	p.T274T		NM_005546	NP_005537	Q08881	ITK_HUMAN	IL2-inducible T-cell kinase	274	SH2.				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								---	---	---	---
CYFIP2	26999	broad.mit.edu	37	5	156738719	156738719	+	Missense_Mutation	SNP	A	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:156738719A>C	uc003lwq.2	+	13	1178	c.1040A>C	c.(1039-1041)GAG>GCG	p.E347A	CYFIP2_uc011ddn.1_Missense_Mutation_p.E321A|CYFIP2_uc011ddo.1_Missense_Mutation_p.E151A|CYFIP2_uc003lwr.2_Missense_Mutation_p.E347A|CYFIP2_uc003lws.2_Missense_Mutation_p.E347A|CYFIP2_uc003lwt.2_Missense_Mutation_p.E225A|CYFIP2_uc011ddp.1_Missense_Mutation_p.E81A	NM_001037333	NP_001032410	Q96F07	CYFP2_HUMAN	cytoplasmic FMR1 interacting protein 2	347					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	156747680	156747680	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:156747680G>A	uc003lwq.2	+	17	1679	c.1541G>A	c.(1540-1542)CGA>CAA	p.R514Q	CYFIP2_uc011ddn.1_Missense_Mutation_p.R488Q|CYFIP2_uc011ddo.1_Missense_Mutation_p.R318Q|CYFIP2_uc003lwr.2_Missense_Mutation_p.R514Q|CYFIP2_uc003lws.2_Missense_Mutation_p.R514Q|CYFIP2_uc003lwt.2_Missense_Mutation_p.R392Q|CYFIP2_uc011ddp.1_Missense_Mutation_p.R248Q	NM_001037333	NP_001032410	Q96F07	CYFP2_HUMAN	cytoplasmic FMR1 interacting protein 2	514					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)															---	---	---	---
C1QTNF2	114898	broad.mit.edu	37	5	159776388	159776388	+	Silent	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:159776388G>A	uc003lyd.2	-	3	784	c.780C>T	c.(778-780)AAC>AAT	p.N260N		NM_031908	NP_114114	Q9BXJ5	C1QT2_HUMAN	C1q and tumor necrosis factor related protein 2	215	C1q.					collagen				skin(1)	1	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)															---	---	---	---
GABRB2	2561	broad.mit.edu	37	5	160758044	160758044	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:160758044T>C	uc003lys.1	-	9	1141	c.923A>G	c.(922-924)TAC>TGC	p.Y308C	GABRB2_uc011deh.1_Missense_Mutation_p.Y147C|GABRB2_uc003lyr.1_Missense_Mutation_p.Y308C|GABRB2_uc003lyt.1_Missense_Mutation_p.Y308C|GABRB2_uc010jiu.1_Missense_Mutation_p.Y245C	NM_021911	NP_068711	P47870	GBRB2_HUMAN	gamma-aminobutyric acid (GABA) A receptor, beta	308	Helical; (Probable).				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)													---	---	---	---
ODZ2	57451	broad.mit.edu	37	5	167645400	167645400	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:167645400C>T	uc010jjd.2	+	23	4477	c.4477C>T	c.(4477-4479)CGC>TGC	p.R1493C	ODZ2_uc003lzr.3_Missense_Mutation_p.R1263C|ODZ2_uc003lzt.3_Missense_Mutation_p.R866C|ODZ2_uc010jje.2_Missense_Mutation_p.R757C	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	167645477	167645477	+	Missense_Mutation	SNP	T	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:167645477T>A	uc010jjd.2	+	23	4554	c.4554T>A	c.(4552-4554)AAT>AAA	p.N1518K	ODZ2_uc003lzr.3_Missense_Mutation_p.N1288K|ODZ2_uc003lzt.3_Missense_Mutation_p.N891K|ODZ2_uc010jje.2_Missense_Mutation_p.N782K	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	167673789	167673789	+	Missense_Mutation	SNP	C	T	T	rs141225541	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:167673789C>T	uc010jjd.2	+	27	5818	c.5818C>T	c.(5818-5820)CGT>TGT	p.R1940C	ODZ2_uc003lzr.3_Missense_Mutation_p.R1710C|ODZ2_uc003lzt.3_Missense_Mutation_p.R1313C|ODZ2_uc010jje.2_Missense_Mutation_p.R1204C	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)														---	---	---	---
FBLL1	345630	broad.mit.edu	37	5	167957367	167957367	+	Silent	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:167957367C>T	uc011dep.1	+	1	786	c.573C>T	c.(571-573)TCC>TCT	p.S191S		NR_024356				RecName: Full=rRNA/tRNA 2'-O-methyltransferase fibrillarin-like protein 1;          EC=2.1.1.-;												0																		---	---	---	---
SLIT3	6586	broad.mit.edu	37	5	168093525	168093525	+	Silent	SNP	C	A	A	rs143047334	byFrequency	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:168093525C>A	uc003mab.2	-	36	4926	c.4506G>T	c.(4504-4506)ACG>ACT	p.T1502T	SLIT3_uc010jjg.2_Silent_p.T1509T	NM_003062	NP_003053	O75094	SLIT3_HUMAN	slit homolog 3 precursor	1502	CTCK.				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	168112694	168112694	+	Nonsense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:168112694G>A	uc003mab.2	-	31	3973	c.3553C>T	c.(3553-3555)CAG>TAG	p.Q1185*	SLIT3_uc010jjg.2_Nonsense_Mutation_p.Q1192*	NM_003062	NP_003053	O75094	SLIT3_HUMAN	slit homolog 3 precursor	1185	Laminin G-like.				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)															---	---	---	---
STK10	6793	broad.mit.edu	37	5	171532673	171532673	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:171532673G>A	uc003mbo.1	-	7	1157	c.857C>T	c.(856-858)GCG>GTG	p.A286V		NM_005990	NP_005981	O94804	STK10_HUMAN	serine/threonine kinase 10	286	Protein kinase.						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)															---	---	---	---
DUSP1	1843	broad.mit.edu	37	5	172196107	172196107	+	Silent	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:172196107C>T	uc003mbv.1	-	4	1010	c.762G>A	c.(760-762)GTG>GTA	p.V254V	DUSP1_uc011dez.1_Silent_p.V112V|DUSP1_uc003mbu.1_Silent_p.V142V	NM_004417	NP_004408	P28562	DUS1_HUMAN	dual specificity phosphatase 1	254	Tyrosine-protein phosphatase.				cell cycle|endoderm formation|inactivation of MAPK activity	nucleoplasm	MAP kinase tyrosine/serine/threonine phosphatase activity|non-membrane spanning protein tyrosine phosphatase activity|protein binding			breast(2)|ovary(1)	3	Renal(175;0.000159)|Lung NSC(126;0.00431)|all_lung(126;0.00729)	all_hematologic(541;4.11e-18)|Breast(839;0.00637)|Medulloblastoma(196;0.0208)|all_neural(177;0.0416)|Ovarian(839;0.15)	Kidney(164;7.24e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000516)	GBM - Glioblastoma multiforme(465;0.0103)														---	---	---	---
CDHR2	54825	broad.mit.edu	37	5	176022647	176022647	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:176022647G>A	uc003mem.1	+	32	3973	c.3907G>A	c.(3907-3909)GCT>ACT	p.A1303T	CDHR2_uc003men.1_Missense_Mutation_p.A1303T	NM_017675	NP_060145	Q9BYE9	CDHR2_HUMAN	protocadherin LKC precursor	1303	Cytoplasmic (Potential).				homophilic cell adhesion|negative regulation of cell growth	apical plasma membrane|cell junction|integral to membrane	calcium ion binding|protein binding			ovary(2)	2																		---	---	---	---
NSD1	64324	broad.mit.edu	37	5	176638884	176638884	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:176638884C>T	uc003mfr.3	+	5	3622	c.3484C>T	c.(3484-3486)CGT>TGT	p.R1162C	NSD1_uc003mft.3_Missense_Mutation_p.R893C|NSD1_uc003mfs.1_Missense_Mutation_p.R1059C|NSD1_uc011dfx.1_Missense_Mutation_p.R810C	NM_022455	NP_071900	Q96L73	NSD1_HUMAN	nuclear receptor binding SET domain protein 1	1162					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	176638998	176638998	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:176638998C>T	uc003mfr.3	+	5	3736	c.3598C>T	c.(3598-3600)CGG>TGG	p.R1200W	NSD1_uc003mft.3_Missense_Mutation_p.R931W|NSD1_uc003mfs.1_Missense_Mutation_p.R1097W|NSD1_uc011dfx.1_Missense_Mutation_p.R848W	NM_022455	NP_071900	Q96L73	NSD1_HUMAN	nuclear receptor binding SET domain protein 1	1200					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)			---	---	---	---
DBN1	1627	broad.mit.edu	37	5	176893949	176893949	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:176893949G>A	uc003mgy.2	-	7	842	c.670C>T	c.(670-672)CGC>TGC	p.R224C	DBN1_uc003mgx.2_Missense_Mutation_p.R226C|DBN1_uc010jkn.1_Missense_Mutation_p.R174C|DBN1_uc003mgz.1_Missense_Mutation_p.R161C	NM_004395	NP_004386	Q16643	DREB_HUMAN	drebrin 1 isoform a	224					actin filament organization|regulation of dendrite development|regulation of neuronal synaptic plasticity	actomyosin|cytoplasm|dendrite	actin binding|profilin binding			breast(3)|ovary(1)|lung(1)|skin(1)	6	all_cancers(89;2.17e-05)|Renal(175;0.000269)|Lung NSC(126;0.0014)|all_lung(126;0.0025)	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)															---	---	---	---
N4BP3	23138	broad.mit.edu	37	5	177548247	177548247	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:177548247G>A	uc003mik.1	+	4	1248	c.1001G>A	c.(1000-1002)CGC>CAC	p.R334H	N4BP3_uc003mil.1_5'UTR	NM_015111	NP_055926	O15049	N4BP3_HUMAN	Nedd4 binding protein 3	334	Potential.					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)													OREG0017096	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
NHP2	55651	broad.mit.edu	37	5	177577890	177577890	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:177577890G>A	uc003mir.2	-	3	478	c.335C>T	c.(334-336)ACG>ATG	p.T112M	NHP2_uc003mis.2_Intron	NM_017838	NP_060308	Q9NX24	NHP2_HUMAN	nucleolar protein family A, member 2 isoform a	112					rRNA pseudouridine synthesis	Cajal body|nucleolus|small nucleolar ribonucleoprotein complex	protein binding|snoRNA binding				0																		---	---	---	---
CLK4	57396	broad.mit.edu	37	5	178050348	178050348	+	Missense_Mutation	SNP	G	A	A	rs144043842	byFrequency;by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:178050348G>A	uc003mjf.1	-	2	178	c.70C>T	c.(70-72)CGT>TGT	p.R24C	CLK4_uc003mjg.1_5'UTR|CLK4_uc010jku.1_5'UTR|CLK4_uc003mjh.1_5'UTR|CLK4_uc010jkv.1_RNA|CLK4_uc011dgg.1_Missense_Mutation_p.R24C|CLK4_uc011dgh.1_5'UTR|CLK4_uc011dgi.1_Missense_Mutation_p.R24C|CLK4_uc011dgj.1_Missense_Mutation_p.R24C|CLK4_uc003mji.2_Missense_Mutation_p.R24C|CLK4_uc010jkw.1_Missense_Mutation_p.R24C	NM_020666	NP_065717	Q9HAZ1	CLK4_HUMAN	CDC-like kinase 4	24						nucleus	ATP binding|protein serine/threonine kinase activity|protein tyrosine kinase activity			ovary(1)	1	all_cancers(89;0.000969)|Renal(175;0.000159)|all_epithelial(37;0.000451)|Lung NSC(126;0.00545)|all_lung(126;0.00918)	all_cancers(40;0.0272)|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)	all cancers(165;0.235)														---	---	---	---
ZNF354A	6940	broad.mit.edu	37	5	178140264	178140264	+	Silent	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:178140264T>C	uc003mjj.2	-	5	813	c.615A>G	c.(613-615)CAA>CAG	p.Q205Q		NM_005649	NP_005640	O60765	Z354A_HUMAN	zinc finger protein 354A	205					regulation of transcription from RNA polymerase II promoter|sensory perception of sound|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(2)|skin(1)	3	all_cancers(89;0.000536)|Renal(175;0.000159)|all_epithelial(37;0.000221)|Lung NSC(126;0.00308)|all_lung(126;0.00536)	all_cancers(40;0.0452)|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)	all cancers(165;0.185)														---	---	---	---
ZFP2	80108	broad.mit.edu	37	5	178358990	178358990	+	Missense_Mutation	SNP	A	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:178358990A>C	uc003mjn.1	+	5	1185	c.676A>C	c.(676-678)AGC>CGC	p.S226R	ZFP2_uc010jky.2_Missense_Mutation_p.S226R|ZFP2_uc010jkx.1_Missense_Mutation_p.S226R	NM_030613	NP_085116	Q6ZN57	ZFP2_HUMAN	zinc finger protein 2 homolog	226	C2H2-type 5.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)|pancreas(1)|skin(1)	3	all_cancers(89;0.000639)|all_epithelial(37;0.000109)|Renal(175;0.000159)|Lung NSC(126;0.00199)|all_lung(126;0.00351)	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;0.00655)|GBM - Glioblastoma multiforme(465;0.0302)|OV - Ovarian serous cystadenocarcinoma(192;0.0615)|Epithelial(171;0.111)														---	---	---	---
HNRNPH1	3187	broad.mit.edu	37	5	179044545	179044545	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:179044545C>T	uc003mkf.3	-	9	1133	c.1027G>A	c.(1027-1029)GCA>ACA	p.A343T	HNRNPH1_uc011dgn.1_Missense_Mutation_p.A73T|HNRNPH1_uc003mkg.3_Missense_Mutation_p.A251T|HNRNPH1_uc003mke.3_Missense_Mutation_p.A343T|HNRNPH1_uc003mkh.3_Missense_Mutation_p.A343T	NM_005520	NP_005511	P31943	HNRH1_HUMAN	heterogeneous nuclear ribonucleoprotein H1	343	RRM 3.|2 X 16 AA Gly-rich approximate repeats.				regulation of RNA splicing	actin cytoskeleton|catalytic step 2 spliceosome|cytoplasm|heterogeneous nuclear ribonucleoprotein complex|nucleoplasm	nucleotide binding|poly(U) RNA binding|protein binding				0																		---	---	---	---
C5orf45	51149	broad.mit.edu	37	5	179271188	179271188	+	Silent	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:179271188G>A	uc003mla.2	-	4	299	c.255C>T	c.(253-255)AAC>AAT	p.N85N	C5orf45_uc003mky.2_Silent_p.N82N|C5orf45_uc011dgt.1_Silent_p.N85N|C5orf45_uc011dgu.1_Intron|C5orf45_uc003mlc.2_Intron|C5orf45_uc003mlb.2_Translation_Start_Site	NM_016175	NP_057259	Q6NTE8	CE045_HUMAN	hypothetical protein LOC51149 isoform 1	85											0																		---	---	---	---
BTNL9	153579	broad.mit.edu	37	5	180486680	180486680	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:180486680G>A	uc003mmt.2	+	11	1657	c.1426G>A	c.(1426-1428)GAC>AAC	p.D476N		NM_152547	NP_689760	Q6UXG8	BTNL9_HUMAN	butyrophilin-like 9 precursor	476	Cytoplasmic (Potential).|B30.2/SPRY.					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)															---	---	---	---
Unknown	0	broad.mit.edu	37	5	180651722	180651722	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:180651722C>T	uc003mnb.1	-	2	490	c.170G>A	c.(169-171)CGT>CAT	p.R57H	TRIM41_uc003mnc.1_Silent_p.D241D|TRIM41_uc003mnd.1_Silent_p.D241D|TRIM41_uc003mne.1_Silent_p.D241D|TRIM41_uc003mnf.1_RNA					Homo sapiens cDNA FLJ36305 fis, clone THYMU2004677.																														---	---	---	---
DUSP22	56940	broad.mit.edu	37	6	348140	348140	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:348140G>A	uc003msx.2	+	6	740	c.301G>A	c.(301-303)GCA>ACA	p.A101T	DUSP22_uc011dhn.1_Missense_Mutation_p.A101T|DUSP22_uc003msy.1_Missense_Mutation_p.A58T	NM_020185	NP_064570	Q9NRW4	DUS22_HUMAN	dual specificity phosphatase 22	101	Tyrosine-protein phosphatase.				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)														---	---	---	---
WRNIP1	56897	broad.mit.edu	37	6	2779551	2779551	+	Silent	SNP	C	T	T	rs142180339		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:2779551C>T	uc003mtz.2	+	4	1502	c.1311C>T	c.(1309-1311)GAC>GAT	p.D437D	WRNIP1_uc003mua.2_Silent_p.D412D	NM_020135	NP_064520	Q96S55	WRIP1_HUMAN	Werner helicase interacting protein isoform 1	437					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)																---	---	---	---
SERPINB9	5272	broad.mit.edu	37	6	2892186	2892186	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:2892186C>T	uc003mug.2	-	6	725	c.604G>A	c.(604-606)GCC>ACC	p.A202T	uc003mue.2_Intron|SERPINB9_uc003muf.2_Missense_Mutation_p.A5T	NM_004155	NP_004146	P50453	SPB9_HUMAN	serpin peptidase inhibitor, clade B, member 9	202					anti-apoptosis|cellular response to estrogen stimulus|immune response|mast cell mediated immunity|regulation of proteolysis	cytosol|extracellular space|nucleus	caspase inhibitor activity|protease binding|serine-type endopeptidase inhibitor activity				0	Ovarian(93;0.0412)	all_hematologic(90;0.108)																---	---	---	---
FARS2	10667	broad.mit.edu	37	6	5369248	5369248	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:5369248A>G	uc010jnv.1	+	2	781	c.445A>G	c.(445-447)ACT>GCT	p.T149A	FARS2_uc003mwr.2_Missense_Mutation_p.T149A|FARS2_uc003mws.1_Missense_Mutation_p.T149A	NM_006567	NP_006558	O95363	SYFM_HUMAN	phenylalanyl-tRNA synthetase 2 precursor	149					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)													---	---	---	---
RREB1	6239	broad.mit.edu	37	6	7211863	7211863	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:7211863T>C	uc003mxc.2	+	8	1018	c.628T>C	c.(628-630)TGC>CGC	p.C210R	RREB1_uc010jnw.2_Missense_Mutation_p.C210R|RREB1_uc003mxb.2_Missense_Mutation_p.C210R|RREB1_uc010jnx.2_Missense_Mutation_p.C210R|RREB1_uc003mxd.2_Missense_Mutation_p.C210R	NM_001003698	NP_001003698	Q92766	RREB1_HUMAN	ras responsive element binding protein 1 isoform	210	C2H2-type 4.				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)																---	---	---	---
DSP	1832	broad.mit.edu	37	6	7558460	7558460	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:7558460C>T	uc003mxp.1	+	3	664	c.385C>T	c.(385-387)CGG>TGG	p.R129W	DSP_uc003mxq.1_Missense_Mutation_p.R129W	NM_004415	NP_004406	P15924	DESP_HUMAN	desmoplakin isoform I	129	Globular 1.|Interacts with plakophilin 1 and junction plakoglobin.				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)														---	---	---	---
SLC35B3	51000	broad.mit.edu	37	6	8422698	8422698	+	Intron	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:8422698T>C	uc010joe.2	-						SLC35B3_uc003mya.2_Intron|SLC35B3_uc003myc.2_Intron|SLC35B3_uc003myb.2_Intron|SLC35B3_uc011did.1_Intron|SLC35B3_uc003myd.2_Intron	NM_001142541	NP_001136013			solute carrier family 35, member B3						transmembrane transport	Golgi membrane|integral to membrane					0	Ovarian(93;0.0569)																	---	---	---	---
GCNT2	2651	broad.mit.edu	37	6	10586417	10586417	+	Intron	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:10586417A>G	uc010joo.2	+						GCNT2_uc010jol.2_Intron|GCNT2_uc010jom.2_Intron|GCNT2_uc010jop.2_Intron|GCNT2_uc003mza.2_Intron|GCNT2_uc003mzc.3_Intron|GCNT2_uc003mzd.2_Intron|GCNT2_uc003mze.2_Silent_p.L65L	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)														---	---	---	---
NEDD9	4739	broad.mit.edu	37	6	11213900	11213900	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:11213900G>A	uc003mzv.2	-	2	240	c.73C>T	c.(73-75)CGC>TGC	p.R25C	NEDD9_uc010joz.2_Missense_Mutation_p.R25C|NEDD9_uc003mzw.3_5'UTR|NEDD9_uc003mzx.2_Missense_Mutation_p.R25C	NM_006403	NP_006394	Q14511	CASL_HUMAN	neural precursor cell expressed, developmentally	25	SH3.				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)															---	---	---	---
PHACTR1	221692	broad.mit.edu	37	6	13053669	13053669	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:13053669G>A	uc010jpc.2	+	5	655	c.323G>A	c.(322-324)CGC>CAC	p.R108H	PHACTR1_uc011dir.1_Missense_Mutation_p.R108H|PHACTR1_uc003nag.1_Missense_Mutation_p.R108H|PHACTR1_uc003nah.1_Missense_Mutation_p.R108H	NM_030948	NP_112210	Q9C0D0	PHAR1_HUMAN	phosphatase and actin regulator 1	108						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)															---	---	---	---
GFOD1	54438	broad.mit.edu	37	6	13365469	13365469	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:13365469G>T	uc003nat.1	-	2	1344	c.679C>A	c.(679-681)CTG>ATG	p.L227M	GFOD1_uc003nas.1_Missense_Mutation_p.L124M	NM_018988	NP_061861	Q9NXC2	GFOD1_HUMAN	glucose-fructose oxidoreductase domain	227						extracellular region	binding|oxidoreductase activity			ovary(2)	2	Breast(50;0.0296)|Ovarian(93;0.0454)	all_hematologic(90;0.135)	Epithelial(50;0.0348)|BRCA - Breast invasive adenocarcinoma(129;0.1)|all cancers(50;0.108)															---	---	---	---
JARID2	3720	broad.mit.edu	37	6	15496543	15496543	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:15496543A>G	uc003nbj.2	+	7	1331	c.1087A>G	c.(1087-1089)AAT>GAT	p.N363D	JARID2_uc011diu.1_Missense_Mutation_p.N227D|JARID2_uc011div.1_Missense_Mutation_p.N191D|JARID2_uc011diw.1_Missense_Mutation_p.N325D	NM_004973	NP_004964	Q92833	JARD2_HUMAN	jumonji, AT rich interactive domain 2 protein	363					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	15508684	15508684	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:15508684T>C	uc003nbj.2	+	12	3089	c.2845T>C	c.(2845-2847)TGG>CGG	p.W949R	JARID2_uc011div.1_Missense_Mutation_p.W777R|JARID2_uc011diw.1_Missense_Mutation_p.C911R	NM_004973	NP_004964	Q92833	JARD2_HUMAN	jumonji, AT rich interactive domain 2 protein	949	JmjC.				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)																---	---	---	---
MYLIP	29116	broad.mit.edu	37	6	16144063	16144063	+	Nonsense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:16144063C>T	uc003nbq.2	+	5	1033	c.796C>T	c.(796-798)CGA>TGA	p.R266*	MYLIP_uc003nbr.2_Nonsense_Mutation_p.R85*	NM_013262	NP_037394	Q8WY64	MYLIP_HUMAN	myosin regulatory light chain interacting	266	FERM.				cellular component movement|nervous system development	cytoplasm|cytoskeleton|extrinsic to membrane	cytoskeletal protein binding|ubiquitin-protein ligase activity|zinc ion binding			pancreas(1)	1	Breast(50;0.0799)|Ovarian(93;0.103)	all_hematologic(90;0.0895)	Epithelial(50;0.241)															---	---	---	---
MBOAT1	154141	broad.mit.edu	37	6	20152949	20152949	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:20152949G>A	uc003ncx.1	-	2	356	c.151C>T	c.(151-153)CGC>TGC	p.R51C	MBOAT1_uc011dji.1_Intron	NM_001080480	NP_001073949	Q6ZNC8	MBOA1_HUMAN	membrane bound O-acyltransferase domain	51	Helical; (Potential).				phospholipid biosynthetic process	integral to membrane	acyltransferase activity				0	all_cancers(95;0.244)|Breast(50;0.0379)|Ovarian(93;0.0473)|all_epithelial(95;0.109)		OV - Ovarian serous cystadenocarcinoma(7;0.00392)|all cancers(50;0.0117)|Epithelial(50;0.0454)															---	---	---	---
DCDC2	51473	broad.mit.edu	37	6	24357701	24357701	+	Missense_Mutation	SNP	G	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:24357701G>C	uc003ndx.2	-	1	580	c.278C>G	c.(277-279)GCC>GGC	p.A93G	DCDC2_uc003ndy.2_Missense_Mutation_p.A93G|KAAG1_uc003ndz.1_5'UTR	NM_016356	NP_057440	Q9UHG0	DCDC2_HUMAN	doublecortin domain containing 2	93	Doublecortin 1.				cellular defense response|intracellular signal transduction|neuron migration					ovary(1)	1		Ovarian(999;0.101)																---	---	---	---
DCDC2	51473	broad.mit.edu	37	6	24358124	24358124	+	5'UTR	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:24358124G>A	uc003ndx.2	-	1					DCDC2_uc003ndy.2_Intron|KAAG1_uc003ndz.1_3'UTR	NM_016356	NP_057440			doublecortin domain containing 2						cellular defense response|intracellular signal transduction|neuron migration					ovary(1)	1		Ovarian(999;0.101)																---	---	---	---
GPLD1	2822	broad.mit.edu	37	6	24475366	24475366	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:24475366G>T	uc003ned.1	-	5	535	c.424C>A	c.(424-426)CTT>ATT	p.L142I	GPLD1_uc010jpr.1_Silent_p.S13S|GPLD1_uc010jps.1_Missense_Mutation_p.L142I|GPLD1_uc003nee.2_Missense_Mutation_p.L142I	NM_001503	NP_001494	P80108	PHLD_HUMAN	glycosylphosphatidylinositol specific	142						extracellular region	glycosylphosphatidylinositol phospholipase D activity			ovary(2)|kidney(1)	3																		---	---	---	---
LRRC16A	55604	broad.mit.edu	37	6	25540238	25540238	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:25540238A>G	uc011djw.1	+	26	2636	c.2260A>G	c.(2260-2262)AGT>GGT	p.S754G	LRRC16A_uc010jpx.2_Missense_Mutation_p.S754G|LRRC16A_uc010jpy.2_Missense_Mutation_p.S754G|LRRC16A_uc003nfa.1_Missense_Mutation_p.S108G	NM_017640	NP_060110	Q5VZK9	LR16A_HUMAN	leucine rich repeat containing 16A	754					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	25727236	25727236	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:25727236A>G	uc003nfd.2	+	1	100	c.100A>G	c.(100-102)ACC>GCC	p.T34A	HIST1H2AA_uc003nfc.2_5'Flank	NM_170610	NP_733759	Q96A08	H2B1A_HUMAN	histone cluster 1, H2ba	34					nucleosome assembly	nucleosome|nucleus	DNA binding			kidney(1)	1																		---	---	---	---
SLC17A1	6568	broad.mit.edu	37	6	25826783	25826783	+	Missense_Mutation	SNP	G	A	A	rs147069707		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:25826783G>A	uc003nfh.3	-	3	229	c.113C>T	c.(112-114)GCG>GTG	p.A38V	SLC17A1_uc011djy.1_RNA|SLC17A1_uc010jqb.1_Missense_Mutation_p.A36V|SLC17A1_uc010jqc.1_Missense_Mutation_p.A36V	NM_005074	NP_005065	Q14916	NPT1_HUMAN	solute carrier family 17 (sodium phosphate),	38				RA -> LM (in Ref. 9; BAA05888).	sodium ion transport|urate metabolic process	integral to plasma membrane|membrane fraction	sodium-dependent phosphate transmembrane transporter activity|symporter activity			ovary(3)|pancreas(1)	4																		---	---	---	---
HIST1H3B	8358	broad.mit.edu	37	6	26031939	26031939	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:26031939C>T	uc003nfs.1	-	1	350	c.350G>A	c.(349-351)CGA>CAA	p.R117Q		NM_003537	NP_003528	P68431	H31_HUMAN	histone cluster 1, H3b	117					blood coagulation|nucleosome assembly|regulation of gene silencing|S phase	nucleoplasm|nucleosome	DNA binding|protein binding	p.R117Q(1)		ovary(2)	2																		---	---	---	---
HIST1H3B	8358	broad.mit.edu	37	6	26032195	26032195	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:26032195C>A	uc003nfs.1	-	1	94	c.94G>T	c.(94-96)GCT>TCT	p.A32S		NM_003537	NP_003528	P68431	H31_HUMAN	histone cluster 1, H3b	32					blood coagulation|nucleosome assembly|regulation of gene silencing|S phase	nucleoplasm|nucleosome	DNA binding|protein binding			ovary(2)	2																		---	---	---	---
HIST1H1C	3006	broad.mit.edu	37	6	26056276	26056276	+	Silent	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:26056276T>C	uc003nfw.2	-	1	424	c.381A>G	c.(379-381)AAA>AAG	p.K127K		NM_005319	NP_005310	P16403	H12_HUMAN	histone cluster 1, H1c	127					nucleosome assembly	nucleosome|nucleus	DNA binding			ovary(3)|skin(2)	5																		---	---	---	---
HIST1H1T	3010	broad.mit.edu	37	6	26108233	26108233	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:26108233G>A	uc003ngj.2	-	1	132	c.89C>T	c.(88-90)GCT>GTT	p.A30V		NM_005323	NP_005314	P22492	H1T_HUMAN	histone cluster 1, H1t	30					cell differentiation|multicellular organismal development|nucleosome assembly|spermatogenesis	nucleosome	DNA binding			ovary(2)	2																		---	---	---	---
HIST1H2BC	8347	broad.mit.edu	37	6	26123930	26123930	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:26123930T>C	uc003ngk.3	-	1	225	c.203A>G	c.(202-204)AAC>AGC	p.N68S	HIST1H2BC_uc003ngl.2_Missense_Mutation_p.N68S|HIST1H2AC_uc003ngm.2_5'Flank|HIST1H2AC_uc003ngn.2_5'Flank|HIST1H2AC_uc003ngo.2_5'Flank|HIST1H2AC_uc003ngp.2_5'Flank	NM_003526	NP_003517	P62807	H2B1C_HUMAN	histone cluster 1, H2bc	68					defense response to bacterium|nucleosome assembly	nucleosome|nucleus	DNA binding|protein binding			ovary(1)	1																		---	---	---	---
HIST1H4E	8367	broad.mit.edu	37	6	26205189	26205189	+	3'UTR	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:26205189A>G	uc003ngy.2	+	1						NM_003545	NP_003536			histone cluster 1, H4e						CenH3-containing nucleosome assembly at centromere|negative regulation of megakaryocyte differentiation|phosphatidylinositol-mediated signaling|telomere maintenance	nucleoplasm|nucleosome	DNA binding|protein binding			ovary(1)	1		all_hematologic(11;0.196)																---	---	---	---
HIST1H2BH	8345	broad.mit.edu	37	6	26252027	26252027	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:26252027A>G	uc003nhh.2	+	1	149	c.149A>G	c.(148-150)CAC>CGC	p.H50R	HIST1H3F_uc003nhg.1_5'Flank	NM_003524	NP_003515	Q93079	H2B1H_HUMAN	histone cluster 1, H2bh	50					nucleosome assembly	nucleosome|nucleus	DNA binding			ovary(3)	3																		---	---	---	---
BTN2A3	54718	broad.mit.edu	37	6	26431760	26431760	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:26431760A>G	uc011dkl.1	+	6	1708	c.1678A>G	c.(1678-1680)AGT>GGT	p.S560G	BTN2A3_uc011dkm.1_RNA					RecName: Full=Butyrophilin subfamily 2 member A3; Flags: Precursor;												0																		---	---	---	---
BTN2A1	11120	broad.mit.edu	37	6	26459947	26459947	+	Silent	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:26459947C>T	uc003nib.1	+	3	533	c.321C>T	c.(319-321)AGC>AGT	p.S107S	BTN2A1_uc003nic.1_Silent_p.S107S|BTN2A1_uc003nid.1_5'UTR|BTN2A1_uc011dko.1_Silent_p.S46S	NM_007049	NP_008980	Q7KYR7	BT2A1_HUMAN	butyrophilin, subfamily 2, member A1 isoform 1	107	Extracellular (Potential).|Ig-like V-type.				lipid metabolic process	integral to plasma membrane				ovary(1)|skin(1)	2																		---	---	---	---
ZNF322A	79692	broad.mit.edu	37	6	26637570	26637570	+	3'UTR	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:26637570T>C	uc003nil.3	-	4					ZNF322A_uc003nij.2_5'Flank	NM_024639	NP_078915			zinc finger protein 322A						regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	DNA binding|zinc ion binding				0																		---	---	---	---
PRSS16	10279	broad.mit.edu	37	6	27222646	27222646	+	Missense_Mutation	SNP	T	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:27222646T>A	uc003nja.2	+	10	1337	c.1325T>A	c.(1324-1326)GTT>GAT	p.V442D	PRSS16_uc011dkt.1_RNA|PRSS16_uc003njb.2_Missense_Mutation_p.V185D|PRSS16_uc003njd.2_Intron	NM_005865	NP_005856	Q9NQE7	TSSP_HUMAN	protease, serine, 16 precursor	442					protein catabolic process|proteolysis	cytoplasmic membrane-bounded vesicle	serine-type peptidase activity			ovary(2)|central_nervous_system(2)|skin(1)	5																		---	---	---	---
HIST1H2BM	8342	broad.mit.edu	37	6	27783192	27783192	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:27783192G>A	uc003njo.2	+	1	371	c.371G>A	c.(370-372)AGC>AAC	p.S124N	HIST1H2AJ_uc003njn.1_5'Flank	NM_003521	NP_003512	Q99879	H2B1M_HUMAN	histone cluster 1, H2bm	124					nucleosome assembly	nucleosome|nucleus	DNA binding			large_intestine(1)	1																		---	---	---	---
HIST1H1B	3009	broad.mit.edu	37	6	27834672	27834672	+	Silent	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:27834672T>C	uc003njx.2	-	1	688	c.636A>G	c.(634-636)AAA>AAG	p.K212K		NM_005322	NP_005313	P16401	H15_HUMAN	histone cluster 1, H1b	212					nucleosome assembly	nucleosome|nucleus	DNA binding			large_intestine(2)|lung(1)	3																		---	---	---	---
ZNF192	7745	broad.mit.edu	37	6	28120139	28120139	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:28120139A>G	uc003nkn.1	+	5	936	c.752A>G	c.(751-753)AAT>AGT	p.N251S	ZNF192_uc010jqx.1_Missense_Mutation_p.N251S|ZNF192_uc010jqy.1_Missense_Mutation_p.N64S|ZNF192_uc011dkz.1_Missense_Mutation_p.N64S	NM_006298	NP_006289	Q15776	ZN192_HUMAN	zinc finger protein 192	251	KRAB.				viral reproduction	cytoplasm|nucleolus	DNA binding|protein binding|sequence-specific DNA binding transcription factor activity|zinc ion binding				0																		---	---	---	---
ZKSCAN4	387032	broad.mit.edu	37	6	28217607	28217607	+	Silent	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:28217607G>A	uc003nks.1	-	2	673	c.429C>T	c.(427-429)CCC>CCT	p.P143P	ZKSCAN4_uc011dlb.1_5'UTR	NM_019110	NP_061983	Q969J2	ZKSC4_HUMAN	zinc finger with KRAB and SCAN domains 4	143					viral reproduction	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(1)	1																		---	---	---	---
OR12D2	26529	broad.mit.edu	37	6	29365297	29365297	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:29365297C>T	uc003nmf.3	+	1	882	c.821C>T	c.(820-822)GCC>GTC	p.A274V		NM_013936	NP_039224	P58182	O12D2_HUMAN	olfactory receptor, family 12, subfamily D,	274	Helical; Name=7; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)	1																		---	---	---	---
HLA-F	3134	broad.mit.edu	37	6	29692093	29692093	+	Missense_Mutation	SNP	G	A	A	rs147086730	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:29692093G>A	uc010jrl.2	+	3	602	c.478G>A	c.(478-480)GTG>ATG	p.V160M	HLA-F_uc003nnm.3_Missense_Mutation_p.V160M|HLA-F_uc003nno.3_Missense_Mutation_p.V160M|HLA-F_uc011dlx.1_Missense_Mutation_p.V160M|HLA-F_uc011dly.1_RNA	NM_018950	NP_061823	P30511	HLAF_HUMAN	major histocompatibility complex, class I, F	160	Extracellular (Potential).|Alpha-2.				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				0																		---	---	---	---
HLA-A	3105	broad.mit.edu	37	6	29910404	29910404	+	Splice_Site	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:29910404G>A	uc003nol.2	+	1	73	c.73_splice	c.e1+1	p.G25_splice	HLA-G_uc011dmb.1_Intron|HCG4P6_uc003nog.1_Intron|HLA-A_uc010jrq.2_Splice_Site|HLA-A_uc003nok.2_Splice_Site|HLA-A_uc003non.2_Splice_Site_p.G25_splice|HLA-A_uc003noo.2_Splice_Site_p.G25_splice|HLA-A_uc010jrr.2_Splice_Site_p.G25_splice|HLA-A_uc003nom.2_Splice_Site|HLA-A_uc010klp.2_5'Flank|HLA-A_uc011dmc.1_5'Flank|HLA-A_uc011dmd.1_5'Flank	NM_002116	NP_002107			major histocompatibility complex, class I, A						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			upper_aerodigestive_tract(1)|ovary(1)	2														Melanoma_Familial_Clustering_of|Lichen_Sclerosis_et_Atrophicus_Familial_Clustering_of|Osteosarcoma_Familial_Clustering_of|Naso-/Oropharyngeal/Laryngeal_Cancer_Familial_Clustering_of	Multiple Myeloma(9;0.094)			---	---	---	---
HLA-A	3105	broad.mit.edu	37	6	29911276	29911276	+	Missense_Mutation	SNP	T	C	C	rs45572432		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:29911276T>C	uc003nol.2	+	3	575	c.575T>C	c.(574-576)CTC>CCC	p.L192P	HLA-G_uc011dmb.1_Intron|HCG4P6_uc003nog.1_5'Flank|HLA-A_uc010jrq.2_Missense_Mutation_p.L71P|HLA-A_uc003nok.2_Missense_Mutation_p.L71P|HLA-A_uc003non.2_Missense_Mutation_p.L192P|HLA-A_uc003noo.2_Missense_Mutation_p.L192P|HLA-A_uc010jrr.2_Missense_Mutation_p.L192P|HLA-A_uc003nom.2_Missense_Mutation_p.L71P|HLA-A_uc010klp.2_Missense_Mutation_p.L164P|HLA-A_uc011dmc.1_Missense_Mutation_p.L71P|HLA-A_uc011dmd.1_Missense_Mutation_p.L71P	NM_002116	NP_002107	P30443	1A01_HUMAN	major histocompatibility complex, class I, A	192	Extracellular (Potential).|Alpha-2.				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			upper_aerodigestive_tract(1)|ovary(1)	2														Melanoma_Familial_Clustering_of|Lichen_Sclerosis_et_Atrophicus_Familial_Clustering_of|Osteosarcoma_Familial_Clustering_of|Naso-/Oropharyngeal/Laryngeal_Cancer_Familial_Clustering_of	Multiple Myeloma(9;0.094)			---	---	---	---
C6orf136	221545	broad.mit.edu	37	6	30619216	30619216	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:30619216A>G	uc003nqw.3	+	4	930	c.737A>G	c.(736-738)TAC>TGC	p.Y246C	C6orf136_uc003nqx.3_Missense_Mutation_p.Y427C|C6orf136_uc011dmn.1_Missense_Mutation_p.Y112C	NM_001109938	NP_001103408	Q5SQH8	CF136_HUMAN	hypothetical protein LOC221545 isoform 1	246											0																		---	---	---	---
MDC1	9656	broad.mit.edu	37	6	30672091	30672091	+	Silent	SNP	G	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:30672091G>T	uc003nrg.3	-	10	5309	c.4869C>A	c.(4867-4869)ACC>ACA	p.T1623T	MDC1_uc003nrf.3_Intron|MDC1_uc011dmp.1_Silent_p.T1230T	NM_014641	NP_055456	Q14676	MDC1_HUMAN	mediator of DNA-damage checkpoint 1	1623					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	30673602	30673602	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:30673602C>A	uc003nrg.3	-	10	3798	c.3358G>T	c.(3358-3360)GCT>TCT	p.A1120S	MDC1_uc003nrf.3_Intron|MDC1_uc011dmp.1_Missense_Mutation_p.A727S	NM_014641	NP_055456	Q14676	MDC1_HUMAN	mediator of DNA-damage checkpoint 1	1120	Pro-rich.			Missing (in Ref. 2; CAH18685).	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					---	---	---	---
VARS2	57176	broad.mit.edu	37	6	30893746	30893746	+	Silent	SNP	C	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:30893746C>G	uc003nsc.1	+	28	3683	c.3051C>G	c.(3049-3051)ACC>ACG	p.T1017T	VARS2_uc011dmx.1_Silent_p.T1017T|VARS2_uc011dmy.1_Silent_p.T877T|VARS2_uc011dmz.1_Silent_p.T1047T|VARS2_uc011dna.1_Silent_p.T1015T|VARS2_uc011dnb.1_RNA|VARS2_uc011dnc.1_RNA|VARS2_uc011dnd.1_Silent_p.T455T|VARS2_uc010jsg.1_Silent_p.T389T|VARS2_uc010jsh.1_Silent_p.T161T	NM_020442	NP_065175	Q5ST30	SYVM_HUMAN	valyl-tRNA synthetase 2, mitochondrial	1017					valyl-tRNA aminoacylation	mitochondrion	ATP binding|valine-tRNA ligase activity			ovary(3)|central_nervous_system(1)	4																		---	---	---	---
VARS	7407	broad.mit.edu	37	6	31747903	31747903	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:31747903G>A	uc003nxe.2	-	26	3376	c.2953C>T	c.(2953-2955)CGC>TGC	p.R985C	C6orf27_uc011dog.1_5'Flank|C6orf27_uc003nxd.2_5'Flank|C6orf27_uc011doh.1_5'Flank|VARS_uc003nxf.1_5'UTR	NM_006295	NP_006286	P26640	SYVC_HUMAN	valyl-tRNA synthetase	985					translational elongation|valyl-tRNA aminoacylation	cytosol	ATP binding|protein binding|valine-tRNA ligase activity			upper_aerodigestive_tract(1)|ovary(1)|skin(1)	3					L-Valine(DB00161)													---	---	---	---
NEU1	4758	broad.mit.edu	37	6	31828261	31828261	+	Silent	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:31828261G>A	uc003nxq.3	-	4	909	c.753C>T	c.(751-753)TAC>TAT	p.Y251Y	NEU1_uc010jtg.2_RNA|NEU1_uc003nxr.3_RNA|NEU1_uc010jth.2_Silent_p.Y82Y|NEU1_uc003nxs.3_Silent_p.Y251Y	NM_000434	NP_000425	Q99519	NEUR1_HUMAN	neuraminidase precursor	251						cytoplasmic membrane-bounded vesicle|lysosomal lumen|lysosomal membrane|plasma membrane	exo-alpha-sialidase activity|protein binding			ovary(1)	1					Oseltamivir(DB00198)|Zanamivir(DB00558)													---	---	---	---
NEU1	4758	broad.mit.edu	37	6	31829926	31829926	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:31829926C>T	uc003nxq.3	-	2	358	c.202G>A	c.(202-204)GGG>AGG	p.G68R	NEU1_uc010jtg.2_RNA|NEU1_uc003nxr.3_RNA|NEU1_uc010jth.2_Intron|NEU1_uc003nxs.3_Missense_Mutation_p.G68R	NM_000434	NP_000425	Q99519	NEUR1_HUMAN	neuraminidase precursor	68			G -> V (in SIALIDOSIS; type 2; less than 10% of activity).			cytoplasmic membrane-bounded vesicle|lysosomal lumen|lysosomal membrane|plasma membrane	exo-alpha-sialidase activity|protein binding			ovary(1)	1					Oseltamivir(DB00198)|Zanamivir(DB00558)													---	---	---	---
EHMT2	10919	broad.mit.edu	37	6	31856368	31856368	+	Intron	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:31856368G>A	uc003nxz.1	-						EHMT2_uc003nxy.1_Intron|EHMT2_uc011don.1_Intron|EHMT2_uc003nya.1_Intron	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																		---	---	---	---
CFB	629	broad.mit.edu	37	6	31917880	31917880	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:31917880A>G	uc003nyj.3	+	11	1740	c.1462A>G	c.(1462-1464)ACC>GCC	p.T488A	CFB_uc011dor.1_Missense_Mutation_p.T990A|CFB_uc003nyi.2_Missense_Mutation_p.T488A	NM_001710	NP_001701	P00751	CFAB_HUMAN	complement factor B preproprotein	488	Peptidase S1.				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	32049925	32049925	+	Silent	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:32049925G>A	uc003nzl.2	-	9	3826	c.3624C>T	c.(3622-3624)CCC>CCT	p.P1208P		NM_019105	NP_061978	P22105	TENX_HUMAN	tenascin XB isoform 1 precursor	1295	Fibronectin type-III 5.				actin cytoskeleton organization|cell adhesion|collagen metabolic process|elastic fiber assembly|signal transduction	extracellular space|intracellular|proteinaceous extracellular matrix	heparin binding|integrin binding				0																		---	---	---	---
ATF6B	1388	broad.mit.edu	37	6	32088680	32088680	+	Splice_Site	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:32088680C>T	uc003nzn.2	-	8	734	c.701_splice	c.e8-1	p.G234_splice	ATF6B_uc003nzm.1_5'Flank|ATF6B_uc003nzo.2_Splice_Site_p.G231_splice|ATF6B_uc003nzp.1_5'Flank|ATF6B_uc011dpg.1_Intron|ATF6B_uc011dph.1_Intron	NM_004381	NP_004372			activating transcription factor 6 beta isoform						response to unfolded protein|signal transduction	endoplasmic reticulum membrane|integral to membrane|nucleus	protein dimerization activity|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity				0																		---	---	---	---
NOTCH4	4855	broad.mit.edu	37	6	32169877	32169877	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:32169877T>C	uc003obb.2	-	21	3870	c.3731A>G	c.(3730-3732)GAC>GGC	p.D1244G	NOTCH4_uc003oba.2_5'UTR|NOTCH4_uc011dpu.1_Intron|NOTCH4_uc011dpv.1_Intron	NM_004557	NP_004548	Q99466	NOTC4_HUMAN	notch4 preproprotein	1244	LNR 2.|Extracellular (Potential).				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																		---	---	---	---
PSMB9	5698	broad.mit.edu	37	6	32825853	32825853	+	Missense_Mutation	SNP	G	A	A	rs150909909		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:32825853G>A	uc003sga.2	+	5	371	c.296G>A	c.(295-297)CGA>CAA	p.R99Q	PSMB9_uc011dqj.1_Missense_Mutation_p.R67Q	NM_148954	NP_683756	P28065	PSB9_HUMAN	proteasome beta 9 subunit isoform 2 proprotein	111					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																		---	---	---	---
BRD2	6046	broad.mit.edu	37	6	32945556	32945556	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:32945556C>T	uc003ocn.3	+	9	3053	c.1352C>T	c.(1351-1353)GCC>GTC	p.A451V	BRD2_uc003oco.2_RNA|BRD2_uc003ocq.3_Missense_Mutation_p.A451V|BRD2_uc003ocp.3_Missense_Mutation_p.A331V|BRD2_uc010juh.2_Missense_Mutation_p.A451V	NM_005104	NP_005095	P25440	BRD2_HUMAN	bromodomain containing 2	451					spermatogenesis	nucleus	protein serine/threonine kinase activity			central_nervous_system(3)|stomach(2)	5																		---	---	---	---
BRD2	6046	broad.mit.edu	37	6	32945559	32945559	+	Missense_Mutation	SNP	A	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:32945559A>C	uc003ocn.3	+	9	3056	c.1355A>C	c.(1354-1356)AAG>ACG	p.K452T	BRD2_uc003oco.2_RNA|BRD2_uc003ocq.3_Missense_Mutation_p.K452T|BRD2_uc003ocp.3_Missense_Mutation_p.K332T|BRD2_uc010juh.2_Missense_Mutation_p.K452T	NM_005104	NP_005095	P25440	BRD2_HUMAN	bromodomain containing 2	452					spermatogenesis	nucleus	protein serine/threonine kinase activity			central_nervous_system(3)|stomach(2)	5																		---	---	---	---
COL11A2	1302	broad.mit.edu	37	6	33137193	33137193	+	Silent	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:33137193G>A	uc003ocx.1	-	51	3993	c.3765C>T	c.(3763-3765)GGC>GGT	p.G1255G	COL11A2_uc010jul.1_Intron|COL11A2_uc003ocy.1_Silent_p.G1169G|COL11A2_uc003ocz.1_Silent_p.G1148G	NM_080680	NP_542411	P13942	COBA2_HUMAN	collagen, type XI, alpha 2 isoform 1	1255	Triple-helical region.				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																		---	---	---	---
ZBTB9	221504	broad.mit.edu	37	6	33423942	33423942	+	Silent	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:33423942A>G	uc003oeq.2	+	2	1333	c.1065A>G	c.(1063-1065)TCA>TCG	p.S355S		NM_152735	NP_689948	Q96C00	ZBTB9_HUMAN	zinc finger and BTB domain containing 9	355	Gly-rich.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0																		---	---	---	---
ITPR3	3710	broad.mit.edu	37	6	33646405	33646405	+	Intron	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:33646405C>T	uc011drk.1	+							NM_002224	NP_002215			inositol 1,4,5-triphosphate receptor, type 3						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	33653919	33653919	+	Silent	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:33653919G>A	uc011drk.1	+	42	5976	c.5757G>A	c.(5755-5757)ACG>ACA	p.T1919T	ITPR3_uc003oey.2_Silent_p.T6T	NM_002224	NP_002215	Q14573	ITPR3_HUMAN	inositol 1,4,5-triphosphate receptor, type 3	1919	Cytoplasmic (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																		---	---	---	---
SCUBE3	222663	broad.mit.edu	37	6	35212420	35212420	+	Intron	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:35212420C>T	uc003okf.1	+						SCUBE3_uc003okg.1_Intron|SCUBE3_uc003okh.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																		---	---	---	---
BRPF3	27154	broad.mit.edu	37	6	36168662	36168662	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:36168662T>C	uc003olv.3	+	2	787	c.563T>C	c.(562-564)GTA>GCA	p.V188A	BRPF3_uc010jwb.2_Missense_Mutation_p.V188A|BRPF3_uc011dtj.1_RNA|BRPF3_uc010jwc.2_RNA|BRPF3_uc011dtk.1_Missense_Mutation_p.V188A	NM_015695	NP_056510	Q9ULD4	BRPF3_HUMAN	bromodomain and PHD finger containing, 3	188					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																		---	---	---	---
BRPF3	27154	broad.mit.edu	37	6	36177652	36177652	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:36177652A>G	uc003olv.3	+	5	2050	c.1826A>G	c.(1825-1827)GAT>GGT	p.D609G	BRPF3_uc010jwb.2_Missense_Mutation_p.D609G|BRPF3_uc011dtj.1_RNA|BRPF3_uc010jwc.2_RNA|BRPF3_uc011dtk.1_Missense_Mutation_p.D609G	NM_015695	NP_056510	Q9ULD4	BRPF3_HUMAN	bromodomain and PHD finger containing, 3	609	Bromo.				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																		---	---	---	---
DNAH8	1769	broad.mit.edu	37	6	38800200	38800200	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:38800200G>A	uc003ooe.1	+	29	4240	c.3640G>A	c.(3640-3642)GCA>ACA	p.A1214T		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	38890940	38890940	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:38890940A>G	uc003ooe.1	+	70	10718	c.10118A>G	c.(10117-10119)GAA>GGA	p.E3373G	uc003oof.1_RNA	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																		---	---	---	---
MOCS1	4337	broad.mit.edu	37	6	39874764	39874764	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:39874764C>T	uc003opb.2	-	10	1418	c.1280G>A	c.(1279-1281)TGC>TAC	p.C427Y	MOCS1_uc003opa.2_3'UTR|MOCS1_uc003opc.2_Missense_Mutation_p.C411Y|MOCS1_uc003opd.2_3'UTR|MOCS1_uc003ope.2_Missense_Mutation_p.C324Y	NM_005942	NP_005933	Q9NZB8	MOCS1_HUMAN	molybdenum cofactor synthesis-step 1 protein	427	Molybdenum cofactor biosynthesis protein C.				Mo-molybdopterin cofactor biosynthetic process|Mo-molybdopterin cofactor biosynthetic process|water-soluble vitamin metabolic process	cytosol|molybdopterin synthase complex|nucleus	4 iron, 4 sulfur cluster binding|4 iron, 4 sulfur cluster binding|catalytic activity|GTP binding|metal ion binding			ovary(1)|liver(1)|central_nervous_system(1)	3	Ovarian(28;0.0355)|Colorectal(47;0.196)																	---	---	---	---
MOCS1	4337	broad.mit.edu	37	6	39881137	39881137	+	Silent	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:39881137A>G	uc003opb.2	-	5	819	c.681T>C	c.(679-681)GAT>GAC	p.D227D	MOCS1_uc003opa.2_Silent_p.D227D|MOCS1_uc003opc.2_Silent_p.D227D|MOCS1_uc003opd.2_Silent_p.D227D|MOCS1_uc003ope.2_Silent_p.D140D	NM_005942	NP_005933	Q9NZB8	MOCS1_HUMAN	molybdenum cofactor synthesis-step 1 protein	227	Molybdenum cofactor biosynthesis protein A.				Mo-molybdopterin cofactor biosynthetic process|Mo-molybdopterin cofactor biosynthetic process|water-soluble vitamin metabolic process	cytosol|molybdopterin synthase complex|nucleus	4 iron, 4 sulfur cluster binding|4 iron, 4 sulfur cluster binding|catalytic activity|GTP binding|metal ion binding			ovary(1)|liver(1)|central_nervous_system(1)	3	Ovarian(28;0.0355)|Colorectal(47;0.196)																	---	---	---	---
TREML4	285852	broad.mit.edu	37	6	41196729	41196729	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:41196729C>T	uc003oqc.2	+	2	445	c.341C>T	c.(340-342)GCT>GTT	p.A114V	TREML4_uc003oqd.2_RNA	NM_198153	NP_937796	Q6UXN2	TRML4_HUMAN	triggering receptor expressed on myeloid	114	Ig-like V-type.					extracellular region				breast(1)	1	Ovarian(28;0.0327)|Colorectal(47;0.196)																	---	---	---	---
FOXP4	116113	broad.mit.edu	37	6	41556422	41556422	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:41556422G>A	uc003oql.2	+	9	1476	c.1018G>A	c.(1018-1020)GCC>ACC	p.A340T	FOXP4_uc003oqm.2_Missense_Mutation_p.A338T|FOXP4_uc003oqn.2_Missense_Mutation_p.A339T	NM_001012426	NP_001012426	Q8IVH2	FOXP4_HUMAN	forkhead box P4 isoform 1	340					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)																	---	---	---	---
FRS3	10817	broad.mit.edu	37	6	41738995	41738995	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:41738995C>T	uc003orc.1	-	7	1085	c.841G>A	c.(841-843)GCC>ACC	p.A281T		NM_006653	NP_006644	O43559	FRS3_HUMAN	fibroblast growth factor receptor substrate 3	281					fibroblast growth factor receptor signaling pathway	plasma membrane	fibroblast growth factor receptor binding|insulin receptor binding			ovary(2)	2	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	41900411	41900411	+	Silent	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:41900411C>T	uc003orl.2	+	7	1617	c.1281C>T	c.(1279-1281)CGC>CGT	p.R427R		NM_004053	NP_004044	Q13895	BYST_HUMAN	bystin	427					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)															---	---	---	---
TAF8	129685	broad.mit.edu	37	6	42044927	42044927	+	Silent	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:42044927C>T	uc003ors.2	+	8	899	c.870C>T	c.(868-870)ATC>ATT	p.I290I	TAF8_uc003ort.2_Missense_Mutation_p.S331L|TAF8_uc003oru.1_Missense_Mutation_p.S331L|TAF8_uc003orv.1_Silent_p.I290I|TAF8_uc011dun.1_Silent_p.I214I	NM_138572	NP_612639	Q7Z7C8	TAF8_HUMAN	TBP-associated factor 8	290					cell differentiation|maintenance of protein location in nucleus|positive regulation of transcription, DNA-dependent|regulation of fat cell differentiation|transcription, DNA-dependent	perinuclear region of cytoplasm|transcription factor TFIID complex	DNA binding|protein binding			ovary(1)	1	Colorectal(47;0.196)		STAD - Stomach adenocarcinoma(11;0.000204)|Colorectal(64;0.00062)|COAD - Colon adenocarcinoma(64;0.00152)|Epithelial(12;0.00179)															---	---	---	---
TRERF1	55809	broad.mit.edu	37	6	42200463	42200463	+	Silent	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:42200463G>A	uc003osd.2	-	17	3797	c.3234C>T	c.(3232-3234)GGC>GGT	p.G1078G	TRERF1_uc011duq.1_Silent_p.G995G|TRERF1_uc003osb.2_Silent_p.G846G|TRERF1_uc003osc.2_Silent_p.G834G|TRERF1_uc003ose.2_Silent_p.G1098G	NM_033502	NP_277037	Q96PN7	TREF1_HUMAN	transcriptional regulating factor 1	1078	Interacts with CREBBP.				cholesterol catabolic process|homeostatic process|multicellular organismal development|positive regulation of transcription, DNA-dependent|regulation of hormone biosynthetic process|steroid biosynthetic process	nucleus	DNA bending activity|ligand-dependent nuclear receptor transcription coactivator activity|RNA polymerase II transcription cofactor activity|sequence-specific DNA binding transcription factor activity|transcription factor binding|zinc ion binding			ovary(3)|pancreas(1)|skin(1)	5	Colorectal(47;0.196)		Colorectal(64;0.00062)|COAD - Colon adenocarcinoma(64;0.00152)															---	---	---	---
UBR2	23304	broad.mit.edu	37	6	42611965	42611965	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:42611965T>C	uc011dur.1	+	19	2111	c.2111T>C	c.(2110-2112)ATG>ACG	p.M704T	UBR2_uc011dus.1_Missense_Mutation_p.M349T|UBR2_uc010jxv.1_Missense_Mutation_p.M208T|UBR2_uc003osh.2_RNA	NM_015255	NP_056070	Q8IWV8	UBR2_HUMAN	ubiquitin protein ligase E3 component n-recognin	704					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)															---	---	---	---
PTK7	5754	broad.mit.edu	37	6	43098351	43098351	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:43098351G>A	uc003oub.1	+	5	962	c.764G>A	c.(763-765)AGC>AAC	p.S255N	PTK7_uc003ouc.1_Missense_Mutation_p.S255N|PTK7_uc003oud.1_Missense_Mutation_p.S255N|PTK7_uc003oue.1_Missense_Mutation_p.S255N|PTK7_uc003ouf.1_RNA|PTK7_uc003oug.1_RNA|PTK7_uc011dve.1_Missense_Mutation_p.S263N|PTK7_uc010jyj.1_5'Flank|PTK7_uc003oua.2_Missense_Mutation_p.S255N	NM_002821	NP_002812	Q13308	PTK7_HUMAN	PTK7 protein tyrosine kinase 7 isoform a	255	Ig-like C2-type 3.|Extracellular (Potential).				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)															---	---	---	---
CUL9	23113	broad.mit.edu	37	6	43160803	43160803	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:43160803G>A	uc003ouk.2	+	9	2320	c.2245G>A	c.(2245-2247)GTG>ATG	p.V749M	CUL9_uc003oul.2_Missense_Mutation_p.V749M|CUL9_uc010jyk.2_Translation_Start_Site	NM_015089	NP_055904	Q8IWT3	CUL9_HUMAN	p53-associated parkin-like cytoplasmic protein	749					ubiquitin-dependent protein catabolic process	cullin-RING ubiquitin ligase complex|cytoplasm	ATP binding|ubiquitin protein ligase binding|zinc ion binding			ovary(5)|lung(3)|skin(2)|breast(1)|central_nervous_system(1)	12																		---	---	---	---
TTBK1	84630	broad.mit.edu	37	6	43222390	43222390	+	Splice_Site	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:43222390G>A	uc003ouq.1	+	6	855	c.576_splice	c.e6+1	p.P192_splice		NM_032538	NP_115927			tau tubulin kinase 1							cell junction|cytoplasm|nucleus	ATP binding|protein binding|protein serine/threonine kinase activity			lung(4)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)	9			Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|all cancers(41;0.0125)|OV - Ovarian serous cystadenocarcinoma(102;0.0399)															---	---	---	---
ABCC10	89845	broad.mit.edu	37	6	43412904	43412904	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:43412904C>T	uc003ouy.1	+	14	3097	c.2882C>T	c.(2881-2883)TCC>TTC	p.S961F	ABCC10_uc003ouz.1_Missense_Mutation_p.S933F|ABCC10_uc010jyo.1_Missense_Mutation_p.S67F	NM_033450	NP_258261	Q5T3U5	MRP7_HUMAN	ATP-binding cassette, sub-family C, member 10	961	ABC transmembrane type-1 2.					integral to membrane|plasma membrane	ATP binding|ATPase activity, coupled to transmembrane movement of substances			ovary(6)|central_nervous_system(1)	7	all_lung(25;0.00536)		Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|all cancers(41;0.0152)|OV - Ovarian serous cystadenocarcinoma(102;0.0804)															---	---	---	---
VEGFA	7422	broad.mit.edu	37	6	43747429	43747429	+	Intron	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:43747429G>A	uc003owh.2	+						VEGFA_uc003owd.2_Intron|VEGFA_uc003owf.2_Intron|VEGFA_uc003owe.2_Intron|VEGFA_uc003owg.2_Intron|VEGFA_uc003owi.2_Intron|VEGFA_uc003owj.2_Intron|VEGFA_uc010jyx.2_Intron|VEGFA_uc003owk.2_Intron	NM_001025366	NP_001020537			vascular endothelial growth factor A isoform a						basophil chemotaxis|cellular response to hypoxia|induction of positive chemotaxis|induction of positive chemotaxis|platelet activation|platelet degranulation|platelet-derived growth factor receptor signaling pathway|positive regulation of angiogenesis|positive regulation of blood vessel endothelial cell migration|positive regulation of cell adhesion|positive regulation of cell division|positive regulation of endothelial cell proliferation|positive regulation of leukocyte migration|positive regulation of mast cell chemotaxis|positive regulation of peptidyl-tyrosine phosphorylation|positive regulation of vascular endothelial growth factor receptor signaling pathway|positive regulation of vascular permeability|regulation of cell shape|vascular endothelial growth factor receptor signaling pathway|vasculogenesis	cell surface|extracellular space|membrane|platelet alpha granule lumen	cell surface binding|chemoattractant activity|cytokine activity|fibronectin binding|growth factor activity|heparin binding|platelet-derived growth factor receptor binding|protein heterodimerization activity|protein homodimerization activity|vascular endothelial growth factor receptor 1 binding|vascular endothelial growth factor receptor 2 binding|vascular endothelial growth factor receptor binding			ovary(1)|breast(1)	2	all_cancers(18;5.46e-07)|all_epithelial(2;5.96e-08)|Lung NSC(15;0.000157)|all_lung(25;0.000486)|Hepatocellular(11;0.00309)		all cancers(41;0.000413)|Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|STAD - Stomach adenocarcinoma(11;0.0742)|OV - Ovarian serous cystadenocarcinoma(102;0.196)		Atorvastatin(DB01076)|Bevacizumab(DB00112)|Carvedilol(DB01136)|Ginkgo biloba(DB01381)|Gliclazide(DB01120)|Minocycline(DB01017)|Ranibizumab(DB01270)|Simvastatin(DB00641)													---	---	---	---
C6orf223	221416	broad.mit.edu	37	6	43970788	43970788	+	Silent	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:43970788G>A	uc003own.2	+	4	672	c.654G>A	c.(652-654)CGG>CGA	p.R218R	uc003owm.1_Intron|C6orf223_uc003owo.2_Silent_p.R198R	NM_153246	NP_694978	Q8N319	CF223_HUMAN	hypothetical protein LOC221416	218											0	all_cancers(18;2.28e-07)|all_epithelial(2;1.62e-08)|Lung NSC(15;0.000172)|all_lung(25;0.000533)|Hepatocellular(11;0.00309)|Ovarian(13;0.0437)		all cancers(41;0.00141)|Colorectal(64;0.00337)|COAD - Colon adenocarcinoma(64;0.00536)|STAD - Stomach adenocarcinoma(11;0.217)															---	---	---	---
SUPT3H	8464	broad.mit.edu	37	6	44971423	44971423	+	Silent	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:44971423G>A	uc003oxo.2	-	8	822	c.504C>T	c.(502-504)GAC>GAT	p.D168D	SUPT3H_uc003oxn.1_Silent_p.D157D|SUPT3H_uc011dvv.1_Silent_p.D5D|SUPT3H_uc003oxp.2_Silent_p.D157D|SUPT3H_uc011dvw.1_Silent_p.D71D	NM_181356	NP_852001	O75486	SUPT3_HUMAN	suppressor of Ty 3 homolog isoform 2	239					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																		---	---	---	---
CLIC5	53405	broad.mit.edu	37	6	45870973	45870973	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:45870973C>T	uc003oxv.3	-	6	1191	c.1085G>A	c.(1084-1086)CGC>CAC	p.R362H	CLIC5_uc003oxu.3_Missense_Mutation_p.R203H	NM_001114086	NP_001107558	Q9NZA1	CLIC5_HUMAN	chloride intracellular channel 5 isoform a	362	GST C-terminal.				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																		---	---	---	---
MUT	4594	broad.mit.edu	37	6	49421308	49421308	+	Missense_Mutation	SNP	A	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:49421308A>C	uc003ozg.3	-	5	1328	c.1073T>G	c.(1072-1074)CTT>CGT	p.L358R		NM_000255	NP_000246	P22033	MUTA_HUMAN	methylmalonyl Coenzyme A mutase precursor	358					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)													---	---	---	---
CRISP3	10321	broad.mit.edu	37	6	49701440	49701440	+	Silent	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:49701440G>A	uc003ozs.2	-	5	414	c.399C>T	c.(397-399)AAC>AAT	p.N133N		NM_006061	NP_006052	P54108	CRIS3_HUMAN	cysteine-rich secretory protein 3 precursor	133					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)															---	---	---	---
MCM3	4172	broad.mit.edu	37	6	52137140	52137140	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:52137140G>A	uc003pan.1	-	12	1896	c.1786C>T	c.(1786-1788)CGC>TGC	p.R596C	MCM3_uc011dwu.1_Missense_Mutation_p.R550C	NM_002388	NP_002379	P25205	MCM3_HUMAN	minichromosome maintenance complex component 3	596					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)																	---	---	---	---
MCM3	4172	broad.mit.edu	37	6	52148164	52148164	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:52148164A>G	uc003pan.1	-	2	229	c.119T>C	c.(118-120)ATC>ACC	p.I40T	MCM3_uc011dwu.1_Intron	NM_002388	NP_002379	P25205	MCM3_HUMAN	minichromosome maintenance complex component 3	40					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)																	---	---	---	---
EFHC1	114327	broad.mit.edu	37	6	52334255	52334255	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:52334255G>A	uc003pap.3	+	7	1477	c.1262G>A	c.(1261-1263)CGT>CAT	p.R421H	EFHC1_uc011dwv.1_Missense_Mutation_p.R330H|EFHC1_uc011dww.1_Missense_Mutation_p.R402H	NM_018100	NP_060570	Q5JVL4	EFHC1_HUMAN	EF-hand domain (C-terminal) containing 1	421	DM10 3.					axoneme|neuronal cell body	calcium ion binding|protein C-terminus binding			ovary(2)|skin(1)	3	Lung NSC(77;0.109)																	---	---	---	---
ICK	22858	broad.mit.edu	37	6	52895867	52895867	+	Silent	SNP	T	C	C	rs143876718		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:52895867T>C	uc003pbh.2	-	6	844	c.354A>G	c.(352-354)AAA>AAG	p.K118K	ICK_uc003pbi.2_Silent_p.K118K|ICK_uc003pbj.2_Silent_p.K118K	NM_016513	NP_057597	Q9UPZ9	ICK_HUMAN	intestinal cell kinase	118	Protein 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)																	---	---	---	---
LGSN	51557	broad.mit.edu	37	6	63990353	63990353	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:63990353C>T	uc003peh.2	-	4	1137	c.1103G>A	c.(1102-1104)CGT>CAT	p.R368H	LGSN_uc003pei.2_3'UTR	NM_016571	NP_057655	Q5TDP6	LGSN_HUMAN	lengsin, lens protein with glutamine synthetase	368					glutamine biosynthetic process		glutamate-ammonia ligase activity			skin(2)	2					L-Glutamic Acid(DB00142)													---	---	---	---
EYS	346007	broad.mit.edu	37	6	66063394	66063394	+	Silent	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:66063394T>C	uc011dxu.1	-	9	1954	c.1416A>G	c.(1414-1416)AAA>AAG	p.K472K	EYS_uc003peq.2_Silent_p.K472K|EYS_uc003per.1_Silent_p.K472K	NM_001142800	NP_001136272	Q5T1H1	EYS_HUMAN	eyes shut homolog isoform 1	472					response to stimulus|visual perception	extracellular region	calcium ion binding			lung(4)|ovary(1)|skin(1)	6																		---	---	---	---
DDX43	55510	broad.mit.edu	37	6	74104684	74104684	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:74104684G>A	uc003pgw.2	+	1	400	c.56G>A	c.(55-57)CGA>CAA	p.R19Q	OOEP_uc003pgv.3_5'UTR|DDX43_uc011dyn.1_RNA	NM_018665	NP_061135	Q9NXZ2	DDX43_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 43	19						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	75848296	75848296	+	Missense_Mutation	SNP	T	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:75848296T>A	uc003phs.2	-	29	5264	c.5098A>T	c.(5098-5100)ACC>TCC	p.T1700S	COL12A1_uc003pht.2_Missense_Mutation_p.T536S	NM_004370	NP_004361	Q99715	COCA1_HUMAN	collagen, type XII, alpha 1 long isoform	1700	Fibronectin type-III 12.				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																		---	---	---	---
PHIP	55023	broad.mit.edu	37	6	79680516	79680516	+	Nonsense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:79680516C>T	uc003pir.2	-	25	3205	c.2979G>A	c.(2977-2979)TGG>TGA	p.W993*	PHIP_uc003piq.2_Nonsense_Mutation_p.W17*|PHIP_uc011dyp.1_Nonsense_Mutation_p.W992*	NM_017934	NP_060404	Q8WWQ0	PHIP_HUMAN	pleckstrin homology domain interacting protein	993	Mediates interaction with IRS1 (By similarity).				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)														---	---	---	---
BCKDHB	594	broad.mit.edu	37	6	80877510	80877510	+	Silent	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:80877510T>C	uc003pjd.2	+	4	526	c.459T>C	c.(457-459)ATT>ATC	p.I153I	BCKDHB_uc003pje.2_Silent_p.I153I	NM_000056	NP_000047	P21953	ODBB_HUMAN	branched chain keto acid dehydrogenase E1 beta	153					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)														---	---	---	---
FAM46A	55603	broad.mit.edu	37	6	82459944	82459944	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:82459944C>T	uc003pjg.2	-	3	1115	c.797G>A	c.(796-798)GGC>GAC	p.G266D	FAM46A_uc003pjf.2_Missense_Mutation_p.G285D	NM_017633	NP_060103	Q96IP4	FA46A_HUMAN	hypothetical protein LOC55603	266											0		all_cancers(76;6.74e-06)|Acute lymphoblastic leukemia(125;3.41e-06)|all_hematologic(105;0.000282)|all_epithelial(107;0.0104)		BRCA - Breast invasive adenocarcinoma(397;0.0428)														---	---	---	---
TPBG	7162	broad.mit.edu	37	6	83075159	83075159	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:83075159G>A	uc003pjn.3	+	3	1417	c.481G>A	c.(481-483)GCT>ACT	p.A161T	TPBG_uc010kbj.2_Missense_Mutation_p.A161T|TPBG_uc003pjo.2_Missense_Mutation_p.A161T	NM_006670	NP_006661	Q13641	TPBG_HUMAN	trophoblast glycoprotein precursor	161	Extracellular (Potential).|LRR 3.				cell adhesion	integral to plasma membrane				central_nervous_system(1)	1		all_cancers(76;0.000805)|Acute lymphoblastic leukemia(125;3.85e-06)|all_hematologic(105;0.0017)|all_epithelial(107;0.0897)		BRCA - Breast invasive adenocarcinoma(397;0.107)														---	---	---	---
DOPEY1	23033	broad.mit.edu	37	6	83810525	83810525	+	Silent	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:83810525T>C	uc003pjs.1	+	4	500	c.240T>C	c.(238-240)CAT>CAC	p.H80H	DOPEY1_uc011dyy.1_Silent_p.H80H|DOPEY1_uc010kbl.1_Silent_p.H80H	NM_015018	NP_055833	Q5JWR5	DOP1_HUMAN	dopey family member 1	80					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)														---	---	---	---
TBX18	9096	broad.mit.edu	37	6	85472260	85472260	+	Splice_Site	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:85472260A>G	uc003pkl.1	-	2	497	c.497_splice	c.e2+1	p.R166_splice	TBX18_uc010kbq.1_Splice_Site_p.R8_splice	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)														---	---	---	---
HTR1E	3354	broad.mit.edu	37	6	87725184	87725184	+	Silent	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:87725184C>T	uc003pli.2	+	2	835	c.132C>T	c.(130-132)ATC>ATT	p.I44I		NM_000865	NP_000856	P28566	5HT1E_HUMAN	5-hydroxytryptamine (serotonin) receptor 1E	44	Helical; Name=1; (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)													---	---	---	---
RARS2	57038	broad.mit.edu	37	6	88240617	88240617	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:88240617A>G	uc003pme.2	-	9	716	c.656T>C	c.(655-657)GTA>GCA	p.V219A	RARS2_uc003pmb.2_Missense_Mutation_p.V44A|RARS2_uc003pmc.2_Missense_Mutation_p.V44A|RARS2_uc003pmd.2_5'UTR|RARS2_uc003pmf.2_RNA	NM_020320	NP_064716	Q5T160	SYRM_HUMAN	arginyl-tRNA synthetase 2, mitochondrial	219					arginyl-tRNA aminoacylation	mitochondrial matrix	arginine-tRNA ligase activity|ATP binding|protein binding			ovary(2)|central_nervous_system(1)	3		all_cancers(76;3.93e-06)|Acute lymphoblastic leukemia(125;3.55e-10)|Prostate(29;3.51e-09)|all_hematologic(105;3.29e-06)|all_epithelial(107;0.00575)		BRCA - Breast invasive adenocarcinoma(108;0.0456)														---	---	---	---
GABRR1	2569	broad.mit.edu	37	6	89888752	89888752	+	Missense_Mutation	SNP	G	A	A	rs118018352	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:89888752G>A	uc003pna.2	-	10	1632	c.1177C>T	c.(1177-1179)CGC>TGC	p.R393C	GABRR1_uc011dzv.1_Missense_Mutation_p.R370C	NM_002042	NP_002033	P24046	GBRR1_HUMAN	gamma-aminobutyric acid (GABA) receptor, rho 1	393	Cytoplasmic (Probable).				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)													---	---	---	---
GABRR2	2570	broad.mit.edu	37	6	89975444	89975444	+	Silent	SNP	G	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:89975444G>C	uc003pnb.2	-	7	860	c.852C>G	c.(850-852)CGC>CGG	p.R284R	GABRR2_uc011dzx.1_Silent_p.R160R	NM_002043	NP_002034	P28476	GBRR2_HUMAN	gamma-aminobutyric acid (GABA) receptor, rho 2	284	Extracellular (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				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)														---	---	---	---
ANKRD6	22881	broad.mit.edu	37	6	90331672	90331672	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:90331672G>T	uc003pni.3	+	10	1165	c.824G>T	c.(823-825)AGG>ATG	p.R275M	ANKRD6_uc003pne.3_Missense_Mutation_p.R275M|ANKRD6_uc003pnf.3_Intron|ANKRD6_uc011dzy.1_Missense_Mutation_p.R275M|ANKRD6_uc010kcd.2_Missense_Mutation_p.R216M|LYRM2_uc010kce.1_Intron|LYRM2_uc003png.2_Intron|ANKRD6_uc003pnh.3_Translation_Start_Site|LYRM2_uc010kcf.1_Intron|ANKRD6_uc003pnj.3_Translation_Start_Site	NM_014942	NP_055757	Q9Y2G4	ANKR6_HUMAN	ankyrin repeat domain 6	275							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	90432809	90432809	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:90432809C>A	uc003pnn.1	-	40	5948	c.5832G>T	c.(5830-5832)TGG>TGT	p.W1944C		NM_014611	NP_055426	Q9NU22	MDN1_HUMAN	MDN1, midasin homolog	1944					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	90564550	90564550	+	Missense_Mutation	SNP	T	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:90564550T>A	uc003pnr.2	+	4	335	c.139T>A	c.(139-141)TCC>ACC	p.S47T	CASP8AP2_uc003pns.2_Missense_Mutation_p.S47T|CASP8AP2_uc003pnt.2_Missense_Mutation_p.S47T|CASP8AP2_uc011dzz.1_Missense_Mutation_p.S47T	NM_001137667	NP_001131139	Q9UKL3	C8AP2_HUMAN	caspase 8 associated protein 2	47					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)														---	---	---	---
MAP3K7	6885	broad.mit.edu	37	6	91263236	91263236	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:91263236C>T	uc003pnz.1	-	7	839	c.677G>A	c.(676-678)CGG>CAG	p.R226Q	MAP3K7_uc003poa.1_Missense_Mutation_p.R226Q|MAP3K7_uc003pob.1_Missense_Mutation_p.R226Q|MAP3K7_uc003poc.1_Missense_Mutation_p.R226Q	NM_145331	NP_663304	O43318	M3K7_HUMAN	mitogen-activated protein kinase kinase kinase 7	226	Protein kinase.				activation of MAPK activity|activation of NF-kappaB-inducing kinase activity|histone H3 acetylation|I-kappaB phosphorylation|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 interleukin-2 production|positive regulation of JUN kinase activity|positive regulation of NF-kappaB transcription factor activity|positive regulation of T cell cytokine production|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|transforming growth factor beta receptor signaling pathway	Ada2/Gcn5/Ada3 transcription activator complex|cytosol|endosome membrane	ATP binding|magnesium ion binding|MAP kinase kinase kinase activity|protein binding|protein binding			ovary(2)|lung(2)|upper_aerodigestive_tract(1)|stomach(1)	6		all_cancers(76;6.4e-08)|Acute lymphoblastic leukemia(125;1.43e-09)|Prostate(29;9.32e-09)|all_hematologic(105;3.69e-06)|all_epithelial(107;0.000187)|Ovarian(999;0.0164)		OV - Ovarian serous cystadenocarcinoma(136;2.05e-11)|all cancers(137;3.25e-11)|GBM - Glioblastoma multiforme(226;0.0416)|BRCA - Breast invasive adenocarcinoma(108;0.0429)														---	---	---	---
EPHA7	2045	broad.mit.edu	37	6	93956542	93956542	+	Silent	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:93956542A>G	uc003poe.2	-	15	2935	c.2694T>C	c.(2692-2694)AAT>AAC	p.N898N	EPHA7_uc003pof.2_Silent_p.N893N|EPHA7_uc011eac.1_Silent_p.N894N	NM_004440	NP_004431	Q15375	EPHA7_HUMAN	ephrin receptor EphA7 precursor	898	Cytoplasmic (Potential).					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)														---	---	---	---
GPR63	81491	broad.mit.edu	37	6	97246426	97246426	+	Silent	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:97246426C>T	uc010kcl.2	-	3	1660	c.1182G>A	c.(1180-1182)CCG>CCA	p.P394P	GPR63_uc003pou.2_Silent_p.P394P	NM_001143957	NP_001137429	Q9BZJ6	GPR63_HUMAN	G protein-coupled receptor 63	394	Cytoplasmic (Potential).					integral to membrane|plasma membrane	G-protein coupled receptor activity|protein binding			upper_aerodigestive_tract(1)|ovary(1)	2		all_cancers(76;6.89e-05)|Acute lymphoblastic leukemia(125;7.02e-10)|all_hematologic(75;1.23e-06)|all_epithelial(107;0.0618)|Colorectal(196;0.0721)		BRCA - Breast invasive adenocarcinoma(108;0.0912)														---	---	---	---
FBXL4	26235	broad.mit.edu	37	6	99365430	99365430	+	Silent	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:99365430A>G	uc003ppf.1	-	4	1036	c.678T>C	c.(676-678)CAT>CAC	p.H226H	FBXL4_uc003ppg.1_Silent_p.H226H|FBXL4_uc003pph.1_Intron	NM_012160	NP_036292	Q9UKA2	FBXL4_HUMAN	F-box and leucine-rich repeat protein 4	226					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)														---	---	---	---
SFRS18	25957	broad.mit.edu	37	6	99850594	99850594	+	Intron	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:99850594C>T	uc003ppo.3	-						SFRS18_uc003ppl.2_5'Flank|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)														---	---	---	---
ASCC3	10973	broad.mit.edu	37	6	101247320	101247320	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:101247320A>G	uc003pqk.2	-	7	1585	c.1256T>C	c.(1255-1257)ATT>ACT	p.I419T	ASCC3_uc011eai.1_Missense_Mutation_p.I321T|ASCC3_uc003pql.2_Missense_Mutation_p.I419T	NM_006828	NP_006819	Q8N3C0	HELC1_HUMAN	activating signal cointegrator 1 complex subunit	419					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)														---	---	---	---
HACE1	57531	broad.mit.edu	37	6	105198241	105198241	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:105198241A>G	uc003pqu.1	-	20	2595	c.2318T>C	c.(2317-2319)ATA>ACA	p.I773T	HACE1_uc010kcy.1_Missense_Mutation_p.I255T|HACE1_uc010kcz.1_Missense_Mutation_p.I558T|HACE1_uc010kcx.1_Missense_Mutation_p.I182T|HACE1_uc003pqt.1_Missense_Mutation_p.I426T	NM_020771	NP_065822	Q8IYU2	HACE1_HUMAN	HECT domain and ankyrin repeat containing, E3	773	HECT.				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)														---	---	---	---
PDSS2	57107	broad.mit.edu	37	6	107531718	107531718	+	Silent	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:107531718A>G	uc003prt.2	-	6	1223	c.933T>C	c.(931-933)TTT>TTC	p.F311F	PDSS2_uc011eak.1_Silent_p.F175F|PDSS2_uc011eal.1_Intron|PDSS2_uc003pru.2_Silent_p.F311F	NM_020381	NP_065114	Q86YH6	DLP1_HUMAN	prenyl diphosphate synthase, subunit 2	311					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)														---	---	---	---
NR2E1	7101	broad.mit.edu	37	6	108502083	108502083	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:108502083T>C	uc003psg.2	+	7	1567	c.812T>C	c.(811-813)GTG>GCG	p.V271A		NM_003269	NP_003260	Q9Y466	NR2E1_HUMAN	nuclear receptor subfamily 2, group E, member 1	271	Ligand-binding (By similarity).				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	108645027	108645027	+	Splice_Site	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:108645027A>G	uc003psj.2	+	2	326	c.140_splice	c.e2-2	p.A47_splice		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)														---	---	---	---
WASF1	8936	broad.mit.edu	37	6	110424599	110424599	+	Missense_Mutation	SNP	G	A	A	rs141943257		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:110424599G>A	uc003ptv.1	-	9	1712	c.875C>T	c.(874-876)CCG>CTG	p.P292L	WASF1_uc003ptw.1_Missense_Mutation_p.P292L|WASF1_uc003ptx.1_Missense_Mutation_p.P292L|WASF1_uc003pty.1_Missense_Mutation_p.P292L	NM_003931	NP_003922	Q92558	WASF1_HUMAN	Wiskott-Aldrich syndrome protein family member	292					actin filament polymerization|cellular component movement	actin cytoskeleton	actin binding				0		all_cancers(87;1.18e-05)|Acute lymphoblastic leukemia(125;2.66e-08)|all_hematologic(75;1.13e-06)|all_epithelial(87;0.00159)|Colorectal(196;0.0488)		OV - Ovarian serous cystadenocarcinoma(136;0.0364)|Epithelial(106;0.051)|all cancers(137;0.0687)														---	---	---	---
SLC16A10	117247	broad.mit.edu	37	6	111498697	111498697	+	Silent	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:111498697T>C	uc003pus.2	+	3	946	c.771T>C	c.(769-771)AGT>AGC	p.S257S	SLC16A10_uc003pur.3_Silent_p.S257S|SLC16A10_uc003put.2_5'UTR	NM_018593	NP_061063	Q8TF71	MOT10_HUMAN	solute carrier family 16, member 10	257	Extracellular (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)														---	---	---	---
SLC16A10	117247	broad.mit.edu	37	6	111498728	111498728	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:111498728T>C	uc003pus.2	+	3	977	c.802T>C	c.(802-804)TCC>CCC	p.S268P	SLC16A10_uc003pur.3_Missense_Mutation_p.S268P|SLC16A10_uc003put.2_5'UTR	NM_018593	NP_061063	Q8TF71	MOT10_HUMAN	solute carrier family 16, member 10	268	Extracellular (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)														---	---	---	---
TSPYL1	7259	broad.mit.edu	37	6	116599705	116599705	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:116599705C>A	uc003pwp.3	-	1	1576	c.1289G>T	c.(1288-1290)AGG>ATG	p.R430M	DSE_uc011ebf.1_Intron|DSE_uc003pwq.1_5'Flank|DSE_uc003pwr.2_5'Flank|DSE_uc003pws.2_5'Flank	NM_003309	NP_003300	Q9H0U9	TSYL1_HUMAN	TSPY-like 1	430					nucleosome assembly	nucleolus					0		all_cancers(87;0.0144)|all_epithelial(87;0.021)|Colorectal(196;0.234)		all cancers(137;0.0235)|OV - Ovarian serous cystadenocarcinoma(136;0.0469)|GBM - Glioblastoma multiforme(226;0.0503)|Epithelial(106;0.094)														---	---	---	---
RSPH4A	345895	broad.mit.edu	37	6	116953571	116953571	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:116953571G>T	uc003pxe.2	+	6	2263	c.2118G>T	c.(2116-2118)GAG>GAT	p.E706D	RSPH4A_uc010kee.2_3'UTR	NM_001010892	NP_001010892	Q5TD94	RSH4A_HUMAN	radial spoke head 4 homolog A isoform 1	706					cilium axoneme assembly|cilium movement	cytoplasm|cytoskeleton|radial spoke					0														Kartagener_syndrome				---	---	---	---
ROS1	6098	broad.mit.edu	37	6	117687383	117687383	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:117687383A>G	uc003pxp.1	-	18	2867	c.2668T>C	c.(2668-2670)TAC>CAC	p.Y890H	ROS1_uc011ebi.1_RNA|GOPC_uc003pxq.1_Intron	NM_002944	NP_002935	P08922	ROS_HUMAN	proto-oncogene c-ros-1 protein precursor	890	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								---	---	---	---
DCBLD1	285761	broad.mit.edu	37	6	117865728	117865728	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:117865728G>A	uc003pxs.2	+	13	1608	c.1483G>A	c.(1483-1485)GCT>ACT	p.A495T	GOPC_uc003pxq.1_Intron|DCBLD1_uc003pxr.1_Silent_p.R493R|DCBLD1_uc003pxt.1_Missense_Mutation_p.A150T	NM_173674	NP_775945	Q8N8Z6	DCBD1_HUMAN	discoidin, CUB and LCCL domain containing 1	495	Cytoplasmic (Potential).				cell adhesion	integral to membrane				ovary(1)	1		all_cancers(87;0.171)		GBM - Glioblastoma multiforme(226;0.0447)|OV - Ovarian serous cystadenocarcinoma(136;0.0921)|all cancers(137;0.125)														---	---	---	---
GOPC	57120	broad.mit.edu	37	6	117888134	117888134	+	Missense_Mutation	SNP	C	T	T	rs115242892	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:117888134C>T	uc003pxu.2	-	8	1371	c.1141G>A	c.(1141-1143)GTA>ATA	p.V381I	GOPC_uc003pxq.1_Missense_Mutation_p.V154I|DCBLD1_uc003pxs.2_Intron|GOPC_uc003pxv.2_Missense_Mutation_p.V373I	NM_020399	NP_065132	Q9HD26	GOPC_HUMAN	golgi associated PDZ and coiled-coil motif	381					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								---	---	---	---
GOPC	57120	broad.mit.edu	37	6	117890761	117890761	+	Nonsense_Mutation	SNP	C	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:117890761C>A	uc003pxu.2	-	7	1281	c.1051G>T	c.(1051-1053)GAA>TAA	p.E351*	GOPC_uc003pxq.1_Nonsense_Mutation_p.E124*|DCBLD1_uc003pxs.2_Intron|GOPC_uc003pxv.2_Nonsense_Mutation_p.E343*	NM_020399	NP_065132	Q9HD26	GOPC_HUMAN	golgi associated PDZ and coiled-coil motif	351	PDZ.				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								---	---	---	---
ASF1A	25842	broad.mit.edu	37	6	119228731	119228731	+	Silent	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:119228731A>G	uc011ebn.1	+	4	904	c.567A>G	c.(565-567)TCA>TCG	p.S189S		NM_014034	NP_054753	Q9Y294	ASF1A_HUMAN	ASF1 anti-silencing function 1 homolog A	189	Required for interaction with HIRA.				chromatin modification|DNA repair|loss of chromatin silencing|nucleosome assembly|transcription, DNA-dependent	chromatin remodeling complex	chromatin binding|histone binding				0		all_cancers(87;0.122)|all_epithelial(87;0.179)		GBM - Glioblastoma multiforme(226;0.0633)|OV - Ovarian serous cystadenocarcinoma(136;0.188)														---	---	---	---
MCM9	254394	broad.mit.edu	37	6	119243179	119243179	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:119243179A>G	uc003pyh.2	-	4	957	c.694T>C	c.(694-696)TGC>CGC	p.C232R		NM_153255	NP_694987	Q9NXL9	MCM9_HUMAN	minichromosome maintenance complex component 9	232					DNA replication		ATP binding|DNA binding|nucleoside-triphosphatase activity			ovary(1)	1		all_cancers(87;0.122)|all_epithelial(87;0.179)		GBM - Glioblastoma multiforme(226;0.0676)|OV - Ovarian serous cystadenocarcinoma(136;0.194)														---	---	---	---
C6orf174	387104	broad.mit.edu	37	6	127767690	127767690	+	3'UTR	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:127767690T>C	uc003qbd.2	-	11					C6orf174_uc003qbc.2_Missense_Mutation_p.N592D|C6orf174_uc003qba.2_Intron|C6orf174_uc003qbb.2_Missense_Mutation_p.N475D|KIAA0408_uc011ebs.1_Missense_Mutation_p.N592D	NM_001012279	NP_001012279			hypothetical protein LOC387104 precursor							integral to membrane				breast(3)|ovary(2)|skin(1)	6				GBM - Glioblastoma multiforme(226;0.026)|all cancers(137;0.161)														---	---	---	---
C6orf174	387104	broad.mit.edu	37	6	127836152	127836152	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:127836152C>A	uc003qbd.2	-	3	2007	c.1142G>T	c.(1141-1143)AGG>ATG	p.R381M		NM_001012279	NP_001012279	Q5TF21	CF174_HUMAN	hypothetical protein LOC387104 precursor	381	Potential.					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	129486813	129486813	+	Silent	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:129486813T>C	uc003qbn.2	+	9	1404	c.1299T>C	c.(1297-1299)GCT>GCC	p.A433A	LAMA2_uc003qbo.2_Silent_p.A433A	NM_000426	NP_000417	P24043	LAMA2_HUMAN	laminin alpha 2 subunit isoform a precursor	433	Laminin EGF-like 3.				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)														---	---	---	---
LAMA2	3908	broad.mit.edu	37	6	129635895	129635895	+	Silent	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:129635895C>T	uc003qbn.2	+	24	3612	c.3507C>T	c.(3505-3507)TTC>TTT	p.F1169F	LAMA2_uc003qbo.2_Silent_p.F1169F	NM_000426	NP_000417	P24043	LAMA2_HUMAN	laminin alpha 2 subunit isoform a precursor	1169	Laminin EGF-like 14; first part.				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)														---	---	---	---
EPB41L2	2037	broad.mit.edu	37	6	131199301	131199301	+	Silent	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:131199301C>T	uc003qch.2	-	14	2168	c.1986G>A	c.(1984-1986)CCG>CCA	p.P662P	EPB41L2_uc003qce.1_Silent_p.P40P|EPB41L2_uc003qcf.1_RNA|EPB41L2_uc003qcg.1_Intron|EPB41L2_uc011eby.1_Intron|EPB41L2_uc003qci.2_Intron|EPB41L2_uc010kfk.2_Intron|EPB41L2_uc010kfl.1_Intron|EPB41L2_uc003qcj.1_Silent_p.P7P	NM_001431	NP_001422	O43491	E41L2_HUMAN	erythrocyte membrane protein band 4.1-like 2	662	Spectrin--actin-binding.				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)														---	---	---	---
ENPP3	5169	broad.mit.edu	37	6	132014659	132014659	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:132014659T>C	uc003qcu.3	+	16	1654	c.1307T>C	c.(1306-1308)TTC>TCC	p.F436S	ENPP3_uc010kfq.2_RNA|ENPP3_uc003qcv.2_Missense_Mutation_p.F436S	NM_005021	NP_005012	O14638	ENPP3_HUMAN	ectonucleotide pyrophosphatase/phosphodiesterase	436	Extracellular (Potential).|Phosphodiesterase.				immune response|nucleoside triphosphate catabolic process|phosphate metabolic process	extracellular region|integral to plasma membrane|perinuclear region of cytoplasm	metal ion binding|nucleic acid binding|nucleoside-triphosphate diphosphatase activity|nucleotide diphosphatase activity|phosphodiesterase I activity|polysaccharide binding|scavenger receptor activity			ovary(3)|skin(1)	4	Breast(56;0.0753)			GBM - Glioblastoma multiforme(226;0.0252)|OV - Ovarian serous cystadenocarcinoma(155;0.0511)														---	---	---	---
ENPP1	5167	broad.mit.edu	37	6	132176075	132176075	+	Silent	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:132176075G>A	uc011ecf.1	+	6	647	c.627G>A	c.(625-627)ACG>ACA	p.T209T		NM_006208	NP_006199	P22413	ENPP1_HUMAN	ectonucleotide pyrophosphatase/phosphodiesterase	209	Phosphodiesterase.|Extracellular (Potential).				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)													---	---	---	---
ENPP1	5167	broad.mit.edu	37	6	132185719	132185719	+	Intron	SNP	G	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:132185719G>T	uc011ecf.1	+						ENPP1_uc003qcy.2_Intron	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)													---	---	---	---
MOXD1	26002	broad.mit.edu	37	6	132636774	132636774	+	Missense_Mutation	SNP	G	A	A	rs146636600		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:132636774G>A	uc003qdf.2	-	10	1607	c.1508C>T	c.(1507-1509)ACG>ATG	p.T503M	MOXD1_uc003qde.2_Missense_Mutation_p.T435M	NM_015529	NP_056344	Q6UVY6	MOXD1_HUMAN	monooxygenase, DBH-like 1 isoform 2	503	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)														---	---	---	---
TAAR5	9038	broad.mit.edu	37	6	132910473	132910473	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:132910473C>T	uc003qdk.2	-	1	405	c.353G>A	c.(352-354)TGC>TAC	p.C118Y		NM_003967	NP_003958	O14804	TAAR5_HUMAN	trace amine associated receptor 5	118	Helical; Name=3; (Potential).				synaptic transmission	integral to plasma membrane	G-protein coupled receptor activity			skin(1)	1	Breast(56;0.112)			OV - Ovarian serous cystadenocarcinoma(155;0.00604)|GBM - Glioblastoma multiforme(226;0.015)														---	---	---	---
KIAA1244	57221	broad.mit.edu	37	6	138607188	138607188	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:138607188C>T	uc003qhu.2	+	15	2567	c.2567C>T	c.(2566-2568)GCA>GTA	p.A856V		NM_020340	NP_065073	Q5TH69	BIG3_HUMAN	brefeldin A-inhibited guanine	856					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)														---	---	---	---
GPR126	57211	broad.mit.edu	37	6	142691368	142691368	+	Silent	SNP	A	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:142691368A>C	uc010khc.2	+	4	918	c.507A>C	c.(505-507)GTA>GTC	p.V169V	GPR126_uc010khd.2_Silent_p.V169V|GPR126_uc010khe.2_Silent_p.V169V|GPR126_uc010khf.2_Silent_p.V169V|GPR126_uc003qix.2_Silent_p.V169V	NM_020455	NP_065188	Q86SQ4	GP126_HUMAN	G protein-coupled receptor 126 alpha 1	169	Pentaxin.|Extracellular (Potential).				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)														---	---	---	---
PLAGL1	5325	broad.mit.edu	37	6	144263221	144263221	+	Silent	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:144263221T>C	uc003qjv.2	-	3	1998	c.732A>G	c.(730-732)TTA>TTG	p.L244L	PLAGL1_uc003qjx.2_Silent_p.L244L|PLAGL1_uc003qjy.2_Silent_p.L244L|PLAGL1_uc010khl.2_Silent_p.L244L|PLAGL1_uc010khm.2_Silent_p.L244L|PLAGL1_uc003qjz.2_Silent_p.L244L|PLAGL1_uc003qka.2_Silent_p.L244L|PLAGL1_uc003qkb.2_Silent_p.L192L|PLAGL1_uc003qkc.2_Silent_p.L244L|PLAGL1_uc003qkd.2_Silent_p.L192L|PLAGL1_uc003qke.2_Silent_p.L244L|PLAGL1_uc003qkf.2_Silent_p.L244L|PLAGL1_uc003qkg.2_Silent_p.L192L|PLAGL1_uc003qkh.2_Silent_p.L244L|PLAGL1_uc003qki.2_Silent_p.L192L|PLAGL1_uc003qkj.2_Silent_p.L244L|PLAGL1_uc003qkk.2_Silent_p.L192L|PLAGL1_uc003qkl.2_Silent_p.L192L|PLAGL1_uc003qkm.2_Silent_p.L244L|PLAGL1_uc010khn.2_Silent_p.L244L|PLAGL1_uc003qkn.2_Silent_p.L192L|PLAGL1_uc003qko.2_Silent_p.L244L|PLAGL1_uc003qkp.2_Silent_p.L192L|PLAGL1_uc003qjw.2_Silent_p.L192L	NM_002656	NP_002647	Q9UM63	PLAL1_HUMAN	pleiomorphic adenoma gene-like 1 isoform 1	244					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)												OREG0017707	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
UTRN	7402	broad.mit.edu	37	6	144744768	144744768	+	Intron	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:144744768T>C	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)														---	---	---	---
SASH1	23328	broad.mit.edu	37	6	148869531	148869531	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:148869531A>G	uc003qme.1	+	20	4056	c.3581A>G	c.(3580-3582)TAC>TGC	p.Y1194C	SASH1_uc003qmf.1_Missense_Mutation_p.Y604C	NM_015278	NP_056093	O94885	SASH1_HUMAN	SAM and SH3 domain containing 1	1194	SAM 2.						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)														---	---	---	---
C6orf72	116254	broad.mit.edu	37	6	149903589	149903589	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:149903589G>T	uc003qmq.1	+	7	758	c.731G>T	c.(730-732)TGG>TTG	p.W244L		NM_138785	NP_620140	Q9NU53	CF072_HUMAN	hypothetical protein LOC116254 precursor	244	Extracellular (Potential).					integral to membrane					0		Ovarian(120;0.0907)		OV - Ovarian serous cystadenocarcinoma(155;9.66e-12)|GBM - Glioblastoma multiforme(68;0.171)														---	---	---	---
RAET1E	135250	broad.mit.edu	37	6	150210713	150210713	+	Silent	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:150210713T>C	uc003qnl.1	-	3	453	c.393A>G	c.(391-393)GAA>GAG	p.E131E	uc003qni.1_Intron|RAET1E_uc003qnj.2_Silent_p.E131E|RAET1E_uc003qnk.1_Silent_p.E95E|RAET1E_uc010kih.1_RNA	NM_139165	NP_631904	Q8TD07	N2DL4_HUMAN	retinoic acid early transcript 1E precursor	131	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)														---	---	---	---
SYNE1	23345	broad.mit.edu	37	6	152551832	152551832	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:152551832C>A	uc010kiw.2	-	115	21647	c.21045G>T	c.(21043-21045)CAG>CAT	p.Q7015H	SYNE1_uc010kiv.2_Missense_Mutation_p.Q1539H|SYNE1_uc003qos.3_Missense_Mutation_p.Q1539H|SYNE1_uc003qot.3_Missense_Mutation_p.Q6944H|SYNE1_uc003qou.3_Missense_Mutation_p.Q7015H	NM_182961	NP_892006	Q8NF91	SYNE1_HUMAN	spectrin repeat containing, nuclear envelope 1	7015	HAT 9.|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	152651622	152651622	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:152651622A>G	uc010kiw.2	-	78	14800	c.14198T>C	c.(14197-14199)CTG>CCG	p.L4733P	SYNE1_uc003qot.3_Missense_Mutation_p.L4662P|SYNE1_uc003qou.3_Missense_Mutation_p.L4733P|SYNE1_uc010kiz.2_Missense_Mutation_p.L488P	NM_182961	NP_892006	Q8NF91	SYNE1_HUMAN	spectrin repeat containing, nuclear envelope 1	4733	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	152793467	152793467	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:152793467G>A	uc010kiw.2	-	15	2034	c.1432C>T	c.(1432-1434)CCA>TCA	p.P478S	SYNE1_uc003qot.3_Missense_Mutation_p.P485S|SYNE1_uc003qou.3_Missense_Mutation_p.P478S|SYNE1_uc010kjb.1_Missense_Mutation_p.P461S|SYNE1_uc003qpa.1_Missense_Mutation_p.P478S|SYNE1_uc003qox.1_5'UTR|SYNE1_uc003qoz.2_5'UTR|SYNE1_uc003qoy.2_Missense_Mutation_p.P45S	NM_182961	NP_892006	Q8NF91	SYNE1_HUMAN	spectrin repeat containing, nuclear envelope 1	478	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)			---	---	---	---
MTRF1L	54516	broad.mit.edu	37	6	153315696	153315696	+	Silent	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:153315696G>A	uc003qpi.3	-	4	744	c.639C>T	c.(637-639)CGC>CGT	p.R213R	MTRF1L_uc003qpl.3_Silent_p.R213R|MTRF1L_uc011efa.1_Silent_p.R177R|MTRF1L_uc003qpj.3_Silent_p.R71R|MTRF1L_uc003qpk.3_Silent_p.R177R	NM_019041	NP_061914	Q9UGC7	RF1ML_HUMAN	mitochondrial translational release factor	213						mitochondrion	translation release factor activity, codon specific				0		Ovarian(120;0.125)		OV - Ovarian serous cystadenocarcinoma(155;4.24e-10)|BRCA - Breast invasive adenocarcinoma(81;0.0888)														---	---	---	---
Unknown	0	broad.mit.edu	37	6	153603496	153603496	+	IGR	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:153603496G>A								RGS17 (151107 upstream) : OPRM1 (728140 downstream)																																			---	---	---	---
RBM16	22828	broad.mit.edu	37	6	155131212	155131212	+	Silent	SNP	A	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:155131212A>T	uc003qqa.2	+	13	1522	c.1290A>T	c.(1288-1290)CGA>CGT	p.R430R	RBM16_uc011efj.1_Silent_p.R496R|RBM16_uc011efk.1_Silent_p.R475R|RBM16_uc003qpz.2_Silent_p.R430R|RBM16_uc010kji.2_Silent_p.R451R	NM_014892	NP_055707	Q9UPN6	SCAF8_HUMAN	RNA-binding motif protein 16	430	Arg-rich.				mRNA processing|RNA splicing	nuclear matrix|spliceosomal complex	nucleotide binding|RNA binding|RNA polymerase core enzyme binding				0		Ovarian(120;0.196)		OV - Ovarian serous cystadenocarcinoma(155;2.33e-15)|BRCA - Breast invasive adenocarcinoma(81;0.00524)														---	---	---	---
TIAM2	26230	broad.mit.edu	37	6	155504476	155504476	+	Missense_Mutation	SNP	C	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:155504476C>G	uc003qqb.2	+	16	4179	c.2906C>G	c.(2905-2907)ACT>AGT	p.T969S	TIAM2_uc003qqe.2_Missense_Mutation_p.T969S|TIAM2_uc010kjj.2_Missense_Mutation_p.T502S|TIAM2_uc003qqf.2_Missense_Mutation_p.T345S|TIAM2_uc011efl.1_Missense_Mutation_p.T305S|TIAM2_uc003qqg.2_Missense_Mutation_p.T281S	NM_012454	NP_036586	Q8IVF5	TIAM2_HUMAN	T-cell lymphoma invasion and metastasis 2	969	PDZ.				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	157522399	157522399	+	Silent	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:157522399G>A	uc003qqn.2	+	18	4769	c.4617G>A	c.(4615-4617)GCG>GCA	p.A1539A	ARID1B_uc003qqo.2_Silent_p.A1499A|ARID1B_uc003qqp.2_Silent_p.A1486A	NM_017519	NP_059989	Q8NFD5	ARI1B_HUMAN	AT rich interactive domain 1B (SWI1-like)	1544	Pro-rich.				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)														---	---	---	---
ZDHHC14	79683	broad.mit.edu	37	6	158074618	158074618	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:158074618G>A	uc003qqt.2	+	8	1524	c.1027G>A	c.(1027-1029)GGC>AGC	p.G343S	ZDHHC14_uc003qqs.2_Missense_Mutation_p.G343S|ZDHHC14_uc010kjn.2_5'UTR	NM_024630	NP_078906	Q8IZN3	ZDH14_HUMAN	zinc finger, DHHC-type containing 14 isoform 1	343						integral to membrane	acyltransferase activity|zinc ion binding			ovary(1)|skin(1)	2		Breast(66;0.00586)|Ovarian(120;0.123)		OV - Ovarian serous cystadenocarcinoma(65;2.9e-17)|BRCA - Breast invasive adenocarcinoma(81;5.8e-05)														---	---	---	---
TULP4	56995	broad.mit.edu	37	6	158900814	158900814	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:158900814G>A	uc003qrf.2	+	7	2415	c.1058G>A	c.(1057-1059)CGG>CAG	p.R353Q	TULP4_uc011efo.1_Missense_Mutation_p.R353Q|TULP4_uc003qrg.2_Missense_Mutation_p.R353Q	NM_020245	NP_064630	Q9NRJ4	TULP4_HUMAN	tubby like protein 4 isoform 1	353					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)														---	---	---	---
TAGAP	117289	broad.mit.edu	37	6	159457697	159457697	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:159457697C>T	uc003qrz.2	-	10	1690	c.1358G>A	c.(1357-1359)CGG>CAG	p.R453Q	TAGAP_uc011eft.1_Missense_Mutation_p.R390Q|TAGAP_uc003qsa.2_Missense_Mutation_p.R275Q	NM_054114	NP_473455	Q8N103	TAGAP_HUMAN	T-cell activation Rho GTPase-activating protein	453					regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol	GTPase activator activity|guanyl-nucleotide exchange factor activity			ovary(1)	1		Breast(66;0.000776)|Ovarian(120;0.0303)		OV - Ovarian serous cystadenocarcinoma(65;2.16e-16)|BRCA - Breast invasive adenocarcinoma(81;5.87e-06)														---	---	---	---
IGF2R	3482	broad.mit.edu	37	6	160448260	160448260	+	Silent	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:160448260C>T	uc003qta.2	+	6	838	c.690C>T	c.(688-690)CCC>CCT	p.P230P		NM_000876	NP_000867	P11717	MPRI_HUMAN	insulin-like growth factor 2 receptor precursor	230	2.|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)														---	---	---	---
PLG	5340	broad.mit.edu	37	6	161139427	161139427	+	Nonsense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:161139427C>T	uc003qtm.3	+	8	952	c.889C>T	c.(889-891)CAG>TAG	p.Q297*		NM_000301	NP_000292	P00747	PLMN_HUMAN	plasminogen	297	Kringle 3.				extracellular matrix disassembly|fibrinolysis|negative regulation of cell proliferation|negative regulation of cell-substrate adhesion|negative regulation of fibrinolysis|platelet activation|platelet degranulation|positive regulation of fibrinolysis|proteolysis|tissue remodeling	extracellular space|extrinsic to external side of plasma membrane|platelet alpha granule lumen	apolipoprotein binding|cell surface binding|serine-type endopeptidase activity			skin(3)|ovary(1)	4				OV - Ovarian serous cystadenocarcinoma(65;5.24e-17)|BRCA - Breast invasive adenocarcinoma(81;7.08e-06)	Aminocaproic Acid(DB00513)|Streptokinase(DB00086)|Tranexamic Acid(DB00302)|Urokinase(DB00013)													---	---	---	---
T	6862	broad.mit.edu	37	6	166580975	166580975	+	Silent	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:166580975G>A	uc003quu.1	-	2	598	c.105C>T	c.(103-105)GGC>GGT	p.G35G	T_uc003qut.1_Silent_p.G35G|T_uc003quv.1_Silent_p.G35G	NM_003181	NP_003172	O15178	BRAC_HUMAN	transcription factor T	35					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				---	---	---	---
UNC93A	54346	broad.mit.edu	37	6	167708164	167708164	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:167708164G>A	uc003qvq.2	+	2	422	c.247G>A	c.(247-249)GTG>ATG	p.V83M	UNC93A_uc003qvr.2_Missense_Mutation_p.V83M	NM_018974	NP_061847	Q86WB7	UN93A_HUMAN	unc-93 homolog A isoform 1	83	Helical; (Potential).					integral to membrane|plasma membrane					0		Breast(66;7.62e-05)|Ovarian(120;0.105)		OV - Ovarian serous cystadenocarcinoma(33;2.22e-20)|BRCA - Breast invasive adenocarcinoma(81;6.17e-07)|GBM - Glioblastoma multiforme(31;0.00492)														---	---	---	---
THBS2	7058	broad.mit.edu	37	6	169641857	169641857	+	Silent	SNP	C	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:169641857C>A	uc003qwt.2	-	6	1139	c.891G>T	c.(889-891)GTG>GTT	p.V297V		NM_003247	NP_003238	P35442	TSP2_HUMAN	thrombospondin 2 precursor	297					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)														---	---	---	---
TBP	6908	broad.mit.edu	37	6	170870901	170870901	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:170870901C>A	uc003qxt.2	+	3	309	c.77C>A	c.(76-78)CCT>CAT	p.P26H	TBP_uc003qxu.2_Missense_Mutation_p.P26H|TBP_uc011ehf.1_Missense_Mutation_p.P6H|TBP_uc011ehg.1_Missense_Mutation_p.P26H	NM_003194	NP_003185	P20226	TBP_HUMAN	TATA box binding protein	26					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)														---	---	---	---
PRKAR1B	5575	broad.mit.edu	37	7	716930	716930	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:716930T>C	uc003siu.1	-	5	482	c.376A>G	c.(376-378)ACT>GCT	p.T126A	PRKAR1B_uc003siv.2_Missense_Mutation_p.T126A|PRKAR1B_uc003siw.1_Missense_Mutation_p.T126A	NM_002735	NP_002726	P31321	KAP1_HUMAN	protein kinase, cAMP-dependent, regulatory, type	126	Dimerization and phosphorylation.				activation of phospholipase C activity|activation of protein kinase A activity|blood coagulation|cellular response to glucagon stimulus|energy reserve metabolic process|nerve growth factor receptor signaling pathway|protein phosphorylation|regulation of insulin secretion|transmembrane transport|water transport	cAMP-dependent protein kinase complex|cytosol	cAMP binding|cAMP-dependent protein kinase regulator activity				0		Ovarian(82;0.0779)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0181)|Epithelial(4;5.75e-19)|OV - Ovarian serous cystadenocarcinoma(56;2.01e-18)|all cancers(6;3.96e-16)|BRCA - Breast invasive adenocarcinoma(126;0.152)														---	---	---	---
FOXK1	221937	broad.mit.edu	37	7	4796751	4796751	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:4796751G>A	uc003snc.1	+	5	1187	c.1177G>A	c.(1177-1179)GCA>ACA	p.A393T	FOXK1_uc003sna.1_Missense_Mutation_p.A230T	NM_001037165	NP_001032242	P85037	FOXK1_HUMAN	forkhead box K1	393	Fork-head.				cell differentiation|embryo development|muscle organ development|pattern specification process|regulation of sequence-specific DNA binding transcription factor activity|tissue development	transcription factor complex	DNA bending activity|double-stranded DNA binding|magnesium ion 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			upper_aerodigestive_tract(1)|skin(1)	2		Ovarian(82;0.0175)		UCEC - Uterine corpus endometrioid carcinoma (126;0.101)|OV - Ovarian serous cystadenocarcinoma(56;7.43e-15)														---	---	---	---
RNF216	54476	broad.mit.edu	37	7	5752403	5752403	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:5752403T>C	uc003soy.1	-	12	1944	c.1754A>G	c.(1753-1755)TAC>TGC	p.Y585C	RNF216_uc010ksz.1_Missense_Mutation_p.Y207C|RNF216_uc010kta.1_Missense_Mutation_p.Y207C|RNF216_uc011jwj.1_Missense_Mutation_p.Y207C|RNF216_uc003sox.1_Missense_Mutation_p.Y642C	NM_207116	NP_996999	Q9NWF9	RN216_HUMAN	ring finger protein 216 isoform b	585	IBR-type.				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)														---	---	---	---
EIF2AK1	27102	broad.mit.edu	37	7	6066538	6066538	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:6066538T>C	uc003spp.2	-	14	1731	c.1585A>G	c.(1585-1587)ACA>GCA	p.T529A	EIF2AK1_uc003spq.2_Missense_Mutation_p.T528A|EIF2AK1_uc011jwm.1_Missense_Mutation_p.T405A	NM_014413	NP_055228	Q9BQI3	E2AK1_HUMAN	eukaryotic translation initiation factor 2-alpha	529	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)														---	---	---	---
ZNF12	7559	broad.mit.edu	37	7	6731942	6731942	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:6731942G>A	uc003sqt.1	-	5	1185	c.631C>T	c.(631-633)CGT>TGT	p.R211C	ZNF12_uc011jxa.1_Missense_Mutation_p.R49C|ZNF12_uc003sqs.1_Missense_Mutation_p.R173C	NM_016265	NP_057349	P17014	ZNF12_HUMAN	zinc finger protein 12 isoform a	211					negative regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0		Ovarian(82;0.0776)		UCEC - Uterine corpus endometrioid carcinoma (126;0.0231)														---	---	---	---
GLCCI1	113263	broad.mit.edu	37	7	8110703	8110703	+	Silent	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:8110703G>A	uc003srk.2	+	6	1678	c.1119G>A	c.(1117-1119)CCG>CCA	p.P373P		NM_138426	NP_612435	Q86VQ1	GLCI1_HUMAN	glucocorticoid induced transcript 1	373											0		Ovarian(82;0.0608)		UCEC - Uterine corpus endometrioid carcinoma (126;0.206)														---	---	---	---
PHF14	9678	broad.mit.edu	37	7	11030425	11030425	+	Silent	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:11030425C>T	uc003sry.1	+	4	1431	c.996C>T	c.(994-996)GAC>GAT	p.D332D	PHF14_uc011jxi.1_Silent_p.D47D|PHF14_uc003srz.2_Silent_p.D332D|PHF14_uc011jxj.1_Silent_p.D47D	NM_014660	NP_055475	O94880	PHF14_HUMAN	PHD finger protein 14 isoform 2	332	PHD-type 1.						zinc ion binding			kidney(2)|skin(1)	3				UCEC - Uterine corpus endometrioid carcinoma (126;0.205)														---	---	---	---
THSD7A	221981	broad.mit.edu	37	7	11675814	11675814	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:11675814C>A	uc003ssf.3	-	2	1217	c.965G>T	c.(964-966)GGA>GTA	p.G322V		NM_015204	NP_056019	Q9UPZ6	THS7A_HUMAN	thrombospondin, type I, domain containing 7A	322	Extracellular (Potential).					integral to membrane				ovary(3)	3				UCEC - Uterine corpus endometrioid carcinoma (126;0.163)											HNSCC(18;0.044)			---	---	---	---
ETV1	2115	broad.mit.edu	37	7	13946171	13946171	+	Nonsense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:13946171G>A	uc011jxq.1	-	12	1733	c.994C>T	c.(994-996)CGA>TGA	p.R332*	ETV1_uc011jxn.1_Nonsense_Mutation_p.R292*|ETV1_uc011jxo.1_Nonsense_Mutation_p.R229*|ETV1_uc011jxp.1_Nonsense_Mutation_p.R274*|ETV1_uc003ssw.3_Nonsense_Mutation_p.R309*|ETV1_uc003ssx.2_RNA|ETV1_uc011jxr.1_Nonsense_Mutation_p.R314*|ETV1_uc011jxs.1_Nonsense_Mutation_p.R314*|ETV1_uc010ktv.2_Silent_p.G200G	NM_004956	NP_004947	P50549	ETV1_HUMAN	ets variant gene 1 isoform a	332					transcription from RNA polymerase II promoter	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity		TMPRSS2/ETV1(24)|EWSR1/ETV1(7)	prostate(24)|soft_tissue(4)|bone(3)|lung(2)|central_nervous_system(1)|ovary(1)	35								T	EWSR1|TMPRSS2|SLC45A3|C15orf21|HNRNPA2B1. ACSL3	Ewing sarcoma|prostate								---	---	---	---
PRPS1L1	221823	broad.mit.edu	37	7	18067207	18067207	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:18067207G>T	uc003stz.2	-	1	280	c.199C>A	c.(199-201)CTA>ATA	p.L67I		NM_175886	NP_787082	P21108	PRPS3_HUMAN	phosphoribosyl pyrophosphate synthetase 1-like	67					nucleoside metabolic process|ribonucleoside monophosphate biosynthetic process		ATP binding|kinase activity|magnesium ion binding|protein homodimerization activity|ribose phosphate diphosphokinase activity			ovary(1)	1	Lung NSC(10;0.0385)|all_lung(11;0.0736)																	---	---	---	---
TWIST1	7291	broad.mit.edu	37	7	19156400	19156400	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:19156400C>T	uc003sum.2	-	1	896	c.545G>A	c.(544-546)CGG>CAG	p.R182Q		NM_000474	NP_000465	Q15672	TWST1_HUMAN	twist	182	Sufficient for transactivation activity (By similarity).				aortic valve morphogenesis|cellular response to hypoxia|embryonic camera-type eye formation|embryonic cranial skeleton morphogenesis|eyelid development in camera-type eye|muscle organ development|negative regulation of DNA damage response, signal transduction by p53 class mediator|negative regulation of histone phosphorylation|negative regulation of osteoblast differentiation|negative regulation of phosphatidylinositol 3-kinase cascade|negative regulation of transcription from RNA polymerase II promoter|positive regulation of angiogenesis|positive regulation of cell motility|positive regulation of epithelial to mesenchymal transition|positive regulation of fatty acid beta-oxidation|positive regulation of monocyte chemotactic protein-1 production|positive regulation of transcription from RNA polymerase II promoter|positive regulation of transcription regulatory region DNA binding|positive regulation of tumor necrosis factor production|regulation of bone mineralization	nucleus	bHLH transcription factor binding|E-box binding|sequence-specific DNA binding RNA polymerase II transcription factor activity				0														Saethre-Chotzen_syndrome				---	---	---	---
FERD3L	222894	broad.mit.edu	37	7	19184950	19184950	+	Silent	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:19184950C>T	uc003suo.1	-	1	95	c.36G>A	c.(34-36)ACG>ACA	p.T12T	uc003sun.1_RNA	NM_152898	NP_690862	Q96RJ6	FER3L_HUMAN	nephew of atonal 3	12					negative regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding			large_intestine(1)	1																		---	---	---	---
ITGB8	3696	broad.mit.edu	37	7	20420427	20420427	+	Silent	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:20420427C>T	uc003suu.2	+	5	1479	c.774C>T	c.(772-774)GAC>GAT	p.D258D	ITGB8_uc011jyh.1_Silent_p.D123D|ITGB8_uc003sut.2_Silent_p.D258D	NM_002214	NP_002205	P26012	ITB8_HUMAN	integrin, beta 8 precursor	258	VWFA.|Extracellular (Potential).				cell-matrix adhesion|integrin-mediated signaling pathway|placenta blood vessel development	integrin complex	protein binding|receptor activity			skin(3)	3																		---	---	---	---
ITGB8	3696	broad.mit.edu	37	7	20444255	20444255	+	Silent	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:20444255T>C	uc003suu.2	+	11	2397	c.1692T>C	c.(1690-1692)CAT>CAC	p.H564H	ITGB8_uc011jyh.1_Silent_p.H429H	NM_002214	NP_002205	P26012	ITB8_HUMAN	integrin, beta 8 precursor	564	III.|Cysteine-rich tandem repeats.|Extracellular (Potential).				cell-matrix adhesion|integrin-mediated signaling pathway|placenta blood vessel development	integrin complex	protein binding|receptor activity			skin(3)	3																		---	---	---	---
DNAH11	8701	broad.mit.edu	37	7	21675608	21675608	+	Missense_Mutation	SNP	G	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:21675608G>C	uc003svc.2	+	26	4666	c.4635G>C	c.(4633-4635)CAG>CAC	p.Q1545H		NM_003777	NP_003768	Q96DT5	DYH11_HUMAN	dynein, axonemal, heavy chain 11	1545	Stem (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				---	---	---	---
FAM126A	84668	broad.mit.edu	37	7	23023597	23023597	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:23023597G>A	uc003svm.3	-	3	374	c.119C>T	c.(118-120)TCT>TTT	p.S40F	FAM126A_uc003svn.3_5'UTR|FAM126A_uc011jyr.1_Intron	NM_032581	NP_115970	Q9BYI3	HYCCI_HUMAN	family with sequence similarity 126, member A	40						cytoplasm|membrane	signal transducer activity			central_nervous_system(1)	1																		---	---	---	---
C7orf30	115416	broad.mit.edu	37	7	23340629	23340629	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:23340629T>C	uc003swd.1	+	2	460	c.428T>C	c.(427-429)GTG>GCG	p.V143A		NM_138446	NP_612455	Q96EH3	CG030_HUMAN	hypothetical protein LOC115416	143						mitochondrion					0			GBM - Glioblastoma multiforme(13;0.154)															---	---	---	---
DFNA5	1687	broad.mit.edu	37	7	24749884	24749884	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:24749884C>T	uc010kus.1	-	6	909	c.821G>A	c.(820-822)GGG>GAG	p.G274E	DFNA5_uc003swz.2_Missense_Mutation_p.G110E|DFNA5_uc003sxa.1_Missense_Mutation_p.G274E|DFNA5_uc010kut.1_Missense_Mutation_p.G110E	NM_001127453	NP_001120925	O60443	DFNA5_HUMAN	deafness, autosomal dominant 5 protein isoform	274					sensory perception of sound					ovary(1)	1																		---	---	---	---
C7orf31	136895	broad.mit.edu	37	7	25181885	25181885	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:25181885C>T	uc003sxn.1	-	9	1487	c.926G>A	c.(925-927)CGA>CAA	p.R309Q	C7orf31_uc003sxm.1_Missense_Mutation_p.R151Q	NM_138811	NP_620166	Q8N865	CG031_HUMAN	hypothetical protein LOC136895	309											0																		---	---	---	---
HOXA1	3198	broad.mit.edu	37	7	27134225	27134225	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:27134225C>T	uc003sye.2	-	2	936	c.842G>A	c.(841-843)CGA>CAA	p.R281Q	HOXA1_uc003syd.2_3'UTR|uc003syg.2_5'Flank	NM_005522	NP_005513	P49639	HXA1_HUMAN	homeobox A1 isoform a	281	Homeobox.					nucleus	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			ovary(3)	3																		---	---	---	---
HOXA4	3201	broad.mit.edu	37	7	27169078	27169078	+	Silent	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:27169078C>T	uc003sym.3	-	2	776	c.729G>A	c.(727-729)CGG>CGA	p.R243R	HOXA3_uc003syk.2_5'Flank	NM_002141	NP_002132	Q00056	HXA4_HUMAN	homeobox A4	243	Homeobox.					nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			breast(1)	1																		---	---	---	---
PDE1C	5137	broad.mit.edu	37	7	31793018	31793018	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:31793018G>A	uc003tcm.1	-	18	2579	c.2110C>T	c.(2110-2112)CAT>TAT	p.H704Y	PDE1C_uc003tcn.1_Missense_Mutation_p.H704Y|PDE1C_uc003tco.1_Missense_Mutation_p.H764Y	NM_005020	NP_005011	Q14123	PDE1C_HUMAN	phosphodiesterase 1C	704					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)															---	---	---	---
KBTBD2	25948	broad.mit.edu	37	7	32909202	32909202	+	Silent	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:32909202A>G	uc003tdb.2	-	4	2286	c.1627T>C	c.(1627-1629)TTA>CTA	p.L543L	AVL9_uc011kai.1_Intron	NM_015483	NP_056298	Q8IY47	KBTB2_HUMAN	kelch repeat and BTB (POZ) domain containing 2	543	Kelch 5.			L -> S (in Ref. 6; CAB55994).							0			GBM - Glioblastoma multiforme(11;0.0499)															---	---	---	---
DPY19L1	23333	broad.mit.edu	37	7	35057484	35057484	+	Intron	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:35057484A>G	uc003tem.3	-							NM_015283	NP_056098			dpy-19-like 1							integral to membrane					0																		---	---	---	---
ANLN	54443	broad.mit.edu	37	7	36463475	36463475	+	Silent	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:36463475T>C	uc003tff.2	+	15	2730	c.2526T>C	c.(2524-2526)AAT>AAC	p.N842N	ANLN_uc011kaz.1_Silent_p.N754N|ANLN_uc003tfg.2_Silent_p.N805N|ANLN_uc010kxe.2_Silent_p.N804N	NM_018685	NP_061155	Q9NQW6	ANLN_HUMAN	anillin, actin binding protein	842	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																		---	---	---	---
ELMO1	9844	broad.mit.edu	37	7	37264527	37264527	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:37264527C>T	uc003tfk.1	-	9	965	c.658G>A	c.(658-660)GCG>ACG	p.A220T	ELMO1_uc011kbc.1_Missense_Mutation_p.A124T|ELMO1_uc010kxg.1_Missense_Mutation_p.A220T	NM_014800	NP_055615	Q92556	ELMO1_HUMAN	engulfment and cell motility 1 isoform 1	220					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																		---	---	---	---
AMPH	273	broad.mit.edu	37	7	38429435	38429435	+	Silent	SNP	C	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:38429435C>A	uc003tgu.2	-	20	2019	c.1950G>T	c.(1948-1950)CTG>CTT	p.L650L	AMPH_uc003tgv.2_Silent_p.L608L|AMPH_uc003tgt.2_Silent_p.L535L	NM_001635	NP_001626	P49418	AMPH_HUMAN	amphiphysin isoform 1	650	SH3.				endocytosis|synaptic transmission	actin cytoskeleton|cell junction|synaptic vesicle membrane				ovary(3)|liver(1)|skin(1)	5																		---	---	---	---
VPS41	27072	broad.mit.edu	37	7	38803046	38803046	+	Intron	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:38803046A>G	uc003tgy.2	-						VPS41_uc003tgz.2_Intron|VPS41_uc010kxn.2_Intron	NM_014396	NP_055211			vacuolar protein sorting 41 isoform 1						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																		---	---	---	---
POU6F2	11281	broad.mit.edu	37	7	39491263	39491263	+	Silent	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:39491263C>T	uc003thb.1	+	8	1407	c.1365C>T	c.(1363-1365)TCC>TCT	p.S455S		NM_007252	NP_009183	P78424	PO6F2_HUMAN	POU class 6 homeobox 2 isoform 1	455	Ser-rich.				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																		---	---	---	---
YKT6	10652	broad.mit.edu	37	7	44247770	44247770	+	Silent	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:44247770C>T	uc003tkm.2	+	5	589	c.432C>T	c.(430-432)GCC>GCT	p.A144A	YKT6_uc011kbv.1_Silent_p.A144A	NM_006555	NP_006546	O15498	YKT6_HUMAN	YKT6 v-SNARE protein	144	v-SNARE coiled-coil homology.				ER to Golgi vesicle-mediated transport|protein transport|retrograde transport, endosome to Golgi|vesicle docking involved in exocytosis|vesicle targeting	cytoplasmic vesicle membrane|cytosol|endoplasmic reticulum|endosome|Golgi membrane|integral to plasma membrane|mitochondrion|SNARE complex	protein-cysteine S-palmitoleyltransferase activity|SNAP receptor activity				0																		---	---	---	---
NPC1L1	29881	broad.mit.edu	37	7	44561718	44561718	+	Missense_Mutation	SNP	A	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:44561718A>T	uc003tlb.2	-	11	2817	c.2761T>A	c.(2761-2763)TCC>ACC	p.S921T	NPC1L1_uc003tlc.2_Missense_Mutation_p.S921T|NPC1L1_uc011kbw.1_Missense_Mutation_p.S875T|NPC1L1_uc003tla.2_5'Flank	NM_013389	NP_037521	Q9UHC9	NPCL1_HUMAN	Niemann-Pick C1-like protein 1 isoform 1	921	Cytoplasmic (Potential).				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)													---	---	---	---
NPC1L1	29881	broad.mit.edu	37	7	44579806	44579806	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:44579806G>A	uc003tlb.2	-	2	246	c.190C>T	c.(190-192)CGC>TGC	p.R64C	NPC1L1_uc003tlc.2_Missense_Mutation_p.R64C|NPC1L1_uc011kbw.1_Missense_Mutation_p.R64C|NPC1L1_uc003tld.2_Missense_Mutation_p.R64C	NM_013389	NP_037521	Q9UHC9	NPCL1_HUMAN	Niemann-Pick C1-like protein 1 isoform 1	64	Extracellular (Potential).				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)													---	---	---	---
ZMIZ2	83637	broad.mit.edu	37	7	44800184	44800184	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:44800184C>T	uc003tlr.2	+	9	1355	c.1232C>T	c.(1231-1233)TCG>TTG	p.S411L	ZMIZ2_uc003tlq.2_Missense_Mutation_p.S353L|ZMIZ2_uc003tls.2_Missense_Mutation_p.S385L|ZMIZ2_uc003tlt.2_Missense_Mutation_p.S34L|ZMIZ2_uc010kyj.2_5'UTR	NM_031449	NP_113637	Q8NF64	ZMIZ2_HUMAN	zinc finger, MIZ-type containing 2 isoform 1	411					positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	nuclear replication fork	ligand-dependent nuclear receptor transcription coactivator activity|protein binding|zinc ion binding			ovary(2)|large_intestine(2)|breast(1)	5																		---	---	---	---
MYO1G	64005	broad.mit.edu	37	7	45005249	45005249	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:45005249C>T	uc003tmh.2	-	17	2512	c.2368G>A	c.(2368-2370)GCA>ACA	p.A790T	MYO1G_uc003tmf.2_Missense_Mutation_p.A233T|MYO1G_uc003tmg.2_Missense_Mutation_p.A552T|MYO1G_uc010kym.2_Missense_Mutation_p.A675T	NM_033054	NP_149043	B0I1T2	MYO1G_HUMAN	myosin IG	790						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	45108136	45108136	+	Silent	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:45108136C>T	uc003tmo.2	+	5	713	c.567C>T	c.(565-567)CCC>CCT	p.P189P	CCM2_uc003tmn.2_RNA|CCM2_uc003tmp.2_Silent_p.P131P|CCM2_uc003tmq.2_RNA|CCM2_uc003tmr.2_Intron|CCM2_uc011kcb.1_Silent_p.P152P|CCM2_uc011kcc.1_Intron|CCM2_uc003tms.2_Silent_p.P210P	NM_031443	NP_113631	Q9BSQ5	CCM2_HUMAN	cerebral cavernous malformation 2 isoform 2	189	PID.				endothelial tube morphogenesis|integrin-mediated signaling pathway|stress-activated MAPK cascade|vasculogenesis	cytoplasm	protein binding				0														Familial_Cerebral_Cavernous_Angioma				---	---	---	---
ABCA13	154664	broad.mit.edu	37	7	48391926	48391926	+	Silent	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:48391926T>C	uc003toq.2	+	31	10555	c.10530T>C	c.(10528-10530)CCT>CCC	p.P3510P	ABCA13_uc010kys.1_Silent_p.P584P|ABCA13_uc003tos.1_Silent_p.P336P	NM_152701	NP_689914	Q86UQ4	ABCAD_HUMAN	ATP binding cassette, sub-family A (ABC1),	3510					transport	integral to membrane	ATP binding|ATPase activity			ovary(5)|central_nervous_system(4)|skin(1)	10																		---	---	---	---
EGFR	1956	broad.mit.edu	37	7	55270272	55270272	+	Silent	SNP	C	T	T	rs140117937		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:55270272C>T	uc003tqk.2	+	27	3471	c.3225C>T	c.(3223-3225)GGC>GGT	p.G1075G	EGFR_uc010kzg.1_Silent_p.G1030G|EGFR_uc011kco.1_Silent_p.G1022G	NM_005228	NP_005219	P00533	EGFR_HUMAN	epidermal growth factor receptor isoform a	1075	Cytoplasmic (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			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)			---	---	---	---
ZNF680	340252	broad.mit.edu	37	7	63982075	63982075	+	Missense_Mutation	SNP	C	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:63982075C>G	uc003tta.2	-	4	1230	c.1057G>C	c.(1057-1059)GAA>CAA	p.E353Q	ZNF680_uc010kzr.2_Missense_Mutation_p.E280Q	NM_178558	NP_848653	Q8NEM1	ZN680_HUMAN	zinc finger protein 680 isoform 1	353	C2H2-type 7.				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)																---	---	---	---
ZNF117	51351	broad.mit.edu	37	7	64441790	64441790	+	Silent	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:64441790T>C	uc003ttr.2	-	3	1294	c.9A>G	c.(7-9)AGA>AGG	p.R3R		NM_015852	NP_056936	Q03924	ZN117_HUMAN	zinc finger protein 117	3						nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			skin(1)	1		Lung NSC(55;0.0295)|all_lung(88;0.0691)																---	---	---	---
TPST1	8460	broad.mit.edu	37	7	65705701	65705701	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:65705701T>C	uc003tuw.2	+	2	641	c.289T>C	c.(289-291)TGT>CGT	p.C97R	TPST1_uc010kzy.2_Intron|TPST1_uc010kzz.2_Missense_Mutation_p.C97R|TPST1_uc010laa.2_Missense_Mutation_p.C97R	NM_003596	NP_003587	O60507	TPST1_HUMAN	tyrosylprotein sulfotransferase 1	97	Lumenal (Potential).				inflammatory response|peptidyl-tyrosine sulfation	Golgi membrane|integral to membrane|membrane fraction	protein-tyrosine sulfotransferase activity				0																		---	---	---	---
AUTS2	26053	broad.mit.edu	37	7	70255336	70255336	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:70255336T>C	uc003tvw.3	+	19	3877	c.3134T>C	c.(3133-3135)ATG>ACG	p.M1045T	AUTS2_uc003tvx.3_Missense_Mutation_p.M1021T|AUTS2_uc011keg.1_Missense_Mutation_p.M497T	NM_015570	NP_056385	Q8WXX7	AUTS2_HUMAN	autism susceptibility candidate 2 isoform 1	1045										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)														---	---	---	---
FKBP6	8468	broad.mit.edu	37	7	72754741	72754741	+	Silent	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:72754741G>A	uc003tya.2	+	6	822	c.690G>A	c.(688-690)CTG>CTA	p.L230L	FKBP6_uc003twz.2_Silent_p.L200L|FKBP6_uc011kew.1_Silent_p.L225L|FKBP6_uc010lbe.1_RNA	NM_003602	NP_003593	O75344	FKBP6_HUMAN	FK506 binding protein 6 isoform a	230	TPR 2.				protein folding	membrane	FK506 binding|peptidyl-prolyl cis-trans isomerase activity				0		Lung NSC(55;0.0908)|all_lung(88;0.198)																---	---	---	---
BAZ1B	9031	broad.mit.edu	37	7	72925157	72925157	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:72925157A>G	uc003tyc.2	-	2	478	c.133T>C	c.(133-135)TAC>CAC	p.Y45H		NM_032408	NP_115784	Q9UIG0	BAZ1B_HUMAN	bromodomain adjacent to zinc finger domain, 1B	45	WAC.|Mediates the tyrosine-protein kinase activity.				ATP-dependent chromatin remodeling|chromatin-mediated maintenance of transcription|DNA replication-dependent nucleosome disassembly|double-strand break repair|heart morphogenesis|transcription, DNA-dependent	WINAC complex	ATP binding|chromatin binding|histone acetyl-lysine binding|histone kinase activity|non-membrane spanning protein tyrosine kinase activity|protein complex scaffold|vitamin D receptor activator activity|vitamin D receptor binding|zinc ion binding			ovary(4)|upper_aerodigestive_tract(1)|breast(1)|skin(1)	7		Lung NSC(55;0.0659)|all_lung(88;0.152)																---	---	---	---
GTF2IRD1	9569	broad.mit.edu	37	7	73935638	73935638	+	Intron	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:73935638G>A	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																		---	---	---	---
NCF1	653361	broad.mit.edu	37	7	74197386	74197386	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:74197386G>A	uc003ubb.2	+	6	626	c.556G>A	c.(556-558)GTA>ATA	p.V186I	NCF1_uc010lbs.1_Missense_Mutation_p.V186I|NCF1_uc011kfh.1_Missense_Mutation_p.R105H	NM_000265	NP_000256	P14598	NCF1_HUMAN	neutrophil cytosolic factor 1	186	SH3 1.				cell communication|cellular defense response|innate immune response|protein targeting to membrane|respiratory burst|superoxide anion generation	cytosol|NADPH oxidase complex|soluble fraction	electron carrier activity|GTP binding|GTPase activity|phosphatidylinositol binding|SH3 domain binding|superoxide-generating NADPH oxidase activity			skin(1)	1																		---	---	---	---
FGL2	10875	broad.mit.edu	37	7	76826259	76826259	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:76826259T>C	uc003ugb.2	-	2	697	c.657A>G	c.(655-657)ATA>ATG	p.I219M	CCDC146_uc003ufz.1_Intron|CCDC146_uc003uga.2_Intron	NM_006682	NP_006673	Q14314	FGL2_HUMAN	fibrinogen-like 2 precursor	219	Fibrinogen C-terminal.				signal transduction	fibrinogen complex	receptor binding			skin(2)	2																		---	---	---	---
RSBN1L	222194	broad.mit.edu	37	7	77379153	77379153	+	Silent	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:77379153G>A	uc010ldt.1	+	3	1160	c.1116G>A	c.(1114-1116)CTG>CTA	p.L372L	RSBN1L_uc003ugm.2_Silent_p.L154L	NM_198467	NP_940869	Q6PCB5	RSBNL_HUMAN	round spermatid basic protein 1-like	372						nucleus				ovary(1)	1																		---	---	---	---
CACNA2D1	781	broad.mit.edu	37	7	81589149	81589149	+	Intron	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:81589149C>T	uc003uhr.1	-						CACNA2D1_uc011kgy.1_Intron	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	82580543	82580543	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:82580543T>C	uc003uhx.2	-	6	9650	c.9361A>G	c.(9361-9363)ATT>GTT	p.I3121V	PCLO_uc003uhv.2_Missense_Mutation_p.I3121V|PCLO_uc010lec.2_Missense_Mutation_p.I86V	NM_033026	NP_149015	Q9Y6V0	PCLO_HUMAN	piccolo isoform 1	3052					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	82585003	82585003	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:82585003G>A	uc003uhx.2	-	5	5555	c.5266C>T	c.(5266-5268)CGC>TGC	p.R1756C	PCLO_uc003uhv.2_Missense_Mutation_p.R1756C	NM_033026	NP_149015	Q9Y6V0	PCLO_HUMAN	piccolo isoform 1	1687					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	82585766	82585766	+	Missense_Mutation	SNP	A	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:82585766A>T	uc003uhx.2	-	5	4792	c.4503T>A	c.(4501-4503)GAT>GAA	p.D1501E	PCLO_uc003uhv.2_Missense_Mutation_p.D1501E	NM_033026	NP_149015	Q9Y6V0	PCLO_HUMAN	piccolo isoform 1	1432					cytoskeleton organization|synaptic vesicle exocytosis	cell junction|cytoskeleton|synaptic vesicle	calcium ion binding|calcium-dependent phospholipid binding|profilin binding|transporter activity			ovary(7)	7																		---	---	---	---
SEMA3D	223117	broad.mit.edu	37	7	84642132	84642132	+	Silent	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:84642132G>A	uc003uic.2	-	15	1774	c.1734C>T	c.(1732-1734)GGC>GGT	p.G578G	SEMA3D_uc010led.2_Silent_p.G578G|SEMA3D_uc003uib.2_Silent_p.G217G	NM_152754	NP_689967	O95025	SEM3D_HUMAN	semaphorin 3D precursor	578	PSI.				cell differentiation|nervous system development	extracellular region|membrane	receptor activity			ovary(3)|large_intestine(2)	5																		---	---	---	---
ABCB4	5244	broad.mit.edu	37	7	87092182	87092182	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:87092182C>T	uc003uiv.1	-	4	254	c.178G>A	c.(178-180)GGT>AGT	p.G60S	ABCB4_uc003uiw.1_Missense_Mutation_p.G60S|ABCB4_uc003uix.1_Missense_Mutation_p.G60S|ABCB4_uc003uiy.2_Missense_Mutation_p.G60S	NM_018849	NP_061337	P21439	MDR3_HUMAN	ATP-binding cassette, subfamily B, member 4	60	ABC transmembrane type-1 1.|Helical; (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	87179315	87179315	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:87179315A>G	uc003uiz.1	-	14	1824	c.1406T>C	c.(1405-1407)ATC>ACC	p.I469T	ABCB1_uc011khc.1_Missense_Mutation_p.I405T	NM_000927	NP_000918	P08183	MDR1_HUMAN	ATP-binding cassette, subfamily B, member 1	469	ABC transporter 1.|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)													---	---	---	---
ADAM22	53616	broad.mit.edu	37	7	87564473	87564473	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:87564473G>A	uc003ujn.2	+	2	297	c.218G>A	c.(217-219)CGG>CAG	p.R73Q	ADAM22_uc003uji.1_Missense_Mutation_p.R72Q|ADAM22_uc003ujj.1_Missense_Mutation_p.R73Q|ADAM22_uc003ujk.1_Missense_Mutation_p.R73Q|ADAM22_uc003ujl.1_Missense_Mutation_p.R73Q|ADAM22_uc003ujm.2_Missense_Mutation_p.R73Q|ADAM22_uc003ujo.2_Missense_Mutation_p.R73Q|ADAM22_uc003ujp.1_Missense_Mutation_p.R125Q	NM_021723	NP_068369	Q9P0K1	ADA22_HUMAN	ADAM metallopeptidase domain 22 isoform 1	73					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)															---	---	---	---
STEAP4	79689	broad.mit.edu	37	7	87913520	87913520	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:87913520A>G	uc003ujs.2	-	2	170	c.65T>C	c.(64-66)GTA>GCA	p.V22A	STEAP4_uc010lek.2_Missense_Mutation_p.V22A|STEAP4_uc003ujt.2_Missense_Mutation_p.V22A	NM_024636	NP_078912	Q687X5	STEA4_HUMAN	tumor necrosis factor, alpha-induced protein 9	22					fat cell differentiation|ion transport|iron ion homeostasis	Golgi membrane|integral to membrane|plasma membrane	electron carrier activity|flavin adenine dinucleotide binding|iron ion binding|oxidoreductase activity				0	Esophageal squamous(14;0.00802)																	---	---	---	---
ZNF804B	219578	broad.mit.edu	37	7	88964026	88964026	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:88964026A>G	uc011khi.1	+	4	2268	c.1730A>G	c.(1729-1731)AAT>AGT	p.N577S		NM_181646	NP_857597	A4D1E1	Z804B_HUMAN	zinc finger protein 804B	577						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)			---	---	---	---
FZD1	8321	broad.mit.edu	37	7	90895547	90895547	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:90895547C>T	uc003ula.2	+	1	1765	c.1352C>T	c.(1351-1353)GCC>GTC	p.A451V		NM_003505	NP_003496	Q9UP38	FZD1_HUMAN	frizzled 1 precursor	451	Helical; Name=4; (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	91691718	91691718	+	Silent	SNP	G	A	A	rs138928104	byFrequency	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:91691718G>A	uc003ulg.2	+	24	6120	c.5895G>A	c.(5893-5895)GAG>GAA	p.E1965E	AKAP9_uc003ulf.2_Silent_p.E1965E|AKAP9_uc003uli.2_Silent_p.E1588E	NM_005751	NP_005742	Q99996	AKAP9_HUMAN	A-kinase anchor protein 9 isoform 2	1977	Potential.|Glu-rich.				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								---	---	---	---
C7orf64	84060	broad.mit.edu	37	7	92164257	92164257	+	Silent	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:92164257G>A	uc003ulz.2	+	4	1031	c.990G>A	c.(988-990)GCG>GCA	p.A330A	C7orf64_uc003uma.2_Silent_p.A330A	NM_032120	NP_115496	Q5RL73	CG064_HUMAN	hypothetical protein LOC84060	330							nucleotide binding			ovary(2)	2																		---	---	---	---
SAMD9	54809	broad.mit.edu	37	7	92731228	92731228	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:92731228G>A	uc003umf.2	-	3	4439	c.4183C>T	c.(4183-4185)CTC>TTC	p.L1395F	SAMD9_uc003umg.2_Missense_Mutation_p.L1395F	NM_017654	NP_060124	Q5K651	SAMD9_HUMAN	sterile alpha motif domain containing 9	1395						cytoplasm				ovary(3)|skin(2)|breast(1)|central_nervous_system(1)	7	all_cancers(62;5.71e-11)|all_epithelial(64;3.25e-10)|Breast(17;0.000675)|Lung NSC(181;0.0969)|all_lung(186;0.125)		STAD - Stomach adenocarcinoma(171;0.000302)															---	---	---	---
SAMD9L	219285	broad.mit.edu	37	7	92763996	92763996	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:92763996T>C	uc003umh.1	-	5	2505	c.1289A>G	c.(1288-1290)AAG>AGG	p.K430R	SAMD9L_uc003umj.1_Missense_Mutation_p.K430R|SAMD9L_uc003umi.1_Missense_Mutation_p.K430R|SAMD9L_uc010lfb.1_Missense_Mutation_p.K430R|SAMD9L_uc003umk.1_Missense_Mutation_p.K430R|SAMD9L_uc010lfc.1_Missense_Mutation_p.K430R|SAMD9L_uc010lfd.1_Missense_Mutation_p.K430R|SAMD9L_uc011khx.1_Intron	NM_152703	NP_689916	Q8IVG5	SAM9L_HUMAN	sterile alpha motif domain containing 9-like	430										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)															---	---	---	---
COL1A2	1278	broad.mit.edu	37	7	94056606	94056606	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:94056606C>T	uc003ung.1	+	48	3737	c.3266C>T	c.(3265-3267)GCT>GTT	p.A1089V	COL1A2_uc011kib.1_Intron	NM_000089	NP_000080	P08123	CO1A2_HUMAN	alpha 2 type I collagen precursor	1089					axon guidance|blood vessel development|collagen fibril organization|leukocyte migration|odontogenesis|platelet activation|regulation of blood pressure|Rho protein signal transduction|skeletal system development|skin morphogenesis|transforming growth factor beta receptor signaling pathway	collagen type I|extracellular space|plasma membrane	extracellular matrix structural constituent|identical protein binding|platelet-derived growth factor binding|protein binding, bridging		COL1A2/PLAG1(3)	soft_tissue(3)|central_nervous_system(3)|ovary(2)|skin(1)	9	all_cancers(62;2.46e-09)|all_epithelial(64;2.7e-08)		STAD - Stomach adenocarcinoma(171;0.0031)		Collagenase(DB00048)										HNSCC(75;0.22)			---	---	---	---
PPP1R9A	55607	broad.mit.edu	37	7	94791291	94791291	+	Intron	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:94791291C>T	uc003unp.2	+						PPP1R9A_uc010lfj.2_Intron|PPP1R9A_uc011kif.1_Intron|PPP1R9A_uc003unq.2_Intron|PPP1R9A_uc011kig.1_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)			---	---	---	---
LMTK2	22853	broad.mit.edu	37	7	97822648	97822648	+	Silent	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:97822648C>T	uc003upd.1	+	11	3164	c.2871C>T	c.(2869-2871)GAC>GAT	p.D957D		NM_014916	NP_055731	Q8IWU2	LMTK2_HUMAN	lemur tyrosine kinase 2 precursor	957					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	98519479	98519479	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:98519479C>T	uc003upp.2	+	21	2935	c.2726C>T	c.(2725-2727)TCG>TTG	p.S909L	TRRAP_uc011kis.1_Missense_Mutation_p.S909L|TRRAP_uc003upr.2_Missense_Mutation_p.S601L	NM_003496	NP_003487	Q9Y4A5	TRRAP_HUMAN	transformation/transcription domain-associated	909					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	98574180	98574180	+	Silent	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:98574180G>A	uc003upp.2	+	54	8222	c.8013G>A	c.(8011-8013)GCG>GCA	p.A2671A	TRRAP_uc011kis.1_Silent_p.A2653A|TRRAP_uc003upr.2_Silent_p.A2370A	NM_003496	NP_003487	Q9Y4A5	TRRAP_HUMAN	transformation/transcription domain-associated	2671					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)															---	---	---	---
ZNF498	221785	broad.mit.edu	37	7	99227435	99227435	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:99227435A>G	uc003url.1	+	8	1754	c.1427A>G	c.(1426-1428)CAC>CGC	p.H476R	ZNF498_uc003urm.1_Missense_Mutation_p.H312R|ZNF498_uc010lge.1_Missense_Mutation_p.H312R|ZNF498_uc003urn.2_Intron|ZNF498_uc010lgf.1_Missense_Mutation_p.H404R|ZNF498_uc003uro.1_Missense_Mutation_p.H260R	NM_145115	NP_660090	Q6NSZ9	ZN498_HUMAN	zinc finger and SCAN domain containing 25	476	C2H2-type 5.				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)																	---	---	---	---
CYP3A5	1577	broad.mit.edu	37	7	99250381	99250381	+	Missense_Mutation	SNP	C	T	T	rs149081683	byFrequency;by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:99250381C>T	uc003urq.2	-	11	1135	c.1048G>A	c.(1048-1050)GTG>ATG	p.V350M	ZNF498_uc003urn.2_Intron|CYP3A5_uc003urp.2_Missense_Mutation_p.V170M|CYP3A5_uc003urr.2_Missense_Mutation_p.V237M|CYP3A5_uc011kiy.1_Missense_Mutation_p.V340M|CYP3A5_uc003urs.2_Translation_Start_Site|CYP3A5_uc010lgg.2_Intron	NM_000777	NP_000768	P20815	CP3A5_HUMAN	cytochrome P450, family 3, subfamily A,	350					alkaloid catabolic process|drug catabolic process|oxidative demethylation|steroid metabolic process|xenobiotic metabolic process	endoplasmic reticulum membrane|microsome	aromatase activity|electron carrier activity|heme binding|oxygen binding				0	all_epithelial(64;2.77e-08)|Lung NSC(181;0.00396)|all_lung(186;0.00659)|Esophageal squamous(72;0.0166)				Alfentanil(DB00802)|Clopidogrel(DB00758)|Cyclosporine(DB00091)|Daunorubicin(DB00694)|Indinavir(DB00224)|Irinotecan(DB00762)|Ketoconazole(DB01026)|Lapatinib(DB01259)|Mephenytoin(DB00532)|Midazolam(DB00683)|Mifepristone(DB00834)|Phenytoin(DB00252)|Quinine(DB00468)|Saquinavir(DB01232)|Tacrolimus(DB00864)|Troleandomycin(DB01361)|Verapamil(DB00661)|Vincristine(DB00541)													---	---	---	---
ZKSCAN1	7586	broad.mit.edu	37	7	99621176	99621176	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:99621176C>T	uc003usk.1	+	2	266	c.47C>T	c.(46-48)GCT>GTT	p.A16V	ZKSCAN1_uc003usj.2_Missense_Mutation_p.A15V|ZKSCAN1_uc003usl.1_5'UTR|ZKSCAN1_uc003usm.1_Intron	NM_003439	NP_003430	P17029	ZKSC1_HUMAN	zinc finger protein 36	16					viral reproduction	mitochondrion|nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(3)	3	Lung NSC(181;0.0211)|all_lung(186;0.0323)|Esophageal squamous(72;0.0439)		STAD - Stomach adenocarcinoma(171;0.129)															---	---	---	---
ZNF3	7551	broad.mit.edu	37	7	99669739	99669739	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:99669739C>T	uc003usq.2	-	6	675	c.368G>A	c.(367-369)GGT>GAT	p.G123D	ZNF3_uc003usp.2_Intron|ZNF3_uc003usr.2_Missense_Mutation_p.G123D|ZNF3_uc010lgj.2_Missense_Mutation_p.G87D|ZNF3_uc003uss.2_Missense_Mutation_p.G130D|ZNF3_uc003ust.3_Missense_Mutation_p.G123D	NM_032924	NP_116313	P17036	ZNF3_HUMAN	zinc finger protein 3 isoform 2	123	KRAB.				cell differentiation|leukocyte activation|multicellular organismal development	nucleus	DNA binding|identical protein binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(1)	1	Lung NSC(181;0.0181)|all_lung(186;0.0284)|Esophageal squamous(72;0.0439)	Ovarian(593;2.06e-05)|Myeloproliferative disorder(862;0.0122)|Breast(660;0.029)	STAD - Stomach adenocarcinoma(171;0.129)															---	---	---	---
COPS6	10980	broad.mit.edu	37	7	99686961	99686961	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:99686961C>A	uc003usu.2	+	2	156	c.125C>A	c.(124-126)GCT>GAT	p.A42D	COPS6_uc011kjf.1_Missense_Mutation_p.A42D	NM_006833	NP_006824	Q7L5N1	CSN6_HUMAN	COP9 signalosome subunit 6	42	MPN.				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)															---	---	---	---
TAF6	6878	broad.mit.edu	37	7	99705180	99705180	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:99705180C>T	uc003uti.2	-	15	1804	c.1723G>A	c.(1723-1725)GTC>ATC	p.V575I	AP4M1_uc003utd.2_Intron|TAF6_uc003utg.2_Missense_Mutation_p.V497I|TAF6_uc003uth.2_Missense_Mutation_p.V632I|TAF6_uc003utk.2_Missense_Mutation_p.V575I|TAF6_uc011kji.1_Missense_Mutation_p.V612I|TAF6_uc003utj.2_Missense_Mutation_p.V565I|TAF6_uc003utl.2_Missense_Mutation_p.V565I|TAF6_uc003utm.2_Missense_Mutation_p.V575I	NM_139315	NP_647476	P49848	TAF6_HUMAN	TBP-associated factor 6 isoform alpha	575					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)																	---	---	---	---
TAF6	6878	broad.mit.edu	37	7	99708887	99708887	+	Nonsense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:99708887G>A	uc003uti.2	-	10	1039	c.958C>T	c.(958-960)CGA>TGA	p.R320*	TAF6_uc003utg.2_Nonsense_Mutation_p.R242*|TAF6_uc003uth.2_Nonsense_Mutation_p.R377*|TAF6_uc003utk.2_Nonsense_Mutation_p.R320*|TAF6_uc011kji.1_Nonsense_Mutation_p.R357*|TAF6_uc003utj.2_Nonsense_Mutation_p.R310*|TAF6_uc003utl.2_Nonsense_Mutation_p.R320*|TAF6_uc003utm.2_Nonsense_Mutation_p.R320*|TAF6_uc003utn.1_RNA	NM_139315	NP_647476	P49848	TAF6_HUMAN	TBP-associated factor 6 isoform alpha	320					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)																	---	---	---	---
SPDYE3	441272	broad.mit.edu	37	7	99913460	99913460	+	Silent	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:99913460A>G	uc003uug.1	+	2	363	c.123A>G	c.(121-123)TCA>TCG	p.S41S		NM_001004351	NP_001004351	A6NKU9	SPDE3_HUMAN	speedy homolog E3	418											0																		---	---	---	---
PCOLCE	5118	broad.mit.edu	37	7	100200090	100200090	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:100200090C>T	uc003uvo.2	+	1	209	c.11C>T	c.(10-12)GCA>GTA	p.A4V	uc011kjy.1_RNA|PCOLCE_uc011kkb.1_Missense_Mutation_p.A4V|PCOLCE_uc010lhb.1_RNA	NM_002593	NP_002584	Q15113	PCOC1_HUMAN	procollagen C-endopeptidase enhancer	4					multicellular organismal development	extracellular space	collagen binding|heparin binding|peptidase activator activity				0	Lung NSC(181;0.0261)|all_lung(186;0.0392)|Esophageal squamous(72;0.0439)																	---	---	---	---
ZAN	7455	broad.mit.edu	37	7	100334228	100334228	+	Missense_Mutation	SNP	G	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:100334228G>C	uc003uwj.2	+	4	394	c.229G>C	c.(229-231)GCC>CCC	p.A77P	ZAN_uc003uwk.2_Missense_Mutation_p.A77P|ZAN_uc003uwl.2_RNA|ZAN_uc010lhh.2_RNA|ZAN_uc010lhi.2_RNA	NM_003386	NP_003377	Q9Y493	ZAN_HUMAN	zonadhesin isoform 3	77	MAM 1.|Extracellular (Potential).				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)															---	---	---	---
Unknown	0	broad.mit.edu	37	7	100549789	100549789	+	5'Flank	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:100549789G>A	uc003uxk.1	+						uc003uxl.1_5'Flank					Homo sapiens MUC3B mRNA for intestinal mucin, partial cds.																														---	---	---	---
MUC17	140453	broad.mit.edu	37	7	100677971	100677971	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:100677971C>T	uc003uxp.1	+	3	3327	c.3274C>T	c.(3274-3276)CCA>TCA	p.P1092S	MUC17_uc010lho.1_RNA	NM_001040105	NP_001035194	Q685J3	MUC17_HUMAN	mucin 17 precursor	1092	Extracellular (Potential).|Ser-rich.|59 X approximate tandem repeats.|16.					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)																	---	---	---	---
MUC17	140453	broad.mit.edu	37	7	100684372	100684372	+	Silent	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:100684372T>C	uc003uxp.1	+	3	9728	c.9675T>C	c.(9673-9675)ACT>ACC	p.T3225T	MUC17_uc010lho.1_RNA	NM_001040105	NP_001035194	Q685J3	MUC17_HUMAN	mucin 17 precursor	3225	Extracellular (Potential).|Ser-rich.|59 X approximate tandem repeats.|52.					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)																	---	---	---	---
TRIM56	81844	broad.mit.edu	37	7	100730993	100730993	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:100730993G>A	uc003uxq.2	+	3	631	c.400G>A	c.(400-402)GGG>AGG	p.G134R	TRIM56_uc003uxr.2_Missense_Mutation_p.G134R	NM_030961	NP_112223	Q9BRZ2	TRI56_HUMAN	tripartite motif-containing 56	134	B box-type 1.				defense response to virus|interferon-beta production|protein K63-linked ubiquitination|response to type I interferon	cytoplasm	ubiquitin-protein ligase activity|zinc ion binding			kidney(1)|central_nervous_system(1)|skin(1)	3	Lung NSC(181;0.136)|all_lung(186;0.182)																	---	---	---	---
EMID2	136227	broad.mit.edu	37	7	101196614	101196614	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:101196614C>T	uc010lhy.1	+	11	1223	c.1031C>T	c.(1030-1032)CCT>CTT	p.P344L	EMID2_uc003uyo.1_Missense_Mutation_p.P346L	NM_133457	NP_597714	Q96A83	EMID2_HUMAN	EMI domain containing 2	346	Collagen-like 2.					collagen				ovary(1)	1	Lung NSC(181;0.215)																	---	---	---	---
SH2B2	10603	broad.mit.edu	37	7	101943949	101943949	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:101943949G>A	uc011kko.1	+	2	289	c.244G>A	c.(244-246)GCG>ACG	p.A82T		NM_020979	NP_066189	O14492	SH2B2_HUMAN	SH2B adaptor protein 2	39					blood coagulation|insulin receptor signaling pathway|intracellular signal transduction	cytosol|plasma membrane	JAK pathway signal transduction adaptor activity|SH3/SH2 adaptor activity|signal transducer activity				0																		---	---	---	---
ORAI2	80228	broad.mit.edu	37	7	102079426	102079426	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:102079426C>A	uc010lhz.1	+	3	258	c.23C>A	c.(22-24)CCT>CAT	p.P8H	ORAI2_uc003uzj.2_Missense_Mutation_p.P8H|ORAI2_uc003uzk.2_Missense_Mutation_p.P8H|ORAI2_uc011kks.1_Intron	NM_001126340	NP_001119812	Q96SN7	ORAI2_HUMAN	ORAI calcium release-activated calcium modulator	8						integral to membrane	protein binding			ovary(1)|kidney(1)	2																		---	---	---	---
FBXL13	222235	broad.mit.edu	37	7	102473331	102473331	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:102473331A>G	uc003vaq.2	-	18	2237	c.1810T>C	c.(1810-1812)TAC>CAC	p.Y604H	FBXL13_uc010liq.1_Intron|FBXL13_uc010lir.1_Intron|FBXL13_uc003var.2_Intron|FBXL13_uc003vas.2_Missense_Mutation_p.Y576H	NM_145032	NP_659469	Q8NEE6	FXL13_HUMAN	F-box and leucine-rich repeat protein 13 isoform	604	LRR 15.										0																		---	---	---	---
DNAJC2	27000	broad.mit.edu	37	7	102962369	102962369	+	Intron	SNP	T	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:102962369T>A	uc003vbo.2	-						PMPCB_uc011kll.1_Intron|DNAJC2_uc003vbn.2_Intron|DNAJC2_uc010lix.2_Intron|DNAJC2_uc003vbp.2_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																		---	---	---	---
MLL5	55904	broad.mit.edu	37	7	104703826	104703826	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:104703826C>T	uc003vcm.2	+	5	749	c.215C>T	c.(214-216)CCG>CTG	p.P72L	MLL5_uc010lja.1_5'UTR|MLL5_uc010ljb.1_Missense_Mutation_p.P72L|MLL5_uc003vcl.2_Missense_Mutation_p.P72L|MLL5_uc010ljc.2_Missense_Mutation_p.P72L	NM_182931	NP_891847	Q8IZD2	MLL5_HUMAN	myeloid/lymphoid or mixed-lineage leukemia 5	72					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																		---	---	---	---
PUS7	54517	broad.mit.edu	37	7	105098261	105098261	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:105098261C>A	uc003vcx.2	-	16	2181	c.1962G>T	c.(1960-1962)CAG>CAT	p.Q654H	PUS7_uc010lji.2_Missense_Mutation_p.Q660H|PUS7_uc003vcy.2_Missense_Mutation_p.Q654H|PUS7_uc003vcz.1_Missense_Mutation_p.Q654H	NM_019042	NP_061915	Q96PZ0	PUS7_HUMAN	pseudouridylate synthase 7 homolog	654					pseudouridine synthesis|tRNA processing		pseudouridine synthase activity|RNA binding			breast(1)	1																		---	---	---	---
COG5	10466	broad.mit.edu	37	7	107194737	107194737	+	Silent	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:107194737C>T	uc003ved.2	-	3	903	c.378G>A	c.(376-378)TCG>TCA	p.S126S	COG5_uc003vec.2_Silent_p.S126S|COG5_uc003vee.2_Silent_p.S126S	NM_181733	NP_859422	Q9UP83	COG5_HUMAN	component of oligomeric golgi complex 5 isoform	126					intra-Golgi vesicle-mediated transport|protein transport	cytosol|Golgi membrane|Golgi transport complex|nucleus	protein binding			central_nervous_system(2)|skin(2)	4																		---	---	---	---
SLC26A3	1811	broad.mit.edu	37	7	107423266	107423266	+	Silent	SNP	T	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:107423266T>A	uc003ver.2	-	11	1498	c.1287A>T	c.(1285-1287)GGA>GGT	p.G429G	SLC26A3_uc003ves.2_Silent_p.G394G	NM_000111	NP_000102	P40879	S26A3_HUMAN	solute carrier family 26, member 3	429	Helical; (Potential).				excretion	integral to membrane|membrane fraction	inorganic anion exchanger activity|secondary active sulfate transmembrane transporter activity|sequence-specific DNA binding transcription factor activity|transcription cofactor activity			ovary(3)|skin(1)	4																		---	---	---	---
LAMB1	3912	broad.mit.edu	37	7	107593992	107593992	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:107593992A>G	uc003vew.2	-	22	3397	c.3062T>C	c.(3061-3063)CTC>CCC	p.L1021P	LAMB1_uc003vev.2_Missense_Mutation_p.L1045P	NM_002291	NP_002282	P07942	LAMB1_HUMAN	laminin, beta 1 precursor	1021	Laminin EGF-like 10.				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)													---	---	---	---
LAMB4	22798	broad.mit.edu	37	7	107684198	107684198	+	Silent	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:107684198T>C	uc010ljo.1	-	29	4554	c.4470A>G	c.(4468-4470)TTA>TTG	p.L1490L	LAMB4_uc003vey.2_Silent_p.L1490L|LAMB4_uc010ljp.1_Silent_p.L459L	NM_007356	NP_031382	A4D0S4	LAMB4_HUMAN	laminin, beta 4 precursor	1490	Domain I.				cell adhesion	basement membrane				ovary(4)|breast(2)|large_intestine(1)|skin(1)	8																		---	---	---	---
LAMB4	22798	broad.mit.edu	37	7	107703429	107703429	+	Silent	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:107703429G>A	uc010ljo.1	-	23	3156	c.3072C>T	c.(3070-3072)TGC>TGT	p.C1024C	LAMB4_uc003vey.2_Silent_p.C1024C|LAMB4_uc010ljp.1_5'UTR	NM_007356	NP_031382	A4D0S4	LAMB4_HUMAN	laminin, beta 4 precursor	1024	Laminin EGF-like 11.				cell adhesion	basement membrane				ovary(4)|breast(2)|large_intestine(1)|skin(1)	8																		---	---	---	---
LAMB4	22798	broad.mit.edu	37	7	107710147	107710147	+	Intron	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:107710147A>G	uc010ljo.1	-						LAMB4_uc003vey.2_Intron	NM_007356	NP_031382			laminin, beta 4 precursor						cell adhesion	basement membrane				ovary(4)|breast(2)|large_intestine(1)|skin(1)	8																		---	---	---	---
DOCK4	9732	broad.mit.edu	37	7	111629091	111629091	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:111629091G>A	uc003vfx.2	-	6	712	c.443C>T	c.(442-444)GCC>GTC	p.A148V	DOCK4_uc003vfy.2_Missense_Mutation_p.A148V|DOCK4_uc003vga.1_5'UTR|DOCK4_uc010ljt.1_Missense_Mutation_p.A148V|DOCK4_uc003vgb.1_Missense_Mutation_p.A72V	NM_014705	NP_055520	Q8N1I0	DOCK4_HUMAN	dedicator of cytokinesis 4	148					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)																---	---	---	---
ZNF277	11179	broad.mit.edu	37	7	111980942	111980942	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:111980942A>G	uc003vge.2	+	11	1154	c.1025A>G	c.(1024-1026)CAG>CGG	p.Q342R	ZNF277_uc003vgf.2_Missense_Mutation_p.Q264R|ZNF277_uc003vgg.2_Missense_Mutation_p.Q167R	NM_021994	NP_068834	Q9NRM2	ZN277_HUMAN	zinc finger protein (C2H2 type) 277	342						nucleus	DNA binding|protein binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(2)|breast(2)	4																		---	---	---	---
MDFIC	29969	broad.mit.edu	37	7	114562635	114562635	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:114562635G>A	uc003vhf.2	+	1	427	c.164G>A	c.(163-165)CGG>CAG	p.R55Q	MDFIC_uc003vhg.2_5'Flank	NM_199072	NP_951038	Q9P1T7	MDFIC_HUMAN	MyoD family inhibitor domain containing protein	Error:Variant_position_missing_in_Q9P1T7_after_alignment					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																OREG0003787	type=REGULATORY REGION|Gene=MDFIC|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay	---	---	---	---
MET	4233	broad.mit.edu	37	7	116339531	116339531	+	Silent	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:116339531T>C	uc003vij.2	+	2	580	c.393T>C	c.(391-393)ATT>ATC	p.I131I	MET_uc010lkh.2_Silent_p.I131I|MET_uc011knc.1_Silent_p.I131I|MET_uc011knd.1_Silent_p.I131I|MET_uc011kne.1_Silent_p.I131I|MET_uc011knf.1_Silent_p.I131I|MET_uc011kng.1_Silent_p.I131I|MET_uc011knh.1_Silent_p.I131I|MET_uc011kni.1_Silent_p.I131I|MET_uc003vii.1_Silent_p.I150I|MET_uc010lkg.2_Silent_p.I131I|MET_uc011kmz.1_Silent_p.I131I|MET_uc011kna.1_Silent_p.I131I|MET_uc011knb.1_Silent_p.I131I	NM_000245	NP_000236	P08581	MET_HUMAN	met proto-oncogene isoform b precursor	131	Extracellular (Potential).|Sema.				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)				---	---	---	---
ASZ1	136991	broad.mit.edu	37	7	117022121	117022121	+	Splice_Site	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:117022121A>G	uc003vjb.2	-	8	951	c.888_splice	c.e8+1	p.K296_splice	ASZ1_uc011kno.1_Splice_Site_p.K296_splice|ASZ1_uc011knp.1_Splice_Site_p.K88_splice	NM_130768	NP_570124			ankyrin repeat, SAM and basic leucine zipper						cell differentiation|DNA methylation involved in gamete generation|gene silencing by RNA|male meiosis|multicellular organismal development|piRNA metabolic process|spermatogenesis	pi-body	signal transducer activity			central_nervous_system(2)|ovary(1)	3	Lung NSC(10;0.00156)|all_lung(10;0.00175)		STAD - Stomach adenocarcinoma(10;0.000512)															---	---	---	---
CCDC136	64753	broad.mit.edu	37	7	128450375	128450375	+	Silent	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:128450375C>T	uc003vnv.1	+	12	2350	c.1983C>T	c.(1981-1983)CCC>CCT	p.P661P	CCDC136_uc003vnu.1_Intron|CCDC136_uc003vnw.1_Intron|CCDC136_uc003vnx.1_Silent_p.P477P|CCDC136_uc010llq.1_5'UTR|CCDC136_uc003vny.1_Silent_p.P271P	NM_022742	NP_073579	Q96JN2	CC136_HUMAN	coiled-coil domain containing 136	661						integral to membrane	protein binding			ovary(2)	2																		---	---	---	---
FLNC	2318	broad.mit.edu	37	7	128480937	128480937	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:128480937G>A	uc003vnz.3	+	11	1935	c.1726G>A	c.(1726-1728)GCC>ACC	p.A576T	FLNC_uc003voa.3_Missense_Mutation_p.A576T	NM_001458	NP_001449	Q14315	FLNC_HUMAN	gamma filamin isoform a	576	Filamin 4.				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	128494938	128494938	+	Silent	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:128494938C>T	uc003vnz.3	+	42	7316	c.7107C>T	c.(7105-7107)TGC>TGT	p.C2369C	FLNC_uc003voa.3_Silent_p.C2336C	NM_001458	NP_001449	Q14315	FLNC_HUMAN	gamma filamin isoform a	2369	Filamin 21.				cell junction assembly	cytoskeleton|cytosol|plasma membrane|sarcomere	actin binding			breast(5)|large_intestine(3)|ovary(2)|central_nervous_system(1)|skin(1)	12																		---	---	---	---
IRF5	3663	broad.mit.edu	37	7	128588012	128588012	+	Silent	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:128588012C>T	uc003vog.2	+	8	1108	c.987C>T	c.(985-987)CGC>CGT	p.R329R	IRF5_uc003voh.2_Silent_p.R313R|IRF5_uc010llt.2_Silent_p.R237R|IRF5_uc003voi.2_Silent_p.R313R|IRF5_uc003voj.3_Silent_p.R313R|IRF5_uc010llw.1_3'UTR	NM_002200	NP_002191	Q13568	IRF5_HUMAN	interferon regulatory factor 5 isoform a	323					interferon-gamma-mediated signaling pathway|type I interferon-mediated signaling pathway	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity				0																		---	---	---	---
NRF1	4899	broad.mit.edu	37	7	129357144	129357144	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:129357144C>T	uc003voz.2	+	9	1268	c.1151C>T	c.(1150-1152)TCG>TTG	p.S384L	NRF1_uc003vpa.2_Missense_Mutation_p.S384L|NRF1_uc011kpa.1_Missense_Mutation_p.S223L|NRF1_uc003vpb.2_Missense_Mutation_p.S384L	NM_005011	NP_005002	Q16656	NRF1_HUMAN	nuclear respiratory factor 1	384	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																		---	---	---	---
KLHDC10	23008	broad.mit.edu	37	7	129761973	129761973	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:129761973T>C	uc003vpj.1	+	5	845	c.710T>C	c.(709-711)TTA>TCA	p.L237S	KLHDC10_uc003vpk.1_Missense_Mutation_p.L208S|KLHDC10_uc010lmb.1_Missense_Mutation_p.L134S	NM_014997	NP_055812	Q6PID8	KLD10_HUMAN	kelch domain containing 10	237	Kelch 3.										0																		---	---	---	---
C7orf45	136263	broad.mit.edu	37	7	129847829	129847829	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:129847829T>C	uc003vpp.2	+	1	126	c.79T>C	c.(79-81)TAT>CAT	p.Y27H	TMEM209_uc003vpn.2_5'Flank|TMEM209_uc010lmc.1_5'Flank|TMEM209_uc003vpo.2_5'Flank	NM_145268	NP_660311	Q8WWF3	CG045_HUMAN	hypothetical protein LOC136263	27						integral to membrane					0	Melanoma(18;0.0435)																	---	---	---	---
C7orf45	136263	broad.mit.edu	37	7	129855966	129855966	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:129855966C>T	uc003vpp.2	+	3	438	c.391C>T	c.(391-393)CGC>TGC	p.R131C		NM_145268	NP_660311	Q8WWF3	CG045_HUMAN	hypothetical protein LOC136263	131						integral to membrane					0	Melanoma(18;0.0435)																	---	---	---	---
CPA2	1358	broad.mit.edu	37	7	129916516	129916516	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:129916516G>A	uc003vpq.2	+	7	653	c.634G>A	c.(634-636)GCC>ACC	p.A212T	CPA2_uc011kpc.1_Missense_Mutation_p.A212T	NM_001869	NP_001860	P48052	CBPA2_HUMAN	carboxypeptidase A2 (pancreatic) precursor	212					proteolysis|vacuolar protein catabolic process	extracellular region|vacuole	metallocarboxypeptidase activity|zinc ion binding			ovary(1)	1	Melanoma(18;0.0435)																	---	---	---	---
CPA2	1358	broad.mit.edu	37	7	129919348	129919348	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:129919348C>A	uc003vpq.2	+	9	852	c.833C>A	c.(832-834)CCC>CAC	p.P278H		NM_001869	NP_001860	P48052	CBPA2_HUMAN	carboxypeptidase A2 (pancreatic) precursor	278					proteolysis|vacuolar protein catabolic process	extracellular region|vacuole	metallocarboxypeptidase activity|zinc ion binding			ovary(1)	1	Melanoma(18;0.0435)																	---	---	---	---
MKLN1	4289	broad.mit.edu	37	7	131113795	131113795	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:131113795C>A	uc011kpm.1	+	9	915	c.851C>A	c.(850-852)ACT>AAT	p.T284N	MKLN1_uc011kpl.1_Missense_Mutation_p.T261N|MKLN1_uc010lmh.2_Missense_Mutation_p.T284N|MKLN1_uc003vqs.2_Missense_Mutation_p.T77N	NM_013255	NP_037387	Q9UL63	MKLN1_HUMAN	muskelin 1, intracellular mediator containing	284	Kelch 1.				signal transduction	cytoplasm	protein binding			breast(1)	1	Melanoma(18;0.162)																	---	---	---	---
PLXNA4	91584	broad.mit.edu	37	7	131833340	131833340	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:131833340T>C	uc003vra.3	-	26	4955	c.4726A>G	c.(4726-4728)AAT>GAT	p.N1576D		NM_020911	NP_065962	Q9HCM2	PLXA4_HUMAN	plexin A4 isoform 1	1576	Cytoplasmic (Potential).					integral to membrane|intracellular|plasma membrane				ovary(1)	1																		---	---	---	---
BPGM	669	broad.mit.edu	37	7	134346724	134346724	+	Silent	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:134346724G>A	uc003vrv.2	+	3	1006	c.465G>A	c.(463-465)TCG>TCA	p.S155S	BPGM_uc003vrw.2_Silent_p.S155S|BPGM_uc003vrx.2_Silent_p.S155S	NM_199186	NP_954655	P07738	PMGE_HUMAN	bisphosphoglycerate mutase	155					glycolysis|respiratory gaseous exchange		2,3-bisphospho-D-glycerate 2-phosphohydrolase activity|bisphosphoglycerate mutase activity|phosphoglycerate mutase activity				0																		---	---	---	---
TMEM140	55281	broad.mit.edu	37	7	134849758	134849758	+	3'UTR	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:134849758A>G	uc003vsi.2	+	2					C7orf49_uc003vsh.2_Intron	NM_018295	NP_060765			transmembrane protein 140							integral to membrane				large_intestine(1)	1																		---	---	---	---
LUZP6	767558	broad.mit.edu	37	7	135636362	135636362	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:135636362C>T	uc003vte.3	-	2	445	c.89G>A	c.(88-90)CGG>CAG	p.R30Q	LUZP6_uc010lmv.2_Intron	NM_145808	NP_665807	Q538Z0	LUZP6_HUMAN	myotrophin	Error:Variant_position_missing_in_Q538Z0_after_alignment											0																		---	---	---	---
SVOPL	136306	broad.mit.edu	37	7	138329518	138329518	+	Missense_Mutation	SNP	C	T	T	rs144436781	byFrequency	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:138329518C>T	uc011kqh.1	-	8	733	c.733G>A	c.(733-735)GTT>ATT	p.V245I	SVOPL_uc003vue.2_Missense_Mutation_p.V93I	NM_001139456	NP_001132928	Q8N434	SVOPL_HUMAN	SVOP-like isoform 1	245						integral to membrane	transmembrane transporter activity				0																		---	---	---	---
ATP6V0A4	50617	broad.mit.edu	37	7	138444576	138444576	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:138444576C>T	uc003vuf.2	-	7	798	c.560G>A	c.(559-561)CGG>CAG	p.R187Q	ATP6V0A4_uc003vug.2_Missense_Mutation_p.R187Q|ATP6V0A4_uc003vuh.2_Missense_Mutation_p.R187Q	NM_130841	NP_570856	Q9HBG4	VPP4_HUMAN	ATPase, H+ transporting, lysosomal V0 subunit	187	Cytoplasmic (Potential).				cellular iron ion homeostasis|excretion|insulin receptor signaling pathway|ossification|regulation of pH|sensory perception of sound|transferrin transport	apical plasma membrane|brush border membrane|endosome membrane|integral to membrane|proton-transporting two-sector ATPase complex, proton-transporting domain	ATPase binding|hydrogen ion transmembrane transporter activity			pancreas(1)	1																		---	---	---	---
KIAA1549	57670	broad.mit.edu	37	7	138588471	138588471	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:138588471C>T	uc011kql.1	-	8	3581	c.3532G>A	c.(3532-3534)GTC>ATC	p.V1178I	KIAA1549_uc003vuk.3_Missense_Mutation_p.V1128I|KIAA1549_uc011kqj.1_Missense_Mutation_p.V1178I	NM_020910	NP_065961	Q9HCM3	K1549_HUMAN	hypothetical protein LOC57670 isoform 1	1178						integral to membrane			KIAA1549/BRAF(229)	central_nervous_system(229)|pancreas(1)	230								O	BRAF	pilocytic astrocytoma								---	---	---	---
HIPK2	28996	broad.mit.edu	37	7	139311428	139311428	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:139311428T>C	uc003vvf.3	-	6	1712	c.1538A>G	c.(1537-1539)GAC>GGC	p.D513G	HIPK2_uc003vvd.3_Missense_Mutation_p.D513G	NM_022740	NP_073577	Q9H2X6	HIPK2_HUMAN	homeodomain interacting protein kinase 2 isoform	513	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)																	---	---	---	---
MGAM	8972	broad.mit.edu	37	7	141795366	141795366	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:141795366G>A	uc003vwy.2	+	41	4826	c.4772G>A	c.(4771-4773)AGA>AAA	p.R1591K		NM_004668	NP_004659	O43451	MGA_HUMAN	maltase-glucoamylase	1591	Glucoamylase.|Lumenal (Potential).				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)													---	---	---	---
TRYX3	136541	broad.mit.edu	37	7	141955044	141955044	+	Silent	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:141955044A>G	uc003vxb.2	-	3	587	c.267T>C	c.(265-267)CAT>CAC	p.H89H	TRYX3_uc003vxc.3_Silent_p.H89H	NM_001001317	NP_001001317	Q8IYP2	PRS58_HUMAN	trypsin X3 precursor	89	Peptidase S1.				proteolysis	extracellular region	serine-type endopeptidase activity				0	Melanoma(164;0.0272)																	---	---	---	---
PRSS1	5644	broad.mit.edu	37	7	142458439	142458439	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:142458439T>C	uc003wak.2	+	2	91	c.74T>C	c.(73-75)GTT>GCT	p.V25A	uc011krr.1_Intron|uc003vzp.2_Intron|uc011ksh.1_Intron|uc011ksi.1_Intron|uc003vzw.1_Intron|uc010loj.1_Intron|uc003wad.2_Intron|uc003wag.1_Intron|TRY6_uc011ksn.1_Intron|PRSS1_uc011ksm.1_Intron|PRSS1_uc003wam.2_5'Flank	NM_002769	NP_002760	P07477	TRY1_HUMAN	protease, serine, 1 preproprotein	25	Peptidase S1.				digestion|proteolysis	extracellular space	metal ion binding|protein binding|serine-type endopeptidase activity			large_intestine(1)|central_nervous_system(1)	2	Melanoma(164;0.047)	all_cancers(3;2.14e-49)|Acute lymphoblastic leukemia(3;7.3e-185)|all_hematologic(3;1.1e-165)	all cancers(2;0.000126)|Colorectal(2;0.000157)|Epithelial(2;0.000191)|COAD - Colon adenocarcinoma(2;0.00189)											Hereditary_Pancreatitis				---	---	---	---
C7orf34	135927	broad.mit.edu	37	7	142637536	142637536	+	Silent	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:142637536G>A	uc003wca.2	+	2	347	c.306G>A	c.(304-306)TCG>TCA	p.S102S		NM_178829	NP_849151	Q96L11	CG034_HUMAN	hypothetical protein LOC135927	77						extracellular region					0	Melanoma(164;0.059)																	---	---	---	---
OR2F1	26211	broad.mit.edu	37	7	143657648	143657648	+	Silent	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:143657648T>C	uc003wds.1	+	1	629	c.585T>C	c.(583-585)AAT>AAC	p.N195N		NM_012369	NP_036501	Q13607	OR2F1_HUMAN	olfactory receptor, family 2, subfamily F,	195	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			skin(2)|ovary(1)	3	Melanoma(164;0.0903)																	---	---	---	---
CUL1	8454	broad.mit.edu	37	7	148427296	148427296	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:148427296A>G	uc010lpg.2	+	2	608	c.82A>G	c.(82-84)ATC>GTC	p.I28V	CUL1_uc003wey.2_Missense_Mutation_p.I28V|CUL1_uc003wez.2_5'UTR	NM_003592	NP_003583	Q13616	CUL1_HUMAN	cullin 1	28					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)															---	---	---	---
EZH2	2146	broad.mit.edu	37	7	148515124	148515124	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:148515124C>T	uc003wfd.1	-	10	1236	c.1070G>A	c.(1069-1071)CGG>CAG	p.R357Q	EZH2_uc011kug.1_Missense_Mutation_p.R348Q|EZH2_uc003wfb.1_Missense_Mutation_p.R362Q|EZH2_uc003wfc.1_Missense_Mutation_p.R318Q|EZH2_uc011kuh.1_Missense_Mutation_p.R348Q|EZH2_uc011kui.1_Missense_Mutation_p.R357Q|EZH2_uc011kuj.1_RNA	NM_004456	NP_004447	Q15910	EZH2_HUMAN	enhancer of zeste 2 isoform a	357					negative regulation of retinoic acid receptor signaling pathway|negative regulation of transcription, DNA-dependent|transcription, DNA-dependent	ESC/E(Z) complex	DNA binding|histone-lysine N-methyltransferase activity|protein binding			haematopoietic_and_lymphoid_tissue(180)|skin(2)|large_intestine(1)	183	Melanoma(164;0.15)		OV - Ovarian serous cystadenocarcinoma(82;0.00239)					Mis		DLBCL								---	---	---	---
ZNF398	57541	broad.mit.edu	37	7	148875833	148875833	+	Missense_Mutation	SNP	A	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:148875833A>C	uc003wfl.2	+	6	1144	c.869A>C	c.(868-870)AAG>ACG	p.K290T	ZNF398_uc011kul.1_Missense_Mutation_p.K119T|ZNF398_uc011kum.1_Missense_Mutation_p.K295T	NM_170686	NP_733787	Q8TD17	ZN398_HUMAN	zinc finger 398 isoform a	290					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)															---	---	---	---
ZNF398	57541	broad.mit.edu	37	7	148876640	148876640	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:148876640G>A	uc003wfl.2	+	6	1951	c.1676G>A	c.(1675-1677)CGC>CAC	p.R559H	ZNF398_uc011kul.1_Missense_Mutation_p.R388H|ZNF398_uc011kum.1_Missense_Mutation_p.R564H	NM_170686	NP_733787	Q8TD17	ZN398_HUMAN	zinc finger 398 isoform a	559	C2H2-type 8.				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)															---	---	---	---
KRBA1	84626	broad.mit.edu	37	7	149420939	149420939	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:149420939G>A	uc003wfz.2	+	8	1286	c.887G>A	c.(886-888)CGG>CAG	p.R296Q	KRBA1_uc010lpj.2_RNA|KRBA1_uc003wga.2_RNA|KRBA1_uc003wgb.2_5'UTR	NM_032534	NP_115923	A5PL33	KRBA1_HUMAN	KRAB A domain containing 1	296										ovary(1)|central_nervous_system(1)	2	Melanoma(164;0.165)|Ovarian(565;0.177)		OV - Ovarian serous cystadenocarcinoma(82;0.00625)															---	---	---	---
ABP1	26	broad.mit.edu	37	7	150554905	150554905	+	Silent	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:150554905G>A	uc003why.1	+	3	5565	c.1347G>A	c.(1345-1347)GTG>GTA	p.V449V	ABP1_uc003whz.1_Silent_p.V449V|ABP1_uc003wia.1_Silent_p.V449V	NM_001091	NP_001082	P19801	ABP1_HUMAN	amiloride binding protein 1 precursor	449					amine metabolic process	extracellular space|peroxisome	copper ion binding|diamine oxidase activity|heparin binding|histamine oxidase activity|methylputrescine oxidase activity|primary amine oxidase activity|propane-1,3-diamine oxidase activity|quinone binding			ovary(2)|breast(2)|skin(2)	6	all_neural(206;0.219)		OV - Ovarian serous cystadenocarcinoma(82;0.0121)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)	Amiloride(DB00594)|Spermine(DB00127)													---	---	---	---
KCNH2	3757	broad.mit.edu	37	7	150647423	150647423	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:150647423C>T	uc003wic.2	-	9	2244	c.2231G>A	c.(2230-2232)CGA>CAA	p.R744Q	KCNH2_uc003wib.2_Missense_Mutation_p.R404Q|KCNH2_uc011kux.1_Missense_Mutation_p.R648Q|KCNH2_uc003wid.2_Missense_Mutation_p.R404Q|KCNH2_uc003wie.2_Missense_Mutation_p.R744Q	NM_000238	NP_000229	Q12809	KCNH2_HUMAN	voltage-gated potassium channel, subfamily H,	744	Cytoplasmic (Potential).|cNMP.				blood circulation|muscle contraction|regulation of heart contraction|regulation of transcription, DNA-dependent	voltage-gated potassium channel complex	delayed rectifier potassium channel activity|two-component sensor activity			skin(3)|ovary(1)	4	all_neural(206;0.219)		OV - Ovarian serous cystadenocarcinoma(82;0.0121)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)	Amiodarone(DB01118)|Amsacrine(DB00276)|Astemizole(DB00637)|Carvedilol(DB01136)|Cisapride(DB00604)|Dofetilide(DB00204)|Halofantrine(DB01218)|Ibutilide(DB00308)|Pimozide(DB01100)|Propafenone(DB01182)|Quinidine(DB00908)|Sertindole(DB06144)|Sotalol(DB00489)|Terfenadine(DB00342)|Verapamil(DB00661)													---	---	---	---
ACCN3	9311	broad.mit.edu	37	7	150749636	150749636	+	Intron	SNP	C	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:150749636C>A	uc003win.2	+						ACCN3_uc003wio.2_Intron|ACCN3_uc003wip.2_Intron|ACCN3_uc003wiq.2_Intron	NM_004769	NP_004760			amiloride-sensitive cation channel 3 isoform a						sensory perception|signal transduction	cytoplasm|integral to plasma membrane	ligand-gated sodium channel activity			ovary(1)|central_nervous_system(1)	2			OV - Ovarian serous cystadenocarcinoma(82;0.0121)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)														---	---	---	---
CDK5	1020	broad.mit.edu	37	7	150751338	150751338	+	Silent	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:150751338G>A	uc003wir.1	-	11	814	c.753C>T	c.(751-753)GTC>GTT	p.V251V		NM_004935	NP_004926	Q00535	CDK5_HUMAN	cyclin-dependent kinase 5 isoform 1	251	Protein kinase.				activation of pro-apoptotic gene products|blood coagulation|cell division|cell proliferation|embryo development|negative regulation of transcription, DNA-dependent|positive regulation of neuron apoptosis	axon|cytosol|dendrite|growth cone|lamellipodium|membrane|neuromuscular junction|neuronal cell body	acetylcholine receptor activator activity|ATP binding|cyclin-dependent protein kinase activity|ErbB-2 class receptor binding|ErbB-3 class receptor binding|tau-protein kinase activity			lung(1)|central_nervous_system(1)	2		Breast(660;0.159)|Ovarian(593;0.182)	OV - Ovarian serous cystadenocarcinoma(82;0.0121)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)|LUSC - Lung squamous cell carcinoma(290;0.008)|Lung(243;0.00942)|BRCA - Breast invasive adenocarcinoma(188;0.242)														---	---	---	---
ABCF2	10061	broad.mit.edu	37	7	150916160	150916160	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:150916160G>A	uc003wjp.2	-	8	1118	c.1007C>T	c.(1006-1008)GCA>GTA	p.A336V	ABCF2_uc003wjo.1_Missense_Mutation_p.A336V	NM_007189	NP_009120	Q9UG63	ABCF2_HUMAN	ATP-binding cassette, sub-family F, member 2	336						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)														---	---	---	---
HTR5A	3361	broad.mit.edu	37	7	154862965	154862965	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:154862965C>T	uc003wlu.1	+	1	420	c.356C>T	c.(355-357)GCG>GTG	p.A119V	uc011kvt.1_Missense_Mutation_p.A17T|uc003wlt.2_Missense_Mutation_p.A17T	NM_024012	NP_076917	P47898	5HT5A_HUMAN	5-hydroxytryptamine receptor 5A	119	Helical; Name=3; (By similarity).					integral to plasma membrane	serotonin receptor activity			ovary(2)|large_intestine(1)	3	all_neural(206;0.119)	all_hematologic(28;0.0592)	OV - Ovarian serous cystadenocarcinoma(82;0.0238)	UCEC - Uterine corpus endometrioid carcinoma (81;0.171)														---	---	---	---
PTPRN2	5799	broad.mit.edu	37	7	157369296	157369296	+	Intron	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:157369296G>A	uc003wno.2	-						PTPRN2_uc003wnp.2_Intron|PTPRN2_uc003wnq.2_Intron|PTPRN2_uc003wnr.2_Intron|PTPRN2_uc011kwa.1_Intron|uc011kwb.1_5'Flank|MIR153-2_hsa-mir-153-2|MI0000464_5'Flank	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	157874049	157874049	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:157874049G>A	uc003wno.2	-	11	1785	c.1664C>T	c.(1663-1665)ACC>ATC	p.T555I	PTPRN2_uc003wnp.2_Missense_Mutation_p.T538I|PTPRN2_uc003wnq.2_Missense_Mutation_p.T526I|PTPRN2_uc003wnr.2_Missense_Mutation_p.T517I|PTPRN2_uc011kwa.1_Missense_Mutation_p.T578I	NM_002847	NP_002838	Q92932	PTPR2_HUMAN	protein tyrosine phosphatase, receptor type, N	555	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)														---	---	---	---
PTPRN2	5799	broad.mit.edu	37	7	157926586	157926586	+	Missense_Mutation	SNP	C	T	T	rs142388788		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:157926586C>T	uc003wno.2	-	9	1460	c.1339G>A	c.(1339-1341)GTC>ATC	p.V447I	PTPRN2_uc003wnp.2_Missense_Mutation_p.V430I|PTPRN2_uc003wnq.2_Missense_Mutation_p.V447I|PTPRN2_uc003wnr.2_Missense_Mutation_p.V409I|PTPRN2_uc011kwa.1_Missense_Mutation_p.V470I	NM_002847	NP_002838	Q92932	PTPR2_HUMAN	protein tyrosine phosphatase, receptor type, N	447	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)														---	---	---	---
ESYT2	57488	broad.mit.edu	37	7	158552195	158552195	+	Silent	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:158552195A>G	uc003wob.1	-	13	1611	c.1545T>C	c.(1543-1545)GAT>GAC	p.D515D	ESYT2_uc003woc.1_Silent_p.D339D|ESYT2_uc003wod.1_Silent_p.D515D|ESYT2_uc003woa.1_Silent_p.D71D	NM_020728	NP_065779	A0FGR8	ESYT2_HUMAN	family with sequence similarity 62 (C2 domain	543	C2 2.					integral to membrane|plasma membrane				central_nervous_system(2)|kidney(1)	3																		---	---	---	---
ESYT2	57488	broad.mit.edu	37	7	158560398	158560398	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:158560398C>T	uc003wob.1	-	8	1081	c.1015G>A	c.(1015-1017)GTT>ATT	p.V339I	ESYT2_uc003woc.1_Missense_Mutation_p.V163I|ESYT2_uc003wod.1_Missense_Mutation_p.V339I	NM_020728	NP_065779	A0FGR8	ESYT2_HUMAN	family with sequence similarity 62 (C2 domain	367						integral to membrane|plasma membrane				central_nervous_system(2)|kidney(1)	3																		---	---	---	---
WDR60	55112	broad.mit.edu	37	7	158672581	158672581	+	Silent	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:158672581A>G	uc003woe.3	+	5	938	c.780A>G	c.(778-780)CGA>CGG	p.R260R	WDR60_uc010lqv.2_RNA	NM_018051	NP_060521	Q8WVS4	WDR60_HUMAN	WD repeat domain 60	260										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	401445	401445	+	Missense_Mutation	SNP	A	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:401445A>T	uc003wox.2	+	7	918	c.652A>T	c.(652-654)ATG>TTG	p.M218L	FBXO25_uc003woy.2_Missense_Mutation_p.M218L|FBXO25_uc003woz.2_Missense_Mutation_p.M151L|FBXO25_uc003wpa.2_Missense_Mutation_p.M1L	NM_183421	NP_904357	Q8TCJ0	FBX25_HUMAN	F-box only protein 25 isoform 1	218						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)														---	---	---	---
DLGAP2	9228	broad.mit.edu	37	8	1497704	1497704	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:1497704A>G	uc003wpl.2	+	2	942	c.845A>G	c.(844-846)GAC>GGC	p.D282G	DLGAP2_uc003wpm.2_Missense_Mutation_p.D282G	NM_004745	NP_004736	Q9P1A6	DLGP2_HUMAN	discs large-associated protein 2	361					neuron-neuron synaptic transmission	cell junction|neurofilament|postsynaptic density|postsynaptic membrane	protein binding				0		Ovarian(12;0.0271)|Hepatocellular(245;0.0838)|Colorectal(14;0.0846)		BRCA - Breast invasive adenocarcinoma(11;0.000169)|READ - Rectum adenocarcinoma(644;0.171)														---	---	---	---
DLGAP2	9228	broad.mit.edu	37	8	1513881	1513881	+	Silent	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:1513881C>T	uc003wpl.2	+	3	1120	c.1023C>T	c.(1021-1023)ACC>ACT	p.T341T	DLGAP2_uc003wpm.2_Silent_p.T341T	NM_004745	NP_004736	Q9P1A6	DLGP2_HUMAN	discs large-associated protein 2	420					neuron-neuron synaptic transmission	cell junction|neurofilament|postsynaptic density|postsynaptic membrane	protein binding				0		Ovarian(12;0.0271)|Hepatocellular(245;0.0838)|Colorectal(14;0.0846)		BRCA - Breast invasive adenocarcinoma(11;0.000169)|READ - Rectum adenocarcinoma(644;0.171)														---	---	---	---
DLGAP2	9228	broad.mit.edu	37	8	1624732	1624732	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:1624732C>T	uc003wpl.2	+	8	2093	c.1996C>T	c.(1996-1998)CGC>TGC	p.R666C	DLGAP2_uc003wpm.2_Missense_Mutation_p.R652C	NM_004745	NP_004736	Q9P1A6	DLGP2_HUMAN	discs large-associated protein 2	745					neuron-neuron synaptic transmission	cell junction|neurofilament|postsynaptic density|postsynaptic membrane	protein binding				0		Ovarian(12;0.0271)|Hepatocellular(245;0.0838)|Colorectal(14;0.0846)		BRCA - Breast invasive adenocarcinoma(11;0.000169)|READ - Rectum adenocarcinoma(644;0.171)														---	---	---	---
MYOM2	9172	broad.mit.edu	37	8	2007345	2007345	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:2007345T>C	uc003wpx.3	+	6	770	c.632T>C	c.(631-633)GTA>GCA	p.V211A	MYOM2_uc011kwi.1_Intron	NM_003970	NP_003961	P54296	MYOM2_HUMAN	myomesin 2	211	Ig-like C2-type 1.				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)														---	---	---	---
MYOM2	9172	broad.mit.edu	37	8	2026918	2026918	+	Nonsense_Mutation	SNP	C	T	T	rs143448287	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:2026918C>T	uc003wpx.3	+	12	1504	c.1366C>T	c.(1366-1368)CGA>TGA	p.R456*	MYOM2_uc011kwi.1_Intron	NM_003970	NP_003961	P54296	MYOM2_HUMAN	myomesin 2	456	Fibronectin type-III 1.				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)														---	---	---	---
MYOM2	9172	broad.mit.edu	37	8	2040264	2040264	+	Missense_Mutation	SNP	A	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:2040264A>C	uc003wpx.3	+	16	2057	c.1919A>C	c.(1918-1920)GAC>GCC	p.D640A	MYOM2_uc011kwi.1_Missense_Mutation_p.D65A	NM_003970	NP_003961	P54296	MYOM2_HUMAN	myomesin 2	640	Fibronectin type-III 3.				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)														---	---	---	---
MYOM2	9172	broad.mit.edu	37	8	2092753	2092753	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:2092753T>C	uc003wpx.3	+	37	4384	c.4246T>C	c.(4246-4248)TAC>CAC	p.Y1416H	MYOM2_uc011kwi.1_Missense_Mutation_p.Y841H	NM_003970	NP_003961	P54296	MYOM2_HUMAN	myomesin 2	1416	Ig-like C2-type 5.				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	2836280	2836280	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:2836280C>T	uc011kwk.1	-	55	8813	c.8423G>A	c.(8422-8424)CGT>CAT	p.R2808H	CSMD1_uc011kwj.1_Missense_Mutation_p.R2137H|CSMD1_uc010lrg.2_Missense_Mutation_p.R818H	NM_033225	NP_150094	Q96PZ7	CSMD1_HUMAN	CUB and Sushi multiple domains 1 precursor	2808	Extracellular (Potential).|Sushi 20.					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	2876070	2876070	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:2876070G>A	uc011kwk.1	-	52	8351	c.7961C>T	c.(7960-7962)ACG>ATG	p.T2654M	CSMD1_uc011kwj.1_Missense_Mutation_p.T1983M|CSMD1_uc010lrg.2_Intron	NM_033225	NP_150094	Q96PZ7	CSMD1_HUMAN	CUB and Sushi multiple domains 1 precursor	2654	Extracellular (Potential).|Sushi 17.					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)														---	---	---	---
AGPAT5	55326	broad.mit.edu	37	8	6599174	6599174	+	Intron	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:6599174T>C	uc003wqo.2	+						AGPAT5_uc011kwm.1_Intron	NM_018361	NP_060831			1-acylglycerol-3-phosphate O-acyltransferase 5						phospholipid biosynthetic process	integral to membrane|mitochondrion	1-acylglycerol-3-phosphate O-acyltransferase activity				0			STAD - Stomach adenocarcinoma(24;0.0578)	READ - Rectum adenocarcinoma(644;0.156)|COAD - Colon adenocarcinoma(149;0.191)														---	---	---	---
PPP1R3B	79660	broad.mit.edu	37	8	8998664	8998664	+	Silent	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:8998664G>A	uc003wsn.3	-	2	663	c.498C>T	c.(496-498)TTC>TTT	p.F166F	PPP1R3B_uc003wso.3_Silent_p.F165F	NM_024607	NP_078883	Q86XI6	PPR3B_HUMAN	protein phosphatase 1, regulatory (inhibitor)	166	CBM21.				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	10480543	10480543	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:10480543C>T	uc003wtc.2	-	2	398	c.169G>A	c.(169-171)GCC>ACC	p.A57T		NM_178857	NP_849188	Q8IWN7	RP1L1_HUMAN	retinitis pigmentosa 1-like 1	57					intracellular signal transduction					ovary(4)|breast(3)|central_nervous_system(1)	8				COAD - Colon adenocarcinoma(149;0.0811)														---	---	---	---
SOX7	83595	broad.mit.edu	37	8	10689208	10689208	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:10689208C>T	uc011kwz.1	-	4	301	c.268G>A	c.(268-270)GAA>AAA	p.E90K	PINX1_uc003wth.2_Missense_Mutation_p.E90K|PINX1_uc003wti.2_Missense_Mutation_p.E90K	NM_031439	NP_113627	Q9BT81	SOX7_HUMAN	SRY-box 7	Error:Variant_position_missing_in_Q9BT81_after_alignment					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	11058385	11058385	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:11058385C>T	uc003wtk.1	-	1	491	c.464G>A	c.(463-465)CGC>CAC	p.R155H		NM_173683	NP_775954	Q5GH73	XKR6_HUMAN	XK, Kell blood group complex subunit-related	155						integral to membrane				ovary(1)|skin(1)	2				Lung(29;0.0407)|COAD - Colon adenocarcinoma(149;0.0555)														---	---	---	---
BLK	640	broad.mit.edu	37	8	11414286	11414286	+	Nonsense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:11414286C>T	uc003wty.2	+	9	1473	c.892C>T	c.(892-894)CGA>TGA	p.R298*	BLK_uc003wtz.2_Nonsense_Mutation_p.R227*	NM_001715	NP_001706	P51451	BLK_HUMAN	B lymphoid tyrosine kinase	298	Protein kinase.				intracellular protein kinase cascade|positive regulation of insulin secretion		ATP binding|non-membrane spanning protein tyrosine kinase activity			large_intestine(1)|stomach(1)|ovary(1)	3			STAD - Stomach adenocarcinoma(15;0.00391)	COAD - Colon adenocarcinoma(149;0.207)														---	---	---	---
BLK	640	broad.mit.edu	37	8	11414358	11414358	+	Intron	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:11414358C>T	uc003wty.2	+						BLK_uc003wtz.2_Intron	NM_001715	NP_001706			B lymphoid tyrosine kinase						intracellular protein kinase cascade|positive regulation of insulin secretion		ATP binding|non-membrane spanning protein tyrosine kinase activity			large_intestine(1)|stomach(1)|ovary(1)	3			STAD - Stomach adenocarcinoma(15;0.00391)	COAD - Colon adenocarcinoma(149;0.207)														---	---	---	---
DLC1	10395	broad.mit.edu	37	8	12943308	12943308	+	3'UTR	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:12943308T>C	uc003wwm.2	-	18					DLC1_uc003wwk.1_3'UTR|DLC1_uc003wwl.1_3'UTR|DLC1_uc011kxx.1_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																		---	---	---	---
DLC1	10395	broad.mit.edu	37	8	12957706	12957706	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:12957706C>T	uc003wwm.2	-	9	2584	c.2140G>A	c.(2140-2142)GTG>ATG	p.V714M	DLC1_uc003wwk.1_Missense_Mutation_p.V277M|DLC1_uc003wwl.1_Missense_Mutation_p.V311M|DLC1_uc011kxx.1_Missense_Mutation_p.V203M	NM_182643	NP_872584	Q96QB1	RHG07_HUMAN	deleted in liver cancer 1 isoform 1	714					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																		---	---	---	---
TUSC3	7991	broad.mit.edu	37	8	15397967	15397967	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:15397967C>T	uc003wwt.2	+	1	238	c.28C>T	c.(28-30)CGT>TGT	p.R10C	TUSC3_uc003wwr.2_Missense_Mutation_p.R10C|TUSC3_uc003wws.2_Missense_Mutation_p.R10C|TUSC3_uc003wwu.2_Missense_Mutation_p.R10C|TUSC3_uc003wwv.2_Missense_Mutation_p.R10C|TUSC3_uc003www.2_Missense_Mutation_p.R10C|TUSC3_uc003wwx.2_RNA|TUSC3_uc003wwy.2_Missense_Mutation_p.R10C	NM_006765	NP_006756	Q13454	TUSC3_HUMAN	tumor suppressor candidate 3 isoform a	10					cell redox homeostasis|post-translational protein modification|protein N-linked glycosylation via asparagine	integral to membrane|oligosaccharyltransferase complex				ovary(2)|central_nervous_system(1)	3				Colorectal(111;0.113)														---	---	---	---
MTMR7	9108	broad.mit.edu	37	8	17228561	17228561	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:17228561G>A	uc003wxm.2	-	3	534	c.295C>T	c.(295-297)CGC>TGC	p.R99C		NM_004686	NP_004677	Q9Y216	MTMR7_HUMAN	myotubularin related protein 7	99							protein tyrosine phosphatase activity			skin(1)	1				Colorectal(111;0.112)														---	---	---	---
SLC7A2	6542	broad.mit.edu	37	8	17419564	17419564	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:17419564C>T	uc011kyc.1	+	10	1785	c.1616C>T	c.(1615-1617)GCC>GTC	p.A539V	SLC7A2_uc011kyd.1_Missense_Mutation_p.A578V|SLC7A2_uc011kye.1_Missense_Mutation_p.A579V|SLC7A2_uc011kyf.1_Missense_Mutation_p.A539V	NM_001008539	NP_001008539	P52569	CTR2_HUMAN	solute carrier family 7, member 2 isoform 2	539	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)													---	---	---	---
MTUS1	57509	broad.mit.edu	37	8	17507405	17507405	+	Missense_Mutation	SNP	T	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:17507405T>A	uc003wxv.2	-	13	3925	c.3451A>T	c.(3451-3453)AAT>TAT	p.N1151Y	MTUS1_uc003wxt.2_Missense_Mutation_p.N398Y|MTUS1_uc011kyg.1_Missense_Mutation_p.N296Y|MTUS1_uc010lsy.2_RNA|MTUS1_uc003wxw.2_Missense_Mutation_p.N1097Y|MTUS1_uc003wxs.2_Missense_Mutation_p.N317Y	NM_001001924	NP_001001924	Q9ULD2	MTUS1_HUMAN	mitochondrial tumor suppressor 1 isoform 1	1151	Potential.					Golgi apparatus|microtubule|microtubule organizing center|mitochondrion|nucleus|plasma membrane|spindle				ovary(1)|skin(1)	2				Colorectal(111;0.0778)														---	---	---	---
ATP6V1B2	526	broad.mit.edu	37	8	20068766	20068766	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:20068766A>G	uc003wzp.2	+	6	756	c.542A>G	c.(541-543)AAC>AGC	p.N181S		NM_001693	NP_001684	P21281	VATB2_HUMAN	vacuolar H+ATPase B2	181					ATP hydrolysis coupled proton transport|cellular iron ion homeostasis|insulin receptor signaling pathway|transferrin transport	cytosol|endomembrane system|Golgi apparatus|melanosome|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				0				Colorectal(74;0.0535)|COAD - Colon adenocarcinoma(73;0.211)														---	---	---	---
LZTS1	11178	broad.mit.edu	37	8	20107641	20107641	+	Silent	SNP	C	T	T	rs35939758		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:20107641C>T	uc003wzr.2	-	3	1494	c.1383G>A	c.(1381-1383)GCG>GCA	p.A461A	LZTS1_uc010ltg.1_Silent_p.A461A	NM_021020	NP_066300	Q9Y250	LZTS1_HUMAN	leucine zipper, putative tumor suppressor 1	461					cell cycle|termination of RNA polymerase III transcription|transcription elongation from RNA polymerase III promoter	cell junction|dendritic spine|Golgi apparatus|nucleolus|nucleoplasm|postsynaptic density|postsynaptic membrane	DNA binding|protein binding|sequence-specific DNA binding transcription factor activity			ovary(1)	1				Colorectal(74;0.0511)|COAD - Colon adenocarcinoma(73;0.207)														---	---	---	---
EPB49	2039	broad.mit.edu	37	8	21925081	21925081	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:21925081C>T	uc011kyt.1	+	4	366	c.137C>T	c.(136-138)GCC>GTC	p.A46V	EPB49_uc010ltl.2_Missense_Mutation_p.A46V|EPB49_uc011kys.1_Missense_Mutation_p.A21V|EPB49_uc010ltn.2_Missense_Mutation_p.A21V|EPB49_uc011kyu.1_Missense_Mutation_p.A46V|EPB49_uc011kyv.1_Missense_Mutation_p.A46V|EPB49_uc010ltq.2_Missense_Mutation_p.A46V	NM_001114136	NP_001107608	Q08495	DEMA_HUMAN	erythrocyte membrane protein band 4.9 isoform 1	46					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)														---	---	---	---
NUDT18	79873	broad.mit.edu	37	8	21964803	21964803	+	3'UTR	SNP	C	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:21964803C>A	uc003xaq.1	-	6					NUDT18_uc003xar.1_3'UTR	NM_024815	NP_079091			nudix (nucleoside diphosphate linked moiety								hydrolase activity|metal ion binding|protein binding				0				Colorectal(74;0.00185)|COAD - Colon adenocarcinoma(73;0.0608)|READ - Rectum adenocarcinoma(5;0.0986)														---	---	---	---
BMP1	649	broad.mit.edu	37	8	22054843	22054843	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:22054843G>A	uc003xbg.2	+	15	2261	c.2017G>A	c.(2017-2019)GTC>ATC	p.V673I	BMP1_uc003xba.2_Missense_Mutation_p.V673I|BMP1_uc003xbb.2_Missense_Mutation_p.V673I|BMP1_uc003xbe.2_RNA|BMP1_uc003xbc.2_Missense_Mutation_p.V422I|BMP1_uc003xbd.2_RNA|BMP1_uc003xbf.2_Missense_Mutation_p.V422I|BMP1_uc011kzc.1_Missense_Mutation_p.V422I|BMP1_uc003xbh.2_RNA|BMP1_uc003xbi.2_RNA	NM_006129	NP_006120	P13497	BMP1_HUMAN	bone morphogenetic protein 1 isoform 3	673	CUB 3.				cartilage condensation|cell differentiation|lipid metabolic process|lipoprotein metabolic process|ossification|positive regulation of cartilage development|proteolysis	extracellular space	calcium ion binding|cytokine activity|growth factor activity|metalloendopeptidase activity|zinc ion binding			ovary(2)|breast(1)	3				Colorectal(74;0.00229)|COAD - Colon adenocarcinoma(73;0.0661)|READ - Rectum adenocarcinoma(644;0.11)														---	---	---	---
PIWIL2	55124	broad.mit.edu	37	8	22163439	22163439	+	Splice_Site	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:22163439G>A	uc003xbn.2	+	13	1604	c.1456_splice	c.e13-1	p.L486_splice	PIWIL2_uc011kzf.1_Splice_Site_p.L486_splice|PIWIL2_uc010ltv.2_Splice_Site_p.L486_splice	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)														---	---	---	---
PIWIL2	55124	broad.mit.edu	37	8	22165551	22165551	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:22165551C>T	uc003xbn.2	+	14	1799	c.1651C>T	c.(1651-1653)CGT>TGT	p.R551C	PIWIL2_uc011kzf.1_Missense_Mutation_p.R551C|PIWIL2_uc010ltv.2_Missense_Mutation_p.R551C	NM_018068	NP_060538	Q8TC59	PIWL2_HUMAN	piwi-like 2	551					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)														---	---	---	---
PIWIL2	55124	broad.mit.edu	37	8	22165552	22165552	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:22165552G>A	uc003xbn.2	+	14	1800	c.1652G>A	c.(1651-1653)CGT>CAT	p.R551H	PIWIL2_uc011kzf.1_Missense_Mutation_p.R551H|PIWIL2_uc010ltv.2_Missense_Mutation_p.R551H	NM_018068	NP_060538	Q8TC59	PIWL2_HUMAN	piwi-like 2	551					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)														---	---	---	---
TNFRSF10C	8794	broad.mit.edu	37	8	22973103	22973103	+	Silent	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:22973103C>T	uc003xcy.2	+	4	564	c.363C>T	c.(361-363)TCC>TCT	p.S121S	TNFRSF10C_uc011kzr.1_RNA	NM_003841	NP_003832	O14798	TR10C_HUMAN	tumor necrosis factor receptor superfamily,	121	TNFR-Cys 3.				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)														---	---	---	---
TNFRSF10D	8793	broad.mit.edu	37	8	23003316	23003316	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:23003316T>C	uc003xcz.1	-	5	693	c.601A>G	c.(601-603)ACC>GCC	p.T201A		NM_003840	NP_003831	Q9UBN6	TR10D_HUMAN	tumor necrosis factor receptor superfamily,	201	Extracellular (Potential).				anti-apoptosis|apoptosis	integral to 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)														---	---	---	---
ADAM28	10863	broad.mit.edu	37	8	24188764	24188764	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:24188764C>T	uc003xdy.2	+	12	1288	c.1205C>T	c.(1204-1206)ACA>ATA	p.T402I	ADAM28_uc003xdx.2_Missense_Mutation_p.T402I|ADAM28_uc011kzz.1_Missense_Mutation_p.T169I|ADAM28_uc011laa.1_RNA|ADAM28_uc010lua.2_Missense_Mutation_p.T89I	NM_014265	NP_055080	Q9UKQ2	ADA28_HUMAN	ADAM metallopeptidase domain 28 isoform 1	402	Extracellular (Potential).				proteolysis|spermatogenesis	extracellular region|integral to membrane|plasma membrane	metalloendopeptidase activity|zinc ion binding			skin(3)|lung(1)|central_nervous_system(1)	5		Prostate(55;0.0959)		Colorectal(74;0.0129)|COAD - Colon adenocarcinoma(73;0.0434)|BRCA - Breast invasive adenocarcinoma(99;0.175)														---	---	---	---
CDCA2	157313	broad.mit.edu	37	8	25365050	25365050	+	Missense_Mutation	SNP	T	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:25365050T>A	uc003xep.1	+	15	3347	c.2868T>A	c.(2866-2868)GAT>GAA	p.D956E	PPP2R2A_uc003xek.2_Intron|CDCA2_uc011lae.1_3'UTR|CDCA2_uc003xeq.1_Missense_Mutation_p.D941E|CDCA2_uc003xer.1_Missense_Mutation_p.D619E	NM_152562	NP_689775	Q69YH5	CDCA2_HUMAN	cell division cycle associated 2	956					cell division|mitosis	cytoplasm|nucleus					0		all_cancers(63;0.0378)|Ovarian(32;0.000878)|all_epithelial(46;0.0162)|Breast(100;0.0164)|Prostate(55;0.191)		UCEC - Uterine corpus endometrioid carcinoma (27;0.022)|Epithelial(17;1.37e-11)|Colorectal(74;0.0129)|COAD - Colon adenocarcinoma(73;0.0443)														---	---	---	---
SCARA3	51435	broad.mit.edu	37	8	27509080	27509080	+	Silent	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:27509080G>A	uc003xga.1	+	3	303	c.162G>A	c.(160-162)TCG>TCA	p.S54S	SCARA3_uc003xgb.1_Silent_p.S54S	NM_016240	NP_057324	Q6AZY7	SCAR3_HUMAN	scavenger receptor class A, member 3 isoform 1	54	Cytoplasmic (Potential).				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)														---	---	---	---
ESCO2	157570	broad.mit.edu	37	8	27646366	27646366	+	Silent	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:27646366C>T	uc003xgg.2	+	7	1217	c.1134C>T	c.(1132-1134)GAC>GAT	p.D378D	ESCO2_uc010luy.1_RNA	NM_001017420	NP_001017420	Q56NI9	ESCO2_HUMAN	establishment of cohesion 1 homolog 2	378					cell cycle|post-translational protein acetylation|regulation of DNA replication	chromatin|nucleus	acyltransferase activity|metal ion binding			central_nervous_system(1)	1		Ovarian(32;0.000953)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0204)|KIRC - Kidney renal clear cell carcinoma(542;0.0955)|Kidney(114;0.115)|Colorectal(74;0.132)										SC_Phocomelia_syndrome				---	---	---	---
EXTL3	2137	broad.mit.edu	37	8	28575711	28575711	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:28575711G>A	uc003xgz.1	+	3	2728	c.2135G>A	c.(2134-2136)GGC>GAC	p.G712D		NM_001440	NP_001431	O43909	EXTL3_HUMAN	exostoses-like 3	712	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	29003951	29003951	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:29003951T>C	uc003xhh.3	-	18	2190	c.2131A>G	c.(2131-2133)ACA>GCA	p.T711A	KIF13B_uc003xhj.2_Missense_Mutation_p.T608A	NM_015254	NP_056069	Q9NQT8	KI13B_HUMAN	kinesin family member 13B	711					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)														---	---	---	---
KIF13B	23303	broad.mit.edu	37	8	29035024	29035024	+	Silent	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:29035024G>A	uc003xhh.3	-	9	851	c.792C>T	c.(790-792)GGC>GGT	p.G264G	KIF13B_uc003xhj.2_Silent_p.G161G|KIF13B_uc010lvf.1_Silent_p.G200G	NM_015254	NP_056069	Q9NQT8	KI13B_HUMAN	kinesin family member 13B	264	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)												OREG0018684	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
GTF2E2	2961	broad.mit.edu	37	8	30437887	30437887	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:30437887T>C	uc003xig.2	-	7	923	c.670A>G	c.(670-672)ACT>GCT	p.T224A		NM_002095	NP_002086	P29084	T2EB_HUMAN	general transcription factor IIE, polypeptide 2,	224					regulation of transcription, DNA-dependent|transcription elongation from RNA polymerase II promoter|transcription initiation from RNA polymerase II promoter|viral reproduction	transcription factor TFIIE complex	DNA binding|protein binding				0				KIRC - Kidney renal clear cell carcinoma(542;0.113)|Kidney(114;0.135)														---	---	---	---
PPP2CB	5516	broad.mit.edu	37	8	30655261	30655261	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:30655261G>T	uc003xik.2	-	4	557	c.322C>A	c.(322-324)CCA>ACA	p.P108T		NM_004156	NP_004147	P62714	PP2AB_HUMAN	protein phosphatase 2, catalytic subunit, beta	108					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)													---	---	---	---
TEX15	56154	broad.mit.edu	37	8	30705843	30705843	+	Missense_Mutation	SNP	A	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:30705843A>T	uc003xil.2	-	1	691	c.691T>A	c.(691-693)TAC>AAC	p.Y231N		NM_031271	NP_112561	Q9BXT5	TEX15_HUMAN	testis expressed 15	231										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	30954301	30954301	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:30954301T>C	uc003xio.3	+	17	2704	c.1916T>C	c.(1915-1917)GTA>GCA	p.V639A	WRN_uc010lvk.2_Missense_Mutation_p.V106A	NM_000553	NP_000544	Q14191	WRN_HUMAN	Werner syndrome protein	639	Helicase ATP-binding.				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	30958428	30958428	+	Missense_Mutation	SNP	A	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:30958428A>T	uc003xio.3	+	18	2833	c.2045A>T	c.(2044-2046)GAT>GTT	p.D682V	WRN_uc010lvk.2_Missense_Mutation_p.D149V	NM_000553	NP_000544	Q14191	WRN_HUMAN	Werner syndrome protein	682	Helicase ATP-binding.				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	30969229	30969229	+	Silent	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:30969229T>C	uc003xio.3	+	19	2975	c.2187T>C	c.(2185-2187)GGT>GGC	p.G729G	WRN_uc010lvk.2_Silent_p.G196G	NM_000553	NP_000544	Q14191	WRN_HUMAN	Werner syndrome protein	729					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	30999056	30999056	+	Silent	SNP	A	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:30999056A>T	uc003xio.3	+	25	3866	c.3078A>T	c.(3076-3078)GGA>GGT	p.G1026G	WRN_uc010lvk.2_Silent_p.G493G	NM_000553	NP_000544	Q14191	WRN_HUMAN	Werner syndrome protein	1026					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	32463136	32463136	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:32463136G>A	uc003xiv.2	+	3	852	c.335G>A	c.(334-336)TGC>TAC	p.C112Y	NRG1_uc003xip.2_Missense_Mutation_p.C327Y|NRG1_uc003xir.2_Missense_Mutation_p.C112Y|NRG1_uc010lvl.2_Missense_Mutation_p.C112Y|NRG1_uc010lvm.2_Missense_Mutation_p.C112Y|NRG1_uc010lvn.2_Missense_Mutation_p.C112Y|NRG1_uc003xis.2_Missense_Mutation_p.C112Y|NRG1_uc011lbf.1_Missense_Mutation_p.C112Y|NRG1_uc010lvo.2_Missense_Mutation_p.C112Y|NRG1_uc003xiu.2_Missense_Mutation_p.C112Y|NRG1_uc003xiw.2_Missense_Mutation_p.C112Y|NRG1_uc003xit.2_Missense_Mutation_p.C112Y|NRG1_uc010lvr.2_5'UTR|NRG1_uc010lvs.2_5'UTR|NRG1_uc010lvp.2_Missense_Mutation_p.C78Y|NRG1_uc010lvq.2_Missense_Mutation_p.C78Y|NRG1_uc003xix.2_Missense_Mutation_p.C2Y	NM_013964	NP_039258	Q02297	NRG1_HUMAN	neuregulin 1 isoform HRG-alpha	112	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)														---	---	---	---
NRG1	3084	broad.mit.edu	37	8	32621854	32621854	+	Silent	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:32621854G>A	uc003xiv.2	+	12	2374	c.1857G>A	c.(1855-1857)TCG>TCA	p.S619S	NRG1_uc010lvo.2_3'UTR|NRG1_uc003xiu.2_Silent_p.S624S|NRG1_uc003xiw.2_Silent_p.S616S|NRG1_uc003xit.2_3'UTR|NRG1_uc010lvr.2_Silent_p.S361S|NRG1_uc010lvs.2_Silent_p.S361S|NRG1_uc010lvp.2_Silent_p.S573S|NRG1_uc010lvq.2_Silent_p.S556S|NRG1_uc011lbg.1_3'UTR|NRG1_uc011lbh.1_Silent_p.S462S|NRG1_uc003xja.2_Silent_p.S430S	NM_013964	NP_039258	Q02297	NRG1_HUMAN	neuregulin 1 isoform HRG-alpha	619	Cytoplasmic (Potential).				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)														---	---	---	---
FUT10	84750	broad.mit.edu	37	8	33310884	33310884	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:33310884A>G	uc003xje.2	-	3	582	c.226T>C	c.(226-228)TGG>CGG	p.W76R	FUT10_uc003xjc.2_Missense_Mutation_p.W83R|FUT10_uc003xjd.2_Missense_Mutation_p.W48R|FUT10_uc011lbi.1_Missense_Mutation_p.W126R|FUT10_uc003xjf.2_Missense_Mutation_p.M1T|FUT10_uc003xjg.2_Missense_Mutation_p.W48R|FUT10_uc003xjh.2_Missense_Mutation_p.W76R|FUT10_uc003xji.1_Missense_Mutation_p.W76R	NM_032664	NP_116053	Q6P4F1	FUT10_HUMAN	fucosyltransferase 10	76	Lumenal (Potential).				embryo development|fertilization|hemopoiesis|L-fucose catabolic process|nervous system development|protein folding|protein glycosylation|protein targeting|wound healing	Golgi cisterna membrane|integral to membrane	alpha(1,3)-fucosyltransferase activity			ovary(1)|pancreas(1)	2				KIRC - Kidney renal clear cell carcinoma(67;0.129)|Kidney(114;0.154)														---	---	---	---
C8orf41	80185	broad.mit.edu	37	8	33370057	33370057	+	Silent	SNP	G	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:33370057G>T	uc003xjl.3	-	1	600	c.75C>A	c.(73-75)GCC>GCA	p.A25A	C8orf41_uc003xjk.3_Silent_p.A25A|C8orf41_uc010lvv.2_Silent_p.A25A|C8orf41_uc003xjm.3_Silent_p.A25A|C8orf41_uc003xjn.1_Silent_p.A25A	NM_025115	NP_079391	Q6NXR4	CH041_HUMAN	hypothetical protein LOC80185	25							binding				0				KIRC - Kidney renal clear cell carcinoma(67;0.0923)|Kidney(114;0.111)														---	---	---	---
UNC5D	137970	broad.mit.edu	37	8	35541203	35541203	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:35541203G>A	uc003xjr.1	+	5	1037	c.709G>A	c.(709-711)GTG>ATG	p.V237M	UNC5D_uc003xjs.1_Missense_Mutation_p.V232M|UNC5D_uc003xjt.1_Missense_Mutation_p.V6M	NM_080872	NP_543148	Q6UXZ4	UNC5D_HUMAN	unc-5 homolog D precursor	237	Extracellular (Potential).|Ig-like C2-type.				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)														---	---	---	---
UNC5D	137970	broad.mit.edu	37	8	35606092	35606092	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:35606092G>A	uc003xjr.1	+	12	2142	c.1814G>A	c.(1813-1815)TGT>TAT	p.C605Y	UNC5D_uc003xjs.1_Missense_Mutation_p.C600Y|UNC5D_uc003xju.1_Missense_Mutation_p.C181Y	NM_080872	NP_543148	Q6UXZ4	UNC5D_HUMAN	unc-5 homolog D precursor	605	ZU5.|Cytoplasmic (Potential).				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	36673184	36673184	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:36673184A>G	uc010lvw.2	+	9	1061	c.974A>G	c.(973-975)TAT>TGT	p.Y325C	KCNU1_uc003xjw.2_RNA	NM_001031836	NP_001027006	A8MYU2	KCNU1_HUMAN	potassium channel, subfamily U, member 1	325	Cytoplasmic (Potential).					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)														---	---	---	---
BRF2	55290	broad.mit.edu	37	8	37702444	37702444	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:37702444C>T	uc003xkk.2	-	4	934	c.824G>A	c.(823-825)CGG>CAG	p.R275Q		NM_018310	NP_060780	Q9HAW0	BRF2_HUMAN	RNA polymerase III transcription initiation	275					regulation of transcription, DNA-dependent|transcription from RNA polymerase III promoter|transcription initiation, DNA-dependent	nucleoplasm	protein binding|zinc ion binding				0		Lung NSC(58;0.118)|all_lung(54;0.195)	BRCA - Breast invasive adenocarcinoma(5;2.75e-24)|LUSC - Lung squamous cell carcinoma(8;1.81e-10)															---	---	---	---
RAB11FIP1	80223	broad.mit.edu	37	8	37732355	37732355	+	Missense_Mutation	SNP	A	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:37732355A>T	uc003xkm.1	-	3	1344	c.1300T>A	c.(1300-1302)TCC>ACC	p.S434T	RAB11FIP1_uc010lvz.1_Missense_Mutation_p.S282T|RAB11FIP1_uc003xkn.1_Missense_Mutation_p.S434T|RAB11FIP1_uc003xkl.1_5'Flank|RAB11FIP1_uc003xko.1_5'Flank|RAB11FIP1_uc003xkp.1_Missense_Mutation_p.S282T	NM_001002814	NP_001002814	Q6WKZ4	RFIP1_HUMAN	RAB11 family interacting protein 1 isoform 3	434					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	37756792	37756792	+	Silent	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:37756792C>T	uc003xkm.1	-	1	212	c.168G>A	c.(166-168)GTG>GTA	p.V56V	RAB11FIP1_uc010lvz.1_Intron|RAB11FIP1_uc003xkn.1_Silent_p.V56V	NM_001002814	NP_001002814	Q6WKZ4	RFIP1_HUMAN	RAB11 family interacting protein 1 isoform 3	56	C2.				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)															---	---	---	---
ADRB3	155	broad.mit.edu	37	8	37823768	37823768	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:37823768C>T	uc003xkr.1	-	1	417	c.220G>A	c.(220-222)GTG>ATG	p.V74M		NM_000025	NP_000016	P13945	ADRB3_HUMAN	adrenergic, beta-3-, receptor	74	Helical; Name=2; (By similarity).				carbohydrate metabolic process|energy reserve metabolic process|positive regulation of MAPKKK cascade	integral to plasma membrane|receptor complex	beta3-adrenergic receptor activity|protein homodimerization activity			lung(2)	2	Colorectal(12;0.00627)	Lung NSC(58;0.118)|all_lung(54;0.195)	LUSC - Lung squamous cell carcinoma(8;1.37e-11)		Norepinephrine(DB00368)|Pindolol(DB00960)|Propranolol(DB00571)													---	---	---	---
BAG4	9530	broad.mit.edu	37	8	38050285	38050285	+	Missense_Mutation	SNP	A	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:38050285A>T	uc003xky.1	+	2	632	c.350A>T	c.(349-351)TAT>TTT	p.Y117F	BAG4_uc003xkz.1_Intron	NM_004874	NP_004865	O95429	BAG4_HUMAN	BCL2-associated athanogene 4	117					anti-apoptosis|apoptosis|protein folding	cytoplasm|nucleus	receptor signaling protein activity			ovary(1)	1	Colorectal(12;0.000442)	all_lung(54;0.00787)|Lung NSC(58;0.0295)|Hepatocellular(245;0.121)																---	---	---	---
DDHD2	23259	broad.mit.edu	37	8	38090665	38090665	+	Missense_Mutation	SNP	T	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:38090665T>A	uc003xlb.2	+	2	530	c.153T>A	c.(151-153)GAT>GAA	p.D51E	DDHD2_uc003xla.2_Missense_Mutation_p.D51E|DDHD2_uc003xlc.2_Missense_Mutation_p.D51E|DDHD2_uc011lbl.1_5'UTR	NM_015214	NP_056029	O94830	DDHD2_HUMAN	DDHD domain containing 2 isoform 1	51	WWE.				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)															---	---	---	---
FGFR1	2260	broad.mit.edu	37	8	38271334	38271334	+	Intron	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:38271334G>A	uc003xlp.2	-						FGFR1_uc010lwf.2_Intron|FGFR1_uc011lbo.1_Intron|FGFR1_uc011lbp.1_Intron|FGFR1_uc011lbq.1_Intron|FGFR1_uc010lwk.2_Intron	NM_023110	NP_075598			fibroblast growth factor receptor 1 isoform 1						axon guidance|cell growth|insulin receptor signaling pathway|MAPKKK cascade|positive regulation of cell proliferation|skeletal system development	extracellular region|integral to plasma membrane|membrane fraction	ATP binding|fibroblast growth factor receptor activity|heparin binding|protein homodimerization activity			lung(5)|central_nervous_system(5)|stomach(2)|breast(2)|ovary(1)	15	all_cancers(2;9.05e-47)|all_epithelial(2;2.64e-50)|all_lung(3;1.71e-23)|Lung NSC(2;3.61e-23)|Colorectal(12;0.000442)	Breast(189;1.48e-05)|all_lung(54;0.00354)|Lung NSC(58;0.0138)|Hepatocellular(245;0.065)	Epithelial(3;3.96e-34)|all cancers(3;3.06e-30)|BRCA - Breast invasive adenocarcinoma(5;2.28e-21)|COAD - Colon adenocarcinoma(9;0.24)		Palifermin(DB00039)		1	T	BCR|FOP|ZNF198|CEP1	MPD|NHL		Pfeiffer syndrome|Kallman syndrome						---	---	---	---
HTRA4	203100	broad.mit.edu	37	8	38831866	38831866	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:38831866G>T	uc003xmj.2	+	1	199	c.84G>T	c.(82-84)TGG>TGT	p.W28C		NM_153692	NP_710159	P83105	HTRA4_HUMAN	HtrA serine peptidase 4 precursor	28					proteolysis|regulation of cell growth	extracellular region	insulin-like growth factor binding|serine-type endopeptidase activity				0		all_lung(54;0.0344)|Hepatocellular(245;0.0512)|Lung NSC(58;0.0955)	LUSC - Lung squamous cell carcinoma(45;1.5e-07)															---	---	---	---
HTRA4	203100	broad.mit.edu	37	8	38839190	38839190	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:38839190G>A	uc003xmj.2	+	6	1133	c.1018G>A	c.(1018-1020)GTC>ATC	p.V340I		NM_153692	NP_710159	P83105	HTRA4_HUMAN	HtrA serine peptidase 4 precursor	340	Serine protease.				proteolysis|regulation of cell growth	extracellular region	insulin-like growth factor binding|serine-type endopeptidase activity				0		all_lung(54;0.0344)|Hepatocellular(245;0.0512)|Lung NSC(58;0.0955)	LUSC - Lung squamous cell carcinoma(45;1.5e-07)															---	---	---	---
NKX6-3	157848	broad.mit.edu	37	8	41504745	41504745	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:41504745C>A	uc003xoa.2	-	1	134	c.130G>T	c.(130-132)GCA>TCA	p.A44S	NKX6-3_uc010lxa.1_Missense_Mutation_p.A44S	NM_152568	NP_689781	A6NJ46	NKX63_HUMAN	NK6 homeobox 3	Error:Variant_position_missing_in_A6NJ46_after_alignment						nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity				0	Ovarian(28;0.00541)|Colorectal(14;0.0202)|Lung SC(25;0.211)	all_lung(54;0.0131)|Lung NSC(58;0.0363)|Esophageal squamous(32;0.0844)|Hepatocellular(245;0.154)	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	41519367	41519367	+	Missense_Mutation	SNP	A	T	T	rs1060133		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:41519367A>T	uc003xok.2	-	41	5655	c.5571T>A	c.(5569-5571)GAT>GAA	p.D1857E	NKX6-3_uc010lxa.1_Intron|ANK1_uc003xoh.2_Intron|ANK1_uc003xoi.2_Intron|ANK1_uc003xoj.2_Intron|ANK1_uc003xol.2_Missense_Mutation_p.D1695E|ANK1_uc003xom.2_Intron|ANK1_uc011lcl.1_Intron|ANK1_uc003xod.2_Intron|ANK1_uc003xoc.2_Missense_Mutation_p.D132E|ANK1_uc003xof.2_Intron|MIR486_hsa-mir-486|MI0002470_5'Flank	NM_020476	NP_065209	P16157	ANK1_HUMAN	ankyrin 1 isoform 1	1857	55 kDa regulatory domain.				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	41525881	41525881	+	Silent	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:41525881G>A	uc003xok.2	-	39	5382	c.5298C>T	c.(5296-5298)CCC>CCT	p.P1766P	NKX6-3_uc010lxa.1_Intron|ANK1_uc003xoh.2_Silent_p.P920P|ANK1_uc003xoi.2_Silent_p.P1766P|ANK1_uc003xoj.2_Silent_p.P1766P|ANK1_uc003xol.2_Silent_p.P1604P|ANK1_uc003xom.2_Silent_p.P1807P	NM_020476	NP_065209	P16157	ANK1_HUMAN	ankyrin 1 isoform 1	1766	55 kDa regulatory domain.				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	41561903	41561903	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:41561903C>T	uc003xok.2	-	19	2269	c.2185G>A	c.(2185-2187)GCC>ACC	p.A729T	NKX6-3_uc010lxa.1_Intron|ANK1_uc003xoh.2_Missense_Mutation_p.A37T|ANK1_uc003xoi.2_Missense_Mutation_p.A729T|ANK1_uc003xoj.2_Missense_Mutation_p.A729T|ANK1_uc003xol.2_Missense_Mutation_p.A729T|ANK1_uc003xom.2_Missense_Mutation_p.A762T	NM_020476	NP_065209	P16157	ANK1_HUMAN	ankyrin 1 isoform 1	729	ANK 21.|89 kDa domain.				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)															---	---	---	---
MYST3	7994	broad.mit.edu	37	8	41790109	41790109	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:41790109G>A	uc010lxb.2	-	18	6173	c.5629C>T	c.(5629-5631)CGT>TGT	p.R1877C	MYST3_uc010lxc.2_Missense_Mutation_p.R1877C|MYST3_uc003xon.3_Missense_Mutation_p.R1877C	NM_001099412	NP_001092882	Q92794	MYST3_HUMAN	MYST histone acetyltransferase (monocytic	1877					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	41791385	41791385	+	Silent	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:41791385C>T	uc010lxb.2	-	18	4897	c.4353G>A	c.(4351-4353)GCG>GCA	p.A1451A	MYST3_uc010lxc.2_Silent_p.A1451A|MYST3_uc003xon.3_Silent_p.A1451A	NM_001099412	NP_001092882	Q92794	MYST3_HUMAN	MYST histone acetyltransferase (monocytic	1451					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	41792203	41792203	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:41792203T>C	uc010lxb.2	-	18	4079	c.3535A>G	c.(3535-3537)ATC>GTC	p.I1179V	MYST3_uc010lxc.2_Missense_Mutation_p.I1179V|MYST3_uc003xon.3_Missense_Mutation_p.I1179V	NM_001099412	NP_001092882	Q92794	MYST3_HUMAN	MYST histone acetyltransferase (monocytic	1179					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	41906232	41906232	+	Silent	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:41906232A>G	uc010lxb.2	-	3	808	c.264T>C	c.(262-264)CAT>CAC	p.H88H	MYST3_uc010lxc.2_Silent_p.H88H|MYST3_uc003xon.3_Silent_p.H88H|MYST3_uc010lxd.2_Silent_p.H88H	NM_001099412	NP_001092882	Q92794	MYST3_HUMAN	MYST histone acetyltransferase (monocytic	88	Required for activation of RUNX1-1.|Required for nuclear localization.				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	42012310	42012310	+	Silent	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:42012310G>A	uc003xop.2	+	3	396	c.105G>A	c.(103-105)GCG>GCA	p.A35A	AP3M2_uc003xoo.2_Silent_p.A35A|AP3M2_uc010lxe.2_RNA|AP3M2_uc003xoq.1_5'UTR|AP3M2_uc003xor.1_Silent_p.A35A	NM_001134296	NP_001127768	P53677	AP3M2_HUMAN	adaptor-related protein complex 3, mu 2 subunit	35					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)															---	---	---	---
SLC20A2	6575	broad.mit.edu	37	8	42294708	42294708	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:42294708G>A	uc010lxl.2	-	8	2016	c.1322C>T	c.(1321-1323)GCA>GTA	p.A441V	SLC20A2_uc010lxm.2_Missense_Mutation_p.A441V|SLC20A2_uc003xpe.2_Missense_Mutation_p.A441V|SLC20A2_uc011lcu.1_Missense_Mutation_p.A243V	NM_006749	NP_006740	Q08357	S20A2_HUMAN	solute carrier family 20, member 2	441	Cytoplasmic (Potential).				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	42329722	42329722	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:42329722C>A	uc010lxl.2	-	2	881	c.187G>T	c.(187-189)GGC>TGC	p.G63C	SLC20A2_uc010lxm.2_Missense_Mutation_p.G63C|SLC20A2_uc003xpe.2_Missense_Mutation_p.G63C	NM_006749	NP_006740	Q08357	S20A2_HUMAN	solute carrier family 20, member 2	63	Helical; (Potential).				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)															---	---	---	---
CHRNA6	8973	broad.mit.edu	37	8	42614211	42614211	+	Splice_Site	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:42614211C>T	uc003xpj.2	-	3	310	c.264_splice	c.e3+1	p.H88_splice	CHRNA6_uc011lcw.1_Intron	NM_004198	NP_004189			cholinergic receptor, nicotinic, alpha 6							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	42716913	42716913	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:42716913C>T	uc003xpo.2	-	6	959	c.482G>A	c.(481-483)CGG>CAG	p.R161Q	RNF170_uc011lcx.1_Intron|RNF170_uc010lxp.2_Missense_Mutation_p.R77Q|RNF170_uc003xpm.2_Missense_Mutation_p.R161Q|RNF170_uc003xpp.2_Missense_Mutation_p.R65Q|RNF170_uc003xpn.2_Missense_Mutation_p.R65Q|RNF170_uc003xpq.3_Missense_Mutation_p.R161Q	NM_001160223	NP_001153695	Q96K19	RN170_HUMAN	ring finger protein 170 isoform a	161						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)															---	---	---	---
HGSNAT	138050	broad.mit.edu	37	8	43053101	43053101	+	Intron	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:43053101T>C	uc003xpx.3	+							NM_152419	NP_689632			heparan-alpha-glucosaminide N-acetyltransferase						lysosomal transport|protein oligomerization	integral to membrane|lysosomal membrane	heparan-alpha-glucosaminide N-acetyltransferase activity				0	Prostate(17;0.0119)|Ovarian(28;0.0172)|Lung SC(25;0.184)	all_cancers(86;0.000223)|all_epithelial(80;1.61e-07)|all_lung(54;0.00021)|Lung NSC(58;0.000778)|Hepatocellular(245;0.0524)|Renal(179;0.0822)|Esophageal squamous(32;0.129)	Lung(22;0.0777)|LUSC - Lung squamous cell carcinoma(45;0.17)															---	---	---	---
PRKDC	5591	broad.mit.edu	37	8	48746845	48746845	+	Silent	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:48746845T>C	uc003xqi.2	-	60	8121	c.8064A>G	c.(8062-8064)TTA>TTG	p.L2688L	PRKDC_uc003xqj.2_Silent_p.L2688L|PRKDC_uc011ldh.1_Intron	NM_006904	NP_008835	P78527	PRKDC_HUMAN	protein kinase, DNA-activated, catalytic	2688	KIP-binding.				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	48749012	48749012	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:48749012T>C	uc003xqi.2	-	59	7895	c.7838A>G	c.(7837-7839)CAG>CGG	p.Q2613R	PRKDC_uc003xqj.2_Missense_Mutation_p.Q2613R|PRKDC_uc011ldh.1_Intron	NM_006904	NP_008835	P78527	PRKDC_HUMAN	protein kinase, DNA-activated, catalytic	2613	KIP-binding.				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	48762072	48762072	+	Intron	SNP	A	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:48762072A>C	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					---	---	---	---
UBE2V2	7336	broad.mit.edu	37	8	48955726	48955726	+	Silent	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:48955726T>C	uc003xqm.2	+	2	171	c.150T>C	c.(148-150)ATT>ATC	p.I50I		NM_003350	NP_003341	Q15819	UB2V2_HUMAN	ubiquitin-conjugating enzyme E2v2	50					cell proliferation|DNA double-strand break processing|protein polyubiquitination|regulation of DNA repair	cytoplasm|nucleus|UBC13-MMS2 complex	acid-amino acid ligase activity|protein binding				0		all_cancers(86;0.026)|all_epithelial(80;0.000748)|Lung NSC(129;0.00171)|all_lung(136;0.00196)											Direct_reversal_of_damage|Rad6_pathway					---	---	---	---
SNTG1	54212	broad.mit.edu	37	8	51449296	51449296	+	Nonsense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:51449296G>A	uc010lxy.1	+	12	979	c.608G>A	c.(607-609)TGG>TAG	p.W203*	SNTG1_uc003xqs.1_Nonsense_Mutation_p.W203*|SNTG1_uc010lxz.1_Nonsense_Mutation_p.W203*|SNTG1_uc011ldl.1_RNA	NM_018967	NP_061840	Q9NSN8	SNTG1_HUMAN	syntrophin, gamma 1	203					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)																---	---	---	---
SNTG1	54212	broad.mit.edu	37	8	51569483	51569483	+	Silent	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:51569483C>T	uc010lxy.1	+	15	1235	c.864C>T	c.(862-864)GGC>GGT	p.G288G	SNTG1_uc003xqs.1_Silent_p.G288G|SNTG1_uc010lxz.1_Silent_p.G288G|SNTG1_uc011ldl.1_RNA	NM_018967	NP_061840	Q9NSN8	SNTG1_HUMAN	syntrophin, gamma 1	288	PH.				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)																---	---	---	---
ST18	9705	broad.mit.edu	37	8	53092718	53092718	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:53092718C>T	uc003xqz.2	-	4	397	c.241G>A	c.(241-243)GAT>AAT	p.D81N	ST18_uc011ldq.1_5'UTR|ST18_uc011ldr.1_Missense_Mutation_p.D46N|ST18_uc011lds.1_5'UTR|ST18_uc003xra.2_Missense_Mutation_p.D81N|ST18_uc003xrb.2_Missense_Mutation_p.D81N|ST18_uc010lyb.2_RNA	NM_014682	NP_055497	O60284	ST18_HUMAN	suppression of tumorigenicity 18	81						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	53092779	53092779	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:53092779C>A	uc003xqz.2	-	4	336	c.180G>T	c.(178-180)AAG>AAT	p.K60N	ST18_uc011ldq.1_5'UTR|ST18_uc011ldr.1_Missense_Mutation_p.K25N|ST18_uc011lds.1_5'UTR|ST18_uc003xra.2_Missense_Mutation_p.K60N|ST18_uc003xrb.2_Missense_Mutation_p.K60N|ST18_uc010lyb.2_RNA	NM_014682	NP_055497	O60284	ST18_HUMAN	suppression of tumorigenicity 18	60						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)																---	---	---	---
OPRK1	4986	broad.mit.edu	37	8	54163342	54163342	+	Nonsense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:54163342G>A	uc003xrh.1	-	1	631	c.256C>T	c.(256-258)CGA>TGA	p.R86*	OPRK1_uc003xri.1_Nonsense_Mutation_p.R86*|OPRK1_uc010lyc.1_5'UTR	NM_000912	NP_000903	P41145	OPRK_HUMAN	opioid receptor, kappa 1	86	Cytoplasmic (Potential).				behavior|immune response|inhibition of adenylate cyclase activity by G-protein signaling pathway|sensory perception|synaptic transmission|viral genome replication	integral to plasma membrane	kappa-opioid receptor activity|protein binding			ovary(1)|skin(1)	2		all_epithelial(80;0.066)|Lung NSC(129;0.0804)|all_lung(136;0.136)			Buprenorphine(DB00921)|Butorphanol(DB00611)|Cocaine(DB00907)|Codeine(DB00318)|Dezocine(DB01209)|Hydrocodone(DB00956)|Hydromorphone(DB00327)|Meperidine(DB00454)|Mirtazapine(DB00370)|Morphine(DB00295)|Nalbuphine(DB00844)|Naltrexone(DB00704)|Oxycodone(DB00497)|Pentazocine(DB00652)|Propoxyphene(DB00647)|Tramadol(DB00193)													---	---	---	---
TCEA1	6917	broad.mit.edu	37	8	54896934	54896934	+	Missense_Mutation	SNP	T	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:54896934T>A	uc003xru.2	-	7	990	c.667A>T	c.(667-669)ATG>TTG	p.M223L	TCEA1_uc003xrv.2_Missense_Mutation_p.M202L|TCEA1_uc011ldw.1_Intron|TCEA1_uc010lyg.2_RNA	NM_006756	NP_006747	P23193	TCEA1_HUMAN	transcription elongation factor A 1 isoform 1	223	TFIIS central.				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								---	---	---	---
LYPLA1	10434	broad.mit.edu	37	8	54974845	54974845	+	Silent	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:54974845A>G	uc003xry.2	-	5	449	c.255T>C	c.(253-255)GAT>GAC	p.D85D	LYPLA1_uc011ldx.1_Silent_p.D80D|LYPLA1_uc003xrz.2_Silent_p.D64D	NM_006330	NP_006321	O75608	LYPA1_HUMAN	lysophospholipase 1	85					fatty acid metabolic process|nitric oxide metabolic process|regulation of nitric-oxide synthase activity	cytosol	lysophospholipase activity|palmitoyl-(protein) hydrolase activity			central_nervous_system(1)	1		Lung NSC(129;0.109)|all_epithelial(80;0.11)|all_lung(136;0.181)	OV - Ovarian serous cystadenocarcinoma(7;8.48e-07)|Epithelial(17;9.29e-05)|all cancers(17;0.000689)															---	---	---	---
RP1	6101	broad.mit.edu	37	8	55538894	55538894	+	Missense_Mutation	SNP	A	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:55538894A>C	uc003xsd.1	+	4	2600	c.2452A>C	c.(2452-2454)AGT>CGT	p.S818R	RP1_uc011ldy.1_Intron	NM_006269	NP_006260	P56715	RP1_HUMAN	retinitis pigmentosa RP1 protein	818					axoneme assembly|intracellular signal transduction|photoreceptor cell maintenance|photoreceptor cell outer segment organization|phototransduction, visible light|retinal cone cell development|retinal rod cell development	cilium axoneme|cytoplasm|microtubule|microtubule associated complex|photoreceptor connecting cilium|photoreceptor inner segment|photoreceptor outer segment	microtubule binding			skin(7)|ovary(4)|pancreas(1)	12		all_lung(136;0.0831)|Lung NSC(129;0.109)|all_epithelial(80;0.123)	OV - Ovarian serous cystadenocarcinoma(7;4.4e-07)|Epithelial(17;3.37e-05)|all cancers(17;0.000285)															---	---	---	---
RP1	6101	broad.mit.edu	37	8	55541977	55541977	+	Silent	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:55541977A>G	uc003xsd.1	+	4	5683	c.5535A>G	c.(5533-5535)GAA>GAG	p.E1845E	RP1_uc011ldy.1_Intron	NM_006269	NP_006260	P56715	RP1_HUMAN	retinitis pigmentosa RP1 protein	1845					axoneme assembly|intracellular signal transduction|photoreceptor cell maintenance|photoreceptor cell outer segment organization|phototransduction, visible light|retinal cone cell development|retinal rod cell development	cilium axoneme|cytoplasm|microtubule|microtubule associated complex|photoreceptor connecting cilium|photoreceptor inner segment|photoreceptor outer segment	microtubule binding			skin(7)|ovary(4)|pancreas(1)	12		all_lung(136;0.0831)|Lung NSC(129;0.109)|all_epithelial(80;0.123)	OV - Ovarian serous cystadenocarcinoma(7;4.4e-07)|Epithelial(17;3.37e-05)|all cancers(17;0.000285)															---	---	---	---
XKR4	114786	broad.mit.edu	37	8	56436672	56436672	+	Silent	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:56436672C>T	uc003xsf.2	+	3	1871	c.1839C>T	c.(1837-1839)GAC>GAT	p.D613D		NM_052898	NP_443130	Q5GH76	XKR4_HUMAN	XK, Kell blood group complex subunit-related	613						integral to membrane				pancreas(2)	2			Epithelial(17;0.000117)|all cancers(17;0.000836)															---	---	---	---
XKR4	114786	broad.mit.edu	37	8	56436734	56436734	+	Missense_Mutation	SNP	A	G	G	rs144622902		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:56436734A>G	uc003xsf.2	+	3	1933	c.1901A>G	c.(1900-1902)TAC>TGC	p.Y634C		NM_052898	NP_443130	Q5GH76	XKR4_HUMAN	XK, Kell blood group complex subunit-related	634						integral to membrane				pancreas(2)	2			Epithelial(17;0.000117)|all cancers(17;0.000836)															---	---	---	---
LYN	4067	broad.mit.edu	37	8	56882275	56882275	+	Splice_Site	SNP	G	T	T	rs67338202		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:56882275G>T	uc003xsk.3	+	10	1256	c.974_splice	c.e10-1	p.G325_splice	LYN_uc003xsl.3_Splice_Site_p.G304_splice	NM_002350	NP_002341			Yamaguchi sarcoma viral (v-yes-1) oncogene						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	56912084	56912084	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:56912084A>G	uc003xsk.3	+	12	1594	c.1312A>G	c.(1312-1314)ACC>GCC	p.T438A	LYN_uc003xsl.3_Missense_Mutation_p.T417A	NM_002350	NP_002341	P07948	LYN_HUMAN	Yamaguchi sarcoma viral (v-yes-1) oncogene	438	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)															---	---	---	---
PLAG1	5324	broad.mit.edu	37	8	57080750	57080750	+	Nonsense_Mutation	SNP	C	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:57080750C>A	uc003xsq.3	-	2	530	c.79G>T	c.(79-81)GAA>TAA	p.E27*	PLAG1_uc003xsr.3_Nonsense_Mutation_p.E27*|PLAG1_uc010lyi.2_Nonsense_Mutation_p.E27*|PLAG1_uc010lyj.2_Intron	NM_001114635	NP_001108107	Q6DJT9	PLAG1_HUMAN	pleiomorphic adenoma gene 1 isoform b	27	Interacts with KPNA2.					nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding		CTNNB1/PLAG1(60)|FGFR1_ENST00000447712/PLAG1(28)|CHCHD7/PLAG1(12)|LIFR_ENST00000263409/PLAG1(10)|HAS2/PLAG1(10)|COL1A2/PLAG1(3)|TCEA1_ENST00000521604/PLAG1(3)	salivary_gland(113)|soft_tissue(13)|lung(1)|central_nervous_system(1)|breast(1)	129		all_lung(136;0.0548)|Lung NSC(129;0.0718)|all_epithelial(80;0.125)	Epithelial(17;0.00179)|all cancers(17;0.0125)					T	TCEA1|LIFR|CTNNB1|CHCHD7	salivary adenoma								---	---	---	---
CHD7	55636	broad.mit.edu	37	8	61766036	61766036	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:61766036C>T	uc003xue.2	+	31	7229	c.6752C>T	c.(6751-6753)TCG>TTG	p.S2251L		NM_017780	NP_060250	Q9P2D1	CHD7_HUMAN	chromodomain helicase DNA binding protein 7	2251	Glu-rich.				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	61773647	61773647	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:61773647A>G	uc003xue.2	+	35	8270	c.7793A>G	c.(7792-7794)CAC>CGC	p.H2598R		NM_017780	NP_060250	Q9P2D1	CHD7_HUMAN	chromodomain helicase DNA binding protein 7	2598					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)															---	---	---	---
CLVS1	157807	broad.mit.edu	37	8	62289211	62289211	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:62289211T>C	uc003xuh.2	+	3	827	c.503T>C	c.(502-504)GTC>GCC	p.V168A	CLVS1_uc003xug.2_Missense_Mutation_p.S167P|CLVS1_uc003xui.2_RNA|CLVS1_uc010lyp.2_Missense_Mutation_p.V168A	NM_173519	NP_775790	Q8IUQ0	CLVS1_HUMAN	retinaldehyde binding protein 1-like 1	168	CRAL-TRIO.				lysosome organization	clathrin-coated vesicle|early endosome membrane|trans-Golgi network	phosphatidylinositol-3,5-bisphosphate binding|transporter activity			skin(4)|ovary(1)	5																		---	---	---	---
MTFR1	9650	broad.mit.edu	37	8	66617028	66617028	+	Silent	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:66617028G>A	uc003xvm.2	+	5	593	c.381G>A	c.(379-381)GAG>GAA	p.E127E	MTFR1_uc011lep.1_Silent_p.E127E|MTFR1_uc003xvn.2_Silent_p.E94E|MTFR1_uc003xvo.1_Silent_p.E117E	NM_014637	NP_055452	Q15390	MTFR1_HUMAN	mitochondrial fission regulator 1 isoform 1	127						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)															---	---	---	---
SGK3	23678	broad.mit.edu	37	8	67759535	67759535	+	Silent	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:67759535A>G	uc003xwr.2	+	15	1481	c.1182A>G	c.(1180-1182)GAA>GAG	p.E394E	SGK3_uc003xwp.2_Silent_p.E388E|SGK3_uc003xwt.2_Silent_p.E394E|SGK3_uc003xwu.2_Silent_p.E362E	NM_001033578	NP_001028750	Q96BR1	SGK3_HUMAN	serum/glucocorticoid regulated kinase 3 isoform	394	Protein kinase.				cell communication|response to stress	cytoplasmic membrane-bounded vesicle|early endosome	ATP binding|phosphatidylinositol binding|protein serine/threonine kinase activity			ovary(1)|large_intestine(1)|lung(1)|breast(1)	4	Breast(64;0.186)	Lung NSC(129;0.0908)|all_lung(136;0.152)	Epithelial(68;0.0046)|OV - Ovarian serous cystadenocarcinoma(28;0.0112)|all cancers(69;0.0141)|BRCA - Breast invasive adenocarcinoma(89;0.206)															---	---	---	---
COPS5	10987	broad.mit.edu	37	8	67963491	67963491	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:67963491T>C	uc003xxe.2	-	6	1076	c.745A>G	c.(745-747)ACG>GCG	p.T249A	COPS5_uc003xxd.2_Missense_Mutation_p.T185A|COPS5_uc003xxf.2_Missense_Mutation_p.T294A|COPS5_uc010lyu.1_RNA|COPS5_uc010lyv.1_Missense_Mutation_p.T249A	NM_006837	NP_006828	Q92905	CSN5_HUMAN	COP9 signalosome subunit 5	249					cullin deneddylation|transcription from RNA polymerase II promoter	eukaryotic translation initiation factor 3 complex|signalosome	metal ion binding|metallopeptidase activity|protein binding|transcription coactivator activity|translation initiation factor activity			ovary(1)|skin(1)	2	Breast(64;0.214)	Lung NSC(129;0.0908)|all_lung(136;0.152)	Epithelial(68;0.00389)|OV - Ovarian serous cystadenocarcinoma(28;0.00691)|all cancers(69;0.0205)|BRCA - Breast invasive adenocarcinoma(89;0.153)															---	---	---	---
COPS5	10987	broad.mit.edu	37	8	67963497	67963497	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:67963497C>A	uc003xxe.2	-	6	1070	c.739G>T	c.(739-741)GTG>TTG	p.V247L	COPS5_uc003xxd.2_Missense_Mutation_p.V183L|COPS5_uc003xxf.2_Missense_Mutation_p.V292L|COPS5_uc010lyu.1_RNA|COPS5_uc010lyv.1_Missense_Mutation_p.V247L	NM_006837	NP_006828	Q92905	CSN5_HUMAN	COP9 signalosome subunit 5	247					cullin deneddylation|transcription from RNA polymerase II promoter	eukaryotic translation initiation factor 3 complex|signalosome	metal ion binding|metallopeptidase activity|protein binding|transcription coactivator activity|translation initiation factor activity			ovary(1)|skin(1)	2	Breast(64;0.214)	Lung NSC(129;0.0908)|all_lung(136;0.152)	Epithelial(68;0.00389)|OV - Ovarian serous cystadenocarcinoma(28;0.00691)|all cancers(69;0.0205)|BRCA - Breast invasive adenocarcinoma(89;0.153)															---	---	---	---
PREX2	80243	broad.mit.edu	37	8	68950493	68950493	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:68950493G>A	uc003xxv.1	+	7	832	c.805G>A	c.(805-807)GAT>AAT	p.D269N	PREX2_uc003xxu.1_Missense_Mutation_p.D269N|PREX2_uc011lez.1_Missense_Mutation_p.D204N	NM_024870	NP_079146	Q70Z35	PREX2_HUMAN	DEP domain containing 2 isoform a	269	PH.				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	69351850	69351850	+	Silent	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:69351850T>C	uc010lyz.2	+	2	235	c.186T>C	c.(184-186)TCT>TCC	p.S62S	C8orf34_uc010lyx.1_Silent_p.S62S|C8orf34_uc010lyy.1_Silent_p.S62S|C8orf34_uc003xyb.2_Silent_p.S37S	NM_052958	NP_443190	Q49A92	CH034_HUMAN	hypothetical protein LOC116328	62					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)															---	---	---	---
SULF1	23213	broad.mit.edu	37	8	70513887	70513887	+	Splice_Site	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:70513887A>G	uc010lza.1	+	10	1603	c.886_splice	c.e10-2	p.L296_splice	SULF1_uc003xyd.2_Splice_Site_p.L296_splice|SULF1_uc003xye.2_Splice_Site_p.L296_splice|SULF1_uc003xyf.2_Splice_Site_p.L296_splice|SULF1_uc003xyg.2_Splice_Site_p.L296_splice|SULF1_uc003xyh.1_Splice_Site	NM_015170	NP_055985			sulfatase 1 precursor						apoptosis|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			central_nervous_system(3)|ovary(2)|pancreas(1)|skin(1)	7	Breast(64;0.0654)		Epithelial(68;0.0124)|OV - Ovarian serous cystadenocarcinoma(28;0.0265)|all cancers(69;0.0534)															---	---	---	---
SLCO5A1	81796	broad.mit.edu	37	8	70667703	70667703	+	Missense_Mutation	SNP	G	A	A	rs144396521		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:70667703G>A	uc003xyl.2	-	4	1921	c.1214C>T	c.(1213-1215)GCG>GTG	p.A405V	SLCO5A1_uc010lzb.2_Missense_Mutation_p.A405V|SLCO5A1_uc011lfa.1_Intron|SLCO5A1_uc003xyk.2_Missense_Mutation_p.A405V|SLCO5A1_uc010lzc.2_Missense_Mutation_p.A405V	NM_030958	NP_112220	Q9H2Y9	SO5A1_HUMAN	solute carrier organic anion transporter family,	405	Cytoplasmic (Potential).					integral to membrane|plasma membrane	transporter activity			ovary(3)|upper_aerodigestive_tract(1)	4	Breast(64;0.0654)		Epithelial(68;0.0141)|OV - Ovarian serous cystadenocarcinoma(28;0.0315)|all cancers(69;0.0594)															---	---	---	---
SLCO5A1	81796	broad.mit.edu	37	8	70744582	70744582	+	Silent	SNP	G	A	A	rs145247874		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:70744582G>A	uc003xyl.2	-	2	1034	c.327C>T	c.(325-327)TCC>TCT	p.S109S	SLCO5A1_uc010lzb.2_Silent_p.S109S|SLCO5A1_uc011lfa.1_RNA|SLCO5A1_uc003xyk.2_Silent_p.S109S|SLCO5A1_uc010lzc.2_Silent_p.S109S	NM_030958	NP_112220	Q9H2Y9	SO5A1_HUMAN	solute carrier organic anion transporter family,	109	Cytoplasmic (Potential).					integral to membrane|plasma membrane	transporter activity			ovary(3)|upper_aerodigestive_tract(1)	4	Breast(64;0.0654)		Epithelial(68;0.0141)|OV - Ovarian serous cystadenocarcinoma(28;0.0315)|all cancers(69;0.0594)													OREG0018815	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
TRPA1	8989	broad.mit.edu	37	8	72964828	72964828	+	Intron	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:72964828G>A	uc003xza.2	-						uc011lff.1_RNA|uc003xyy.2_RNA	NM_007332	NP_015628			ankyrin-like protein 1							integral to plasma membrane				ovary(4)|lung(1)|kidney(1)	6			Epithelial(68;0.223)		Menthol(DB00825)													---	---	---	---
TRPA1	8989	broad.mit.edu	37	8	72987588	72987588	+	Silent	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:72987588G>A	uc003xza.2	-	1	232	c.57C>T	c.(55-57)GGC>GGT	p.G19G		NM_007332	NP_015628	O75762	TRPA1_HUMAN	ankyrin-like protein 1	19	Cytoplasmic (Potential).					integral to plasma membrane				ovary(4)|lung(1)|kidney(1)	6			Epithelial(68;0.223)		Menthol(DB00825)													---	---	---	---
KCNB2	9312	broad.mit.edu	37	8	73480139	73480139	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:73480139C>T	uc003xzb.2	+	2	758	c.170C>T	c.(169-171)CCC>CTC	p.P57L		NM_004770	NP_004761	Q92953	KCNB2_HUMAN	potassium voltage-gated channel, Shab-related	57	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)															---	---	---	---
KCNB2	9312	broad.mit.edu	37	8	73480430	73480430	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:73480430G>A	uc003xzb.2	+	2	1049	c.461G>A	c.(460-462)CGA>CAA	p.R154Q		NM_004770	NP_004761	Q92953	KCNB2_HUMAN	potassium voltage-gated channel, Shab-related	154	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)															---	---	---	---
RDH10	157506	broad.mit.edu	37	8	74235026	74235026	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:74235026A>G	uc003xzi.2	+	5	1143	c.883A>G	c.(883-885)ATC>GTC	p.I295V	RDH10_uc003xzj.2_Missense_Mutation_p.I130V|uc003xzk.1_Intron	NM_172037	NP_742034	Q8IZV5	RDH10_HUMAN	retinol dehydrogenase 10	295					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)															---	---	---	---
PI15	51050	broad.mit.edu	37	8	75756321	75756321	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:75756321G>A	uc003yal.2	+	3	558	c.379G>A	c.(379-381)GTA>ATA	p.V127I	uc003yak.1_Intron|PI15_uc003yam.2_Missense_Mutation_p.V127I	NM_015886	NP_056970	O43692	PI15_HUMAN	protease inhibitor 15 preproprotein	127						extracellular region	peptidase inhibitor activity			central_nervous_system(2)|ovary(1)	3	Breast(64;0.137)		BRCA - Breast invasive adenocarcinoma(89;0.104)|Epithelial(68;0.118)															---	---	---	---
HNF4G	3174	broad.mit.edu	37	8	76465396	76465396	+	Silent	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:76465396T>C	uc003yaq.2	+	6	738	c.468T>C	c.(466-468)TAT>TAC	p.Y156Y	HNF4G_uc003yar.2_Silent_p.Y193Y	NM_004133	NP_004124	Q14541	HNF4G_HUMAN	hepatocyte nuclear factor 4, gamma	156					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)															---	---	---	---
ZFHX4	79776	broad.mit.edu	37	8	77763896	77763896	+	Missense_Mutation	SNP	T	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:77763896T>A	uc003yav.2	+	10	4991	c.4604T>A	c.(4603-4605)GTC>GAC	p.V1535D	ZFHX4_uc003yau.1_Missense_Mutation_p.V1580D|ZFHX4_uc003yaw.1_Missense_Mutation_p.V1535D	NM_024721	NP_078997	Q86UP3	ZFHX4_HUMAN	zinc finger homeodomain 4	1535						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)			---	---	---	---
ZBTB10	65986	broad.mit.edu	37	8	81426179	81426179	+	Silent	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:81426179T>C	uc003ybx.3	+	3	2494	c.1896T>C	c.(1894-1896)GGT>GGC	p.G632G	ZBTB10_uc003ybv.3_Silent_p.G340G|ZBTB10_uc003ybw.3_Silent_p.G632G|ZBTB10_uc010lzt.2_Silent_p.G630G	NM_001105539	NP_001099009	Q96DT7	ZBT10_HUMAN	zinc finger and BTB domain containing 10 isoform	632					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)															---	---	---	---
LRRCC1	85444	broad.mit.edu	37	8	86027654	86027654	+	Silent	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:86027654A>G	uc003ycw.2	+	6	919	c.765A>G	c.(763-765)TTA>TTG	p.L255L	LRRCC1_uc010lzz.1_Intron|LRRCC1_uc010maa.1_Intron|LRRCC1_uc003ycx.2_Silent_p.L162L|LRRCC1_uc003ycy.2_Silent_p.L235L	NM_033402	NP_208325	Q9C099	LRCC1_HUMAN	sodium channel associated protein 2 isoform a	255					cell division|mitosis	centriole|nucleus					0																		---	---	---	---
CA1	759	broad.mit.edu	37	8	86250550	86250550	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:86250550T>C	uc003ydh.2	-	4	366	c.166A>G	c.(166-168)ACA>GCA	p.T56A	CA13_uc003ydf.1_Intron|CA1_uc010mae.1_Missense_Mutation_p.T56A|CA1_uc003ydi.2_Missense_Mutation_p.T56A	NM_001738	NP_001729	P00915	CAH1_HUMAN	carbonic anhydrase I	56					one-carbon metabolic process	Golgi apparatus	carbonate dehydratase activity|zinc ion binding			ovary(1)|central_nervous_system(1)	2		all_lung(136;4.89e-06)			Acetazolamide(DB00819)|Amlodipine(DB00381)|Bendroflumethiazide(DB00436)|Benzthiazide(DB00562)|Brinzolamide(DB01194)|Chlorothiazide(DB00880)|Cyclothiazide(DB00606)|Diazoxide(DB01119)|Dichlorphenamide(DB01144)|Ethinamate(DB01031)|Ethoxzolamide(DB00311)|Hydrochlorothiazide(DB00999)|Hydroflumethiazide(DB00774)|Levetiracetam(DB01202)|Methazolamide(DB00703)|Methyclothiazide(DB00232)|Quinethazone(DB01325)|Trichlormethiazide(DB01021)|Verapamil(DB00661)|Zonisamide(DB00909)													---	---	---	---
CA2	760	broad.mit.edu	37	8	86386591	86386591	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:86386591T>G	uc003ydk.2	+	4	570	c.390T>G	c.(388-390)TTT>TTG	p.F130L		NM_000067	NP_000058	P00918	CAH2_HUMAN	carbonic anhydrase II	130					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)													---	---	---	---
PSKH2	85481	broad.mit.edu	37	8	87076642	87076642	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:87076642A>G	uc011lfy.1	-	2	404	c.404T>C	c.(403-405)ATG>ACG	p.M135T		NM_033126	NP_149117	Q96QS6	KPSH2_HUMAN	protein serine kinase H2	135	Protein kinase.						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	87473533	87473533	+	Silent	SNP	A	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:87473533A>T	uc003ydt.2	+	23	2860	c.2580A>T	c.(2578-2580)GGA>GGT	p.G860G		NM_007013	NP_008944	Q9H0M0	WWP1_HUMAN	WW domain containing E3 ubiquitin protein ligase	860	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	87541258	87541258	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:87541258A>G	uc003ydv.2	+	4	380	c.218A>G	c.(217-219)CAG>CGG	p.Q73R		NM_003909	NP_003900	O75131	CPNE3_HUMAN	copine III	73	C2 1.				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	87541261	87541261	+	Missense_Mutation	SNP	A	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:87541261A>T	uc003ydv.2	+	4	383	c.221A>T	c.(220-222)AAA>ATA	p.K74I		NM_003909	NP_003900	O75131	CPNE3_HUMAN	copine III	74	C2 1.				lipid metabolic process|vesicle-mediated transport	cytosol	calcium-dependent phospholipid binding|protein serine/threonine kinase activity|transporter activity			ovary(1)|skin(1)	2																		---	---	---	---
CNGB3	54714	broad.mit.edu	37	8	87660042	87660042	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:87660042T>C	uc003ydx.2	-	8	1023	c.977A>G	c.(976-978)AAT>AGT	p.N326S	CNGB3_uc010maj.2_Missense_Mutation_p.N188S	NM_019098	NP_061971	Q9NQW8	CNGB3_HUMAN	cyclic nucleotide gated channel beta 3	326	Extracellular (Potential).				signal transduction|visual perception	integral to membrane	cGMP binding			ovary(2)|pancreas(1)	3																		---	---	---	---
CNGB3	54714	broad.mit.edu	37	8	87660065	87660065	+	Silent	SNP	C	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:87660065C>A	uc003ydx.2	-	8	1000	c.954G>T	c.(952-954)GGG>GGT	p.G318G	CNGB3_uc010maj.2_Silent_p.G180G	NM_019098	NP_061971	Q9NQW8	CNGB3_HUMAN	cyclic nucleotide gated channel beta 3	318	Helical; Name=H3; (Potential).				signal transduction|visual perception	integral to membrane	cGMP binding			ovary(2)|pancreas(1)	3																		---	---	---	---
DCAF4L2	138009	broad.mit.edu	37	8	88885347	88885347	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:88885347G>T	uc003ydz.2	-	1	950	c.853C>A	c.(853-855)CTG>ATG	p.L285M		NM_152418	NP_689631	Q8NA75	DC4L2_HUMAN	WD repeat domain 21C	285	WD 1.									ovary(1)	1																		---	---	---	---
CALB1	793	broad.mit.edu	37	8	91072912	91072912	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:91072912A>G	uc003yel.1	-	10	799	c.617T>C	c.(616-618)ATA>ACA	p.I206T	CALB1_uc011lge.1_Missense_Mutation_p.I149T	NM_004929	NP_004920	P05937	CALB1_HUMAN	calbindin 1	206	4.|EF-hand 5.					nucleus	calcium ion binding|vitamin D binding			pancreas(1)	1			BRCA - Breast invasive adenocarcinoma(11;0.00953)															---	---	---	---
FAM92A1	137392	broad.mit.edu	37	8	94713594	94713594	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:94713594G>A	uc010maq.2	+	2	272	c.169G>A	c.(169-171)GCG>ACG	p.A57T	FAM92A1_uc003yfu.1_RNA|FAM92A1_uc003yfv.3_RNA	NM_145269	NP_660312	A1XBS5	F92A1_HUMAN	hypothetical protein LOC137392	57											0	Breast(36;2.4e-06)		BRCA - Breast invasive adenocarcinoma(8;0.0168)															---	---	---	---
RBM12B	389677	broad.mit.edu	37	8	94747043	94747043	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:94747043C>A	uc003yfz.2	-	3	1789	c.1596G>T	c.(1594-1596)GAG>GAT	p.E532D		NM_203390	NP_976324	Q8IXT5	RB12B_HUMAN	RNA binding motif protein 12B	532							nucleotide binding|RNA binding				0	Breast(36;4.14e-07)		BRCA - Breast invasive adenocarcinoma(8;0.0168)															---	---	---	---
RBM12B	389677	broad.mit.edu	37	8	94747533	94747533	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:94747533C>T	uc003yfz.2	-	3	1299	c.1106G>A	c.(1105-1107)CGT>CAT	p.R369H		NM_203390	NP_976324	Q8IXT5	RB12B_HUMAN	RNA binding motif protein 12B	369							nucleotide binding|RNA binding				0	Breast(36;4.14e-07)		BRCA - Breast invasive adenocarcinoma(8;0.0168)															---	---	---	---
RAD54B	25788	broad.mit.edu	37	8	95403830	95403830	+	Intron	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:95403830C>T	uc003ygk.2	-						RAD54B_uc010may.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					---	---	---	---
PLEKHF2	79666	broad.mit.edu	37	8	96166490	96166490	+	Missense_Mutation	SNP	A	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:96166490A>C	uc003yhn.1	+	2	465	c.218A>C	c.(217-219)AAA>ACA	p.K73T		NM_024613	NP_078889	Q9H8W4	PKHF2_HUMAN	phafin 2	73	PH.					transport vesicle	metal ion binding|protein binding			ovary(2)	2	Breast(36;3.18e-05)																	---	---	---	---
MTDH	92140	broad.mit.edu	37	8	98701290	98701290	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:98701290T>C	uc003yhz.2	+	5	1098	c.770T>C	c.(769-771)GTT>GCT	p.V257A	MTDH_uc010mbf.2_5'Flank	NM_178812	NP_848927	Q86UE4	LYRIC_HUMAN	metadherin	257	Cytoplasmic (Potential).				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)															---	---	---	---
MATN2	4147	broad.mit.edu	37	8	99028797	99028797	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:99028797G>A	uc003yic.2	+	11	1834	c.1603G>A	c.(1603-1605)GGT>AGT	p.G535S	MATN2_uc010mbh.1_Missense_Mutation_p.G494S|MATN2_uc003yid.2_Missense_Mutation_p.G535S|MATN2_uc003yie.1_Missense_Mutation_p.G535S|MATN2_uc010mbi.1_Missense_Mutation_p.G368S|MATN2_uc010mbj.1_Missense_Mutation_p.G34S	NM_002380	NP_002371	O00339	MATN2_HUMAN	matrilin 2 isoform a precursor	535	EGF-like 8.					proteinaceous extracellular matrix	calcium ion binding			ovary(2)	2	Breast(36;1.43e-06)		OV - Ovarian serous cystadenocarcinoma(57;0.244)															---	---	---	---
C8orf47	203111	broad.mit.edu	37	8	99101589	99101589	+	Missense_Mutation	SNP	C	T	T	rs146451719	byFrequency	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:99101589C>T	uc003yih.1	+	2	492	c.344C>T	c.(343-345)CCG>CTG	p.P115L		NM_173549	NP_775820	Q6P6B1	CH047_HUMAN	hypothetical protein LOC203111	115											0	Breast(36;2.31e-06)		OV - Ovarian serous cystadenocarcinoma(57;0.214)															---	---	---	---
OSR2	116039	broad.mit.edu	37	8	99961774	99961774	+	Silent	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:99961774G>A	uc003yir.2	+	2	1129	c.594G>A	c.(592-594)AGG>AGA	p.R198R	OSR2_uc010mbn.2_Silent_p.R198R|OSR2_uc003yiq.2_Silent_p.R198R|OSR2_uc011lgx.1_Silent_p.R319R	NM_001142462	NP_001135934	Q8N2R0	OSR2_HUMAN	odd-skipped related 2 isoform a	198					bone morphogenesis|chondrocyte differentiation|embryonic digit morphogenesis|embryonic forelimb morphogenesis|embryonic hindlimb morphogenesis|embryonic leg joint morphogenesis|embryonic skeletal joint morphogenesis|eyelid development in camera-type eye|head development|mesonephros development|metanephros development|middle ear morphogenesis|negative regulation of transcription from RNA polymerase II promoter|odontogenesis|osteoblast proliferation|palate development|positive regulation of bone mineralization|positive regulation of epithelial cell proliferation|positive regulation of transcription from RNA polymerase II promoter	nucleus	sequence-specific DNA binding|zinc ion binding			central_nervous_system(1)	1	Breast(36;4.14e-07)		OV - Ovarian serous cystadenocarcinoma(57;0.0136)															---	---	---	---
OSR2	116039	broad.mit.edu	37	8	99961783	99961783	+	Silent	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:99961783G>A	uc003yir.2	+	2	1138	c.603G>A	c.(601-603)ACG>ACA	p.T201T	OSR2_uc010mbn.2_Silent_p.T201T|OSR2_uc003yiq.2_Silent_p.T201T|OSR2_uc011lgx.1_Silent_p.T322T	NM_001142462	NP_001135934	Q8N2R0	OSR2_HUMAN	odd-skipped related 2 isoform a	201	C2H2-type 2.				bone morphogenesis|chondrocyte differentiation|embryonic digit morphogenesis|embryonic forelimb morphogenesis|embryonic hindlimb morphogenesis|embryonic leg joint morphogenesis|embryonic skeletal joint morphogenesis|eyelid development in camera-type eye|head development|mesonephros development|metanephros development|middle ear morphogenesis|negative regulation of transcription from RNA polymerase II promoter|odontogenesis|osteoblast proliferation|palate development|positive regulation of bone mineralization|positive regulation of epithelial cell proliferation|positive regulation of transcription from RNA polymerase II promoter	nucleus	sequence-specific DNA binding|zinc ion binding			central_nervous_system(1)	1	Breast(36;4.14e-07)		OV - Ovarian serous cystadenocarcinoma(57;0.0136)															---	---	---	---
OSR2	116039	broad.mit.edu	37	8	99961842	99961842	+	Intron	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:99961842G>A	uc003yir.2	+						OSR2_uc010mbn.2_Intron|OSR2_uc003yiq.2_Intron|OSR2_uc011lgx.1_Intron	NM_001142462	NP_001135934			odd-skipped related 2 isoform a						bone morphogenesis|chondrocyte differentiation|embryonic digit morphogenesis|embryonic forelimb morphogenesis|embryonic hindlimb morphogenesis|embryonic leg joint morphogenesis|embryonic skeletal joint morphogenesis|eyelid development in camera-type eye|head development|mesonephros development|metanephros development|middle ear morphogenesis|negative regulation of transcription from RNA polymerase II promoter|odontogenesis|osteoblast proliferation|palate development|positive regulation of bone mineralization|positive regulation of epithelial cell proliferation|positive regulation of transcription from RNA polymerase II promoter	nucleus	sequence-specific DNA binding|zinc ion binding			central_nervous_system(1)	1	Breast(36;4.14e-07)		OV - Ovarian serous cystadenocarcinoma(57;0.0136)															---	---	---	---
VPS13B	157680	broad.mit.edu	37	8	100160103	100160103	+	Silent	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:100160103T>C	uc003yiv.2	+	14	1989	c.1878T>C	c.(1876-1878)CCT>CCC	p.P626P	VPS13B_uc003yiw.2_Silent_p.P626P|VPS13B_uc003yit.2_Silent_p.P626P|VPS13B_uc003yiu.1_Silent_p.P626P|VPS13B_uc003yix.1_Silent_p.P97P	NM_017890	NP_060360	Q7Z7G8	VP13B_HUMAN	vacuolar protein sorting 13B isoform 5	626					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	100523417	100523417	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:100523417G>A	uc003yiv.2	+	29	4496	c.4385G>A	c.(4384-4386)CGC>CAC	p.R1462H	VPS13B_uc003yiw.2_Missense_Mutation_p.R1437H|VPS13B_uc003yix.1_Missense_Mutation_p.R932H	NM_017890	NP_060360	Q7Z7G8	VP13B_HUMAN	vacuolar protein sorting 13B isoform 5	1462					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	100729516	100729516	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:100729516C>T	uc003yiv.2	+	37	6758	c.6647C>T	c.(6646-6648)GCT>GTT	p.A2216V	VPS13B_uc003yiw.2_Missense_Mutation_p.A2191V	NM_017890	NP_060360	Q7Z7G8	VP13B_HUMAN	vacuolar protein sorting 13B isoform 5	2216					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	100861096	100861096	+	Silent	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:100861096A>G	uc003yiv.2	+	55	10221	c.10110A>G	c.(10108-10110)GCA>GCG	p.A3370A	VPS13B_uc003yiw.2_Silent_p.A3345A	NM_017890	NP_060360	Q7Z7G8	VP13B_HUMAN	vacuolar protein sorting 13B isoform 5	3370					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)															---	---	---	---
RGS22	26166	broad.mit.edu	37	8	100974909	100974909	+	Intron	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:100974909A>G	uc003yjb.1	-						RGS22_uc003yja.1_Intron|RGS22_uc003yjc.1_Intron	NM_015668	NP_056483			regulator of G-protein signaling 22						negative regulation of signal transduction	cytoplasm|plasma membrane	GTPase activator activity|signal transducer activity			ovary(3)|skin(2)|breast(1)|central_nervous_system(1)	7			Epithelial(11;6.71e-08)|all cancers(13;4.19e-06)|OV - Ovarian serous cystadenocarcinoma(57;0.000469)|STAD - Stomach adenocarcinoma(118;0.169)															---	---	---	---
SNX31	169166	broad.mit.edu	37	8	101596342	101596342	+	Silent	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:101596342T>C	uc003yjr.2	-	12	1318	c.1167A>G	c.(1165-1167)GAA>GAG	p.E389E	SNX31_uc011lha.1_Silent_p.E184E|SNX31_uc011lhb.1_Silent_p.E290E	NM_152628	NP_689841	Q8N9S9	SNX31_HUMAN	sorting nexin 31	389					cell communication|protein transport		phosphatidylinositol binding				0	all_cancers(14;4.01e-05)|all_epithelial(15;1.26e-07)|Lung NSC(17;0.000453)|all_lung(17;0.00125)		Epithelial(11;1.21e-11)|all cancers(13;2.62e-09)|OV - Ovarian serous cystadenocarcinoma(57;3.22e-06)|STAD - Stomach adenocarcinoma(118;0.206)															---	---	---	---
GRHL2	79977	broad.mit.edu	37	8	102571028	102571028	+	Silent	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:102571028C>T	uc010mbu.2	+	4	996	c.666C>T	c.(664-666)GAC>GAT	p.D222D	GRHL2_uc011lhi.1_Silent_p.D222D	NM_024915	NP_079191	Q6ISB3	GRHL2_HUMAN	transcription factor CP2-like 3	222						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)															---	---	---	---
UBR5	51366	broad.mit.edu	37	8	103297739	103297739	+	Splice_Site	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:103297739A>G	uc003ykr.1	-	39	5517	c.5484_splice	c.e39+1	p.Q1828_splice	UBR5_uc003yks.1_Splice_Site_p.Q1828_splice	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)															---	---	---	---
UBR5	51366	broad.mit.edu	37	8	103326070	103326070	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:103326070C>A	uc003ykr.1	-	16	2002	c.1969G>T	c.(1969-1971)GTT>TTT	p.V657F	UBR5_uc003yks.1_Missense_Mutation_p.V657F	NM_015902	NP_056986	O95071	UBR5_HUMAN	ubiquitin protein ligase E3 component n-recognin	657					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	103354874	103354874	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:103354874G>A	uc003ykr.1	-	9	958	c.925C>T	c.(925-927)CGT>TGT	p.R309C	UBR5_uc003yks.1_Missense_Mutation_p.R309C	NM_015902	NP_056986	O95071	UBR5_HUMAN	ubiquitin protein ligase E3 component n-recognin	309					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)															---	---	---	---
BAALC	79870	broad.mit.edu	37	8	104240243	104240243	+	Silent	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:104240243T>C	uc003yld.2	+	3	559	c.354T>C	c.(352-354)CCT>CCC	p.P118P	BAALC_uc003yle.2_3'UTR|uc003ylf.2_Intron|BAALC_uc003ylg.2_Silent_p.P64P|BAALC_uc010mcc.2_RNA	NM_024812	NP_079088	Q8WXS3	BAALC_HUMAN	brain and acute leukemia, cytoplasmic isoform 1	153						centrosome|membrane|nucleus					0			OV - Ovarian serous cystadenocarcinoma(57;3.49e-05)|STAD - Stomach adenocarcinoma(118;0.133)															---	---	---	---
FZD6	8323	broad.mit.edu	37	8	104342146	104342146	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:104342146C>T	uc003ylh.2	+	6	2089	c.1805C>T	c.(1804-1806)GCG>GTG	p.A602V	FZD6_uc003ylj.2_Missense_Mutation_p.A602V|FZD6_uc011lhn.1_Missense_Mutation_p.A568V|FZD6_uc011lho.1_Missense_Mutation_p.A297V|FZD6_uc011lhp.1_Missense_Mutation_p.A547V	NM_003506	NP_003497	O60353	FZD6_HUMAN	frizzled 6 isoform a precursor	602	Cytoplasmic (Potential).				angiogenesis|axonogenesis|cell proliferation in midbrain|establishment of planar polarity|G-protein signaling, coupled to cGMP nucleotide second messenger|gonad development|inner ear morphogenesis|negative regulation of canonical Wnt receptor signaling pathway|negative regulation of sequence-specific DNA binding transcription factor activity|neural tube closure|non-canonical Wnt receptor signaling pathway	apical part of cell|apicolateral plasma membrane|cytoplasm|integral to plasma membrane|neuron projection membrane	G-protein coupled receptor activity|PDZ domain binding|Wnt receptor activity|Wnt-protein binding			central_nervous_system(1)|skin(1)	2			OV - Ovarian serous cystadenocarcinoma(57;2.86e-05)|STAD - Stomach adenocarcinoma(118;0.197)															---	---	---	---
FZD6	8323	broad.mit.edu	37	8	104343586	104343586	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:104343586A>G	uc003ylh.2	+	7	2254	c.1970A>G	c.(1969-1971)GAT>GGT	p.D657G	FZD6_uc003ylj.2_Missense_Mutation_p.D657G|FZD6_uc011lhn.1_Missense_Mutation_p.D623G|FZD6_uc011lho.1_Missense_Mutation_p.D352G|FZD6_uc011lhp.1_Missense_Mutation_p.D602G	NM_003506	NP_003497	O60353	FZD6_HUMAN	frizzled 6 isoform a precursor	657	Cytoplasmic (Potential).				angiogenesis|axonogenesis|cell proliferation in midbrain|establishment of planar polarity|G-protein signaling, coupled to cGMP nucleotide second messenger|gonad development|inner ear morphogenesis|negative regulation of canonical Wnt receptor signaling pathway|negative regulation of sequence-specific DNA binding transcription factor activity|neural tube closure|non-canonical Wnt receptor signaling pathway	apical part of cell|apicolateral plasma membrane|cytoplasm|integral to plasma membrane|neuron projection membrane	G-protein coupled receptor activity|PDZ domain binding|Wnt receptor activity|Wnt-protein binding			central_nervous_system(1)|skin(1)	2			OV - Ovarian serous cystadenocarcinoma(57;2.86e-05)|STAD - Stomach adenocarcinoma(118;0.197)															---	---	---	---
SLC25A32	81034	broad.mit.edu	37	8	104413783	104413783	+	Missense_Mutation	SNP	A	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:104413783A>C	uc003yll.2	-	6	1076	c.773T>G	c.(772-774)TTT>TGT	p.F258C	SLC25A32_uc011lhr.1_Missense_Mutation_p.F126C	NM_030780	NP_110407	Q9H2D1	MFTC_HUMAN	solute carrier family 25, member 32	258	Solcar 3.				folic acid metabolic process|mitochondrial transport	integral to membrane|mitochondrial inner membrane	binding|folic acid transporter activity			ovary(1)	1			OV - Ovarian serous cystadenocarcinoma(57;2.79e-06)|STAD - Stomach adenocarcinoma(118;0.197)		Folic Acid(DB00158)													---	---	---	---
DCAF13	25879	broad.mit.edu	37	8	104447872	104447872	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:104447872G>A	uc003yln.2	+	8	1537	c.1260G>A	c.(1258-1260)ATG>ATA	p.M420I	DCAF13_uc003ylm.1_Missense_Mutation_p.M153I|DCAF13_uc003ylo.2_Missense_Mutation_p.M131I	NM_015420	NP_056235	Q9NV06	DCA13_HUMAN	WD repeats and SOF1 domain containing	268	WD 5.				rRNA processing	CUL4 RING ubiquitin ligase complex|nucleolus|ribonucleoprotein complex				breast(1)	1																		---	---	---	---
RIMS2	9699	broad.mit.edu	37	8	104924318	104924318	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:104924318G>A	uc003yls.2	+	4	1305	c.1064G>A	c.(1063-1065)CGT>CAT	p.R355H	RIMS2_uc003ylp.2_Missense_Mutation_p.R577H|RIMS2_uc003ylw.2_Missense_Mutation_p.R385H|RIMS2_uc003ylq.2_Missense_Mutation_p.R385H|RIMS2_uc003ylr.2_Missense_Mutation_p.R432H|RIMS2_uc003ylt.2_5'UTR	NM_014677	NP_055492	Q9UQ26	RIMS2_HUMAN	regulating synaptic membrane exocytosis 2	655					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)			---	---	---	---
LRP12	29967	broad.mit.edu	37	8	105509302	105509302	+	Missense_Mutation	SNP	A	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:105509302A>C	uc003yma.2	-	5	1573	c.1478T>G	c.(1477-1479)GTC>GGC	p.V493G	LRP12_uc003ymb.2_Missense_Mutation_p.V474G|LRP12_uc003ylz.2_5'Flank	NM_013437	NP_038465	Q9Y561	LRP12_HUMAN	low density lipoprotein-related protein 12	493	Helical; (Potential).				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	105511659	105511659	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:105511659C>A	uc003yma.2	-	4	456	c.361G>T	c.(361-363)GCT>TCT	p.A121S	LRP12_uc003ymb.2_Missense_Mutation_p.A102S	NM_013437	NP_038465	Q9Y561	LRP12_HUMAN	low density lipoprotein-related protein 12	121	Extracellular (Potential).|CUB 1.				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)															---	---	---	---
ZFPM2	23414	broad.mit.edu	37	8	106813293	106813293	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:106813293T>C	uc003ymd.2	+	8	1006	c.983T>C	c.(982-984)TTC>TCC	p.F328S	ZFPM2_uc011lhs.1_Missense_Mutation_p.F59S|uc003yme.1_5'Flank	NM_012082	NP_036214	Q8WW38	FOG2_HUMAN	zinc finger protein, multitype 2	328					blood coagulation|negative regulation of fat cell differentiation|outflow tract septum morphogenesis|right ventricular cardiac muscle tissue morphogenesis|ventricular septum morphogenesis	nucleoplasm	DNA binding|RNA polymerase II transcription coactivator activity|transcription corepressor activity|transcription factor binding|zinc ion binding			ovary(4)|large_intestine(1)	5			OV - Ovarian serous cystadenocarcinoma(57;8.28e-08)															---	---	---	---
ANGPT1	284	broad.mit.edu	37	8	108306156	108306156	+	Intron	SNP	C	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:108306156C>A	uc003ymn.2	-						ANGPT1_uc011lhv.1_Intron|ANGPT1_uc003ymo.2_Intron|ANGPT1_uc003ymp.3_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	110100505	110100505	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:110100505A>G	uc003ymz.3	+	1	780	c.764A>G	c.(763-765)AAC>AGC	p.N255S		NM_003301	NP_003292	P34981	TRFR_HUMAN	thyrotropin-releasing hormone receptor	255	Cytoplasmic (Potential).					integral to plasma membrane	thyrotropin-releasing hormone receptor activity			skin(2)|lung(1)	3			OV - Ovarian serous cystadenocarcinoma(57;2.3e-11)															---	---	---	---
NUDCD1	84955	broad.mit.edu	37	8	110257549	110257549	+	Splice_Site	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:110257549A>G	uc003ynb.3	-	9	1570	c.1459_splice	c.e9+1	p.G487_splice	NUDCD1_uc003yna.2_Splice_Site_p.G458_splice|NUDCD1_uc010mcl.2_Splice_Site_p.G400_splice	NM_032869	NP_116258			NudC domain containing 1 isoform 1											ovary(1)|breast(1)	2	all_neural(195;0.219)		OV - Ovarian serous cystadenocarcinoma(57;1.56e-12)															---	---	---	---
PKHD1L1	93035	broad.mit.edu	37	8	110457127	110457127	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:110457127G>A	uc003yne.2	+	38	5133	c.5029G>A	c.(5029-5031)GTG>ATG	p.V1677M		NM_177531	NP_803875	Q86WI1	PKHL1_HUMAN	fibrocystin L precursor	1677	IPT/TIG 9.|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)			---	---	---	---
CSMD3	114788	broad.mit.edu	37	8	113275976	113275976	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:113275976C>A	uc003ynu.2	-	61	9913	c.9754G>T	c.(9754-9756)GGC>TGC	p.G3252C	CSMD3_uc003yns.2_Missense_Mutation_p.G2454C|CSMD3_uc003ynt.2_Missense_Mutation_p.G3212C|CSMD3_uc011lhx.1_Missense_Mutation_p.G3083C	NM_198123	NP_937756	Q7Z407	CSMD3_HUMAN	CUB and Sushi multiple domains 3 isoform 1	3252	Sushi 25.|Extracellular (Potential).					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	113562951	113562951	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:113562951A>G	uc003ynu.2	-	27	4672	c.4513T>C	c.(4513-4515)TTT>CTT	p.F1505L	CSMD3_uc003yns.2_Missense_Mutation_p.F777L|CSMD3_uc003ynt.2_Missense_Mutation_p.F1465L|CSMD3_uc011lhx.1_Missense_Mutation_p.F1401L	NM_198123	NP_937756	Q7Z407	CSMD3_HUMAN	CUB and Sushi multiple domains 3 isoform 1	1505	Extracellular (Potential).|CUB 8.					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	114326889	114326889	+	Silent	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:114326889T>C	uc003ynu.2	-	2	471	c.312A>G	c.(310-312)CAA>CAG	p.Q104Q	CSMD3_uc003ynt.2_Silent_p.Q64Q|CSMD3_uc011lhx.1_Silent_p.Q104Q|CSMD3_uc010mcx.1_Silent_p.Q104Q|CSMD3_uc003ynx.3_Silent_p.Q104Q	NM_198123	NP_937756	Q7Z407	CSMD3_HUMAN	CUB and Sushi multiple domains 3 isoform 1	104	Extracellular (Potential).|CUB 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)			---	---	---	---
TRPS1	7227	broad.mit.edu	37	8	116617163	116617163	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:116617163A>G	uc003ynz.2	-	3	1453	c.994T>C	c.(994-996)TAT>CAT	p.Y332H	TRPS1_uc011lhy.1_Missense_Mutation_p.Y336H|TRPS1_uc003yny.2_Missense_Mutation_p.Y345H|TRPS1_uc010mcy.2_Missense_Mutation_p.Y332H	NM_014112	NP_054831	Q9UHF7	TRPS1_HUMAN	zinc finger transcription factor TRPS1	332					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				---	---	---	---
UTP23	84294	broad.mit.edu	37	8	117783976	117783976	+	Silent	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:117783976G>A	uc003yoc.2	+	3	746	c.645G>A	c.(643-645)CCG>CCA	p.P215P		NM_032334	NP_115710	Q9BRU9	UTP23_HUMAN	UTP23, small subunit (SSU) processome component,	215					rRNA processing	nucleolus					0																		---	---	---	---
EXT1	2131	broad.mit.edu	37	8	118819481	118819481	+	Silent	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:118819481A>G	uc003yok.1	-	9	2631	c.1858T>C	c.(1858-1860)TTG>CTG	p.L620L		NM_000127	NP_000118	Q16394	EXT1_HUMAN	exostosin 1	620	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				---	---	---	---
NOV	4856	broad.mit.edu	37	8	120428858	120428858	+	Splice_Site	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:120428858T>C	uc003yoq.2	+	1	305	c.84_splice	c.e1+2	p.Q28_splice		NM_002514	NP_002505			nephroblastoma overexpressed precursor						regulation of cell growth		growth factor activity|insulin-like growth factor binding			ovary(2)|skin(2)|kidney(1)	5	all_cancers(13;3.84e-26)|Lung NSC(37;1.19e-08)|Ovarian(258;0.0249)|Hepatocellular(40;0.161)		STAD - Stomach adenocarcinoma(47;0.000507)		Insulin Glargine recombinant(DB00047)|Insulin Lyspro recombinant(DB00046)|Insulin recombinant(DB00030)|Insulin, porcine(DB00071)											OREG0018940	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
NOV	4856	broad.mit.edu	37	8	120431386	120431386	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:120431386C>T	uc003yoq.2	+	4	799	c.578C>T	c.(577-579)GCC>GTC	p.A193V		NM_002514	NP_002505	P48745	NOV_HUMAN	nephroblastoma overexpressed precursor	193					regulation of cell growth		growth factor activity|insulin-like growth factor binding			ovary(2)|skin(2)|kidney(1)	5	all_cancers(13;3.84e-26)|Lung NSC(37;1.19e-08)|Ovarian(258;0.0249)|Hepatocellular(40;0.161)		STAD - Stomach adenocarcinoma(47;0.000507)		Insulin Glargine recombinant(DB00047)|Insulin Lyspro recombinant(DB00046)|Insulin recombinant(DB00030)|Insulin, porcine(DB00071)													---	---	---	---
ENPP2	5168	broad.mit.edu	37	8	120608253	120608253	+	Intron	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:120608253G>A	uc003yot.1	-						ENPP2_uc003yos.1_Intron|ENPP2_uc010mdd.1_Intron	NM_001040092	NP_001035181			autotaxin isoform 2 preproprotein						cellular component movement|chemotaxis|G-protein coupled receptor protein signaling pathway|immune response|phosphate metabolic process|phosphatidylcholine catabolic process|regulation of cell migration	extracellular space|integral to plasma membrane	alkylglycerophosphoethanolamine phosphodiesterase activity|calcium ion binding|lysophospholipase activity|nucleic acid binding|nucleotide diphosphatase activity|phosphodiesterase I activity|polysaccharide binding|scavenger receptor activity|transcription factor binding|zinc ion binding			ovary(2)|central_nervous_system(2)|upper_aerodigestive_tract(1)|large_intestine(1)|kidney(1)	7	Lung NSC(37;5.03e-06)|Ovarian(258;0.0249)|Hepatocellular(40;0.161)		STAD - Stomach adenocarcinoma(47;0.00185)															---	---	---	---
DEPDC6	64798	broad.mit.edu	37	8	120940770	120940770	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:120940770G>A	uc003yow.3	+	2	440	c.253G>A	c.(253-255)GCA>ACA	p.A85T	DEPDC6_uc011lid.1_Intron	NM_022783	NP_073620	Q8TB45	DPTOR_HUMAN	DEP domain containing 6	85	DEP 1.				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)															---	---	---	---
DEPDC6	64798	broad.mit.edu	37	8	121013925	121013925	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:121013925C>T	uc003yow.3	+	5	953	c.766C>T	c.(766-768)CGG>TGG	p.R256W	DEPDC6_uc011lid.1_Missense_Mutation_p.R155W	NM_022783	NP_073620	Q8TB45	DPTOR_HUMAN	DEP domain containing 6	256	Ser-rich.				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)															---	---	---	---
HAS2	3037	broad.mit.edu	37	8	122641249	122641249	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:122641249T>C	uc003yph.2	-	2	870	c.332A>G	c.(331-333)TAC>TGC	p.Y111C		NM_005328	NP_005319	Q92819	HAS2_HUMAN	hyaluronan synthase 2	111	Cytoplasmic (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	123966033	123966033	+	Silent	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:123966033A>G	uc003ypk.1	+	3	2850	c.2283A>G	c.(2281-2283)CCA>CCG	p.P761P		NM_014943	NP_055758	Q9Y6X8	ZHX2_HUMAN	zinc fingers and homeoboxes 2	761						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)															---	---	---	---
WDR67	93594	broad.mit.edu	37	8	124117674	124117674	+	Silent	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:124117674A>G	uc003ypp.1	+	8	1269	c.1179A>G	c.(1177-1179)CAA>CAG	p.Q393Q	WDR67_uc011lig.1_Silent_p.Q393Q|WDR67_uc011lih.1_Silent_p.Q283Q|WDR67_uc003ypq.1_RNA|WDR67_uc003yps.1_Silent_p.Q106Q	NM_145647	NP_663622	Q96DN5	WDR67_HUMAN	WD repeat domain 67 isoform 1	393						centrosome	Rab GTPase activator activity			skin(1)	1	Lung NSC(37;7e-10)|Ovarian(258;0.0205)		STAD - Stomach adenocarcinoma(47;0.00527)															---	---	---	---
ATAD2	29028	broad.mit.edu	37	8	124383512	124383512	+	Silent	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:124383512T>C	uc003yqh.3	-	5	711	c.603A>G	c.(601-603)GAA>GAG	p.E201E	ATAD2_uc011lii.1_5'UTR|ATAD2_uc003yqi.3_RNA|ATAD2_uc003yqj.2_Silent_p.E201E	NM_014109	NP_054828	Q6PL18	ATAD2_HUMAN	ATPase family, AAA domain containing 2	201					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)															---	---	---	---
FER1L6	654463	broad.mit.edu	37	8	124988177	124988177	+	Silent	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:124988177G>A	uc003yqw.2	+	9	929	c.723G>A	c.(721-723)CCG>CCA	p.P241P		NM_001039112	NP_001034201	Q2WGJ9	FR1L6_HUMAN	fer-1-like 6	241	C2 2.|Cytoplasmic (Potential).					integral to membrane				ovary(5)|skin(5)|central_nervous_system(1)	11	Lung NSC(37;4.1e-12)|Ovarian(258;0.00438)|all_neural(195;0.0741)		STAD - Stomach adenocarcinoma(47;0.00186)															---	---	---	---
FER1L6	654463	broad.mit.edu	37	8	125072534	125072534	+	Intron	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:125072534A>G	uc003yqw.2	+						uc003yqy.1_RNA	NM_001039112	NP_001034201			fer-1-like 6							integral to membrane				ovary(5)|skin(5)|central_nervous_system(1)	11	Lung NSC(37;4.1e-12)|Ovarian(258;0.00438)|all_neural(195;0.0741)		STAD - Stomach adenocarcinoma(47;0.00186)															---	---	---	---
FER1L6	654463	broad.mit.edu	37	8	125113359	125113359	+	Silent	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:125113359T>C	uc003yqw.2	+	38	5111	c.4905T>C	c.(4903-4905)GAT>GAC	p.D1635D	uc003yqy.1_Intron	NM_001039112	NP_001034201	Q2WGJ9	FR1L6_HUMAN	fer-1-like 6	1635	C2 6.|Cytoplasmic (Potential).					integral to membrane				ovary(5)|skin(5)|central_nervous_system(1)	11	Lung NSC(37;4.1e-12)|Ovarian(258;0.00438)|all_neural(195;0.0741)		STAD - Stomach adenocarcinoma(47;0.00186)															---	---	---	---
FER1L6	654463	broad.mit.edu	37	8	125131983	125131983	+	Silent	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:125131983C>T	uc003yqw.2	+	41	5732	c.5526C>T	c.(5524-5526)ATC>ATT	p.I1842I	uc003yqy.1_Intron	NM_001039112	NP_001034201	Q2WGJ9	FR1L6_HUMAN	fer-1-like 6	1842	Helical; (Potential).					integral to membrane				ovary(5)|skin(5)|central_nervous_system(1)	11	Lung NSC(37;4.1e-12)|Ovarian(258;0.00438)|all_neural(195;0.0741)		STAD - Stomach adenocarcinoma(47;0.00186)															---	---	---	---
OC90	729330	broad.mit.edu	37	8	133047080	133047080	+	Silent	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:133047080T>C	uc003ytg.2	-	9	681	c.681A>G	c.(679-681)AAA>AAG	p.K227K	OC90_uc011lix.1_Silent_p.E227E	NM_001080399	NP_001073868	Q02509	OC90_HUMAN	otoconin 90	243					lipid catabolic process|phospholipid metabolic process		calcium ion binding|phospholipase A2 activity			ovary(2)|skin(1)	3	Esophageal squamous(12;0.00693)|Ovarian(258;0.00769)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.000805)															---	---	---	---
KCNQ3	3786	broad.mit.edu	37	8	133141607	133141607	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:133141607C>T	uc003ytj.2	-	15	2746	c.2521G>A	c.(2521-2523)GAC>AAC	p.D841N	KCNQ3_uc010mdt.2_Missense_Mutation_p.D829N|uc003yti.2_5'Flank	NM_004519	NP_004510	O43525	KCNQ3_HUMAN	potassium voltage-gated channel KQT-like protein	841					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)															---	---	---	---
LRRC6	23639	broad.mit.edu	37	8	133584615	133584615	+	Missense_Mutation	SNP	A	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:133584615A>T	uc003ytk.2	-	12	1414	c.1340T>A	c.(1339-1341)ATT>AAT	p.I447N	LRRC6_uc003ytl.2_RNA	NM_012472	NP_036604	Q86X45	LRRC6_HUMAN	leucine rich repeat containing 6	447						cytoplasm				ovary(1)|kidney(1)	2	Ovarian(258;0.00352)|Esophageal squamous(12;0.00507)|all_neural(3;0.0052)|Medulloblastoma(3;0.0922)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.000311)															---	---	---	---
PHF20L1	51105	broad.mit.edu	37	8	133836299	133836299	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:133836299G>A	uc003ytt.2	+	13	1955	c.1630G>A	c.(1630-1632)GCA>ACA	p.A544T	PHF20L1_uc003yts.2_Missense_Mutation_p.A544T|PHF20L1_uc011lja.1_Missense_Mutation_p.A518T|PHF20L1_uc003ytu.1_RNA	NM_016018	NP_057102	A8MW92	P20L1_HUMAN	PHD finger protein 20-like 1 isoform 1	544	Lys-rich.						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	133945933	133945933	+	Intron	SNP	C	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:133945933C>A	uc003ytw.2	+						TG_uc010mdw.2_Intron|TG_uc011ljb.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)														---	---	---	---
TG	7038	broad.mit.edu	37	8	134145784	134145784	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:134145784C>A	uc003ytw.2	+	47	8109	c.8068C>A	c.(8068-8070)CCC>ACC	p.P2690T	TG_uc010mdw.2_Missense_Mutation_p.P1449T|TG_uc011ljb.1_Missense_Mutation_p.P1059T|TG_uc011ljc.1_Missense_Mutation_p.P823T	NM_003235	NP_003226	P01266	THYG_HUMAN	thyroglobulin precursor	2690					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)														---	---	---	---
COL22A1	169044	broad.mit.edu	37	8	139697475	139697475	+	Silent	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:139697475G>A	uc003yvd.2	-	38	3390	c.2943C>T	c.(2941-2943)CCC>CCT	p.P981P	COL22A1_uc011ljo.1_Silent_p.P281P	NM_152888	NP_690848	Q8NFW1	COMA1_HUMAN	collagen, type XXII, alpha 1	981	Pro-rich.|Gly-rich.|Collagen-like 8.				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)			---	---	---	---
EIF2C2	27161	broad.mit.edu	37	8	141542214	141542214	+	Nonsense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:141542214G>A	uc003yvn.2	-	19	2549	c.2509C>T	c.(2509-2511)CGA>TGA	p.R837*	EIF2C2_uc010men.2_Nonsense_Mutation_p.R760*|EIF2C2_uc010meo.2_Nonsense_Mutation_p.R803*	NM_012154	NP_036286	Q9UKV8	AGO2_HUMAN	argonaute 2 isoform 1	837					mRNA cleavage involved in gene silencing by miRNA|negative regulation of translation involved in gene silencing by miRNA|negative regulation of translational initiation|pre-miRNA processing|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasmic mRNA processing body|cytosol|micro-ribonucleoprotein complex|mRNA cap binding complex|nucleus|polysome|RNA-induced silencing complex	endoribonuclease activity, cleaving siRNA-paired mRNA|metal ion binding|protein binding|RNA 7-methylguanosine cap binding|siRNA binding|translation initiation factor activity				0	all_cancers(97;2.54e-14)|all_epithelial(106;5.99e-13)|Lung NSC(106;1.45e-05)|all_lung(105;2.07e-05)|Ovarian(258;0.0154)|Acute lymphoblastic leukemia(118;0.155)	Breast(495;0.159)	BRCA - Breast invasive adenocarcinoma(115;0.158)															---	---	---	---
EIF2C2	27161	broad.mit.edu	37	8	141568575	141568575	+	Intron	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:141568575G>A	uc003yvn.2	-						EIF2C2_uc010men.2_Intron|EIF2C2_uc010meo.2_Intron	NM_012154	NP_036286			argonaute 2 isoform 1						mRNA cleavage involved in gene silencing by miRNA|negative regulation of translation involved in gene silencing by miRNA|negative regulation of translational initiation|pre-miRNA processing|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasmic mRNA processing body|cytosol|micro-ribonucleoprotein complex|mRNA cap binding complex|nucleus|polysome|RNA-induced silencing complex	endoribonuclease activity, cleaving siRNA-paired mRNA|metal ion binding|protein binding|RNA 7-methylguanosine cap binding|siRNA binding|translation initiation factor activity				0	all_cancers(97;2.54e-14)|all_epithelial(106;5.99e-13)|Lung NSC(106;1.45e-05)|all_lung(105;2.07e-05)|Ovarian(258;0.0154)|Acute lymphoblastic leukemia(118;0.155)	Breast(495;0.159)	BRCA - Breast invasive adenocarcinoma(115;0.158)															---	---	---	---
DENND3	22898	broad.mit.edu	37	8	142178119	142178119	+	Silent	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:142178119G>A	uc003yvy.2	+	13	1808	c.1530G>A	c.(1528-1530)CCG>CCA	p.P510P	DENND3_uc010mep.2_Silent_p.P471P|DENND3_uc003yvz.1_Silent_p.P194P	NM_014957	NP_055772	A2RUS2	DEND3_HUMAN	DENN/MADD domain containing 3	510										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)															---	---	---	---
BAI1	575	broad.mit.edu	37	8	143569830	143569830	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:143569830T>C	uc003ywm.2	+	13	2597	c.2414T>C	c.(2413-2415)GTC>GCC	p.V805A		NM_001702	NP_001693	O14514	BAI1_HUMAN	brain-specific angiogenesis inhibitor 1	805	Extracellular (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)																	---	---	---	---
GML	2765	broad.mit.edu	37	8	143921918	143921918	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:143921918G>A	uc003yxg.2	+	2	155	c.65G>A	c.(64-66)CGC>CAC	p.R22H		NM_002066	NP_002057	Q99445	GML_HUMAN	glycosylphosphatidylinositol anchored molecule	22					apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|negative regulation of cell proliferation	anchored to membrane|extrinsic to membrane|plasma membrane				central_nervous_system(2)	2	all_cancers(97;4.26e-11)|all_epithelial(106;1.85e-08)|Lung NSC(106;0.000274)|all_lung(105;0.000755)|Medulloblastoma(13;0.00276)|all_neural(13;0.00559)|Ovarian(258;0.0254)|Acute lymphoblastic leukemia(118;0.155)																	---	---	---	---
CYP11B1	1584	broad.mit.edu	37	8	143956433	143956433	+	Silent	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:143956433G>A	uc003yxi.2	-	8	1345	c.1338C>T	c.(1336-1338)GGC>GGT	p.G446G	CYP11B1_uc010mex.2_Silent_p.G145G|CYP11B1_uc003yxh.2_Intron|CYP11B1_uc003yxj.2_Intron|CYP11B1_uc010mey.2_Silent_p.G517G	NM_000497	NP_000488	P15538	C11B1_HUMAN	cytochrome P450, family 11, subfamily B,	446					aldosterone biosynthetic process|cellular response to hormone stimulus|cellular response to potassium ion|cortisol biosynthetic process|glucose homeostasis|immune response|regulation of blood pressure|response to stress|xenobiotic metabolic process	mitochondrial inner membrane	electron carrier activity|steroid 11-beta-monooxygenase activity			ovary(3)	3	all_cancers(97;4.74e-11)|all_epithelial(106;2.06e-08)|Lung NSC(106;0.000228)|all_lung(105;0.000633)|Medulloblastoma(13;0.00276)|all_neural(13;0.00559)|Ovarian(258;0.0254)|Acute lymphoblastic leukemia(118;0.155)				Mitotane(DB00648)									Familial_Hyperaldosteronism_type_I				---	---	---	---
ZNF623	9831	broad.mit.edu	37	8	144733184	144733184	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:144733184G>T	uc003yzd.2	+	1	1231	c.1142G>T	c.(1141-1143)GGG>GTG	p.G381V	ZNF623_uc011lkp.1_Missense_Mutation_p.G341V|ZNF623_uc003yzc.2_Missense_Mutation_p.G341V	NM_014789	NP_055604	O75123	ZN623_HUMAN	zinc finger protein 623 isoform 1	381	C2H2-type 10.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0	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;2.46e-41)|Epithelial(56;5.28e-40)|all cancers(56;5.23e-35)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.146)															---	---	---	---
ZNF623	9831	broad.mit.edu	37	8	144733352	144733352	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:144733352G>T	uc003yzd.2	+	1	1399	c.1310G>T	c.(1309-1311)GGG>GTG	p.G437V	ZNF623_uc011lkp.1_Missense_Mutation_p.G397V|ZNF623_uc003yzc.2_Missense_Mutation_p.G397V	NM_014789	NP_055604	O75123	ZN623_HUMAN	zinc finger protein 623 isoform 1	437	C2H2-type 12.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0	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;2.46e-41)|Epithelial(56;5.28e-40)|all cancers(56;5.23e-35)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.146)															---	---	---	---
SCRIB	23513	broad.mit.edu	37	8	144896004	144896004	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:144896004C>T	uc003yzp.1	-	3	347	c.340G>A	c.(340-342)GGG>AGG	p.G114R	SCRIB_uc003yzo.1_Missense_Mutation_p.G114R|MIR937_hsa-mir-937|MI0005759_5'Flank	NM_015356	NP_056171	Q14160	SCRIB_HUMAN	scribble isoform b	114	LRR 4.|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	144942242	144942242	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:144942242C>T	uc003zaa.1	-	1	5193	c.5180G>A	c.(5179-5181)GGC>GAC	p.G1727D		NM_031308	NP_112598	P58107	EPIPL_HUMAN	epiplakin 1	1727	Plectin 30.					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	144945054	144945054	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:144945054C>T	uc003zaa.1	-	1	2381	c.2368G>A	c.(2368-2370)GAG>AAG	p.E790K		NM_031308	NP_112598	P58107	EPIPL_HUMAN	epiplakin 1	790	Plectin 15.					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	144994245	144994245	+	Silent	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:144994245G>A	uc003zaf.1	-	32	10325	c.10155C>T	c.(10153-10155)GGC>GGT	p.G3385G	PLEC_uc003zab.1_Silent_p.G3248G|PLEC_uc003zac.1_Silent_p.G3252G|PLEC_uc003zad.2_Silent_p.G3248G|PLEC_uc003zae.1_Silent_p.G3216G|PLEC_uc003zag.1_Silent_p.G3226G|PLEC_uc003zah.2_Silent_p.G3234G|PLEC_uc003zaj.2_Silent_p.G3275G	NM_201380	NP_958782	Q15149	PLEC_HUMAN	plectin isoform 1	3385	Globular 2.				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	145002166	145002166	+	Intron	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:145002166G>A	uc003zaf.1	-						PLEC_uc003zab.1_Intron|PLEC_uc003zac.1_Intron|PLEC_uc003zad.2_Intron|PLEC_uc003zae.1_Intron|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																		---	---	---	---
PLEC	5339	broad.mit.edu	37	8	145009056	145009056	+	Silent	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:145009056C>T	uc003zaf.1	-	9	1448	c.1278G>A	c.(1276-1278)CTG>CTA	p.L426L	PLEC_uc003zab.1_Silent_p.L289L|PLEC_uc003zac.1_Silent_p.L293L|PLEC_uc003zad.2_Silent_p.L289L|PLEC_uc003zae.1_Silent_p.L257L|PLEC_uc003zag.1_Silent_p.L267L|PLEC_uc003zah.2_Silent_p.L275L|PLEC_uc003zaj.2_Silent_p.L316L	NM_201380	NP_958782	Q15149	PLEC_HUMAN	plectin isoform 1	426	Globular 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																		---	---	---	---
PLEC	5339	broad.mit.edu	37	8	145009256	145009256	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:145009256A>G	uc003zaf.1	-	8	1329	c.1159T>C	c.(1159-1161)TCC>CCC	p.S387P	PLEC_uc003zab.1_Missense_Mutation_p.S250P|PLEC_uc003zac.1_Missense_Mutation_p.S254P|PLEC_uc003zad.2_Missense_Mutation_p.S250P|PLEC_uc003zae.1_Missense_Mutation_p.S218P|PLEC_uc003zag.1_Missense_Mutation_p.S228P|PLEC_uc003zah.2_Missense_Mutation_p.S236P|PLEC_uc003zaj.2_Missense_Mutation_p.S277P	NM_201380	NP_958782	Q15149	PLEC_HUMAN	plectin isoform 1	387	CH 2.|Globular 1.|Actin-binding.				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																		---	---	---	---
PARP10	84875	broad.mit.edu	37	8	145057415	145057415	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:145057415G>A	uc003zal.3	-	8	2450	c.2342C>T	c.(2341-2343)GCT>GTT	p.A781V	PARP10_uc003zak.3_Missense_Mutation_p.A478V|PARP10_uc011lku.1_Missense_Mutation_p.A793V|PARP10_uc011lkv.1_Intron|PARP10_uc003zam.2_Missense_Mutation_p.A772V	NM_032789	NP_116178	Q53GL7	PAR10_HUMAN	poly (ADP-ribose) polymerase family, member 10	781	Myc binding.					Golgi apparatus|nucleolus	NAD+ ADP-ribosyltransferase activity|nucleotide binding			ovary(2)|upper_aerodigestive_tract(1)|lung(1)|breast(1)|pancreas(1)	6	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;1.31e-40)|Epithelial(56;1.16e-39)|all cancers(56;6.43e-35)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.105)															---	---	---	---
GPAA1	8733	broad.mit.edu	37	8	145139744	145139744	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:145139744C>T	uc003zax.2	+	8	1240	c.1130C>T	c.(1129-1131)GCT>GTT	p.A377V	GPAA1_uc003zav.1_Missense_Mutation_p.A255V|GPAA1_uc003zaw.1_Missense_Mutation_p.A317V	NM_003801	NP_003792	O43292	GPAA1_HUMAN	glycosylphosphatidylinositol anchor attachment	377	Helical; (Potential).				attachment of GPI anchor to protein|C-terminal protein lipidation|protein complex assembly|protein retention in ER lumen	GPI-anchor transamidase complex	tubulin binding				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;3.38e-41)|Epithelial(56;6.02e-40)|all cancers(56;2.11e-35)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.105)															---	---	---	---
GPAA1	8733	broad.mit.edu	37	8	145140209	145140209	+	Silent	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:145140209G>A	uc003zax.2	+	10	1388	c.1278G>A	c.(1276-1278)TCG>TCA	p.S426S		NM_003801	NP_003792	O43292	GPAA1_HUMAN	glycosylphosphatidylinositol anchor attachment	426	Cytoplasmic (Potential).				attachment of GPI anchor to protein|C-terminal protein lipidation|protein complex assembly|protein retention in ER lumen	GPI-anchor transamidase complex	tubulin binding				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;3.38e-41)|Epithelial(56;6.02e-40)|all cancers(56;2.11e-35)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.105)															---	---	---	---
SHARPIN	81858	broad.mit.edu	37	8	145154030	145154030	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:145154030G>T	uc003zba.2	-	7	1485	c.1001C>A	c.(1000-1002)CCC>CAC	p.P334H	SHARPIN_uc003zbb.2_Intron	NM_030974	NP_112236	Q9H0F6	SHRPN_HUMAN	shank-interacting protein-like 1	334					negative regulation of inflammatory response|positive regulation of I-kappaB kinase/NF-kappaB cascade|protein linear polyubiquitination|regulation of CD40 signaling pathway|regulation of tumor necrosis factor-mediated signaling pathway	cytosol|LUBAC complex	polyubiquitin binding|zinc ion binding			ovary(1)	1	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;4.1e-42)|Epithelial(56;1.58e-40)|all cancers(56;6.12e-36)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.105)															---	---	---	---
GPR172A	79581	broad.mit.edu	37	8	145584287	145584287	+	Missense_Mutation	SNP	G	A	A	rs145502954	byFrequency	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:145584287G>A	uc003zcc.1	+	4	1196	c.1039G>A	c.(1039-1041)GTG>ATG	p.V347M	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.V347M|GPR172A_uc003zce.1_Missense_Mutation_p.V347M|GPR172A_uc010mfy.1_Missense_Mutation_p.V347M|GPR172A_uc003zcf.1_Missense_Mutation_p.V347M|GPR172A_uc011llc.1_Missense_Mutation_p.V259M	NM_024531	NP_078807	Q9HAB3	RFT3_HUMAN	G protein-coupled receptor 172A precursor	347	Helical; (Potential).					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)															---	---	---	---
CPSF1	29894	broad.mit.edu	37	8	145620511	145620511	+	Silent	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:145620511G>A	uc003zcj.2	-	28	3231	c.3156C>T	c.(3154-3156)GGC>GGT	p.G1052G	MIR939_hsa-mir-939|MI0005761_5'Flank|CPSF1_uc011lld.1_RNA	NM_013291	NP_037423	Q10570	CPSF1_HUMAN	cleavage and polyadenylation specific factor 1,	1052					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)															---	---	---	---
CPSF1	29894	broad.mit.edu	37	8	145623258	145623258	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:145623258C>T	uc003zcj.2	-	20	2059	c.1984G>A	c.(1984-1986)GAG>AAG	p.E662K		NM_013291	NP_037423	Q10570	CPSF1_HUMAN	cleavage and polyadenylation specific factor 1,	662					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)															---	---	---	---
CPSF1	29894	broad.mit.edu	37	8	145625650	145625650	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:145625650C>T	uc003zcj.2	-	9	922	c.847G>A	c.(847-849)GTC>ATC	p.V283I	CPSF1_uc003zck.1_Missense_Mutation_p.V205I|CPSF1_uc011lle.1_Missense_Mutation_p.V283I|MIR1234_hsa-mir-1234|MI0006324_5'Flank	NM_013291	NP_037423	Q10570	CPSF1_HUMAN	cleavage and polyadenylation specific factor 1,	283					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)															---	---	---	---
VPS28	51160	broad.mit.edu	37	8	145649357	145649357	+	Intron	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:145649357G>A	uc003zcr.1	-						VPS28_uc003zcs.1_Intron|VPS28_uc003zct.1_Silent_p.P205P	NM_016208	NP_057292			vacuolar protein sorting 28 isoform 1						cellular membrane organization|endosome transport|negative regulation of protein ubiquitination|protein transport	cytosol|late endosome membrane|plasma membrane	protein binding				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;8.67e-41)|all cancers(56;1.1e-35)|BRCA - Breast invasive adenocarcinoma(115;0.035)|Colorectal(110;0.055)															---	---	---	---
PPP1R16A	84988	broad.mit.edu	37	8	145722710	145722710	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:145722710C>A	uc003zdd.2	+	2	1046	c.133C>A	c.(133-135)CAG>AAG	p.Q45K	uc003zde.1_Missense_Mutation_p.W135L|PPP1R16A_uc003zdf.2_Missense_Mutation_p.Q45K	NM_032902	NP_116291	Q96I34	PP16A_HUMAN	protein phosphatase 1, regulatory (inhibitor)	45	Potential.			Missing (in Ref. 1; BAC03452).		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)															---	---	---	---
GPT	2875	broad.mit.edu	37	8	145731402	145731402	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:145731402G>A	uc011lli.1	+	8	1001	c.844G>A	c.(844-846)GCG>ACG	p.A282T	GPT_uc011llj.1_Missense_Mutation_p.R304H|GPT_uc003zdh.3_Missense_Mutation_p.A282T	NM_005309	NP_005300	P24298	ALAT1_HUMAN	glutamic pyruvate transaminase	282					gluconeogenesis	cytosol	1-aminocyclopropane-1-carboxylate synthase activity|L-alanine:2-oxoglutarate aminotransferase activity|pyridoxal phosphate binding			ovary(1)|central_nervous_system(1)	2	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)		L-Alanine(DB00160)|L-Glutamic Acid(DB00142)|Pyridoxal Phosphate(DB00114)													---	---	---	---
ZNF16	7564	broad.mit.edu	37	8	146171443	146171443	+	Silent	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:146171443A>G	uc003zet.2	-	3	337	c.150T>C	c.(148-150)TGT>TGC	p.C50C	ZNF16_uc003zeu.2_Silent_p.C50C	NM_001029976	NP_001025147	P17020	ZNF16_HUMAN	zinc finger protein 16	50					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(5)	5	all_cancers(97;8.72e-12)|all_epithelial(106;1.07e-10)|Lung NSC(106;7.18e-05)|all_lung(105;0.00021)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)	Acute lymphoblastic leukemia(644;0.136)	Epithelial(56;3.45e-38)|all cancers(56;3.04e-33)|BRCA - Breast invasive adenocarcinoma(115;0.0424)|Colorectal(110;0.055)	GBM - Glioblastoma multiforme(99;0.02)|KIRC - Kidney renal clear cell carcinoma(644;0.0486)														---	---	---	---
FOXD4	2298	broad.mit.edu	37	9	116942	116942	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:116942G>A	uc003zfz.2	-	1	1476	c.1178C>T	c.(1177-1179)TCG>TTG	p.S393L		NM_207305	NP_997188	Q12950	FOXD4_HUMAN	forkhead box D4	393					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	164038	164038	+	Splice_Site	SNP	C	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:164038C>G	uc003zga.3	-	5	537	c.431_splice	c.e5-1	p.G144_splice	CBWD1_uc010mgs.2_Splice_Site|CBWD1_uc003zgb.3_Splice_Site_p.G108_splice|CBWD1_uc003zgc.3_Splice_Site_p.G144_splice|CBWD1_uc011llr.1_Splice_Site_p.G108_splice	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	370256	370256	+	Silent	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:370256T>C	uc003zgf.2	+	16	1936	c.1824T>C	c.(1822-1824)CCT>CCC	p.P608P	DOCK8_uc010mgu.2_5'UTR|DOCK8_uc010mgv.2_Silent_p.P540P|DOCK8_uc010mgw.1_5'UTR|DOCK8_uc003zgk.2_Silent_p.P66P|DOCK8_uc003zgh.2_RNA	NM_203447	NP_982272	Q8NF50	DOCK8_HUMAN	dedicator of cytokinesis 8	608					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)														---	---	---	---
KANK1	23189	broad.mit.edu	37	9	712851	712851	+	Silent	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:712851C>T	uc003zgl.1	+	7	2734	c.2085C>T	c.(2083-2085)TGC>TGT	p.C695C	KANK1_uc003zgm.2_Silent_p.C695C|KANK1_uc003zgn.1_Silent_p.C695C|KANK1_uc003zgo.1_Silent_p.C695C|KANK1_uc003zgp.1_Silent_p.C695C|KANK1_uc003zgq.2_Silent_p.C537C|KANK1_uc003zgr.1_Silent_p.C537C|KANK1_uc003zgs.1_Silent_p.C537C	NM_015158	NP_055973	Q14678	KANK1_HUMAN	KN motif and ankyrin repeat domains 1 isoform a	695					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)														---	---	---	---
KIAA1432	57589	broad.mit.edu	37	9	5763594	5763594	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:5763594A>G	uc003zji.2	+	18	2423	c.2330A>G	c.(2329-2331)TAC>TGC	p.Y777C	KIAA1432_uc003zjh.2_Missense_Mutation_p.Y777C|KIAA1432_uc003zjl.3_Missense_Mutation_p.Y740C|KIAA1432_uc003zjj.1_Missense_Mutation_p.Y319C	NM_020829	NP_065880	Q4ADV7	RIC1_HUMAN	connexin 43-interacting protein 150 isoform a	856						integral to membrane					0		Acute lymphoblastic leukemia(23;0.154)		GBM - Glioblastoma multiforme(50;0.000525)|Lung(218;0.122)														---	---	---	---
ERMP1	79956	broad.mit.edu	37	9	5787252	5787252	+	Silent	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:5787252C>T	uc003zjm.1	-	15	2661	c.2607G>A	c.(2605-2607)CTG>CTA	p.L869L	ERMP1_uc011lme.1_RNA|ERMP1_uc010mhs.1_Silent_p.L483L	NM_024896	NP_079172	Q7Z2K6	ERMP1_HUMAN	aminopeptidase Fxna	869	Extracellular (Potential).				proteolysis	endoplasmic reticulum membrane|integral to membrane	metal ion binding|metallopeptidase activity			ovary(1)	1		Acute lymphoblastic leukemia(23;0.158)		GBM - Glioblastoma multiforme(50;0.00115)|Lung(218;0.111)														---	---	---	---
KIAA2026	158358	broad.mit.edu	37	9	5923005	5923005	+	Silent	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:5923005A>G	uc003zjq.3	-	8	3207	c.2991T>C	c.(2989-2991)TCT>TCC	p.S997S	KIAA2026_uc010mht.2_Silent_p.S172S	NM_001017969	NP_001017969	Q5HYC2	K2026_HUMAN	hypothetical protein LOC158358	997										ovary(2)|central_nervous_system(1)	3		Acute lymphoblastic leukemia(23;0.158)		GBM - Glioblastoma multiforme(50;0.00155)|Lung(218;0.124)														---	---	---	---
RANBP6	26953	broad.mit.edu	37	9	6012658	6012658	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:6012658T>G	uc003zjr.2	-	1	2961	c.2950A>C	c.(2950-2952)ATA>CTA	p.I984L	RANBP6_uc011lmf.1_Missense_Mutation_p.I632L|RANBP6_uc003zjs.2_Missense_Mutation_p.I572L	NM_012416	NP_036548	O60518	RNBP6_HUMAN	RAN binding protein 6	984	HEAT 7.				protein transport	cytoplasm|nucleus	binding			ovary(3)	3		Acute lymphoblastic leukemia(23;0.158)		GBM - Glioblastoma multiforme(50;0.00522)|Lung(218;0.101)														---	---	---	---
GLDC	2731	broad.mit.edu	37	9	6605128	6605128	+	Intron	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:6605128T>C	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)													---	---	---	---
PTPRD	5789	broad.mit.edu	37	9	8338984	8338984	+	Missense_Mutation	SNP	G	T	T	rs34704234		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:8338984G>T	uc003zkk.2	-	42	6028	c.5317C>A	c.(5317-5319)CCC>ACC	p.P1773T	PTPRD_uc003zkp.2_Missense_Mutation_p.P1367T|PTPRD_uc003zkq.2_Missense_Mutation_p.P1366T|PTPRD_uc003zkr.2_Missense_Mutation_p.P1357T|PTPRD_uc003zks.2_Missense_Mutation_p.P1366T|PTPRD_uc003zkl.2_Missense_Mutation_p.P1764T|PTPRD_uc003zkm.2_Missense_Mutation_p.P1760T|PTPRD_uc003zkn.2_Missense_Mutation_p.P1362T|PTPRD_uc003zko.2_Missense_Mutation_p.P1363T	NM_002839	NP_002830	P23468	PTPRD_HUMAN	protein tyrosine phosphatase, receptor type, D	1773	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)			---	---	---	---
MPDZ	8777	broad.mit.edu	37	9	13168424	13168424	+	Silent	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:13168424T>C	uc010mia.1	-	21	3252	c.3195A>G	c.(3193-3195)GTA>GTG	p.V1065V	MPDZ_uc011lmm.1_5'Flank|MPDZ_uc003zkz.3_5'UTR|MPDZ_uc010mhy.2_Silent_p.V1065V|MPDZ_uc010mhz.2_Silent_p.V1065V|MPDZ_uc011lmn.1_Silent_p.V1065V|MPDZ_uc003zlb.3_Silent_p.V1065V	NM_003829	NP_003820	O75970	MPDZ_HUMAN	multiple PDZ domain protein	1065	PDZ 6.				interspecies interaction between organisms	apical plasma membrane|dendrite|postsynaptic density|postsynaptic membrane|synaptosome|tight junction	protein C-terminus binding			ovary(5)|central_nervous_system(1)	6				GBM - Glioblastoma multiforme(50;2.03e-06)														---	---	---	---
FREM1	158326	broad.mit.edu	37	9	14808043	14808043	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:14808043A>G	uc003zlm.2	-	17	3573	c.2983T>C	c.(2983-2985)TAC>CAC	p.Y995H	FREM1_uc010mic.2_RNA	NM_144966	NP_659403	Q5H8C1	FREM1_HUMAN	FRAS1 related extracellular matrix 1 precursor	995	CSPG 6.				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	17273755	17273755	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:17273755G>A	uc003zmz.2	+	6	900	c.874G>A	c.(874-876)GCA>ACA	p.A292T	CNTLN_uc003zmx.3_Missense_Mutation_p.A292T|CNTLN_uc003zmy.2_Missense_Mutation_p.A292T|CNTLN_uc010mio.2_5'UTR	NM_017738	NP_060208	Q9NXG0	CNTLN_HUMAN	centlein isoform 1	292						centriole|membrane	two-component sensor activity			pancreas(1)	1				GBM - Glioblastoma multiforme(50;6.14e-10)														---	---	---	---
ADAMTSL1	92949	broad.mit.edu	37	9	18777810	18777810	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:18777810A>G	uc003zne.3	+	19	3710	c.3583A>G	c.(3583-3585)ACA>GCA	p.T1195A		NM_001040272	NP_001035362	Q8N6G6	ATL1_HUMAN	ADAMTS-like 1 isoform 4 precursor	1195	Ig-like C2-type 2.					proteinaceous extracellular matrix	metallopeptidase activity|zinc ion binding			ovary(3)|upper_aerodigestive_tract(1)|lung(1)	5				GBM - Glioblastoma multiforme(50;1.29e-17)														---	---	---	---
DENND4C	55667	broad.mit.edu	37	9	19346931	19346931	+	Silent	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:19346931T>C	uc003znq.2	+	18	3342	c.3309T>C	c.(3307-3309)GGT>GGC	p.G1103G	DENND4C_uc011lnc.1_Silent_p.G433G|DENND4C_uc011lnd.1_Silent_p.G391G|DENND4C_uc003znr.2_Silent_p.G391G|DENND4C_uc003zns.2_Silent_p.G285G|DENND4C_uc003znt.2_Silent_p.G285G	NM_017925	NP_060395	Q5VZ89	DEN4C_HUMAN	DENN/MADD domain containing 4C	1103						integral to membrane				ovary(1)|skin(1)	2																		---	---	---	---
SLC24A2	25769	broad.mit.edu	37	9	19786265	19786265	+	Silent	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:19786265G>A	uc003zoa.1	-	1	662	c.600C>T	c.(598-600)CAC>CAT	p.H200H	SLC24A2_uc003zob.1_Silent_p.H200H	NM_020344	NP_065077	Q9UI40	NCKX2_HUMAN	solute carrier family 24	200	Extracellular (Potential).|Alpha-1.				visual perception	integral to membrane|plasma membrane	calcium, potassium:sodium antiporter activity|symporter activity			ovary(3)	3				GBM - Glioblastoma multiforme(1;1.67e-55)|Lung(42;0.0443)														---	---	---	---
IFNA7	3444	broad.mit.edu	37	9	21202170	21202170	+	5'UTR	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:21202170T>C	uc003zop.1	-	1					IFNA14_uc003zoo.1_Intron	NM_021057	NP_066401			interferon, alpha 7 precursor						blood coagulation|cell-cell signaling|regulation of type I interferon-mediated signaling pathway|response to virus|type I interferon-mediated signaling pathway	extracellular space	cytokine activity|interferon-alpha/beta receptor binding				0				GBM - Glioblastoma multiforme(5;4.75e-197)|Lung(24;1.26e-23)|LUSC - Lung squamous cell carcinoma(38;1.4e-13)														---	---	---	---
KLHL9	55958	broad.mit.edu	37	9	21333121	21333121	+	Missense_Mutation	SNP	G	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:21333121G>C	uc003zoy.2	-	1	2309	c.1738C>G	c.(1738-1740)CTT>GTT	p.L580V	KLHL9_uc003zow.2_Intron|KLHL9_uc003zox.2_RNA	NM_018847	NP_061335	Q9P2J3	KLHL9_HUMAN	kelch-like 9	580	Kelch 6.				cytokinesis|mitosis|protein ubiquitination	Cul3-RING ubiquitin ligase complex|midbody				ovary(3)|skin(1)	4				Lung(24;8.52e-27)|LUSC - Lung squamous cell carcinoma(38;1.4e-13)|OV - Ovarian serous cystadenocarcinoma(39;0.118)														---	---	---	---
LINGO2	158038	broad.mit.edu	37	9	27949031	27949031	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:27949031T>C	uc003zqu.1	-	2	1833	c.1639A>G	c.(1639-1641)ATG>GTG	p.M547V	LINGO2_uc010mjf.1_Missense_Mutation_p.M547V|LINGO2_uc003zqv.1_Missense_Mutation_p.M547V	NM_152570	NP_689783	Q7L985	LIGO2_HUMAN	leucine rich repeat and Ig domain containing 2	547	Helical; (Potential).					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)														---	---	---	---
AQP7	364	broad.mit.edu	37	9	33385801	33385801	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:33385801C>T	uc003zst.2	-	7	761	c.589G>A	c.(589-591)GCA>ACA	p.A197T	SUGT1P1_uc010mjq.1_Intron|AQP7_uc003zsu.1_Missense_Mutation_p.A140T|AQP7_uc010mjs.2_Missense_Mutation_p.A105T|AQP7_uc010mjt.2_Missense_Mutation_p.A105T|AQP7_uc011lnx.1_Missense_Mutation_p.A197T|AQP7_uc011lny.1_Missense_Mutation_p.A196T|AQP7_uc003zss.3_Missense_Mutation_p.A105T|AQP7_uc011lnz.1_Missense_Mutation_p.A105T|AQP7_uc011loa.1_Missense_Mutation_p.S65N	NM_001170	NP_001161	O14520	AQP7_HUMAN	aquaporin 7	197	Helical; (Potential).				excretion|generation of precursor metabolites and energy	cell-cell junction|cytoplasm|integral to plasma membrane	glycerol channel activity|water channel activity				0			LUSC - Lung squamous cell carcinoma(29;0.00788)	GBM - Glioblastoma multiforme(74;0.191)														---	---	---	---
UBAP2	55833	broad.mit.edu	37	9	34017053	34017053	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:34017053C>T	uc003ztq.1	-	2	207	c.94G>A	c.(94-96)GTA>ATA	p.V32I	UBAP2_uc011loc.1_5'UTR|UBAP2_uc011lod.1_Intron|UBAP2_uc011loe.1_5'UTR|UBAP2_uc011lof.1_5'UTR|UBAP2_uc011log.1_Missense_Mutation_p.V31I|UBAP2_uc003ztr.2_5'UTR	NM_018449	NP_060919	Q5T6F2	UBAP2_HUMAN	ubiquitin associated protein 2	32										ovary(3)	3			LUSC - Lung squamous cell carcinoma(29;0.00575)	GBM - Glioblastoma multiforme(74;0.168)														---	---	---	---
DNAI1	27019	broad.mit.edu	37	9	34514433	34514433	+	Silent	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:34514433C>T	uc003zum.2	+	17	1804	c.1611C>T	c.(1609-1611)GAC>GAT	p.D537D		NM_012144	NP_036276	Q9UI46	DNAI1_HUMAN	dynein, axonemal, intermediate chain 1	537					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				---	---	---	---
DNAI1	27019	broad.mit.edu	37	9	34514697	34514697	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:34514697A>G	uc003zum.2	+	18	1971	c.1778A>G	c.(1777-1779)TAC>TGC	p.Y593C		NM_012144	NP_036276	Q9UI46	DNAI1_HUMAN	dynein, axonemal, intermediate chain 1	593	WD 4.				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				---	---	---	---
FANCG	2189	broad.mit.edu	37	9	35079527	35079527	+	5'UTR	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:35079527C>T	uc003zwb.1	-	1					FANCG_uc003zwa.1_5'Flank|FANCG_uc010mkj.1_5'UTR|FANCG_uc011lot.1_5'UTR	NM_004629	NP_004620			Fanconi anemia, complementation group G						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				---	---	---	---
RUSC2	9853	broad.mit.edu	37	9	35555539	35555539	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:35555539C>T	uc003zww.2	+	3	2752	c.2497C>T	c.(2497-2499)CCG>TCG	p.P833S	RUSC2_uc010mkq.2_RNA|RUSC2_uc003zwx.3_Missense_Mutation_p.P833S	NM_014806	NP_055621	Q8N2Y8	RUSC2_HUMAN	RUN and SH3 domain containing 2	833						cytosol				ovary(1)	1			Lung(28;0.000837)|LUSC - Lung squamous cell carcinoma(32;0.00109)|STAD - Stomach adenocarcinoma(86;0.194)															---	---	---	---
CCDC107	203260	broad.mit.edu	37	9	35660439	35660439	+	Silent	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:35660439G>A	uc011lox.1	+	3	366	c.300G>A	c.(298-300)AAG>AAA	p.K100K	RMRP_uc003zxh.1_5'Flank|CCDC107_uc011loy.1_Silent_p.K100K|CCDC107_uc003zxj.2_Silent_p.K100K|CCDC107_uc003zxk.2_Silent_p.K100K|C9orf100_uc003zxl.2_RNA|C9orf100_uc003zxm.1_3'UTR	NM_174923	NP_777583	Q8WV48	CC107_HUMAN	coiled-coil domain containing 107 precursor	100						integral to membrane					0	all_epithelial(49;0.217)		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	35736107	35736107	+	Missense_Mutation	SNP	G	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:35736107G>C	uc003zxv.2	+	7	1127	c.674G>C	c.(673-675)AGC>ACC	p.S225T	CREB3_uc010mla.2_Missense_Mutation_p.S144T	NM_006368	NP_006359	O43889	CREB3_HUMAN	cAMP responsive element binding protein 3	249	Cytoplasmic (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)	---	---	---	---
NPR2	4882	broad.mit.edu	37	9	35800753	35800753	+	Silent	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:35800753A>G	uc003zyd.2	+	6	1266	c.1266A>G	c.(1264-1266)GGA>GGG	p.G422G	NPR2_uc010mlb.2_Silent_p.G422G	NM_003995	NP_003986	P20594	ANPRB_HUMAN	natriuretic peptide receptor B precursor	422	Extracellular (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)													---	---	---	---
OR13J1	392309	broad.mit.edu	37	9	35870390	35870390	+	Silent	SNP	C	T	T	rs114188212	byFrequency	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:35870390C>T	uc011lph.1	-	1	9	c.9G>A	c.(7-9)CCG>CCA	p.P3P		NM_001004487	NP_001004487	Q8NGT2	O13J1_HUMAN	olfactory receptor, family 13, subfamily J,	3	Extracellular (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)															---	---	---	---
RECK	8434	broad.mit.edu	37	9	36118927	36118927	+	Silent	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:36118927G>A	uc003zyv.2	+	18	2513	c.2427G>A	c.(2425-2427)TCG>TCA	p.S809S	RECK_uc003zyw.2_Silent_p.S681S|RECK_uc003zyx.2_RNA	NM_021111	NP_066934	O95980	RECK_HUMAN	RECK protein precursor	809						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)															---	---	---	---
RNF38	152006	broad.mit.edu	37	9	36369838	36369838	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:36369838C>T	uc003zzh.2	-	4	639	c.448G>A	c.(448-450)GCA>ACA	p.A150T	RNF38_uc003zzi.2_Missense_Mutation_p.A100T|RNF38_uc003zzj.2_Missense_Mutation_p.A67T|RNF38_uc003zzk.2_Missense_Mutation_p.A67T|RNF38_uc003zzl.2_Missense_Mutation_p.A74T|RNF38_uc003zzm.2_Missense_Mutation_p.A67T	NM_022781	NP_073618	Q9H0F5	RNF38_HUMAN	ring finger protein 38 isoform 1	150							zinc ion binding			central_nervous_system(1)	1			STAD - Stomach adenocarcinoma(86;0.228)															---	---	---	---
CNTNAP3	79937	broad.mit.edu	37	9	39086710	39086710	+	Intron	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:39086710T>C	uc004abi.2	-						CNTNAP3_uc004abj.2_Intron|CNTNAP3_uc011lqr.1_Intron|CNTNAP3_uc004abk.1_Silent_p.V1119V	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)														---	---	---	---
TJP2	9414	broad.mit.edu	37	9	71831387	71831387	+	Intron	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:71831387T>C	uc004ahe.2	+						TJP2_uc011lrs.1_Intron|TJP2_uc004ahb.1_Intron|TJP2_uc011lrt.1_Intron|TJP2_uc004ahd.2_Intron|TJP2_uc004ahf.2_Intron|TJP2_uc011lru.1_Intron|TJP2_uc011lrv.1_Intron	NM_004817	NP_004808			tight junction protein 2 (zona occludens 2)						cellular component disassembly involved in apoptosis	adherens junction|cytoplasm|nucleus|tight junction	guanylate kinase activity|protein binding				0																		---	---	---	---
C9orf135	138255	broad.mit.edu	37	9	72435902	72435902	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:72435902G>A	uc004ahl.2	+	1	172	c.107G>A	c.(106-108)CGC>CAC	p.R36H	C9orf135_uc011lrw.1_5'UTR|C9orf135_uc010moq.2_5'UTR|C9orf135_uc011lrx.1_RNA|C9orf135_uc010mop.2_Missense_Mutation_p.R36H|uc004ahk.2_5'Flank	NM_001010940	NP_001010940	Q5VTT2	CI135_HUMAN	hypothetical protein LOC138255	36	Extracellular (Potential).					integral to membrane				ovary(1)	1																		---	---	---	---
TRPM3	80036	broad.mit.edu	37	9	73152169	73152169	+	Missense_Mutation	SNP	C	T	T	rs141399885	byFrequency	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:73152169C>T	uc004aid.2	-	25	4068	c.3824G>A	c.(3823-3825)CGG>CAG	p.R1275Q	TRPM3_uc004ahu.2_Missense_Mutation_p.R1117Q|TRPM3_uc004ahv.2_Missense_Mutation_p.R1077Q|TRPM3_uc004ahw.2_Missense_Mutation_p.R1147Q|TRPM3_uc004ahx.2_Missense_Mutation_p.R1134Q|TRPM3_uc004ahy.2_Missense_Mutation_p.R1137Q|TRPM3_uc004ahz.2_Missense_Mutation_p.R1124Q|TRPM3_uc004aia.2_Missense_Mutation_p.R1122Q|TRPM3_uc004aib.2_Missense_Mutation_p.R1112Q|TRPM3_uc004aic.2_Missense_Mutation_p.R1275Q	NM_001007471	NP_001007472	Q9HCF6	TRPM3_HUMAN	transient receptor potential cation channel,	1300	Cytoplasmic (Potential).|Potential.					integral to membrane	calcium channel activity			ovary(3)|pancreas(2)|central_nervous_system(2)|skin(2)	9																		---	---	---	---
TRPM3	80036	broad.mit.edu	37	9	73213528	73213528	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:73213528T>C	uc004aid.2	-	20	3063	c.2819A>G	c.(2818-2820)TAC>TGC	p.Y940C	TRPM3_uc004ahu.2_Missense_Mutation_p.Y770C|TRPM3_uc004ahv.2_Missense_Mutation_p.Y742C|TRPM3_uc004ahw.2_Missense_Mutation_p.Y812C|TRPM3_uc004ahx.2_Missense_Mutation_p.Y799C|TRPM3_uc004ahy.2_Missense_Mutation_p.Y802C|TRPM3_uc004ahz.2_Missense_Mutation_p.Y789C|TRPM3_uc004aia.2_Missense_Mutation_p.Y787C|TRPM3_uc004aib.2_Missense_Mutation_p.Y777C|TRPM3_uc004aic.2_Missense_Mutation_p.Y940C	NM_001007471	NP_001007472	Q9HCF6	TRPM3_HUMAN	transient receptor potential cation channel,	965	Helical; (Potential).					integral to membrane	calcium channel activity			ovary(3)|pancreas(2)|central_nervous_system(2)|skin(2)	9																		---	---	---	---
TRPM3	80036	broad.mit.edu	37	9	73218374	73218374	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:73218374C>T	uc004aid.2	-	19	2888	c.2644G>A	c.(2644-2646)GGA>AGA	p.G882R	TRPM3_uc004ahu.2_Missense_Mutation_p.G712R|TRPM3_uc004ahv.2_Missense_Mutation_p.G684R|TRPM3_uc004ahw.2_Missense_Mutation_p.G754R|TRPM3_uc004ahx.2_Missense_Mutation_p.G741R|TRPM3_uc004ahy.2_Missense_Mutation_p.G744R|TRPM3_uc004ahz.2_Missense_Mutation_p.G731R|TRPM3_uc004aia.2_Missense_Mutation_p.G729R|TRPM3_uc004aib.2_Missense_Mutation_p.G719R|TRPM3_uc004aic.2_Missense_Mutation_p.G882R	NM_001007471	NP_001007472	Q9HCF6	TRPM3_HUMAN	transient receptor potential cation channel,	907	Helical; (Potential).					integral to membrane	calcium channel activity			ovary(3)|pancreas(2)|central_nervous_system(2)|skin(2)	9																		---	---	---	---
GDA	9615	broad.mit.edu	37	9	74817483	74817483	+	Intron	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:74817483C>T	uc004aiq.2	+						GDA_uc011lse.1_Intron|GDA_uc011lsf.1_Intron|GDA_uc004air.2_Intron|GDA_uc010mow.1_Intron|GDA_uc004ais.2_Intron|GDA_uc004ait.1_Intron	NM_004293	NP_004284			guanine deaminase						nervous system development|purine base metabolic process|purine nucleotide catabolic process	cytosol	guanine deaminase activity|zinc ion binding			ovary(2)|central_nervous_system(2)|skin(1)	5		Myeloproliferative disorder(762;0.0122)		Lung(182;0.0583)														---	---	---	---
TRPM6	140803	broad.mit.edu	37	9	77376978	77376978	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:77376978C>T	uc004ajl.1	-	26	4847	c.4609G>A	c.(4609-4611)GCT>ACT	p.A1537T	TRPM6_uc004ajk.1_Missense_Mutation_p.A1532T|TRPM6_uc010mpb.1_RNA|TRPM6_uc010mpc.1_Intron|TRPM6_uc010mpd.1_Intron|TRPM6_uc010mpe.1_Intron|TRPM6_uc004ajj.1_Missense_Mutation_p.A493T	NM_017662	NP_060132	Q9BX84	TRPM6_HUMAN	transient receptor potential cation channel,	1537	Cytoplasmic (Potential).				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																		---	---	---	---
TRPM6	140803	broad.mit.edu	37	9	77400880	77400880	+	Silent	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:77400880G>A	uc004ajl.1	-	21	3067	c.2829C>T	c.(2827-2829)TGC>TGT	p.C943C	TRPM6_uc004ajk.1_Silent_p.C938C|TRPM6_uc010mpb.1_RNA|TRPM6_uc010mpc.1_Intron|TRPM6_uc010mpd.1_Intron|TRPM6_uc010mpe.1_Intron|TRPM6_uc004ajm.1_Silent_p.C229C	NM_017662	NP_060132	Q9BX84	TRPM6_HUMAN	transient receptor potential cation channel,	943	Helical; (Potential).				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																		---	---	---	---
PCSK5	5125	broad.mit.edu	37	9	78774052	78774052	+	Silent	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:78774052G>A	uc004ajz.2	+	12	2122	c.1584G>A	c.(1582-1584)TCG>TCA	p.S528S	PCSK5_uc004ajy.2_Silent_p.S528S|PCSK5_uc004aka.2_RNA	NM_006200	NP_006191	Q92824	PCSK5_HUMAN	proprotein convertase subtilisin/kexin type 5	528	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																		---	---	---	---
PRUNE2	158471	broad.mit.edu	37	9	79325492	79325492	+	Silent	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:79325492A>G	uc010mpk.2	-	8	1822	c.1698T>C	c.(1696-1698)CAT>CAC	p.H566H		NM_015225	NP_056040	Q8WUY3	PRUN2_HUMAN	prune homolog 2	566					apoptosis|G1 phase|induction of apoptosis	cytoplasm	metal ion binding|pyrophosphatase activity				0																		---	---	---	---
VPS13A	23230	broad.mit.edu	37	9	79946947	79946947	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:79946947C>A	uc004akr.2	+	46	6273	c.6013C>A	c.(6013-6015)CCA>ACA	p.P2005T	VPS13A_uc004akp.3_Missense_Mutation_p.P2005T|VPS13A_uc004akq.3_Missense_Mutation_p.P2005T|VPS13A_uc004aks.2_Missense_Mutation_p.P1966T|VPS13A_uc004akt.2_Missense_Mutation_p.P345T	NM_033305	NP_150648	Q96RL7	VP13A_HUMAN	vacuolar protein sorting 13A isoform A	2005					Golgi to endosome transport|protein transport	intracellular	protein binding			pancreas(3)|skin(3)|ovary(2)|large_intestine(1)|central_nervous_system(1)	10																		---	---	---	---
TLE1	7088	broad.mit.edu	37	9	84249115	84249115	+	Silent	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:84249115G>A	uc004aly.2	-	7	915	c.474C>T	c.(472-474)CTC>CTT	p.L158L	TLE1_uc004alz.2_Silent_p.L168L|TLE1_uc011lsr.1_Silent_p.L158L|TLE1_uc004ama.1_Silent_p.L158L|TLE1_uc011lss.1_Intron|TLE1_uc004amb.2_Silent_p.L158L	NM_005077	NP_005068	Q04724	TLE1_HUMAN	transducin-like enhancer protein 1	158	Gly/Pro-rich.				negative regulation of Wnt receptor signaling pathway|organ morphogenesis|transcription, DNA-dependent|Wnt receptor signaling pathway		transcription factor binding			ovary(1)|skin(1)	2																		---	---	---	---
GKAP1	80318	broad.mit.edu	37	9	86383795	86383795	+	Nonsense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:86383795G>A	uc004amy.2	-	8	1172	c.676C>T	c.(676-678)CGA>TGA	p.R226*	GKAP1_uc004amz.2_Intron|GKAP1_uc011lsu.1_RNA	NM_025211	NP_079487	Q5VSY0	GKAP1_HUMAN	G kinase anchoring protein 1 isoform a	226					signal transduction	Golgi apparatus					0																		---	---	---	---
C9orf64	84267	broad.mit.edu	37	9	86570294	86570294	+	Splice_Site	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:86570294A>G	uc004anb.2	-	2	845	c.597_splice	c.e2+1	p.E199_splice	C9orf64_uc004anc.2_Splice_Site_p.E58_splice	NM_032307	NP_115683			hypothetical protein LOC84267												0																		---	---	---	---
ZCCHC6	79670	broad.mit.edu	37	9	88937354	88937354	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:88937354C>T	uc004aoq.2	-	14	3129	c.2914G>A	c.(2914-2916)GGT>AGT	p.G972S	ZCCHC6_uc010mqe.2_5'Flank|ZCCHC6_uc011ltf.1_RNA|ZCCHC6_uc004aor.2_RNA|ZCCHC6_uc004aos.2_RNA|ZCCHC6_uc004aot.2_Intron|ZCCHC6_uc004aou.2_Missense_Mutation_p.G972S	NM_024617	NP_078893	Q5VYS8	TUT7_HUMAN	zinc finger, CCHC domain containing 6	972	CCHC-type 1.				RNA 3'-end processing		nucleic acid binding|RNA uridylyltransferase activity|zinc ion binding			ovary(2)	2																		---	---	---	---
SEMA4D	10507	broad.mit.edu	37	9	92003846	92003846	+	Silent	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:92003846G>A	uc004aqo.1	-	12	1463	c.891C>T	c.(889-891)TTC>TTT	p.F297F	SEMA4D_uc011ltm.1_Silent_p.F297F|SEMA4D_uc011ltn.1_RNA|SEMA4D_uc011lto.1_RNA|SEMA4D_uc004aqp.1_Silent_p.F295F	NM_006378	NP_006369	Q92854	SEM4D_HUMAN	semaphorin 4D isoform 1	297	Sema.|Extracellular (Potential).				anti-apoptosis|axon guidance|cell adhesion|immune response	integral to membrane|plasma membrane	receptor activity|receptor binding			ovary(1)|pancreas(1)	2																		---	---	---	---
IARS	3376	broad.mit.edu	37	9	94985709	94985709	+	Missense_Mutation	SNP	A	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:94985709A>T	uc004art.1	-	32	3729	c.3472T>A	c.(3472-3474)TCG>ACG	p.S1158T	IARS_uc004ars.1_Missense_Mutation_p.S951T|IARS_uc004aru.3_Missense_Mutation_p.S1158T|IARS_uc010mqr.2_Missense_Mutation_p.S1048T|IARS_uc010mqt.2_Missense_Mutation_p.S381T	NM_013417	NP_038203	P41252	SYIC_HUMAN	isoleucine tRNA synthetase	1158					isoleucyl-tRNA aminoacylation	cytosol|nucleus|soluble fraction	ATP binding|isoleucine-tRNA ligase activity|protein binding			ovary(1)|skin(1)	2					L-Isoleucine(DB00167)													---	---	---	---
FGD3	89846	broad.mit.edu	37	9	95773547	95773547	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:95773547G>A	uc004asw.2	+	8	1656	c.1028G>A	c.(1027-1029)CGG>CAG	p.R343Q	FGD3_uc004asx.2_Missense_Mutation_p.R343Q|FGD3_uc004asz.2_Missense_Mutation_p.R343Q|FGD3_uc004ata.2_Missense_Mutation_p.R146Q	NM_001083536	NP_001077005	Q5JSP0	FGD3_HUMAN	FYVE, RhoGEF and PH domain containing 3	343					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|Golgi apparatus|lamellipodium|ruffle	metal ion binding|Rho guanyl-nucleotide exchange factor activity|small GTPase binding			ovary(1)|breast(1)	2																		---	---	---	---
FGD3	89846	broad.mit.edu	37	9	95778045	95778045	+	Silent	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:95778045G>A	uc004asw.2	+	10	1837	c.1209G>A	c.(1207-1209)GTG>GTA	p.V403V	FGD3_uc004asx.2_Silent_p.V403V|FGD3_uc004asz.2_Silent_p.V403V|FGD3_uc004ata.2_Silent_p.V206V|FGD3_uc011luc.1_Silent_p.V6V	NM_001083536	NP_001077005	Q5JSP0	FGD3_HUMAN	FYVE, RhoGEF and PH domain containing 3	403	PH 1.				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|Golgi apparatus|lamellipodium|ruffle	metal ion binding|Rho guanyl-nucleotide exchange factor activity|small GTPase binding			ovary(1)|breast(1)	2																		---	---	---	---
C9orf3	84909	broad.mit.edu	37	9	97555117	97555117	+	Missense_Mutation	SNP	C	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:97555117C>G	uc004ava.2	+	3	1170	c.1035C>G	c.(1033-1035)TGC>TGG	p.C345W	C9orf3_uc004aux.1_Missense_Mutation_p.C345W|C9orf3_uc004auy.2_Missense_Mutation_p.C345W|C9orf3_uc004auz.1_Missense_Mutation_p.C345W	NM_032823	NP_116212	Q8N6M6	AMPO_HUMAN	aminopeptidase O	345					leukotriene biosynthetic process|proteolysis	cytoplasm	aminopeptidase activity|metallopeptidase activity|zinc ion binding			ovary(1)	1				OV - Ovarian serous cystadenocarcinoma(323;0.000275)														---	---	---	---
TSTD2	158427	broad.mit.edu	37	9	100367150	100367150	+	Intron	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:100367150A>G	uc004axn.2	-						TSTD2_uc004axo.2_Intron|TSTD2_uc004axp.1_Intron	NM_139246	NP_640339			thiosulfate sulfurtransferase (rhodanese)-like											ovary(2)	2																		---	---	---	---
TSTD2	158427	broad.mit.edu	37	9	100387961	100387961	+	Splice_Site	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:100387961A>G	uc004axn.2	-	3	970	c.482_splice	c.e3+1	p.S161_splice	TSTD2_uc004axo.2_Splice_Site|TSTD2_uc004axp.1_Intron	NM_139246	NP_640339			thiosulfate sulfurtransferase (rhodanese)-like											ovary(2)	2																		---	---	---	---
INVS	27130	broad.mit.edu	37	9	103059376	103059376	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:103059376G>T	uc004bap.1	+	15	3176	c.2964G>T	c.(2962-2964)AAG>AAT	p.K988N	INVS_uc011lve.1_Missense_Mutation_p.K892N|INVS_uc004bao.1_Missense_Mutation_p.K818N|INVS_uc004baq.1_Missense_Mutation_p.K722N|INVS_uc004bar.1_Missense_Mutation_p.K892N|INVS_uc010mtb.1_Missense_Mutation_p.K662N	NM_014425	NP_055240	Q9Y283	INVS_HUMAN	inversin isoform a	988					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)																---	---	---	---
NIPSNAP3A	25934	broad.mit.edu	37	9	107515246	107515246	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:107515246G>A	uc004bch.1	+	3	436	c.331G>A	c.(331-333)GAA>AAA	p.E111K	NIPSNAP3A_uc011lvt.1_Missense_Mutation_p.E111K|NIPSNAP3A_uc011lvu.1_Missense_Mutation_p.E111K	NM_015469	NP_056284	Q9UFN0	NPS3A_HUMAN	nipsnap homolog 3A	111						cytosol					0																		---	---	---	---
ZNF462	58499	broad.mit.edu	37	9	109690802	109690802	+	Nonsense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:109690802C>T	uc004bcz.2	+	3	4898	c.4609C>T	c.(4609-4611)CGA>TGA	p.R1537*	ZNF462_uc010mto.2_Nonsense_Mutation_p.R1385*|ZNF462_uc004bda.2_Nonsense_Mutation_p.R1385*	NM_021224	NP_067047	Q96JM2	ZN462_HUMAN	zinc finger protein 462	1537	C2H2-type 13.				transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(5)	5																		---	---	---	---
PTPN3	5774	broad.mit.edu	37	9	112168734	112168734	+	Intron	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:112168734G>A	uc004bed.2	-						PTPN3_uc004beb.2_Intron|PTPN3_uc004bec.2_Intron|PTPN3_uc010mtu.2_Intron|PTPN3_uc011lwg.1_Intron|PTPN3_uc011lwh.1_Intron|PTPN3_uc011lwd.1_Intron|PTPN3_uc011lwe.1_Intron|PTPN3_uc011lwf.1_Intron	NM_002829	NP_002820			protein tyrosine phosphatase, non-receptor type						negative regulation of membrane protein ectodomain proteolysis|negative regulation of mitotic cell cycle	cytoplasm|cytoskeleton|internal side of plasma membrane	ATPase binding|cytoskeletal protein binding|phosphotyrosine binding|protein tyrosine phosphatase activity			ovary(3)	3																		---	---	---	---
PALM2-AKAP2	445815	broad.mit.edu	37	9	112900134	112900134	+	Silent	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:112900134C>T	uc004bei.2	+	9	3198	c.3006C>T	c.(3004-3006)GGC>GGT	p.G1002G	PALM2-AKAP2_uc004bek.3_Silent_p.G770G|PALM2-AKAP2_uc004bej.3_Silent_p.G770G|PALM2-AKAP2_uc004bel.1_Silent_p.G580G|AKAP2_uc011lwi.1_Silent_p.G628G|AKAP2_uc004bem.2_Silent_p.G628G|PALM2-AKAP2_uc010mtw.1_Silent_p.G588G|AKAP2_uc011lwj.1_Silent_p.G539G|PALM2-AKAP2_uc004ben.2_Silent_p.G539G	NM_001136562	NP_001130034	Q9Y2D5	AKAP2_HUMAN	A kinase (PRKA) anchor protein 2 isoform 2	539							enzyme binding			ovary(3)|central_nervous_system(2)|skin(1)	6																		---	---	---	---
PALM2-AKAP2	445815	broad.mit.edu	37	9	112918628	112918628	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:112918628T>C	uc004bej.3	+	9	3205	c.3025T>C	c.(3025-3027)TCC>CCC	p.S1009P	PALM2-AKAP2_uc004bek.3_Missense_Mutation_p.S1009P|AKAP2_uc011lwi.1_Missense_Mutation_p.S867P|AKAP2_uc004bem.2_Missense_Mutation_p.S867P|AKAP2_uc011lwj.1_Missense_Mutation_p.S778P|PALM2-AKAP2_uc004ben.2_Intron	NM_007203	NP_009134	Q9Y2D5	AKAP2_HUMAN	PALM2-AKAP2 protein isoform 1	778							enzyme binding			ovary(3)|central_nervous_system(2)|skin(1)	6																		---	---	---	---
SVEP1	79987	broad.mit.edu	37	9	113169672	113169672	+	Silent	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:113169672T>C	uc010mtz.2	-	38	8545	c.8208A>G	c.(8206-8208)GGA>GGG	p.G2736G	SVEP1_uc010mty.2_Silent_p.G662G	NM_153366	NP_699197	Q4LDE5	SVEP1_HUMAN	polydom	2736	Sushi 22.				cell adhesion	cytoplasm|extracellular region|membrane	calcium ion binding			ovary(7)	7																		---	---	---	---
SVEP1	79987	broad.mit.edu	37	9	113194276	113194276	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:113194276G>A	uc010mtz.2	-	32	5609	c.5272C>T	c.(5272-5274)CAT>TAT	p.H1758Y	SVEP1_uc010mty.2_5'Flank	NM_153366	NP_699197	Q4LDE5	SVEP1_HUMAN	polydom	1758	EGF-like 7; calcium-binding (Potential).				cell adhesion	cytoplasm|extracellular region|membrane	calcium ion binding			ovary(7)	7																		---	---	---	---
SUSD1	64420	broad.mit.edu	37	9	114825218	114825218	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:114825218T>C	uc004bfu.2	-	13	1890	c.1849A>G	c.(1849-1851)AGT>GGT	p.S617G	SUSD1_uc010mui.2_Missense_Mutation_p.S617G|SUSD1_uc010muj.2_Missense_Mutation_p.S617G	NM_022486	NP_071931	Q6UWL2	SUSD1_HUMAN	sushi domain containing 1 precursor	617	Extracellular (Potential).					integral to membrane	calcium ion binding				0																		---	---	---	---
PRPF4	9128	broad.mit.edu	37	9	116038826	116038826	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:116038826A>G	uc004bgx.2	+	2	79	c.29A>G	c.(28-30)CAG>CGG	p.Q10R	FKBP15_uc010muu.1_5'Flank|CDC26_uc004bgw.2_5'Flank|PRPF4_uc004bgy.2_Splice_Site_p.A10_splice	NM_004697	NP_004688	O43172	PRP4_HUMAN	PRP4 pre-mRNA processing factor 4 homolog	10						Cajal body|nuclear speck|spliceosomal complex|U4/U6 snRNP	protein binding			ovary(2)|pancreas(1)	3																		---	---	---	---
POLE3	54107	broad.mit.edu	37	9	116171145	116171145	+	Silent	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:116171145G>A	uc011lxg.1	-	4	772	c.390C>T	c.(388-390)GAC>GAT	p.D130D	POLE3_uc004bhn.2_Silent_p.D130D|C9orf43_uc004bho.3_5'Flank|C9orf43_uc004bhp.2_5'Flank	NM_017443	NP_059139	Q9NRF9	DPOE3_HUMAN	DNA-directed DNA polymerase epsilon 3	130	Potential.				DNA replication|histone H3 acetylation	Ada2/Gcn5/Ada3 transcription activator complex	DNA-directed DNA polymerase activity|protein binding|sequence-specific DNA binding				0																		---	---	---	---
COL27A1	85301	broad.mit.edu	37	9	116971994	116971994	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:116971994T>C	uc011lxl.1	+	11	2308	c.2308T>C	c.(2308-2310)TCT>CCT	p.S770P	COL27A1_uc004bii.2_RNA|COL27A1_uc010mvd.1_Missense_Mutation_p.S569P	NM_032888	NP_116277	Q8IZC6	CORA1_HUMAN	collagen, type XXVII, alpha 1 precursor	770	Collagen-like 3.|Pro-rich.|Triple-helical region.				cell adhesion		extracellular matrix structural constituent			ovary(3)|skin(1)	4																		---	---	---	---
COL27A1	85301	broad.mit.edu	37	9	117068945	117068945	+	Missense_Mutation	SNP	A	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:117068945A>T	uc011lxl.1	+	58	5084	c.5084A>T	c.(5083-5085)GAC>GTC	p.D1695V	COL27A1_uc004bii.2_RNA|COL27A1_uc011lxn.1_5'Flank	NM_032888	NP_116277	Q8IZC6	CORA1_HUMAN	collagen, type XXVII, alpha 1 precursor	1695	Fibrillar collagen NC1.				cell adhesion		extracellular matrix structural constituent			ovary(3)|skin(1)	4																OREG0019417	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
ORM1	5004	broad.mit.edu	37	9	117087427	117087427	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:117087427A>G	uc004bik.3	+	5	646	c.535A>G	c.(535-537)AAA>GAA	p.K179E	ORM1_uc011lxo.1_Intron	NM_000607	NP_000598	P02763	A1AG1_HUMAN	orosomucoid 1 precursor	179					acute-phase response|regulation of immune system process|transport	extracellular space	protein binding				0		Myeloproliferative disorder(63;0.163)			Acenocoumarol(DB01418)|Alfentanil(DB00802)|Aprindine(DB01429)|Disopyramide(DB00280)|Penbutolol(DB01359)|Phenprocoumon(DB00946)|Quinidine(DB00908)|Tamsulosin(DB00706)													---	---	---	---
AKNA	80709	broad.mit.edu	37	9	117113177	117113177	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:117113177C>A	uc004biq.3	-	14	3318	c.3183G>T	c.(3181-3183)GAG>GAT	p.E1061D	AKNA_uc004bin.3_Missense_Mutation_p.E308D|AKNA_uc004bio.3_Missense_Mutation_p.E521D|AKNA_uc004bip.3_Missense_Mutation_p.E980D|AKNA_uc004bir.3_Missense_Mutation_p.E1061D|AKNA_uc004bis.3_Missense_Mutation_p.E1061D|AKNA_uc010mve.2_Missense_Mutation_p.E942D|AKNA_uc004bit.1_RNA	NM_030767	NP_110394	Q7Z591	AKNA_HUMAN	AT-hook transcription factor	1061					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding			ovary(4)|central_nervous_system(2)	6																		---	---	---	---
TNC	3371	broad.mit.edu	37	9	117826227	117826227	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:117826227T>C	uc004bjj.3	-	12	3970	c.3608A>G	c.(3607-3609)GAC>GGC	p.D1203G	TNC_uc010mvf.2_Missense_Mutation_p.D1203G	NM_002160	NP_002151	P24821	TENA_HUMAN	tenascin C precursor	1203	Fibronectin type-III 7.				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																		---	---	---	---
ASTN2	23245	broad.mit.edu	37	9	119202889	119202889	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:119202889T>C	uc004bjs.1	-	22	3882	c.3781A>G	c.(3781-3783)AGG>GGG	p.R1261G	ASTN2_uc004bjr.1_Missense_Mutation_p.R1257G|ASTN2_uc004bjt.1_Missense_Mutation_p.R1210G|ASTN2_uc004bjp.1_Missense_Mutation_p.R354G|ASTN2_uc004bjq.1_Missense_Mutation_p.R313G|ASTN2_uc011lxr.1_Missense_Mutation_p.R313G|ASTN2_uc011lxs.1_Missense_Mutation_p.R313G|ASTN2_uc011lxt.1_Missense_Mutation_p.R313G|ASTN2_uc004bjo.1_Missense_Mutation_p.R42G	NM_198187	NP_937830	O75129	ASTN2_HUMAN	astrotactin 2 isoform c	1261	Extracellular (Potential).					integral to membrane				skin(4)|ovary(3)|breast(1)|kidney(1)	9																		---	---	---	---
TRIM32	22954	broad.mit.edu	37	9	119460334	119460334	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:119460334C>T	uc004bjx.2	+	2	471	c.313C>T	c.(313-315)CGG>TGG	p.R105W	ASTN2_uc004bjr.1_Intron|ASTN2_uc004bjs.1_Intron|ASTN2_uc004bjt.1_Intron|TRIM32_uc004bjw.2_Missense_Mutation_p.R105W	NM_001099679	NP_001093149	Q13049	TRI32_HUMAN	tripartite motif-containing 32	105	B box-type.				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				---	---	---	---
ASTN2	23245	broad.mit.edu	37	9	119903671	119903671	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:119903671C>T	uc004bjs.1	-	4	1203	c.1102G>A	c.(1102-1104)GGT>AGT	p.G368S	ASTN2_uc004bjr.1_Missense_Mutation_p.G368S|ASTN2_uc004bjt.1_Intron	NM_198187	NP_937830	O75129	ASTN2_HUMAN	astrotactin 2 isoform c	368	Cytoplasmic (Potential).					integral to membrane				skin(4)|ovary(3)|breast(1)|kidney(1)	9																		---	---	---	---
CDK5RAP2	55755	broad.mit.edu	37	9	123301407	123301407	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:123301407G>A	uc004bkf.2	-	6	600	c.419C>T	c.(418-420)TCT>TTT	p.S140F	CDK5RAP2_uc004bkg.2_Missense_Mutation_p.S140F|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_Missense_Mutation_p.S140F|CDK5RAP2_uc004bki.2_5'Flank	NM_018249	NP_060719	Q96SN8	CK5P2_HUMAN	CDK5 regulatory subunit associated protein 2	140					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																		---	---	---	---
CEP110	11064	broad.mit.edu	37	9	123920160	123920160	+	Splice_Site	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:123920160T>C	uc004bkx.1	+	27	4668	c.4637_splice	c.e27+2	p.E1546_splice	CEP110_uc010mvo.1_Splice_Site_p.E215_splice|CEP110_uc004blb.1_Splice_Site_p.E215_splice|CEP110_uc010mvp.1_Splice_Site	NM_007018	NP_008949			centrosomal protein 110kDa						cell division|G2/M transition of mitotic cell cycle	centrosome|cytosol	protein binding				0																		---	---	---	---
GSN	2934	broad.mit.edu	37	9	124065262	124065262	+	Silent	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:124065262C>T	uc004blf.1	+	3	484	c.423C>T	c.(421-423)GGC>GGT	p.G141G	GSN_uc004bld.1_Silent_p.G90G|GSN_uc010mvq.1_Silent_p.G101G|GSN_uc010mvr.1_Silent_p.G101G|GSN_uc010mvu.1_Silent_p.G90G|GSN_uc010mvt.1_Silent_p.G90G|GSN_uc010mvs.1_Silent_p.G90G|GSN_uc004ble.1_Silent_p.G90G|GSN_uc010mvv.1_Silent_p.G90G|GSN_uc011lyh.1_Silent_p.G107G|GSN_uc011lyi.1_Silent_p.G90G|GSN_uc011lyj.1_Silent_p.G114G	NM_000177	NP_000168	P06396	GELS_HUMAN	gelsolin isoform a precursor	141	Actin-severing (Potential).				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																		---	---	---	---
TTLL11	158135	broad.mit.edu	37	9	124751423	124751423	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:124751423C>A	uc004blt.1	-	4	1778	c.1590G>T	c.(1588-1590)AAG>AAT	p.K530N	TTLL11_uc011lyl.1_Intron|TTLL11_uc004blr.2_Intron|TTLL11_uc011lym.1_Intron|TTLL11_uc004blu.1_3'UTR	NM_194252	NP_919228	Q8NHH1	TTL11_HUMAN	tubulin tyrosine ligase-like family, member 11	530	TTL.				protein modification process	cilium|microtubule basal body	tubulin-tyrosine ligase activity				0																		---	---	---	---
OR1J1	347168	broad.mit.edu	37	9	125240071	125240071	+	Silent	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:125240071G>A	uc011lyu.1	-	1	135	c.135C>T	c.(133-135)ATC>ATT	p.I45I	OR1J2_uc004bmj.1_Intron	NM_001004451	NP_001004451	Q8NGS3	OR1J1_HUMAN	olfactory receptor, family 1, subfamily J,	45	Helical; Name=1; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			skin(2)	2																		---	---	---	---
DENND1A	57706	broad.mit.edu	37	9	126641260	126641260	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:126641260C>T	uc004bnz.1	-	2	291	c.58G>A	c.(58-60)GCC>ACC	p.A20T	DENND1A_uc011lzm.1_Intron|DENND1A_uc004boa.1_Missense_Mutation_p.A20T|DENND1A_uc004bob.1_Nonsense_Mutation_p.W4*|DENND1A_uc004boc.2_Nonsense_Mutation_p.W4*	NM_020946	NP_065997	Q8TEH3	DEN1A_HUMAN	DENN/MADD domain containing 1A isoform 1	20						cell junction|clathrin coated vesicle membrane|presynaptic membrane	guanyl-nucleotide exchange factor activity			ovary(2)	2																		---	---	---	---
NR6A1	2649	broad.mit.edu	37	9	127289189	127289189	+	Intron	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:127289189A>G	uc004bor.1	-						NR6A1_uc004boq.1_Intron|NR6A1_uc010mwq.1_Intron	NM_033334	NP_201591			nuclear receptor subfamily 6, group A, member 1						cell proliferation|negative regulation of transcription from RNA polymerase II promoter|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor|spermatogenesis	transcription factor complex	protein homodimerization activity|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|steroid hormone receptor activity|zinc ion binding			ovary(3)	3																		---	---	---	---
OLFML2A	169611	broad.mit.edu	37	9	127549390	127549390	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:127549390C>T	uc004bov.2	+	2	340	c.227C>T	c.(226-228)ACG>ATG	p.T76M	OLFML2A_uc010mwr.1_Missense_Mutation_p.T76M	NM_182487	NP_872293	Q68BL7	OLM2A_HUMAN	olfactomedin-like 2A precursor	76											0																		---	---	---	---
WDR38	401551	broad.mit.edu	37	9	127618161	127618161	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:127618161C>T	uc004box.2	+	4	385	c.329C>T	c.(328-330)ACG>ATG	p.T110M	WDR38_uc011lzn.1_Missense_Mutation_p.T99M|WDR38_uc011lzo.1_Missense_Mutation_p.T110M|WDR38_uc011lzp.1_Missense_Mutation_p.T61M	NM_001045476	NP_001038941	Q5JTN6	WDR38_HUMAN	WD repeat domain 38	110	WD 3.										0																OREG0019485	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
HSPA5	3309	broad.mit.edu	37	9	128000895	128000895	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:128000895C>T	uc004bpn.2	-	6	1464	c.1208G>A	c.(1207-1209)GGT>GAT	p.G403D		NM_005347	NP_005338	P11021	GRP78_HUMAN	heat shock 70kDa protein 5	403					anti-apoptosis|cellular response to glucose starvation|ER-associated protein catabolic process|platelet activation|platelet degranulation|regulation of protein folding in endoplasmic reticulum	cell surface|endoplasmic reticulum chaperone complex|endoplasmic reticulum lumen|ER-Golgi intermediate compartment|integral to endoplasmic reticulum membrane|melanosome|midbody|nucleus|perinuclear region of cytoplasm	ATP binding|ATPase activity|calcium ion binding|caspase inhibitor activity|chaperone binding|misfolded protein binding|protein binding, bridging|protein domain specific binding|ubiquitin protein ligase binding|unfolded protein binding			ovary(3)|skin(1)	4					Antihemophilic Factor(DB00025)										Prostate(1;0.17)			---	---	---	---
ZNF79	7633	broad.mit.edu	37	9	130206787	130206787	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:130206787A>G	uc004bqw.3	+	5	1222	c.808A>G	c.(808-810)ACC>GCC	p.T270A	ZNF79_uc011maf.1_Missense_Mutation_p.T246A|ZNF79_uc011mag.1_Missense_Mutation_p.T246A	NM_007135	NP_009066	Q15937	ZNF79_HUMAN	zinc finger protein 79	270	C2H2-type 3.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			central_nervous_system(1)	1																		---	---	---	---
STXBP1	6812	broad.mit.edu	37	9	130438961	130438961	+	Missense_Mutation	SNP	G	A	A	rs148131665		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:130438961G>A	uc004brl.2	+	15	1485	c.1288G>A	c.(1288-1290)GCC>ACC	p.A430T	STXBP1_uc004brk.2_Missense_Mutation_p.A430T	NM_001032221	NP_001027392	P61764	STXB1_HUMAN	syntaxin binding protein 1 isoform b	430					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																		---	---	---	---
TOR2A	27433	broad.mit.edu	37	9	130495702	130495702	+	Silent	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:130495702G>A	uc004brs.3	-	3	610	c.555C>T	c.(553-555)TAC>TAT	p.Y185Y	TOR2A_uc004brt.3_Silent_p.Y185Y|TOR2A_uc004brw.3_Silent_p.Y185Y|TOR2A_uc011maj.1_3'UTR|TOR2A_uc004bru.3_Silent_p.Y23Y|TOR2A_uc004brv.3_RNA|TOR2A_uc004brx.1_Silent_p.Y23Y	NM_001085347	NP_001078816	Q5JU69	TOR2A_HUMAN	torsin family 2, member A isoform a	185					chaperone mediated protein folding requiring cofactor	endoplasmic reticulum|extracellular region	ATP binding|nucleoside-triphosphatase activity				0																		---	---	---	---
SLC25A25	114789	broad.mit.edu	37	9	130869725	130869725	+	3'UTR	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:130869725G>A	uc004bte.2	+	10					SLC25A25_uc004btb.2_3'UTR|SLC25A25_uc004btc.2_3'UTR|SLC25A25_uc004btd.2_3'UTR|SLC25A25_uc004btf.2_3'UTR	NM_052901	NP_443133			solute carrier family 25, member 25 isoform a						transmembrane transport	integral to membrane|mitochondrial inner membrane	calcium ion binding				0																		---	---	---	---
DNM1	1759	broad.mit.edu	37	9	130982511	130982511	+	Missense_Mutation	SNP	A	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:130982511A>T	uc011mau.1	+	6	827	c.740A>T	c.(739-741)GAC>GTC	p.D247V	DNM1_uc010mxr.2_Missense_Mutation_p.D247V|DNM1_uc011mat.1_Missense_Mutation_p.D247V	NM_004408	NP_004399	Q05193	DYN1_HUMAN	dynamin 1 isoform 1	247					receptor-mediated endocytosis	microtubule	GTP binding|GTPase activity			ovary(2)	2																		---	---	---	---
GOLGA2	2801	broad.mit.edu	37	9	131023762	131023762	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:131023762G>A	uc011maw.1	-	15	1235	c.1222C>T	c.(1222-1224)CGG>TGG	p.R408W	GOLGA2_uc010mxw.2_Intron|GOLGA2_uc004buh.2_5'Flank|GOLGA2_uc004bul.1_Missense_Mutation_p.R309W|uc004bun.2_5'Flank	NM_004486	NP_004477	Q08379	GOGA2_HUMAN	Golgi autoantigen, golgin subfamily a, 2	408	Potential.					Golgi cisterna membrane	protein binding			ovary(1)	1																		---	---	---	---
SPTAN1	6709	broad.mit.edu	37	9	131365838	131365838	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:131365838T>C	uc004bvl.3	+	28	3709	c.3596T>C	c.(3595-3597)GTT>GCT	p.V1199A	SPTAN1_uc011mbh.1_Missense_Mutation_p.V1211A|SPTAN1_uc004bvm.3_Missense_Mutation_p.V1199A|SPTAN1_uc004bvn.3_Missense_Mutation_p.V1179A	NM_003127	NP_003118	Q13813	SPTA2_HUMAN	spectrin, alpha, non-erythrocytic 1	1199					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																		---	---	---	---
SPTAN1	6709	broad.mit.edu	37	9	131395582	131395582	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:131395582T>C	uc004bvl.3	+	56	7501	c.7388T>C	c.(7387-7389)GTG>GCG	p.V2463A	SPTAN1_uc004bvm.3_Missense_Mutation_p.V2468A|SPTAN1_uc004bvn.3_Missense_Mutation_p.V2443A|SPTAN1_uc004bvo.3_Missense_Mutation_p.V230A|SPTAN1_uc004bvp.3_Missense_Mutation_p.V206A	NM_003127	NP_003118	Q13813	SPTA2_HUMAN	spectrin, alpha, non-erythrocytic 1	2463					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	131504917	131504917	+	Silent	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:131504917C>T	uc004bwa.1	-	9	1900	c.1467G>A	c.(1465-1467)ACG>ACA	p.T489T		NM_006336	NP_006327	Q7Z7L7	ZER1_HUMAN	zyg-11 homolog B (C. elegans)-like	489					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																		---	---	---	---
LRRC8A	56262	broad.mit.edu	37	9	131670110	131670110	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:131670110A>G	uc004bwl.3	+	3	921	c.667A>G	c.(667-669)ATC>GTC	p.I223V	LRRC8A_uc010myp.2_Missense_Mutation_p.I223V|LRRC8A_uc010myq.2_Missense_Mutation_p.I223V	NM_019594	NP_062540	Q8IWT6	LRC8A_HUMAN	leucine rich repeat containing 8 family, member	223					pre-B cell differentiation	integral to membrane					0																		---	---	---	---
DOLK	22845	broad.mit.edu	37	9	131708479	131708479	+	Silent	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:131708479C>T	uc004bwr.2	-	1	1534	c.1104G>A	c.(1102-1104)GCG>GCA	p.A368A	NUP188_uc004bws.1_5'Flank|NUP188_uc004bwq.1_Intron	NM_014908	NP_055723	Q9UPQ8	DOLK_HUMAN	dolichol kinase	368	Helical; (Potential).				dolichyl diphosphate biosynthetic process|dolichyl monophosphate biosynthetic process|post-translational protein modification|protein N-linked glycosylation via asparagine	integral to endoplasmic reticulum membrane|membrane fraction	dolichol kinase activity				0																		---	---	---	---
NUP188	23511	broad.mit.edu	37	9	131749911	131749911	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:131749911T>C	uc004bws.1	+	23	2330	c.2308T>C	c.(2308-2310)TAC>CAC	p.Y770H	NUP188_uc004bwu.2_Missense_Mutation_p.Y113H	NM_015354	NP_056169	Q5SRE5	NU188_HUMAN	nucleoporin 188kDa	770					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	131756681	131756681	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:131756681C>T	uc004bws.1	+	28	3069	c.3047C>T	c.(3046-3048)CCG>CTG	p.P1016L	NUP188_uc004bwu.2_Missense_Mutation_p.P359L	NM_015354	NP_056169	Q5SRE5	NU188_HUMAN	nucleoporin 188kDa	1016					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	131765724	131765724	+	Silent	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:131765724T>C	uc004bws.1	+	38	4447	c.4425T>C	c.(4423-4425)CGT>CGC	p.R1475R	NUP188_uc004bwu.2_Silent_p.R818R	NM_015354	NP_056169	Q5SRE5	NU188_HUMAN	nucleoporin 188kDa	1475					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																		---	---	---	---
TOR1B	27348	broad.mit.edu	37	9	132571786	132571786	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:132571786C>T	uc004byk.1	+	5	995	c.935C>T	c.(934-936)ACG>ATG	p.T312M		NM_014506	NP_055321	O14657	TOR1B_HUMAN	torsin family 1, member B (torsin B) precursor	312					chaperone mediated protein folding requiring cofactor|response to unfolded protein	endoplasmic reticulum lumen	ATP binding|nucleoside-triphosphatase activity|unfolded protein binding				0		Ovarian(14;0.0586)																---	---	---	---
FNBP1	23048	broad.mit.edu	37	9	132687277	132687277	+	Missense_Mutation	SNP	A	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:132687277A>T	uc004byw.1	-	9	1168	c.949T>A	c.(949-951)TCC>ACC	p.S317T	FNBP1_uc011mbv.1_Missense_Mutation_p.S317T|FNBP1_uc011mbw.1_Missense_Mutation_p.S317T|FNBP1_uc004bza.2_Missense_Mutation_p.S317T|FNBP1_uc004byz.1_Missense_Mutation_p.S317T|FNBP1_uc004byx.1_Missense_Mutation_p.S238T|FNBP1_uc004byy.1_Missense_Mutation_p.S238T	NM_015033	NP_055848	Q96RU3	FNBP1_HUMAN	formin binding protein 1	317	Interaction with microtubules (By similarity).|Required for self-association and induction of membrane tubulation.				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								---	---	---	---
EXOSC2	23404	broad.mit.edu	37	9	133574784	133574784	+	Intron	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:133574784A>G	uc004bzu.2	+						EXOSC2_uc011mbz.1_Intron|EXOSC2_uc011mca.1_Intron	NM_014285	NP_055100			exosome component 2						exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay|positive regulation of cell growth|rRNA processing	cytosol|exosome (RNase complex)|nucleolus	3'-5'-exoribonuclease activity|7S RNA binding|protein binding			ovary(1)	1		Acute lymphoblastic leukemia(5;0.0508)|all_hematologic(13;0.0588)		OV - Ovarian serous cystadenocarcinoma(145;0.000324)														---	---	---	---
QRFP	347148	broad.mit.edu	37	9	133769056	133769056	+	Missense_Mutation	SNP	C	T	T	rs148387144	byFrequency	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:133769056C>T	uc011mcb.1	-	1	170	c.170G>A	c.(169-171)CGG>CAG	p.R57Q		NM_198180	NP_937823	P83859	OX26_HUMAN	RF(Arg-Phe)amide family 26 amino acid peptide	57					locomotory behavior|neuropeptide signaling pathway|positive regulation of blood pressure|regulation of feeding behavior	extracellular region	neuropeptide hormone activity|orexigenic neuropeptide QRFP receptor binding				0	all_hematologic(7;0.0028)	Myeloproliferative disorder(178;0.204)		OV - Ovarian serous cystadenocarcinoma(145;6.17e-05)|Epithelial(140;0.000267)														---	---	---	---
FAM78A	286336	broad.mit.edu	37	9	134136686	134136686	+	Silent	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:134136686G>A	uc004cak.2	-	2	715	c.375C>T	c.(373-375)AGC>AGT	p.S125S	FAM78A_uc004caj.2_Silent_p.S122S	NM_033387	NP_203745	Q5JUQ0	FA78A_HUMAN	hypothetical protein LOC286336	125										ovary(1)	1	all_hematologic(7;0.0028)	Myeloproliferative disorder(178;0.204)		OV - Ovarian serous cystadenocarcinoma(145;2.15e-05)|Epithelial(140;0.000267)														---	---	---	---
RAPGEF1	2889	broad.mit.edu	37	9	134501740	134501740	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:134501740G>A	uc004cbc.2	-	10	1350	c.1220C>T	c.(1219-1221)ACG>ATG	p.T407M	RAPGEF1_uc004cbb.2_Missense_Mutation_p.T425M|RAPGEF1_uc010mzm.2_RNA|RAPGEF1_uc010mzn.2_Missense_Mutation_p.T412M|RAPGEF1_uc004cbd.2_Missense_Mutation_p.T412M	NM_005312	NP_005303	Q13905	RPGF1_HUMAN	guanine nucleotide-releasing factor 2 isoform a	407					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)														---	---	---	---
BARHL1	56751	broad.mit.edu	37	9	135458451	135458451	+	Silent	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:135458451G>A	uc004cbp.1	+	1	459	c.267G>A	c.(265-267)TCG>TCA	p.S89S		NM_020064	NP_064448	Q9BZE3	BARH1_HUMAN	BarH-like homeobox 1	89						nucleus	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity				0				OV - Ovarian serous cystadenocarcinoma(145;1.79e-06)|Epithelial(140;3.12e-05)														---	---	---	---
GTF3C5	9328	broad.mit.edu	37	9	135919170	135919170	+	Silent	SNP	G	A	A	rs150454891	byFrequency;by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:135919170G>A	uc004cci.3	+	3	766	c.429G>A	c.(427-429)ACG>ACA	p.T143T	GTF3C5_uc010mzz.2_Silent_p.T18T|GTF3C5_uc004ccj.3_Silent_p.T143T	NM_012087	NP_036219	Q9Y5Q8	TF3C5_HUMAN	general transcription factor IIIC, polypeptide 5	143						transcription factor TFIIIC complex	DNA binding|protein binding				0				OV - Ovarian serous cystadenocarcinoma(145;4.01e-06)|Epithelial(140;4e-05)														---	---	---	---
SURF1	6834	broad.mit.edu	37	9	136220629	136220629	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:136220629T>C	uc004cdh.1	-	5	522	c.490A>G	c.(490-492)ACT>GCT	p.T164A	SURF1_uc004cdg.1_Missense_Mutation_p.T55A|SURF2_uc004cdi.2_5'Flank	NM_003172	NP_003163	Q15526	SURF1_HUMAN	surfeit 1	164					aerobic respiration|respiratory chain complex IV assembly	integral to membrane|mitochondrial respiratory chain	cytochrome-c oxidase activity			breast(2)	2				OV - Ovarian serous cystadenocarcinoma(145;5.06e-07)|Epithelial(140;4.25e-06)|all cancers(34;3.93e-05)														---	---	---	---
REXO4	57109	broad.mit.edu	37	9	136277979	136277979	+	Missense_Mutation	SNP	G	A	A	rs139090649		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:136277979G>A	uc004cdm.2	-	3	835	c.635C>T	c.(634-636)GCG>GTG	p.A212V	ADAMTS13_uc004cdp.3_5'Flank|REXO4_uc011mde.1_Missense_Mutation_p.A75V|REXO4_uc011mdf.1_Missense_Mutation_p.A75V|REXO4_uc004cdn.2_5'UTR|REXO4_uc004cdo.2_Intron	NM_020385	NP_065118	Q9GZR2	REXO4_HUMAN	XPMC2 prevents mitotic catastrophe 2 homolog	212						nucleolus	exonuclease activity|nucleic acid binding|sequence-specific DNA binding transcription factor activity				0				OV - Ovarian serous cystadenocarcinoma(145;8.58e-08)|Epithelial(140;9.55e-07)|all cancers(34;1.05e-05)														---	---	---	---
ADAMTS13	11093	broad.mit.edu	37	9	136319604	136319604	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:136319604G>T	uc004cdv.3	+	24	3556	c.3112G>T	c.(3112-3114)GCC>TCC	p.A1038S	ADAMTS13_uc004cdp.3_Missense_Mutation_p.A265S|ADAMTS13_uc004cdt.1_Missense_Mutation_p.A1038S|ADAMTS13_uc004cdu.1_Missense_Mutation_p.A1007S|ADAMTS13_uc004cdw.3_Missense_Mutation_p.A1038S|ADAMTS13_uc004cdx.3_Missense_Mutation_p.A1007S|ADAMTS13_uc004cdz.3_Missense_Mutation_p.A708S|ADAMTS13_uc004cea.1_5'Flank|ADAMTS13_uc004ceb.3_5'Flank	NM_139025	NP_620594	Q76LX8	ATS13_HUMAN	ADAM metallopeptidase with thrombospondin type 1	1038	TSP type-1 7.				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)														---	---	---	---
OLFM1	10439	broad.mit.edu	37	9	138011525	138011525	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:138011525T>C	uc010nar.2	+	6	1275	c.959T>C	c.(958-960)ATC>ACC	p.I320T	OLFM1_uc004cfl.3_Missense_Mutation_p.I302T|OLFM1_uc004cfn.3_Missense_Mutation_p.I71T	NM_014279	NP_055094	Q99784	NOE1_HUMAN	olfactomedin related ER localized protein	320	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)														---	---	---	---
KIAA0649	9858	broad.mit.edu	37	9	138378948	138378948	+	Silent	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:138378948C>T	uc004cfr.1	+	4	3141	c.2592C>T	c.(2590-2592)ACC>ACT	p.T864T		NM_014811	NP_055626	Q5T8A7	K0649_HUMAN	1A6/DRIM (down-regulated in metastasis)	864						nucleolus	protein binding			ovary(2)|central_nervous_system(1)	3				OV - Ovarian serous cystadenocarcinoma(145;6.91e-08)|Epithelial(140;4.69e-07)|all cancers(34;9.33e-06)														---	---	---	---
GLT6D1	360203	broad.mit.edu	37	9	138516425	138516425	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:138516425C>T	uc010nbd.1	-	5	603	c.349G>A	c.(349-351)GCC>ACC	p.A117T		NM_182974	NP_892019	Q7Z4J2	GL6D1_HUMAN	glycosyltransferase 6 domain containing 1	117	Lumenal (Potential).				carbohydrate metabolic process	integral to membrane	transferase activity, transferring hexosyl groups			ovary(1)	1		Myeloproliferative disorder(178;0.0821)		OV - Ovarian serous cystadenocarcinoma(145;4.3e-07)|Epithelial(140;1.58e-06)|all cancers(34;5.36e-05)														---	---	---	---
SNAPC4	6621	broad.mit.edu	37	9	139272104	139272104	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:139272104A>G	uc004chh.2	-	21	4184	c.4175T>C	c.(4174-4176)GTA>GCA	p.V1392A		NM_003086	NP_003077	Q5SXM2	SNPC4_HUMAN	small nuclear RNA activating complex,	1392	SNAPC2-binding.				snRNA transcription from RNA polymerase II promoter|snRNA transcription from RNA polymerase III promoter	snRNA-activating protein complex	DNA binding|sequence-specific DNA binding transcription factor activity				0		Myeloproliferative disorder(178;0.0511)		OV - Ovarian serous cystadenocarcinoma(145;5.31e-06)|Epithelial(140;7.13e-06)														---	---	---	---
SEC16A	9919	broad.mit.edu	37	9	139369273	139369273	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:139369273G>T	uc004chx.2	-	3	3104	c.2795C>A	c.(2794-2796)CCA>CAA	p.P932Q	SEC16A_uc004chv.3_Intron|SEC16A_uc004chw.2_Missense_Mutation_p.P932Q|SEC16A_uc010nbn.2_Missense_Mutation_p.P932Q|SEC16A_uc010nbo.1_Missense_Mutation_p.P932Q	NM_014866	NP_055681	O15027	SC16A_HUMAN	SEC16 homolog A	754					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)														---	---	---	---
SEC16A	9919	broad.mit.edu	37	9	139371344	139371344	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:139371344G>A	uc004chx.2	-	3	1033	c.724C>T	c.(724-726)CCC>TCC	p.P242S	SEC16A_uc004chv.3_5'Flank|SEC16A_uc004chw.2_Missense_Mutation_p.P242S|SEC16A_uc010nbn.2_Missense_Mutation_p.P242S|SEC16A_uc010nbo.1_Missense_Mutation_p.P242S	NM_014866	NP_055681	O15027	SC16A_HUMAN	SEC16 homolog A	64					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)														---	---	---	---
NOTCH1	4851	broad.mit.edu	37	9	139407871	139407871	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:139407871C>T	uc004chz.2	-	14	2326	c.2326G>A	c.(2326-2328)GTG>ATG	p.V776M	NOTCH1_uc004cia.1_Missense_Mutation_p.V6M	NM_017617	NP_060087	P46531	NOTC1_HUMAN	notch1 preproprotein	776	Extracellular (Potential).|EGF-like 20.				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)			---	---	---	---
FBXW5	54461	broad.mit.edu	37	9	139837242	139837242	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:139837242C>T	uc004cjx.2	-	4	656	c.505G>A	c.(505-507)GAG>AAG	p.E169K	FBXW5_uc010nbx.2_5'Flank|FBXW5_uc004cjy.2_5'UTR|FBXW5_uc004cjz.2_5'UTR|C8G_uc004cka.2_5'Flank	NM_018998	NP_061871	Q969U6	FBXW5_HUMAN	F-box and WD repeat domain containing 5	169							catalytic activity|protein binding				0	all_cancers(76;0.11)	Myeloproliferative disorder(178;0.0511)	STAD - Stomach adenocarcinoma(284;0.19)	OV - Ovarian serous cystadenocarcinoma(145;7.8e-06)|Epithelial(140;0.000106)														---	---	---	---
C9orf142	286257	broad.mit.edu	37	9	139887511	139887511	+	Silent	SNP	C	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:139887511C>A	uc004cki.2	+	4	263	c.237C>A	c.(235-237)GCC>GCA	p.A79A		NM_183241	NP_899064	Q9BUH6	CI142_HUMAN	hypothetical protein LOC286257	79											0	all_cancers(76;0.11)	Myeloproliferative disorder(178;0.0821)	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	139910856	139910856	+	Silent	SNP	G	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:139910856G>T	uc011mem.1	-	20	3136	c.2988C>A	c.(2986-2988)ACC>ACA	p.T996T	ABCA2_uc011mel.1_Silent_p.T997T|ABCA2_uc004ckl.1_Silent_p.T927T|ABCA2_uc004ckm.1_Silent_p.T1027T|ABCA2_uc004ckn.1_RNA	NM_001606	NP_001597	Q9BZC7	ABCA2_HUMAN	ATP-binding cassette, sub-family A, member 2	996	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)														---	---	---	---
ABCA2	20	broad.mit.edu	37	9	139912808	139912808	+	Intron	SNP	G	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:139912808G>T	uc011mem.1	-						ABCA2_uc011mel.1_Intron|ABCA2_uc004ckl.1_Intron|ABCA2_uc004ckm.1_Intron|ABCA2_uc004ckn.1_5'Flank|ABCA2_uc004cko.1_Intron	NM_001606	NP_001597			ATP-binding cassette, sub-family A, member 2						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)														---	---	---	---
C9orf140	89958	broad.mit.edu	37	9	139959976	139959976	+	Missense_Mutation	SNP	C	T	T	rs146866219		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:139959976C>T	uc011men.1	-	3	945	c.829G>A	c.(829-831)GCC>ACC	p.A277T		NM_178448	NP_848543	Q86UD0	CI140_HUMAN	tumor specificity and mitosis phase-dependent	277	Potential.					cytoplasm|nucleus				skin(1)	1	all_cancers(76;0.0926)	Myeloproliferative disorder(178;0.0821)	STAD - Stomach adenocarcinoma(284;0.123)	OV - Ovarian serous cystadenocarcinoma(145;3.02e-05)|Epithelial(140;0.000499)														---	---	---	---
PNPLA7	375775	broad.mit.edu	37	9	140355129	140355129	+	Missense_Mutation	SNP	T	C	C	rs144637358		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:140355129T>C	uc004cnf.2	-	33	4164	c.3827A>G	c.(3826-3828)TAC>TGC	p.Y1276C	C9orf167_uc011mew.1_Intron|PNPLA7_uc004cnd.1_Missense_Mutation_p.Y523C|PNPLA7_uc004cne.1_Missense_Mutation_p.Y542C|PNPLA7_uc011mfa.1_Missense_Mutation_p.Y684C|PNPLA7_uc010ncj.1_Missense_Mutation_p.Y1301C|NELF_uc011mey.1_5'Flank|NELF_uc004cna.2_5'Flank|NELF_uc011mez.1_5'Flank|NELF_uc004cmz.2_5'Flank|NELF_uc004cnc.2_5'Flank|NELF_uc004cnb.2_5'Flank	NM_152286	NP_689499	Q6ZV29	PLPL7_HUMAN	patatin-like phospholipase domain containing 7	1276					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)														---	---	---	---
PNPLA7	375775	broad.mit.edu	37	9	140400183	140400183	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:140400183T>C	uc004cnf.2	-	13	1618	c.1281A>G	c.(1279-1281)ATA>ATG	p.I427M	C9orf167_uc011mew.1_Intron|PNPLA7_uc011mfa.1_Intron|PNPLA7_uc010ncj.1_Missense_Mutation_p.I452M	NM_152286	NP_689499	Q6ZV29	PLPL7_HUMAN	patatin-like phospholipase domain containing 7	427				FLHSDEHPGSSVASKSRKSVMVAEIPSTVSQHSESHTDETL ASRKSDAIFRAAKKDLLTLMKLEDSSLLDG -> LCLLPQC LGGLPPTDTSVYSSASSDCCGCSMPVLCIMGHKPHVTVDT (in Ref. 1; BAC86509).	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	140646789	140646789	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:140646789G>A	uc011mfc.1	+	7	1214	c.1177G>A	c.(1177-1179)GGG>AGG	p.G393R	EHMT1_uc004coa.2_Missense_Mutation_p.G393R|EHMT1_uc004cob.1_Missense_Mutation_p.G362R	NM_024757	NP_079033	Q9H9B1	EHMT1_HUMAN	euchromatic histone-lysine N-methyltransferase 1	393					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	140870442	140870442	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:140870442C>T	uc004cog.2	+	12	1772	c.1627C>T	c.(1627-1629)CGG>TGG	p.R543W	CACNA1B_uc011mfd.1_Missense_Mutation_p.R74W	NM_000718	NP_000709	Q00975	CAC1B_HUMAN	calcium channel, voltage-dependent, N type,	543	Cytoplasmic (Potential).|II.				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	140968042	140968042	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:140968042G>A	uc004cog.2	+	32	4922	c.4777G>A	c.(4777-4779)GTC>ATC	p.V1593I	CACNA1B_uc004coi.2_Missense_Mutation_p.V805I|CACNA1B_uc004cok.1_5'Flank|CACNA1B_uc010ncp.1_5'Flank	NM_000718	NP_000709	Q00975	CAC1B_HUMAN	calcium channel, voltage-dependent, N type,	1593	Cytoplasmic (Potential).|IV.				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)													---	---	---	---
ZMYND11	10771	broad.mit.edu	37	10	298376	298376	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:298376C>T	uc010pzt.1	+	15	2203	c.1775C>T	c.(1774-1776)GCG>GTG	p.A592V	ZMYND11_uc010pzu.1_Missense_Mutation_p.A592V|ZMYND11_uc010pzv.1_Missense_Mutation_p.A537V|ZMYND11_uc010pzw.1_Missense_Mutation_p.A507V|ZMYND11_uc001ifm.2_Missense_Mutation_p.A538V|ZMYND11_uc009xhg.2_Missense_Mutation_p.A575V|ZMYND11_uc009xhh.2_Missense_Mutation_p.A466V|ZMYND11_uc010pzy.1_Missense_Mutation_p.A444V	NM_006624	NP_006615	Q15326	ZMY11_HUMAN	zinc finger, MYND domain containing 11 isoform	552	MYND-type.				cell cycle|cell proliferation|interspecies interaction between organisms|negative regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0		all_cancers(4;1.32e-05)|all_lung(4;3.67e-05)|Lung NSC(4;0.000301)|all_epithelial(10;0.000416)|Colorectal(49;0.14)	OV - Ovarian serous cystadenocarcinoma(33;0.132)	Epithelial(11;0.00289)|all cancers(11;0.0108)|Lung(33;0.0689)|OV - Ovarian serous cystadenocarcinoma(14;0.106)														---	---	---	---
DIP2C	22982	broad.mit.edu	37	10	323366	323366	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:323366C>T	uc001ifp.2	-	37	4660	c.4570G>A	c.(4570-4572)GTC>ATC	p.V1524I		NM_014974	NP_055789	Q9Y2E4	DIP2C_HUMAN	DIP2 disco-interacting protein 2 homolog C	1524						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)														---	---	---	---
LARP4B	23185	broad.mit.edu	37	10	859084	859084	+	Nonsense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:859084G>A	uc001ifs.1	-	17	2040	c.1999C>T	c.(1999-2001)CAA>TAA	p.Q667*		NM_015155	NP_055970	Q92615	LAR4B_HUMAN	La ribonucleoprotein domain family, member 4B	667							nucleotide binding|RNA binding			ovary(2)|central_nervous_system(1)	3																		---	---	---	---
GTPBP4	23560	broad.mit.edu	37	10	1058506	1058506	+	Silent	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:1058506G>A	uc001ift.2	+	14	1517	c.1446G>A	c.(1444-1446)CAG>CAA	p.Q482Q	GTPBP4_uc001ifu.2_RNA|GTPBP4_uc010qad.1_Silent_p.Q366Q|GTPBP4_uc010qae.1_Silent_p.Q435Q	NM_012341	NP_036473	Q9BZE4	NOG1_HUMAN	G protein-binding protein CRFG	482					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)														---	---	---	---
IDI2	91734	broad.mit.edu	37	10	1066741	1066741	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:1066741C>T	uc001ifv.1	-	4	397	c.332G>A	c.(331-333)CGT>CAT	p.R111H	C10orf110_uc010qaf.1_5'Flank|C10orf110_uc001ifx.3_5'Flank|C10orf110_uc001ifw.3_5'Flank|C10orf110_uc001ify.3_5'Flank	NM_033261	NP_150286	Q9BXS1	IDI2_HUMAN	isopentenyl-diphosphate delta isomerase 2	111	Nudix hydrolase.				carotenoid biosynthetic process|cholesterol biosynthetic process	cytosol|peroxisome	hydrolase activity|isopentenyl-diphosphate delta-isomerase activity|metal ion binding				0		Colorectal(49;0.235)	OV - Ovarian serous cystadenocarcinoma(33;0.143)	Epithelial(11;0.067)|OV - Ovarian serous cystadenocarcinoma(14;0.169)|all cancers(11;0.192)														---	---	---	---
WDR37	22884	broad.mit.edu	37	10	1170262	1170262	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:1170262C>T	uc001igf.1	+	12	1381	c.1208C>T	c.(1207-1209)GCA>GTA	p.A403V	WDR37_uc009xhm.1_Missense_Mutation_p.A404V|WDR37_uc009xhn.1_RNA|WDR37_uc001igg.1_RNA	NM_014023	NP_054742	Q9Y2I8	WDR37_HUMAN	WD repeat domain 37	403	WD 5.										0		all_epithelial(10;0.0449)|Colorectal(49;0.142)		Epithelial(11;0.134)														---	---	---	---
PFKP	5214	broad.mit.edu	37	10	3155624	3155624	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:3155624G>A	uc001igp.2	+	13	1321	c.1285G>A	c.(1285-1287)GTA>ATA	p.V429I	PFKP_uc001igq.2_Missense_Mutation_p.V421I|PFKP_uc009xhr.2_Missense_Mutation_p.V391I|PFKP_uc009xhs.1_Missense_Mutation_p.V213I|PFKP_uc009xht.2_Missense_Mutation_p.V167I|PFKP_uc009xhu.2_5'UTR	NM_002627	NP_002618	Q01813	K6PP_HUMAN	phosphofructokinase, platelet	429					glycolysis	6-phosphofructokinase complex	6-phosphofructokinase activity|ATP binding|metal ion binding|protein binding			upper_aerodigestive_tract(1)|ovary(1)|lung(1)	3				GBM - Glioblastoma multiforme(1;0.000975)|all cancers(11;0.00351)|Epithelial(11;0.142)														---	---	---	---
ASB13	79754	broad.mit.edu	37	10	5691060	5691060	+	Silent	SNP	G	A	A	rs34459416	byFrequency;by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:5691060G>A	uc001iig.2	-	4	434	c.390C>T	c.(388-390)TCC>TCT	p.S130S	ASB13_uc001iii.2_RNA|ASB13_uc001iih.2_RNA|ASB13_uc009xic.2_Silent_p.S130S	NM_024701	NP_078977	Q8WXK3	ASB13_HUMAN	ankyrin repeat and SOCS box-containing protein	130	ANK 4.				intracellular signal transduction		protein binding			ovary(1)	1				GBM - Glioblastoma multiforme(2;9.59e-09)														---	---	---	---
C10orf18	54906	broad.mit.edu	37	10	5772808	5772808	+	Silent	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:5772808A>G	uc001iij.2	+	11	1471	c.846A>G	c.(844-846)GCA>GCG	p.A282A	C10orf18_uc001iik.2_5'UTR	NM_017782	NP_060252	Q5VWN6	CJ018_HUMAN	hypothetical protein LOC54906	282										ovary(1)|central_nervous_system(1)	2																		---	---	---	---
ANKRD16	54522	broad.mit.edu	37	10	5929819	5929819	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:5929819G>A	uc010qat.1	-	2	1069	c.526C>T	c.(526-528)CAT>TAT	p.H176Y	ANKRD16_uc009xie.2_Missense_Mutation_p.H176Y|ANKRD16_uc009xif.2_Missense_Mutation_p.H176Y|ANKRD16_uc001iiq.2_Missense_Mutation_p.H176Y|FBXO18_uc001iir.2_5'Flank|FBXO18_uc001iis.2_5'Flank|FBXO18_uc009xig.2_5'Flank	NM_019046	NP_061919	Q6P6B7	ANR16_HUMAN	ankyrin repeat domain 16 isoform a	176	ANK 5.										0																		---	---	---	---
ITIH5	80760	broad.mit.edu	37	10	7621772	7621772	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:7621772C>T	uc001ijq.2	-	9	1443	c.1364G>A	c.(1363-1365)TGT>TAT	p.C455Y	ITIH5_uc001ijp.2_Missense_Mutation_p.C241Y|ITIH5_uc001ijr.1_Missense_Mutation_p.C455Y	NM_030569	NP_085046	Q86UX2	ITIH5_HUMAN	inter-alpha trypsin inhibitor heavy chain	455	VWFA.				hyaluronan metabolic process	extracellular region	serine-type endopeptidase inhibitor activity			ovary(2)|central_nervous_system(2)	4																		---	---	---	---
ITIH2	3698	broad.mit.edu	37	10	7763614	7763614	+	Silent	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:7763614G>A	uc001ijs.2	+	8	903	c.741G>A	c.(739-741)GCG>GCA	p.A247A		NM_002216	NP_002207	P19823	ITIH2_HUMAN	inter-alpha globulin inhibitor H2 polypeptide	247					hyaluronan metabolic process	extracellular region	serine-type endopeptidase inhibitor activity			ovary(1)|pancreas(1)|skin(1)	3																		---	---	---	---
CELF2	10659	broad.mit.edu	37	10	11370877	11370877	+	Intron	SNP	G	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:11370877G>T	uc001iki.3	+						CELF2_uc010qbj.1_Intron|CELF2_uc001ikk.2_Intron|CELF2_uc001ikl.3_Intron|CELF2_uc010qbl.1_Intron|CELF2_uc010qbm.1_Intron|CELF2_uc001iko.3_Intron|CELF2_uc001ikp.3_Intron|CELF2_uc010qbn.1_Intron|CELF2_uc010qbo.1_Intron|CELF2_uc010qbp.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																		---	---	---	---
SEC61A2	55176	broad.mit.edu	37	10	12178123	12178123	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:12178123T>C	uc001ile.2	+	3	242	c.95T>C	c.(94-96)GTT>GCT	p.V32A	SEC61A2_uc010qbq.1_Intron|SEC61A2_uc001ilf.3_RNA|SEC61A2_uc001ilh.3_RNA|SEC61A2_uc001ilg.3_Missense_Mutation_p.V32A	NM_018144	NP_060614	Q9H9S3	S61A2_HUMAN	Sec61 alpha form 2 isoform a	32	Cytoplasmic (Potential).					endoplasmic reticulum membrane|integral to membrane	P-P-bond-hydrolysis-driven protein transmembrane transporter activity			ovary(1)	1		Renal(717;0.228)																---	---	---	---
CAMK1D	57118	broad.mit.edu	37	10	12708793	12708793	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:12708793T>C	uc001ilo.2	+	3	518	c.283T>C	c.(283-285)TAC>CAC	p.Y95H	CAMK1D_uc001iln.2_Missense_Mutation_p.Y95H	NM_153498	NP_705718	Q8IU85	KCC1D_HUMAN	calcium/calmodulin-dependent protein kinase ID	95	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)														---	---	---	---
CAMK1D	57118	broad.mit.edu	37	10	12867596	12867596	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:12867596G>A	uc001ilo.2	+	10	1181	c.946G>A	c.(946-948)GTC>ATC	p.V316I	CAMK1D_uc001iln.2_Missense_Mutation_p.V316I	NM_153498	NP_705718	Q8IU85	KCC1D_HUMAN	calcium/calmodulin-dependent protein kinase ID	316	Autoinhibitory domain (By similarity).|Calmodulin-binding (By similarity).					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	13169837	13169837	+	Silent	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:13169837T>C	uc001ilu.1	+	13	1773	c.1335T>C	c.(1333-1335)GAT>GAC	p.D445D	OPTN_uc001ilv.1_Silent_p.D445D|OPTN_uc001ilw.1_Silent_p.D445D|OPTN_uc001ilx.1_Silent_p.D445D|OPTN_uc001ily.1_Silent_p.D439D|OPTN_uc010qbr.1_Silent_p.D388D|OPTN_uc001ilz.1_Silent_p.D439D	NM_001008213	NP_001008214	Q96CV9	OPTN_HUMAN	optineurin	445	Potential.|Interaction with MYO6.|Interaction with HD.				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																		---	---	---	---
FRMD4A	55691	broad.mit.edu	37	10	13824983	13824983	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:13824983T>C	uc001ims.2	-	6	675	c.323A>G	c.(322-324)TAC>TGC	p.Y108C	FRMD4A_uc009xjf.1_Missense_Mutation_p.Y108C|FRMD4A_uc001imt.1_Missense_Mutation_p.Y141C|FRMD4A_uc001imu.1_Missense_Mutation_p.Y124C	NM_018027	NP_060497	Q9P2Q2	FRM4A_HUMAN	FERM domain containing 4A	108	FERM.					cytoplasm|cytoskeleton	binding			ovary(1)|skin(1)|pancreas(1)	3																		---	---	---	---
HSPA14	51182	broad.mit.edu	37	10	14891718	14891718	+	Splice_Site	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:14891718A>G	uc001inf.2	+	6	518	c.377_splice	c.e6-2	p.E126_splice	HSPA14_uc010qbw.1_Splice_Site_p.E126_splice	NM_016299	NP_057383			heat shock 70kDa protein 14 isoform 1						'de novo' cotranslational protein folding	cytosol	ATP binding|protein binding			ovary(2)|breast(2)|lung(1)	5																		---	---	---	---
NMT2	9397	broad.mit.edu	37	10	15154922	15154922	+	Missense_Mutation	SNP	G	A	A	rs146038013		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:15154922G>A	uc001inz.1	-	10	1295	c.1211C>T	c.(1210-1212)ACG>ATG	p.T404M	NMT2_uc001ioa.1_Missense_Mutation_p.T391M|NMT2_uc009xjo.1_Missense_Mutation_p.T404M|NMT2_uc010qbz.1_Missense_Mutation_p.T216M	NM_004808	NP_004799	O60551	NMT2_HUMAN	N-myristoyltransferase 2	404					N-terminal protein myristoylation|protein lipoylation	Golgi apparatus|plasma membrane	glycylpeptide N-tetradecanoyltransferase activity			ovary(1)	1																		---	---	---	---
CUBN	8029	broad.mit.edu	37	10	16990548	16990548	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:16990548G>A	uc001ioo.2	-	35	5190	c.5138C>T	c.(5137-5139)ACG>ATG	p.T1713M		NM_001081	NP_001072	O60494	CUBN_HUMAN	cubilin precursor	1713	CUB 11.				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	17085981	17085981	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:17085981A>G	uc001ioo.2	-	26	3726	c.3674T>C	c.(3673-3675)GTA>GCA	p.V1225A		NM_001081	NP_001072	O60494	CUBN_HUMAN	cubilin precursor	1225	CUB 7.				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	17153060	17153060	+	Intron	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:17153060A>G	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)													---	---	---	---
NEBL	10529	broad.mit.edu	37	10	21097583	21097583	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:21097583C>T	uc001iqi.2	-	26	3014	c.2617G>A	c.(2617-2619)GCG>ACG	p.A873T	NEBL_uc001iqj.2_RNA|NEBL_uc001iqk.2_Intron	NM_006393	NP_006384	O76041	NEBL_HUMAN	nebulette sarcomeric isoform	873	Linker.				regulation of actin filament length		actin binding|structural constituent of muscle			ovary(2)	2																		---	---	---	---
MLLT10	8028	broad.mit.edu	37	10	22021886	22021886	+	Silent	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:22021886A>G	uc001iqs.2	+	19	2673	c.2325A>G	c.(2323-2325)GAA>GAG	p.E775E	MLLT10_uc001iqt.2_Silent_p.E759E|MLLT10_uc001iqv.2_RNA|MLLT10_uc001iqy.2_Silent_p.E759E|MLLT10_uc001ira.2_Silent_p.E216E|MLLT10_uc001irb.2_RNA	NM_004641	NP_004632	P55197	AF10_HUMAN	myeloid/lymphoid or mixed-lineage leukemia	775	Leucine-zipper.|Transactivation domain.				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								---	---	---	---
PIP4K2A	5305	broad.mit.edu	37	10	22830765	22830765	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:22830765T>C	uc001irl.3	-	8	1252	c.1004A>G	c.(1003-1005)AAC>AGC	p.N335S	PIP4K2A_uc010qcu.1_Missense_Mutation_p.N195S	NM_005028	NP_005019	P48426	PI42A_HUMAN	phosphatidylinositol-5-phosphate 4-kinase, type	335	PIPK.						1-phosphatidylinositol-4-phosphate 5-kinase activity|1-phosphatidylinositol-5-phosphate 4-kinase activity|ATP binding			ovary(1)|skin(1)	2																		---	---	---	---
KIAA1217	56243	broad.mit.edu	37	10	24790455	24790455	+	Missense_Mutation	SNP	A	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:24790455A>C	uc001iru.3	+	9	2385	c.1982A>C	c.(1981-1983)CAG>CCG	p.Q661P	KIAA1217_uc001irs.2_Missense_Mutation_p.Q581P|KIAA1217_uc001irt.3_Missense_Mutation_p.Q626P|KIAA1217_uc010qcy.1_Missense_Mutation_p.Q626P|KIAA1217_uc010qcz.1_Missense_Mutation_p.Q626P|KIAA1217_uc001irv.1_Missense_Mutation_p.Q476P|KIAA1217_uc010qda.1_RNA|KIAA1217_uc001irw.2_Missense_Mutation_p.Q344P|KIAA1217_uc001irz.2_Missense_Mutation_p.Q344P|KIAA1217_uc001irx.2_Missense_Mutation_p.Q344P|KIAA1217_uc001iry.2_Missense_Mutation_p.Q344P	NM_019590	NP_062536	Q5T5P2	SKT_HUMAN	sickle tail isoform 1	661	Potential.				embryonic skeletal system development	cytoplasm				ovary(5)|skin(2)	7																		---	---	---	---
ARHGAP21	57584	broad.mit.edu	37	10	24910095	24910095	+	Silent	SNP	G	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:24910095G>T	uc001isb.2	-	9	1216	c.729C>A	c.(727-729)GCC>GCA	p.A243A	ARHGAP21_uc010qdb.1_RNA|ARHGAP21_uc009xkl.1_Silent_p.A243A|ARHGAP21_uc010qdc.1_Silent_p.A78A|ARHGAP21_uc001isc.1_Silent_p.A233A	NM_020824	NP_065875	Q5T5U3	RHG21_HUMAN	Rho GTPase activating protein 21	242					signal transduction	cell junction|cytoplasmic vesicle membrane|cytoskeleton|Golgi membrane	GTPase activator activity|protein binding			ovary(7)|pancreas(1)	8																		---	---	---	---
APBB1IP	54518	broad.mit.edu	37	10	26789826	26789826	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:26789826A>G	uc001iss.2	+	5	560	c.239A>G	c.(238-240)CAG>CGG	p.Q80R	APBB1IP_uc001isr.2_Missense_Mutation_p.Q80R|APBB1IP_uc009xks.1_Missense_Mutation_p.Q80R	NM_019043	NP_061916	Q7Z5R6	AB1IP_HUMAN	amyloid beta (A4) precursor protein-binding,	80					blood coagulation|signal transduction	cytoskeleton|cytosol|focal adhesion|lamellipodium				lung(4)|skin(2)|central_nervous_system(1)	7																		---	---	---	---
PDSS1	23590	broad.mit.edu	37	10	27009168	27009168	+	Silent	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:27009168C>T	uc001isv.2	+	6	535	c.489C>T	c.(487-489)CGC>CGT	p.R163R	PDSS1_uc001isw.2_Silent_p.R163R	NM_014317	NP_055132	Q5T2R2	DPS1_HUMAN	prenyl diphosphate synthase, subunit 1	163					isoprenoid biosynthetic process|ubiquinone biosynthetic process	mitochondrion	metal ion binding|protein heterodimerization activity				0																		---	---	---	---
ANKRD26	22852	broad.mit.edu	37	10	27303481	27303481	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:27303481T>C	uc001ith.2	-	31	4835	c.4663A>G	c.(4663-4665)AAG>GAG	p.K1555E	ANKRD26_uc001itg.2_Missense_Mutation_p.K1242E|ANKRD26_uc009xku.1_Missense_Mutation_p.K1556E	NM_014915	NP_055730	Q9UPS8	ANR26_HUMAN	ankyrin repeat domain 26	1555	Potential.					centrosome				large_intestine(1)|haematopoietic_and_lymphoid_tissue(1)|ovary(1)|skin(1)	4																		---	---	---	---
ANKRD26	22852	broad.mit.edu	37	10	27349302	27349302	+	Silent	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:27349302T>C	uc001ith.2	-	15	1708	c.1536A>G	c.(1534-1536)GGA>GGG	p.G512G	ANKRD26_uc001itg.2_Silent_p.G198G|ANKRD26_uc009xku.1_Silent_p.G512G	NM_014915	NP_055730	Q9UPS8	ANR26_HUMAN	ankyrin repeat domain 26	512						centrosome				large_intestine(1)|haematopoietic_and_lymphoid_tissue(1)|ovary(1)|skin(1)	4																		---	---	---	---
ANKRD26	22852	broad.mit.edu	37	10	27350180	27350180	+	Intron	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:27350180T>C	uc001ith.2	-						ANKRD26_uc001itg.2_Intron|ANKRD26_uc009xku.1_Intron	NM_014915	NP_055730			ankyrin repeat domain 26							centrosome				large_intestine(1)|haematopoietic_and_lymphoid_tissue(1)|ovary(1)|skin(1)	4																		---	---	---	---
PTCHD3	374308	broad.mit.edu	37	10	27687219	27687219	+	3'UTR	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:27687219G>A	uc001itu.2	-	4						NM_001034842	NP_001030014			patched domain containing 3						spermatid development	integral to membrane	hedgehog receptor activity			ovary(2)|pancreas(1)|skin(1)	4																		---	---	---	---
ARMC4	55130	broad.mit.edu	37	10	28149731	28149731	+	Silent	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:28149731A>G	uc009xky.2	-	19	2942	c.2844T>C	c.(2842-2844)CGT>CGC	p.R948R	ARMC4_uc010qds.1_Silent_p.R473R|ARMC4_uc010qdt.1_Silent_p.R640R|ARMC4_uc001itz.2_Silent_p.R948R	NM_018076	NP_060546	Q5T2S8	ARMC4_HUMAN	armadillo repeat containing 4	948	ARM 8.						binding			ovary(4)|skin(2)	6																		---	---	---	---
ARMC4	55130	broad.mit.edu	37	10	28229666	28229666	+	Silent	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:28229666G>A	uc009xky.2	-	13	1910	c.1812C>T	c.(1810-1812)GAC>GAT	p.D604D	ARMC4_uc010qds.1_Silent_p.D129D|ARMC4_uc010qdt.1_Silent_p.D296D|ARMC4_uc001itz.2_Silent_p.D604D|ARMC4_uc010qdu.1_Silent_p.D296D	NM_018076	NP_060546	Q5T2S8	ARMC4_HUMAN	armadillo repeat containing 4	604							binding			ovary(4)|skin(2)	6																		---	---	---	---
SVIL	6840	broad.mit.edu	37	10	29760112	29760112	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:29760112C>A	uc001iut.1	-	31	6343	c.5590G>T	c.(5590-5592)GTG>TTG	p.V1864L	LOC387647_uc001iup.2_Intron|LOC387647_uc001iuq.1_Intron|SVIL_uc010qdw.1_Missense_Mutation_p.V778L|SVIL_uc001iuu.1_Missense_Mutation_p.V1438L	NM_021738	NP_068506	O95425	SVIL_HUMAN	supervillin isoform 2	1864					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)																---	---	---	---
CCNY	219771	broad.mit.edu	37	10	35855066	35855066	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:35855066A>G	uc001iyw.3	+	9	1042	c.862A>G	c.(862-864)AGC>GGC	p.S288G	CCNY_uc001iyu.3_Missense_Mutation_p.S234G|CCNY_uc001iyv.3_Missense_Mutation_p.S234G|CCNY_uc001iyx.3_Missense_Mutation_p.S234G|CCNY_uc009xmb.2_Missense_Mutation_p.S263G|CCNY_uc010qet.1_Missense_Mutation_p.S155G	NM_145012	NP_659449	Q8ND76	CCNY_HUMAN	cyclin Y isoform 1	288					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																		---	---	---	---
FZD8	8325	broad.mit.edu	37	10	35929445	35929445	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:35929445G>A	uc001iyz.1	-	1	918	c.913C>T	c.(913-915)CGC>TGC	p.R305C		NM_031866	NP_114072	Q9H461	FZD8_HUMAN	frizzled 8 precursor	305	Cytoplasmic (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																		---	---	---	---
ALOX5	240	broad.mit.edu	37	10	45920543	45920543	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:45920543G>T	uc001jce.2	+	6	896	c.797G>T	c.(796-798)AGC>ATC	p.S266I	ALOX5_uc009xmt.2_Missense_Mutation_p.S266I|ALOX5_uc010qfg.1_Missense_Mutation_p.S266I	NM_000698	NP_000689	P09917	LOX5_HUMAN	arachidonate 5-lipoxygenase	266	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)													---	---	---	---
ANUBL1	93550	broad.mit.edu	37	10	46135254	46135254	+	Intron	SNP	A	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:46135254A>T	uc001jcp.3	-						ANUBL1_uc001jcl.3_Translation_Start_Site|ANUBL1_uc001jcm.3_Intron|ANUBL1_uc009xmu.2_Intron|ANUBL1_uc001jcn.3_Intron|ANUBL1_uc001jco.3_Intron|ANUBL1_uc001jcq.2_RNA	NM_001128324	NP_001121796			AN1, ubiquitin-like, homolog								zinc ion binding				0																		---	---	---	---
PPYR1	5540	broad.mit.edu	37	10	47086946	47086946	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:47086946G>T	uc001jee.2	+	3	582	c.163G>T	c.(163-165)GGG>TGG	p.G55W	ANXA8_uc001jed.3_Intron|PPYR1_uc009xna.2_Missense_Mutation_p.G55W	NM_005972	NP_005963	P50391	NPY4R_HUMAN	pancreatic polypeptide receptor 1	55	Helical; Name=1; (Potential).				blood circulation|digestion|feeding behavior	integral to plasma membrane				ovary(1)|skin(1)	2																		---	---	---	---
RBP3	5949	broad.mit.edu	37	10	48390105	48390105	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:48390105C>T	uc001jez.2	-	1	887	c.773G>A	c.(772-774)CGG>CAG	p.R258Q		NM_002900	NP_002891	P10745	RET3_HUMAN	retinol-binding protein 3 precursor	258	4 X approximate tandem repeats.|1.				lipid metabolic process|proteolysis|transport|visual perception	interphotoreceptor matrix	retinal binding|serine-type peptidase activity			large_intestine(1)|central_nervous_system(1)	2					Vitamin A(DB00162)													---	---	---	---
RBP3	5949	broad.mit.edu	37	10	48390671	48390671	+	Silent	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:48390671C>T	uc001jez.2	-	1	321	c.207G>A	c.(205-207)ACG>ACA	p.T69T		NM_002900	NP_002891	P10745	RET3_HUMAN	retinol-binding protein 3 precursor	69	4 X approximate tandem repeats.|1.				lipid metabolic process|proteolysis|transport|visual perception	interphotoreceptor matrix	retinal binding|serine-type peptidase activity			large_intestine(1)|central_nervous_system(1)	2					Vitamin A(DB00162)													---	---	---	---
DRGX	644168	broad.mit.edu	37	10	50594854	50594854	+	Silent	SNP	G	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:50594854G>T	uc010qgq.1	-	4	300	c.300C>A	c.(298-300)GCC>GCA	p.A100A		NM_001080520	NP_001073989	A6NNA5	DRGX_HUMAN	dorsal root ganglia homeobox	100					multicellular organismal development	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity				0																		---	---	---	---
SGMS1	259230	broad.mit.edu	37	10	52071156	52071156	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:52071156G>A	uc001jje.2	-	9	1715	c.761C>T	c.(760-762)GCC>GTC	p.A254V	SGMS1_uc010qhk.1_Missense_Mutation_p.A85V|SGMS1_uc009xot.1_RNA	NM_147156	NP_671512	Q86VZ5	SMS1_HUMAN	sphingomyelin synthase 1	260					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																		---	---	---	---
A1CF	29974	broad.mit.edu	37	10	52580312	52580312	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:52580312C>A	uc001jjj.2	-	8	1055	c.867G>T	c.(865-867)AAG>AAT	p.K289N	A1CF_uc010qhn.1_Missense_Mutation_p.K297N|A1CF_uc001jji.2_Missense_Mutation_p.K289N|A1CF_uc001jjh.2_Missense_Mutation_p.K297N|A1CF_uc010qho.1_Missense_Mutation_p.K297N|A1CF_uc009xov.2_Missense_Mutation_p.K289N	NM_138932	NP_620310	Q9NQ94	A1CF_HUMAN	apobec-1 complementation factor isoform 2	289	RRM 3.				cytidine to uridine editing|mRNA modification|mRNA processing|protein stabilization	apolipoprotein B mRNA editing enzyme complex|endoplasmic reticulum|nucleoplasm	nucleotide binding|protein binding|single-stranded RNA binding			central_nervous_system(1)	1																		---	---	---	---
PCDH15	65217	broad.mit.edu	37	10	55626401	55626401	+	Splice_Site	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:55626401C>T	uc001jju.1	-	27	4112	c.3717_splice	c.e27+1	p.L1239_splice	PCDH15_uc010qhq.1_Splice_Site_p.L1244_splice|PCDH15_uc010qhr.1_Splice_Site_p.L1239_splice|PCDH15_uc010qhs.1_Splice_Site_p.L1251_splice|PCDH15_uc010qht.1_Splice_Site_p.L1246_splice|PCDH15_uc010qhu.1_Splice_Site_p.L1239_splice|PCDH15_uc001jjv.1_Intron|PCDH15_uc010qhv.1_Splice_Site_p.L1239_splice|PCDH15_uc010qhw.1_Splice_Site_p.L1202_splice|PCDH15_uc010qhx.1_Splice_Site_p.L1168_splice|PCDH15_uc010qhy.1_Splice_Site_p.L1244_splice|PCDH15_uc010qhz.1_Splice_Site_p.L1239_splice|PCDH15_uc010qia.1_Splice_Site_p.L1217_splice|PCDH15_uc010qib.1_Splice_Site_p.L1217_splice	NM_033056	NP_149045			protocadherin 15 isoform CD1-4 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	55913032	55913032	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:55913032C>T	uc001jju.1	-	14	2007	c.1612G>A	c.(1612-1614)GAA>AAA	p.E538K	PCDH15_uc010qhq.1_Missense_Mutation_p.E543K|PCDH15_uc010qhr.1_Missense_Mutation_p.E538K|PCDH15_uc010qhs.1_Missense_Mutation_p.E550K|PCDH15_uc010qht.1_Missense_Mutation_p.E545K|PCDH15_uc010qhu.1_Missense_Mutation_p.E538K|PCDH15_uc001jjv.1_Missense_Mutation_p.E516K|PCDH15_uc010qhv.1_Missense_Mutation_p.E538K|PCDH15_uc010qhw.1_Missense_Mutation_p.E501K|PCDH15_uc010qhx.1_Missense_Mutation_p.E538K|PCDH15_uc010qhy.1_Missense_Mutation_p.E543K|PCDH15_uc010qhz.1_Missense_Mutation_p.E538K|PCDH15_uc010qia.1_Missense_Mutation_p.E516K|PCDH15_uc010qib.1_Missense_Mutation_p.E516K|PCDH15_uc001jjw.2_Missense_Mutation_p.E538K	NM_033056	NP_149045	Q96QU1	PCD15_HUMAN	protocadherin 15 isoform CD1-4 precursor	538	Cadherin 5.|Extracellular (Potential).				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)			---	---	---	---
RHOBTB1	9886	broad.mit.edu	37	10	62670661	62670661	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:62670661G>A	uc001jli.2	-	5	718	c.280C>T	c.(280-282)CGC>TGC	p.R94C	RHOBTB1_uc001jlh.2_Missense_Mutation_p.R94C|RHOBTB1_uc001jlj.2_Missense_Mutation_p.R94C|RHOBTB1_uc001jlk.2_Missense_Mutation_p.R94C|RHOBTB1_uc009xpe.1_Missense_Mutation_p.R94C|RHOBTB1_uc001jlm.2_Missense_Mutation_p.R94C	NM_014836	NP_055651	O94844	RHBT1_HUMAN	Rho-related BTB domain containing 1	94	Rho-like.				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)																	---	---	---	---
JMJD1C	221037	broad.mit.edu	37	10	64968204	64968204	+	Silent	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:64968204T>C	uc001jmn.2	-	10	3525	c.3225A>G	c.(3223-3225)TCA>TCG	p.S1075S	JMJD1C_uc001jml.2_Silent_p.S856S|JMJD1C_uc001jmm.2_Silent_p.S787S|JMJD1C_uc010qiq.1_Silent_p.S893S|JMJD1C_uc009xpi.2_Silent_p.S893S|JMJD1C_uc009xpj.1_RNA|JMJD1C_uc009xpk.1_Silent_p.S112S	NM_032776	NP_116165	Q15652	JHD2C_HUMAN	jumonji domain containing 1C isoform a	1075					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)																	---	---	---	---
MYPN	84665	broad.mit.edu	37	10	69948681	69948681	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:69948681T>C	uc001jnm.3	+	14	2908	c.2723T>C	c.(2722-2724)TTT>TCT	p.F908S	MYPN_uc001jnn.3_Missense_Mutation_p.F633S|MYPN_uc001jno.3_Missense_Mutation_p.F908S|MYPN_uc009xpt.2_Missense_Mutation_p.F908S|MYPN_uc010qit.1_Missense_Mutation_p.F614S|MYPN_uc010qiu.1_RNA	NM_032578	NP_115967	Q86TC9	MYPN_HUMAN	myopalladin	908				F -> L (in Ref. 2; CAD89906).		nucleus|sarcomere	actin binding			ovary(3)|skin(2)	5																		---	---	---	---
RUFY2	55680	broad.mit.edu	37	10	70136651	70136651	+	Silent	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:70136651A>G	uc001job.2	-	13	1716	c.1389T>C	c.(1387-1389)TCT>TCC	p.S463S	RUFY2_uc001jnz.1_RNA|RUFY2_uc001joa.2_Silent_p.S18S	NM_017987	NP_060457	Q8WXA3	RUFY2_HUMAN	RUN and FYVE domain-containing 2 isoform a	477	Potential.					nucleus	metal ion binding			ovary(1)	1																		---	---	---	---
STOX1	219736	broad.mit.edu	37	10	70645163	70645163	+	Silent	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:70645163G>A	uc001jos.2	+	3	1698	c.1611G>A	c.(1609-1611)TTG>TTA	p.L537L	STOX1_uc001jor.2_Intron|STOX1_uc009xpy.2_Intron|STOX1_uc001joq.2_Silent_p.L427L	NM_001130161	NP_001123633	Q6ZVD7	STOX1_HUMAN	storkhead box 1 isoform a	537						cytoplasm|nucleolus	DNA binding			kidney(1)|skin(1)	2																		---	---	---	---
DDX21	9188	broad.mit.edu	37	10	70721865	70721865	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:70721865G>A	uc001jov.1	+	3	649	c.559G>A	c.(559-561)GCT>ACT	p.A187T	DDX21_uc001jow.1_Missense_Mutation_p.A119T	NM_004728	NP_004719	Q9NR30	DDX21_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 21	187	Q motif.					nucleolus	ATP binding|ATP-dependent RNA helicase activity|protein binding|RNA binding			ovary(2)|kidney(1)	3																		---	---	---	---
SUPV3L1	6832	broad.mit.edu	37	10	70960033	70960033	+	Intron	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:70960033C>T	uc001jpe.1	+						SUPV3L1_uc010qjd.1_Intron	NM_003171	NP_003162			suppressor of var1, 3-like 1 precursor						DNA duplex unwinding	mitochondrial nucleoid|nucleus	ATP binding|DNA binding|DNA helicase activity|RNA binding			urinary_tract(1)|ovary(1)	2																		---	---	---	---
HKDC1	80201	broad.mit.edu	37	10	71010292	71010292	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:71010292T>C	uc001jpf.3	+	12	1853	c.1720T>C	c.(1720-1722)TTT>CTT	p.F574L	HKDC1_uc010qje.1_Missense_Mutation_p.F437L	NM_025130	NP_079406	Q2TB90	HKDC1_HUMAN	hexokinase domain containing 1	574					glycolysis	mitochondrion|nucleus	ATP binding|hexokinase activity			ovary(4)|skin(1)	5																		---	---	---	---
HK1	3098	broad.mit.edu	37	10	71142347	71142347	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:71142347C>T	uc001jpl.3	+	10	1471	c.1370C>T	c.(1369-1371)ACG>ATG	p.T457M	HK1_uc001jpg.3_Missense_Mutation_p.T445M|HK1_uc001jph.3_Missense_Mutation_p.T461M|HK1_uc001jpi.3_Missense_Mutation_p.T461M|HK1_uc001jpj.3_Missense_Mutation_p.T492M|HK1_uc001jpk.3_Missense_Mutation_p.T456M|HK1_uc009xqd.2_Missense_Mutation_p.T335M	NM_000188	NP_000179	P19367	HXK1_HUMAN	hexokinase 1 isoform HKI	457	Regulatory.				glucose transport|glycolysis|transmembrane transport	cytosol|mitochondrial outer membrane|nucleus	ATP binding|glucokinase activity			ovary(1)	1																		---	---	---	---
COL13A1	1305	broad.mit.edu	37	10	71657248	71657248	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:71657248G>A	uc001jpr.1	+	12	1211	c.675G>A	c.(673-675)ATG>ATA	p.M225I	COL13A1_uc001jqj.1_Missense_Mutation_p.M225I|COL13A1_uc001jps.1_Missense_Mutation_p.M196I|COL13A1_uc001jpt.1_Intron|COL13A1_uc001jpu.1_Intron|COL13A1_uc001jpv.1_Missense_Mutation_p.M225I|COL13A1_uc001jpx.1_Missense_Mutation_p.M225I|COL13A1_uc001jpw.1_Intron|COL13A1_uc001jpy.1_Intron|COL13A1_uc001jpz.1_Intron|COL13A1_uc001jqa.1_Missense_Mutation_p.M187I|COL13A1_uc001jqc.1_Missense_Mutation_p.M225I|COL13A1_uc001jqb.1_Missense_Mutation_p.M196I|COL13A1_uc001jql.2_Missense_Mutation_p.M225I|COL13A1_uc001jqd.1_Missense_Mutation_p.M213I|COL13A1_uc001jqe.1_Missense_Mutation_p.M208I|COL13A1_uc001jqf.1_Intron|COL13A1_uc001jqg.1_Missense_Mutation_p.M225I|COL13A1_uc001jqh.1_Missense_Mutation_p.M225I|COL13A1_uc001jqi.1_Missense_Mutation_p.M225I|COL13A1_uc010qjf.1_Intron|COL13A1_uc001jqk.1_Missense_Mutation_p.M85I	NM_005203	NP_005194	Q5TAT6	CODA1_HUMAN	alpha 1 type XIII collagen isoform 1	225	Extracellular (Potential).|Nonhelical region 2 (NC2).				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)													---	---	---	---
KIAA1274	27143	broad.mit.edu	37	10	72299484	72299484	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:72299484T>C	uc001jrd.3	+	15	2155	c.1874T>C	c.(1873-1875)ATC>ACC	p.I625T	KIAA1274_uc001jre.3_5'UTR	NM_014431	NP_055246	Q9ULE6	PALD_HUMAN	KIAA1274	625										ovary(2)|central_nervous_system(1)	3																		---	---	---	---
ADAMTS14	140766	broad.mit.edu	37	10	72500930	72500930	+	Intron	SNP	C	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:72500930C>A	uc001jrh.2	+						ADAMTS14_uc001jrg.2_Intron|ADAMTS14_uc001jri.1_Intron	NM_080722	NP_542453			ADAM metallopeptidase with thrombospondin type 1						collagen catabolic process|proteolysis	proteinaceous extracellular matrix	metalloendopeptidase activity|zinc ion binding			ovary(5)|upper_aerodigestive_tract(1)	6																		---	---	---	---
C10orf27	219793	broad.mit.edu	37	10	72536958	72536958	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:72536958C>T	uc001jrj.1	-	7	1031	c.641G>A	c.(640-642)AGC>AAC	p.S214N	C10orf27_uc010qjm.1_Missense_Mutation_p.S215N|C10orf27_uc009xqh.1_RNA|C10orf27_uc010qjn.1_Missense_Mutation_p.S213N|C10orf27_uc009xqi.1_RNA|C10orf27_uc010qjo.1_Missense_Mutation_p.S234N	NM_152710	NP_689923	Q96M53	SPATL_HUMAN	stromal protein associated with thymii and lymph	214					cell differentiation|multicellular organismal development|spermatogenesis	cytosol				skin(1)	1																		---	---	---	---
SGPL1	8879	broad.mit.edu	37	10	72617373	72617373	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:72617373G>A	uc001jrm.2	+	6	634	c.412G>A	c.(412-414)GCC>ACC	p.A138T		NM_003901	NP_003892	O95470	SGPL1_HUMAN	sphingosine-1-phosphate lyase 1	138	Cytoplasmic (Potential).				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)													---	---	---	---
CDH23	64072	broad.mit.edu	37	10	73490323	73490323	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:73490323C>T	uc001jrx.3	+	30	4054	c.3677C>T	c.(3676-3678)ACG>ATG	p.T1226M	CDH23_uc001jrz.2_Missense_Mutation_p.T842M|C10orf105_uc001jsb.1_Intron|CDH23_uc001jsc.1_Missense_Mutation_p.T34M	NM_022124	NP_071407	Q9H251	CAD23_HUMAN	cadherin-like 23 isoform 1 precursor	1226	Cadherin 12.|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																		---	---	---	---
C10orf54	64115	broad.mit.edu	37	10	73521741	73521741	+	Missense_Mutation	SNP	T	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:73521741T>A	uc001jsd.2	-	2	266	c.125A>T	c.(124-126)TAT>TTT	p.Y42F	CDH23_uc001jrx.3_Intron|C10orf54_uc001jse.2_Intron|C10orf54_uc009xqm.2_Intron|C10orf54_uc001jsf.1_Missense_Mutation_p.Y42F	NM_022153	NP_071436	Q9H7M9	GI24_HUMAN	platelet receptor Gi24 precursor	42	Ig-like.|Extracellular (Potential).					integral to membrane	receptor activity			ovary(1)|breast(1)|central_nervous_system(1)	3																		---	---	---	---
PSAP	5660	broad.mit.edu	37	10	73588695	73588695	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:73588695A>G	uc001jsm.2	-	5	619	c.515T>C	c.(514-516)ATG>ACG	p.M172T		NM_002778	NP_002769	P07602	SAP_HUMAN	prosaposin isoform a preproprotein	172					glycosphingolipid metabolic process|lipid transport|platelet activation|platelet degranulation	extracellular space|Golgi apparatus|integral to membrane|lysosomal lumen	enzyme activator activity|lipid binding			ovary(1)	1																		---	---	---	---
PSAP	5660	broad.mit.edu	37	10	73591638	73591638	+	Missense_Mutation	SNP	C	T	T	rs150701404		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:73591638C>T	uc001jsm.2	-	3	318	c.214G>A	c.(214-216)GCA>ACA	p.A72T		NM_002778	NP_002769	P07602	SAP_HUMAN	prosaposin isoform a preproprotein	72	Saposin B-type 1.				glycosphingolipid metabolic process|lipid transport|platelet activation|platelet degranulation	extracellular space|Golgi apparatus|integral to membrane|lysosomal lumen	enzyme activator activity|lipid binding			ovary(1)	1																		---	---	---	---
SPOCK2	9806	broad.mit.edu	37	10	73848082	73848082	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:73848082C>T	uc001jso.1	-	1	450	c.5G>A	c.(4-6)CGC>CAC	p.R2H	SPOCK2_uc001jsp.2_Missense_Mutation_p.R2H|SPOCK2_uc010qjs.1_Missense_Mutation_p.R2H|SPOCK2_uc010qjt.1_Missense_Mutation_p.R2H	NM_014767	NP_055582	Q92563	TICN2_HUMAN	sparc/osteonectin, cwcv and kazal-like domains	2					extracellular matrix organization|regulation of cell differentiation|signal transduction|synapse assembly	proteinaceous extracellular matrix	calcium ion binding				0																		---	---	---	---
PLA2G12B	84647	broad.mit.edu	37	10	74714308	74714308	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:74714308C>T	uc001jtf.1	-	1	203	c.136G>A	c.(136-138)GTC>ATC	p.V46I	PLA2G12B_uc009xqt.1_5'UTR|PLA2G12B_uc010qjz.1_Missense_Mutation_p.V46I	NM_032562	NP_115951	Q9BX93	PG12B_HUMAN	phospholipase A2, group XIIB precursor	46					lipid catabolic process	extracellular region	calcium ion binding|phospholipase A2 activity			ovary(1)	1	Prostate(51;0.0198)																	---	---	---	---
ECD	11319	broad.mit.edu	37	10	74908110	74908110	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:74908110C>T	uc001jtn.2	-	8	1208	c.965G>A	c.(964-966)TGC>TAC	p.C322Y	ECD_uc009xqx.2_Missense_Mutation_p.C322Y|ECD_uc009xqy.2_Missense_Mutation_p.C279Y|ECD_uc001jto.2_Missense_Mutation_p.C21Y	NM_007265	NP_009196	O95905	SGT1_HUMAN	suppressor of S. cerevisiae gcr2 isoform 1	322					regulation of glycolysis|regulation of transcription, DNA-dependent|transcription from RNA polymerase II promoter	cytoplasm|nucleus	transcription coactivator activity			pancreas(1)	1	Prostate(51;0.0119)																	---	---	---	---
ECD	11319	broad.mit.edu	37	10	74916222	74916222	+	Intron	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:74916222T>C	uc001jtn.2	-						ECD_uc009xqx.2_Intron|ECD_uc009xqy.2_Intron|ECD_uc001jto.2_Intron	NM_007265	NP_009196			suppressor of S. cerevisiae gcr2 isoform 1						regulation of glycolysis|regulation of transcription, DNA-dependent|transcription from RNA polymerase II promoter	cytoplasm|nucleus	transcription coactivator activity			pancreas(1)	1	Prostate(51;0.0119)																	---	---	---	---
ANXA7	310	broad.mit.edu	37	10	75142932	75142932	+	Splice_Site	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:75142932C>T	uc001jtz.2	-	10	1057	c.984_splice	c.e10+1	p.Q328_splice	ANXA7_uc001jua.2_Splice_Site_p.Q306_splice|ANXA7_uc001jub.2_Splice_Site_p.Q266_splice|ANXA7_uc010qki.1_Splice_Site_p.Q216_splice|ANXA7_uc009xre.2_Splice_Site_p.Q235_splice|ANXA7_uc009xrf.1_Splice_Site_p.Q248_splice	NM_004034	NP_004025			annexin VII isoform 2								calcium ion binding|calcium-dependent phospholipid binding|calcium-dependent protein binding			ovary(2)|central_nervous_system(1)	3	Prostate(51;0.0119)																	---	---	---	---
SEC24C	9632	broad.mit.edu	37	10	75506680	75506680	+	Silent	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:75506680G>A	uc001juw.2	+	3	269	c.90G>A	c.(88-90)GGG>GGA	p.G30G	SEC24C_uc010qkn.1_Intron|SEC24C_uc009xrj.1_5'UTR|SEC24C_uc001jux.2_Silent_p.G30G|SEC24C_uc010qko.1_5'UTR|SEC24C_uc010qkp.1_Intron|SEC24C_uc010qkq.1_Intron	NM_004922	NP_004913	P53992	SC24C_HUMAN	SEC24-related protein C	30					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|zinc ion binding			skin(2)|central_nervous_system(1)	3	Prostate(51;0.0112)																	---	---	---	---
SEC24C	9632	broad.mit.edu	37	10	75519969	75519969	+	Silent	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:75519969G>A	uc001juw.2	+	6	854	c.675G>A	c.(673-675)TCG>TCA	p.S225S	SEC24C_uc010qkn.1_RNA|SEC24C_uc009xrj.1_Silent_p.S83S|SEC24C_uc001jux.2_Silent_p.S225S|SEC24C_uc010qko.1_Silent_p.S83S|SEC24C_uc010qkp.1_Intron|SEC24C_uc010qkq.1_Intron	NM_004922	NP_004913	P53992	SC24C_HUMAN	SEC24-related protein C	225					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|zinc ion binding			skin(2)|central_nervous_system(1)	3	Prostate(51;0.0112)																	---	---	---	---
CAMK2G	818	broad.mit.edu	37	10	75602288	75602288	+	Silent	SNP	C	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:75602288C>A	uc001jvv.1	-	11	931	c.807G>T	c.(805-807)ACG>ACT	p.T269T	CAMK2G_uc001jvm.1_Silent_p.T277T|CAMK2G_uc001jvo.1_Silent_p.T277T|CAMK2G_uc001jvq.1_Silent_p.T277T|CAMK2G_uc001jvr.1_Silent_p.T277T|CAMK2G_uc001jvp.1_Silent_p.T277T|CAMK2G_uc001jvs.1_Silent_p.T277T|CAMK2G_uc001jvt.1_RNA|CAMK2G_uc001jvu.1_Silent_p.T255T|CAMK2G_uc010qkv.1_5'UTR|CAMK2G_uc009xrp.1_5'Flank	NM_172171	NP_751911	Q13555	KCC2G_HUMAN	calcium/calmodulin-dependent protein kinase II	277					insulin secretion|interferon-gamma-mediated signaling pathway|synaptic transmission	calcium- and calmodulin-dependent protein kinase complex|cytosol|endocytic vesicle membrane|nucleoplasm|plasma membrane	ATP binding|calcium-dependent protein serine/threonine phosphatase activity|calmodulin binding|calmodulin-dependent protein kinase activity			lung(1)|stomach(1)	2	Prostate(51;0.0112)																	---	---	---	---
MYST4	23522	broad.mit.edu	37	10	76741654	76741654	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:76741654A>G	uc001jwn.1	+	11	2834	c.2341A>G	c.(2341-2343)ATT>GTT	p.I781V	MYST4_uc001jwm.1_Missense_Mutation_p.I489V|MYST4_uc001jwo.1_Missense_Mutation_p.I489V|MYST4_uc001jwp.1_Missense_Mutation_p.I598V	NM_012330	NP_036462	Q8WYB5	MYST4_HUMAN	MYST histone acetyltransferase (monocytic	781	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								---	---	---	---
POLR3A	11128	broad.mit.edu	37	10	79737297	79737297	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:79737297T>C	uc001jzn.2	-	31	4206	c.4112A>G	c.(4111-4113)AAC>AGC	p.N1371S		NM_007055	NP_008986	O14802	RPC1_HUMAN	polymerase (RNA) III (DNA directed) polypeptide	1371					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	81065901	81065901	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:81065901G>A	uc001kaf.2	+	22	3040	c.2468G>A	c.(2467-2469)CGG>CAG	p.R823Q	ZMIZ1_uc001kag.2_Missense_Mutation_p.R699Q|ZMIZ1_uc010qlq.1_5'UTR	NM_020338	NP_065071	Q9ULJ6	ZMIZ1_HUMAN	retinoic acid induced 17	823					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	81070679	81070679	+	Splice_Site	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:81070679A>G	uc001kaf.2	+	24	3408	c.2836_splice	c.e24-2	p.M946_splice	ZMIZ1_uc001kag.2_Splice_Site_p.M822_splice|ZMIZ1_uc010qlq.1_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)															---	---	---	---
SFTPA2	729238	broad.mit.edu	37	10	81317056	81317056	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:81317056C>T	uc001kal.3	-	6	753	c.656G>A	c.(655-657)CGG>CAG	p.R219Q	SFTPA2_uc001kan.3_Missense_Mutation_p.R219Q	NM_006926	NP_008857	Q8IWL1	SFPA2_HUMAN	RecName: Full=Pulmonary surfactant-associated protein A2;          Short=SP-A2;          Short=SP-A;          Short=PSP-A;          Short=PSPA; AltName: Full=Alveolar proteinosis protein; AltName: Full=35 kDa pulmonary surfactant-associated protein; Flags: Precursor;	219	C-type lectin.				cell junction assembly|respiratory gaseous exchange	collagen|extracellular space	sugar binding				0	all_cancers(46;0.197)|Breast(12;0.000326)|Prostate(51;0.00985)|all_epithelial(25;0.0149)		Epithelial(14;0.00957)|all cancers(16;0.0179)|Colorectal(32;0.229)											Pulmonary_Fibrosis_Idiopathic				---	---	---	---
WAPAL	23063	broad.mit.edu	37	10	88257086	88257086	+	Intron	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:88257086T>C	uc001kdo.2	-						WAPAL_uc001kdn.2_Intron|WAPAL_uc009xsw.2_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																		---	---	---	---
OPN4	94233	broad.mit.edu	37	10	88415907	88415907	+	Intron	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:88415907C>T	uc001kdq.2	+						OPN4_uc001kdp.2_Intron|OPN4_uc010qmk.1_Intron	NM_033282	NP_150598			opsin 4 isoform 1						phototransduction|protein-chromophore linkage|regulation of circadian rhythm|rhythmic process|visual perception	integral to membrane|plasma membrane	11-cis retinal binding|G-protein coupled photoreceptor activity			ovary(1)	1																		---	---	---	---
STAMBPL1	57559	broad.mit.edu	37	10	90665418	90665418	+	Splice_Site	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:90665418G>A	uc001kfk.2	+	3	671	c.248_splice	c.e3+1	p.T83_splice	STAMBPL1_uc010qmx.1_Splice_Site_p.T83_splice|STAMBPL1_uc009xto.2_Splice_Site|STAMBPL1_uc001kfl.2_Splice_Site_p.T83_splice|STAMBPL1_uc001kfm.2_5'Flank	NM_020799	NP_065850			STAM binding protein-like 1								metal ion binding|metallopeptidase activity|protein binding			ovary(1)	1		Colorectal(252;0.0381)		Colorectal(12;6.38e-05)|COAD - Colon adenocarcinoma(12;7.75e-05)														---	---	---	---
STAMBPL1	57559	broad.mit.edu	37	10	90674333	90674333	+	Missense_Mutation	SNP	A	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:90674333A>T	uc001kfk.2	+	7	1244	c.821A>T	c.(820-822)GAT>GTT	p.D274V	STAMBPL1_uc010qmx.1_Missense_Mutation_p.D274V|STAMBPL1_uc009xto.2_RNA|STAMBPL1_uc001kfl.2_Missense_Mutation_p.D274V|STAMBPL1_uc001kfn.2_Missense_Mutation_p.D108V	NM_020799	NP_065850	Q96FJ0	STALP_HUMAN	STAM binding protein-like 1	274	MPN.						metal ion binding|metallopeptidase activity|protein binding			ovary(1)	1		Colorectal(252;0.0381)		Colorectal(12;6.38e-05)|COAD - Colon adenocarcinoma(12;7.75e-05)														---	---	---	---
FAS	355	broad.mit.edu	37	10	90771771	90771771	+	Missense_Mutation	SNP	T	C	C	rs144211297	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:90771771T>C	uc001kfr.2	+	7	930	c.584T>C	c.(583-585)GTA>GCA	p.V195A	FAS_uc010qna.1_RNA|FAS_uc001kfs.2_Missense_Mutation_p.V195A|FAS_uc001kft.2_Missense_Mutation_p.V174A|FAS_uc010qnb.1_RNA|FAS_uc010qnc.1_RNA|FAS_uc001kfw.2_Intron|FAS_uc010qnd.1_RNA|FAS_uc010qne.1_RNA|FAS_uc009xtp.2_RNA	NM_000043	NP_000034	P25445	TNR6_HUMAN	tumor necrosis factor receptor superfamily,	195	Cytoplasmic (Potential).				activation of caspase activity|activation of pro-apoptotic gene products|anti-apoptosis|cellular response to mechanical stimulus|positive regulation of necrotic cell death	cytosol|extracellular region|integral to membrane|soluble fraction	identical protein binding|kinase binding			upper_aerodigestive_tract(1)|breast(1)	2		Colorectal(252;0.0161)		Colorectal(12;0.000136)|COAD - Colon adenocarcinoma(12;0.000193)										Autoimmune_Lymphoproliferative_syndrome_type_I				---	---	---	---
KIF20B	9585	broad.mit.edu	37	10	91511151	91511151	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:91511151A>G	uc001kgs.1	+	24	4217	c.4145A>G	c.(4144-4146)GAA>GGA	p.E1382G	KIF20B_uc001kgr.1_Missense_Mutation_p.E1342G|KIF20B_uc001kgt.1_Missense_Mutation_p.E593G|KIF20B_uc009xtw.1_RNA	NM_016195	NP_057279	Q96Q89	KI20B_HUMAN	M-phase phosphoprotein 1	1382					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																		---	---	---	---
BTAF1	9044	broad.mit.edu	37	10	93753606	93753606	+	Splice_Site	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:93753606T>C	uc001khr.2	+	22	3297	c.3199_splice	c.e22+2	p.D1067_splice	BTAF1_uc001kht.1_Splice_Site_p.D505_splice	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)																---	---	---	---
KIF11	3832	broad.mit.edu	37	10	94392424	94392424	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:94392424T>C	uc001kic.2	+	13	1984	c.1676T>C	c.(1675-1677)ATG>ACG	p.M559T	KIF11_uc010qnq.1_Intron	NM_004523	NP_004514	P52732	KIF11_HUMAN	kinesin family member 11	559					blood coagulation|cell division|microtubule-based movement|spindle assembly involved in mitosis	chromatin remodeling complex|cytosol|kinesin complex|microtubule|spindle pole	ATP binding|microtubule motor activity|protein kinase binding			skin(1)	1																		---	---	---	---
KIF11	3832	broad.mit.edu	37	10	94393537	94393537	+	Silent	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:94393537A>G	uc001kic.2	+	14	2168	c.1860A>G	c.(1858-1860)GTA>GTG	p.V620V	KIF11_uc010qnq.1_Intron	NM_004523	NP_004514	P52732	KIF11_HUMAN	kinesin family member 11	620					blood coagulation|cell division|microtubule-based movement|spindle assembly involved in mitosis	chromatin remodeling complex|cytosol|kinesin complex|microtubule|spindle pole	ATP binding|microtubule motor activity|protein kinase binding			skin(1)	1																		---	---	---	---
EXOC6	54536	broad.mit.edu	37	10	94712103	94712103	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:94712103A>G	uc001kig.2	+	15	1556	c.1490A>G	c.(1489-1491)TAT>TGT	p.Y497C	EXOC6_uc010qnr.1_Missense_Mutation_p.Y513C|EXOC6_uc001kie.2_Missense_Mutation_p.Y492C|EXOC6_uc009xub.2_Missense_Mutation_p.Y496C|EXOC6_uc009xuc.2_Missense_Mutation_p.Y394C|EXOC6_uc001kih.2_RNA|EXOC6_uc001kii.2_Missense_Mutation_p.Y71C	NM_019053	NP_061926	Q8TAG9	EXOC6_HUMAN	SEC15-like 1 isoform a	497					protein transport|vesicle docking involved in exocytosis	exocyst				skin(1)	1		Colorectal(252;0.123)																---	---	---	---
CYP26A1	1592	broad.mit.edu	37	10	94834089	94834089	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:94834089C>T	uc001kil.2	+	2	259	c.214C>T	c.(214-216)CGC>TGC	p.R72C	CYP26A1_uc001kik.1_Missense_Mutation_p.R3C|CYP26A1_uc001kim.1_5'UTR	NM_000783	NP_000774	O43174	CP26A_HUMAN	cytochrome P450, family 26, subfamily A,	72					negative regulation of retinoic acid receptor signaling pathway|retinoic acid catabolic process|xenobiotic metabolic process	endoplasmic reticulum membrane|microsome	electron carrier activity|heme binding|oxygen binding|retinoic acid 4-hydroxylase activity|retinoic acid binding			upper_aerodigestive_tract(1)|ovary(1)|breast(1)	3		Colorectal(252;0.122)																---	---	---	---
MYOF	26509	broad.mit.edu	37	10	95163778	95163778	+	Splice_Site	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:95163778A>G	uc001kin.2	-	9	966	c.843_splice	c.e9+1	p.K281_splice	MYOF_uc001kio.2_Splice_Site_p.K281_splice|MYOF_uc001kip.3_Splice_Site_p.K281_splice|MYOF_uc009xuf.2_Splice_Site_p.K263_splice	NM_013451	NP_038479			myoferlin isoform a						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																		---	---	---	---
C10orf4	118924	broad.mit.edu	37	10	95429580	95429580	+	3'UTR	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:95429580G>A	uc001kiz.1	-	14					C10orf4_uc001kiv.1_RNA|C10orf4_uc001kja.1_3'UTR	NM_145246	NP_660289			FRA10AC1 protein							nucleus	protein binding				0		Colorectal(252;0.122)																---	---	---	---
PLCE1	51196	broad.mit.edu	37	10	96014027	96014027	+	Silent	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:96014027T>C	uc001kjk.2	+	10	3994	c.3360T>C	c.(3358-3360)GGT>GGC	p.G1120G	PLCE1_uc010qnx.1_Silent_p.G1120G|PLCE1_uc001kjm.2_Silent_p.G812G	NM_016341	NP_057425	Q9P212	PLCE1_HUMAN	phospholipase C, epsilon 1 isoform 1	1120					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)																---	---	---	---
SORBS1	10580	broad.mit.edu	37	10	97154764	97154764	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:97154764A>G	uc001kkp.2	-	12	1336	c.1291T>C	c.(1291-1293)TCC>CCC	p.S431P	SORBS1_uc001kkl.2_Missense_Mutation_p.S54P|SORBS1_uc001kkn.2_Intron|SORBS1_uc001kkm.2_Missense_Mutation_p.S287P|SORBS1_uc001kko.2_Missense_Mutation_p.S431P|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	Q9BX66	SRBS1_HUMAN	sorbin and SH3 domain containing 1 isoform 3	431	SoHo.				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)														---	---	---	---
PIK3AP1	118788	broad.mit.edu	37	10	98392822	98392822	+	Intron	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:98392822A>G	uc001kmq.2	-						PIK3AP1_uc001kmo.2_5'UTR|PIK3AP1_uc001kmp.2_Intron	NM_152309	NP_689522			phosphoinositide-3-kinase adaptor protein 1							cytoplasm|plasma membrane				upper_aerodigestive_tract(3)|ovary(1)|skin(1)	5		Colorectal(252;0.0442)		Epithelial(162;6.29e-08)|all cancers(201;3.18e-06)														---	---	---	---
GOT1	2805	broad.mit.edu	37	10	101163585	101163585	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:101163585G>A	uc001kpr.2	-	6	897	c.689C>T	c.(688-690)GCA>GTA	p.A230V	GOT1_uc009xwh.2_RNA|GOT1_uc001kpq.1_Intron	NM_002079	NP_002070	P17174	AATC_HUMAN	aspartate aminotransferase 1	230					aspartate catabolic process|cellular response to insulin stimulus|gluconeogenesis|response to glucocorticoid stimulus	cytosol	L-aspartate:2-oxoglutarate aminotransferase activity|pyridoxal phosphate binding				0		Ovarian(717;0.028)|Colorectal(252;0.234)		Epithelial(162;4.76e-10)|all cancers(201;3.84e-08)	L-Aspartic Acid(DB00128)|L-Cysteine(DB00151)|L-Glutamic Acid(DB00142)|Pyridoxal Phosphate(DB00114)													---	---	---	---
ABCC2	1244	broad.mit.edu	37	10	101594271	101594271	+	Silent	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:101594271C>T	uc001kqf.2	+	24	3532	c.3393C>T	c.(3391-3393)GGC>GGT	p.G1131G		NM_000392	NP_000383	Q92887	MRP2_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP),	1131	ABC transmembrane type-1 2.|Helical; Name=15; (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)													---	---	---	---
ERLIN1	10613	broad.mit.edu	37	10	101912065	101912065	+	Silent	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:101912065G>A	uc001kqn.3	-	11	1221	c.870C>T	c.(868-870)GCC>GCT	p.A290A	ERLIN1_uc001kqm.3_Silent_p.A55A|ERLIN1_uc001kqo.3_Silent_p.A290A|ERLIN1_uc010qpm.1_Silent_p.A206A	NM_006459	NP_006450	O75477	ERLN1_HUMAN	ER lipid raft associated 1	288	Lumenal (Potential).				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)														---	---	---	---
PKD2L1	9033	broad.mit.edu	37	10	102057186	102057186	+	Silent	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:102057186G>A	uc001kqx.1	-	5	1292	c.909C>T	c.(907-909)ATC>ATT	p.I303I	PKD2L1_uc009xwm.1_Silent_p.I256I	NM_016112	NP_057196	Q9P0L9	PK2L1_HUMAN	polycystic kidney disease 2-like 1	303	Extracellular (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)														---	---	---	---
FAM178A	55719	broad.mit.edu	37	10	102703850	102703850	+	Missense_Mutation	SNP	A	G	G	rs151321115		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:102703850A>G	uc001krt.3	+	12	3264	c.2722A>G	c.(2722-2724)ACA>GCA	p.T908A	FAM178A_uc001krs.2_Missense_Mutation_p.T908A	NM_018121	NP_060591	Q8IX21	F178A_HUMAN	hypothetical protein LOC55719 isoform 1	908											0																		---	---	---	---
C10orf2	56652	broad.mit.edu	37	10	102750712	102750712	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:102750712G>A	uc001ksf.2	+	4	2354	c.1679G>A	c.(1678-1680)CGG>CAG	p.R560Q	C10orf2_uc001ksg.2_Missense_Mutation_p.R560Q|C10orf2_uc001ksi.2_Missense_Mutation_p.R106Q|C10orf2_uc010qpv.1_Missense_Mutation_p.R106Q|C10orf2_uc001ksh.2_RNA	NM_021830	NP_068602	Q96RR1	PEO1_HUMAN	twinkle isoform A	560	SF4 helicase.				cell death|mitochondrial DNA replication|protein hexamerization|protein homooligomerization|transcription from mitochondrial promoter	mitochondrial nucleoid	5'-3' DNA helicase activity|ATP binding|protease binding|single-stranded DNA binding			ovary(1)	1		Colorectal(252;0.122)|all_hematologic(284;0.152)		Epithelial(162;7.18e-11)|all cancers(201;8.75e-09)|BRCA - Breast invasive adenocarcinoma(275;0.224)														---	---	---	---
LZTS2	84445	broad.mit.edu	37	10	102763459	102763459	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:102763459C>T	uc001ksj.2	+	3	673	c.604C>T	c.(604-606)CCC>TCC	p.P202S	LZTS2_uc010qpw.1_Missense_Mutation_p.P202S|LZTS2_uc001ksk.2_Missense_Mutation_p.P202S|LZTS2_uc001ksl.2_Missense_Mutation_p.P202S|LZTS2_uc001ksm.2_RNA	NM_032429	NP_115805	Q9BRK4	LZTS2_HUMAN	leucine zipper, putative tumor suppressor 2	202	Ser-rich.|Required for centrosomal localization (By similarity).				cell division|mitosis|Wnt receptor signaling pathway	membrane|microtubule|microtubule organizing center				ovary(2)|large_intestine(1)|breast(1)	4				Epithelial(162;7.3e-09)|all cancers(201;3.72e-07)														---	---	---	---
LZTS2	84445	broad.mit.edu	37	10	102763563	102763563	+	Silent	SNP	C	T	T	rs143408611		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:102763563C>T	uc001ksj.2	+	3	777	c.708C>T	c.(706-708)GCC>GCT	p.A236A	LZTS2_uc010qpw.1_Silent_p.A236A|LZTS2_uc001ksk.2_Silent_p.A236A|LZTS2_uc001ksl.2_Silent_p.A236A|LZTS2_uc001ksm.2_RNA	NM_032429	NP_115805	Q9BRK4	LZTS2_HUMAN	leucine zipper, putative tumor suppressor 2	236	Ser-rich.|Required for centrosomal localization (By similarity).				cell division|mitosis|Wnt receptor signaling pathway	membrane|microtubule|microtubule organizing center				ovary(2)|large_intestine(1)|breast(1)	4				Epithelial(162;7.3e-09)|all cancers(201;3.72e-07)														---	---	---	---
SFXN3	81855	broad.mit.edu	37	10	102798400	102798400	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:102798400C>T	uc001ksp.2	+	10	1240	c.784C>T	c.(784-786)CGC>TGC	p.R262C	SFXN3_uc001ksq.2_Missense_Mutation_p.R262C|SFXN3_uc010qpx.1_Missense_Mutation_p.R266C	NM_030971	NP_112233	Q9BWM7	SFXN3_HUMAN	sideroflexin 3	262					iron ion homeostasis	integral to membrane|mitochondrial membrane	cation transmembrane transporter activity			ovary(1)	1		Colorectal(252;0.234)		Epithelial(162;6.98e-09)|all cancers(201;3.55e-07)												OREG0020454	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
PSD	5662	broad.mit.edu	37	10	104173810	104173810	+	Silent	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:104173810G>A	uc001kvg.1	-	5	1796	c.1269C>T	c.(1267-1269)CTC>CTT	p.L423L	PSD_uc001kvh.1_Silent_p.L44L|PSD_uc009xxd.1_Silent_p.L423L	NM_002779	NP_002770	A5PKW4	PSD1_HUMAN	pleckstrin and Sec7 domain containing	423					regulation of ARF protein signal transduction	cytoplasm|plasma membrane|ruffle	ARF guanyl-nucleotide exchange factor activity|signal transducer activity			breast(2)|urinary_tract(1)	3				Epithelial(162;1.27e-08)|all cancers(201;2.85e-07)														---	---	---	---
SFXN2	118980	broad.mit.edu	37	10	104486854	104486854	+	Missense_Mutation	SNP	G	A	A	rs142927441		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:104486854G>A	uc001kwb.2	+	3	438	c.272G>A	c.(271-273)CGC>CAC	p.R91H	SFXN2_uc001kwc.2_RNA|SFXN2_uc001kwd.2_RNA	NM_178858	NP_849189	Q96NB2	SFXN2_HUMAN	sideroflexin 2	91					iron ion homeostasis	integral to membrane	cation transmembrane transporter activity				0		Colorectal(252;0.207)		Epithelial(162;4.53e-09)|all cancers(201;1.2e-07)|BRCA - Breast invasive adenocarcinoma(275;0.218)														---	---	---	---
PDCD11	22984	broad.mit.edu	37	10	105194622	105194622	+	Silent	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:105194622G>A	uc001kwy.1	+	25	3822	c.3735G>A	c.(3733-3735)GGG>GGA	p.G1245G		NM_014976	NP_055791	Q14690	RRP5_HUMAN	programmed cell death 11	1245	S1 motif 11.				mRNA processing|rRNA processing	nucleolus	RNA binding|transcription factor binding			ovary(2)|breast(2)|skin(2)|central_nervous_system(1)	7		Colorectal(252;0.0747)|Breast(234;0.128)		Epithelial(162;7.21e-09)|all cancers(201;1.17e-08)|BRCA - Breast invasive adenocarcinoma(275;0.208)														---	---	---	---
COL17A1	1308	broad.mit.edu	37	10	105793863	105793863	+	Silent	SNP	T	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:105793863T>G	uc001kxr.2	-	52	4165	c.3996A>C	c.(3994-3996)GGA>GGC	p.G1332G	COL17A1_uc001kxq.2_5'Flank	NM_000494	NP_000485	Q9UMD9	COHA1_HUMAN	alpha 1 type XVII collagen	1332	Extracellular (Potential).|Triple-helical region.				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)														---	---	---	---
SORCS3	22986	broad.mit.edu	37	10	106675652	106675652	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:106675652C>T	uc001kyi.1	+	3	984	c.757C>T	c.(757-759)CTC>TTC	p.L253F		NM_014978	NP_055793	Q9UPU3	SORC3_HUMAN	VPS10 domain receptor protein SORCS 3 precursor	253	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)														---	---	---	---
SORCS3	22986	broad.mit.edu	37	10	107023075	107023075	+	Silent	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:107023075T>C	uc001kyi.1	+	27	3839	c.3612T>C	c.(3610-3612)ATT>ATC	p.I1204I		NM_014978	NP_055793	Q9UPU3	SORC3_HUMAN	VPS10 domain receptor protein SORCS 3 precursor	1204	Cytoplasmic (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)														---	---	---	---
SMC3	9126	broad.mit.edu	37	10	112360201	112360201	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:112360201A>G	uc001kze.2	+	22	2558	c.2432A>G	c.(2431-2433)AAC>AGC	p.N811S		NM_005445	NP_005436	Q9UQE7	SMC3_HUMAN	structural maintenance of chromosomes 3	811	Potential.				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)														---	---	---	---
NRAP	4892	broad.mit.edu	37	10	115411638	115411638	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-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	115612881	115612881	+	Nonsense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:115612881G>A	uc001law.2	-	1	979	c.61C>T	c.(61-63)CGA>TGA	p.R21*	NHLRC2_uc001lax.1_5'Flank	NM_014881	NP_055696	Q6PJP8	DCR1A_HUMAN	DNA cross-link repair 1A	21	Nuclear localization region.				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					---	---	---	---
FAM160B1	57700	broad.mit.edu	37	10	116590691	116590691	+	Splice_Site	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:116590691T>C	uc001lcb.2	+	2	459	c.124_splice	c.e2+2	p.D42_splice	FAM160B1_uc001lcc.2_Splice_Site_p.D42_splice	NM_020940	NP_065991			hypothetical protein LOC57700 isoform a											lung(1)	1																		---	---	---	---
TRUB1	142940	broad.mit.edu	37	10	116730205	116730205	+	Intron	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:116730205T>C	uc001lcd.2	+						TRUB1_uc010qsl.1_Intron	NM_139169	NP_631908			TruB pseudouridine (psi) synthase homolog 1						pseudouridine synthesis|tRNA processing		pseudouridine synthase activity|RNA binding				0		Colorectal(252;0.09)|Breast(234;0.174)|Lung NSC(174;0.245)		Epithelial(162;0.00879)|all cancers(201;0.0243)														---	---	---	---
PDZD8	118987	broad.mit.edu	37	10	119043869	119043869	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:119043869T>C	uc001lde.1	-	5	2574	c.2375A>G	c.(2374-2376)CAC>CGC	p.H792R		NM_173791	NP_776152	Q8NEN9	PDZD8_HUMAN	PDZ domain containing 8	792					intracellular signal transduction		metal ion binding				0		Colorectal(252;0.19)		all cancers(201;0.0121)														---	---	---	---
RAB11FIP2	22841	broad.mit.edu	37	10	119799912	119799912	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:119799912C>T	uc001ldj.1	-	2	958	c.518G>A	c.(517-519)GGT>GAT	p.G173D	RAB11FIP2_uc009xyz.1_Missense_Mutation_p.G173D	NM_014904	NP_055719	Q7L804	RFIP2_HUMAN	RAB11 family interacting protein 2	173					protein transport	plasma membrane|recycling endosome membrane	protein homodimerization activity				0		Colorectal(252;0.235)		all cancers(201;0.0238)														---	---	---	---
C10orf46	143384	broad.mit.edu	37	10	120446139	120446139	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:120446139C>T	uc001lds.1	-	8	1524	c.1040G>A	c.(1039-1041)CGG>CAG	p.R347Q	C10orf46_uc010qst.1_RNA	NM_153810	NP_722517	Q86Y37	CJ046_HUMAN	chromosome 10 open reading frame 46	347					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)														---	---	---	---
GRK5	2869	broad.mit.edu	37	10	121196306	121196306	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:121196306G>T	uc001led.2	+	9	1115	c.882G>T	c.(880-882)GAG>GAT	p.E294D	GRK5_uc009xzh.2_Missense_Mutation_p.E189D|GRK5_uc010qta.1_Missense_Mutation_p.E189D	NM_005308	NP_005299	P34947	GRK5_HUMAN	G protein-coupled receptor kinase 5	294	Protein kinase.				G-protein signaling, coupled to cAMP nucleotide second messenger|regulation of G-protein coupled receptor protein signaling pathway|tachykinin receptor signaling pathway	cytoplasm|plasma membrane|soluble fraction	ATP binding|G-protein coupled receptor kinase activity|phospholipid binding|protein kinase C binding|signal transducer activity			lung(2)|stomach(1)	3		Lung NSC(174;0.0971)|all_lung(145;0.127)|Ovarian(717;0.249)		all cancers(201;0.0227)														---	---	---	---
WDR11	55717	broad.mit.edu	37	10	122626212	122626212	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:122626212A>G	uc010qtf.1	+	8	1364	c.1126A>G	c.(1126-1128)AGT>GGT	p.S376G	WDR11_uc010qte.1_Intron|WDR11_uc001lfd.1_5'UTR	NM_018117	NP_060587	Q9BZH6	WDR11_HUMAN	bromodomain and WD repeat domain containing 2	376	WD 3.					integral to membrane					0																		---	---	---	---
PLEKHA1	59338	broad.mit.edu	37	10	124189239	124189239	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:124189239G>A	uc001lge.1	+	12	1123	c.1000G>A	c.(1000-1002)GTC>ATC	p.V334I	PLEKHA1_uc001lgf.1_3'UTR|PLEKHA1_uc001lgg.1_Missense_Mutation_p.V334I	NM_001001974	NP_001001974	Q9HB21	PKHA1_HUMAN	pleckstrin homology domain containing, family A	334					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)																---	---	---	---
HTRA1	5654	broad.mit.edu	37	10	124273774	124273774	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:124273774G>A	uc001lgj.2	+	9	1470	c.1342G>A	c.(1342-1344)GTC>ATC	p.V448I		NM_002775	NP_002766	Q92743	HTRA1_HUMAN	HtrA serine peptidase 1 precursor	448	PDZ.				proteolysis|regulation of cell growth	extracellular space	insulin-like growth factor binding|serine-type endopeptidase activity				0		all_neural(114;0.0765)|Lung NSC(174;0.133)|all_lung(145;0.163)|Breast(234;0.238)																---	---	---	---
DMBT1	1755	broad.mit.edu	37	10	124395581	124395581	+	Missense_Mutation	SNP	G	A	A	rs147966171	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:124395581G>A	uc001lgk.1	+	50	6342	c.6236G>A	c.(6235-6237)CGA>CAA	p.R2079Q	DMBT1_uc001lgl.1_Missense_Mutation_p.R2069Q|DMBT1_uc001lgm.1_Missense_Mutation_p.R1451Q|DMBT1_uc009xzz.1_Missense_Mutation_p.R2078Q|DMBT1_uc010qtx.1_Missense_Mutation_p.R799Q|DMBT1_uc009yab.1_Missense_Mutation_p.R782Q|DMBT1_uc009yac.1_Missense_Mutation_p.R373Q	NM_007329	NP_015568	Q9UGM3	DMBT1_HUMAN	deleted in malignant brain tumors 1 isoform b	2079	CUB 2.				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)																---	---	---	---
LHPP	64077	broad.mit.edu	37	10	126177078	126177078	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:126177078A>G	uc001lhs.1	+	3	421	c.401A>G	c.(400-402)AAC>AGC	p.N134S	LHPP_uc001lht.1_Missense_Mutation_p.N134S|LHPP_uc009yai.1_Missense_Mutation_p.N134S	NM_022126	NP_071409	Q9H008	LHPP_HUMAN	phospholysine phosphohistidine inorganic	134					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)														---	---	---	---
DHX32	55760	broad.mit.edu	37	10	127541004	127541004	+	Silent	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:127541004C>T	uc001ljf.1	-	6	1700	c.1209G>A	c.(1207-1209)CTG>CTA	p.L403L	BCCIP_uc001ljd.3_Intron|DHX32_uc001lje.1_Silent_p.L27L|DHX32_uc001ljg.1_Silent_p.L403L|DHX32_uc009yam.1_Silent_p.L158L	NM_018180	NP_060650	Q7L7V1	DHX32_HUMAN	DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 32	403						mitochondrion|nucleus	ATP binding|helicase activity			breast(2)|ovary(1)|lung(1)	4		all_lung(145;0.00751)|Lung NSC(174;0.0115)|Colorectal(57;0.0846)|all_neural(114;0.0936)																---	---	---	---
DOCK1	1793	broad.mit.edu	37	10	128776225	128776225	+	Silent	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:128776225T>C	uc001ljt.2	+	3	208	c.144T>C	c.(142-144)GGT>GGC	p.G48G	DOCK1_uc010qun.1_Silent_p.G48G	NM_001380	NP_001371	Q14185	DOCK1_HUMAN	dedicator of cytokinesis 1	48	SH3.				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	128944302	128944302	+	Intron	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:128944302C>T	uc001ljt.2	+						DOCK1_uc010qun.1_Intron|FAM196A_uc010quo.1_Intron|FAM196A_uc001ljv.1_Intron|FAM196A_uc001lju.1_Intron|FAM196A_uc009yap.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)														---	---	---	---
NPS	594857	broad.mit.edu	37	10	129347652	129347652	+	Intron	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:129347652C>T	uc001ljx.1	+							NM_001030013	NP_001025184			neuropeptide S precursor						neuropeptide signaling pathway	extracellular region					0																		---	---	---	---
MKI67	4288	broad.mit.edu	37	10	129901948	129901948	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:129901948C>T	uc001lke.2	-	13	8351	c.8156G>A	c.(8155-8157)AGC>AAC	p.S2719N	MKI67_uc001lkf.2_Missense_Mutation_p.S2359N|MKI67_uc009yav.1_Missense_Mutation_p.S2294N|MKI67_uc009yaw.1_Missense_Mutation_p.S1869N	NM_002417	NP_002408	P46013	KI67_HUMAN	antigen identified by monoclonal antibody Ki-67	2719	16 X 122 AA approximate repeats.|15.				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)																---	---	---	---
C10orf93	255352	broad.mit.edu	37	10	134752256	134752256	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:134752256A>G	uc001llt.1	-	5	449	c.373T>C	c.(373-375)TAC>CAC	p.Y125H	C10orf93_uc001llu.2_Missense_Mutation_p.Y125H	NM_173572	NP_775843	Q5SR76	CJ093_HUMAN	hypothetical protein LOC255352	125							binding			pancreas(1)	1		all_cancers(35;1.8e-07)|all_epithelial(44;6.22e-06)|Lung NSC(174;0.0108)|all_lung(145;0.0173)|all_neural(114;0.0726)|Colorectal(31;0.119)|Glioma(114;0.172)|Melanoma(40;0.175)		Epithelial(32;4.28e-05)|OV - Ovarian serous cystadenocarcinoma(35;4.31e-05)|all cancers(32;5.02e-05)														---	---	---	---
CYP2E1	1571	broad.mit.edu	37	10	135345716	135345716	+	Silent	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:135345716T>C	uc001lnj.1	+	4	609	c.576T>C	c.(574-576)AAT>AAC	p.N192N	CYP2E1_uc001lnk.1_Silent_p.N55N|CYP2E1_uc009ybl.1_5'UTR|CYP2E1_uc009ybm.1_Intron|CYP2E1_uc001lnl.1_5'UTR	NM_000773	NP_000764	P05181	CP2E1_HUMAN	cytochrome P450, family 2, subfamily E,	192					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	135351268	135351268	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:135351268T>C	uc001lnj.1	+	8	1202	c.1169T>C	c.(1168-1170)GTG>GCG	p.V390A	CYP2E1_uc001lnk.1_Missense_Mutation_p.V253A|CYP2E1_uc009ybl.1_Missense_Mutation_p.V191A|CYP2E1_uc009ybm.1_Missense_Mutation_p.V44A|CYP2E1_uc001lnl.1_Missense_Mutation_p.V191A	NM_000773	NP_000764	P05181	CP2E1_HUMAN	cytochrome P450, family 2, subfamily E,	390					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				---	---	---	---
RIC8A	60626	broad.mit.edu	37	11	210630	210630	+	Silent	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:210630T>C	uc001log.2	+	4	1111	c.786T>C	c.(784-786)GCT>GCC	p.A262A	RIC8A_uc001lof.2_Silent_p.A262A|RIC8A_uc001loh.2_Silent_p.A255A	NM_021932	NP_068751	Q9NPQ8	RIC8A_HUMAN	resistance to inhibitors of cholinesterase 8	262						cytoplasm|plasma membrane	guanyl-nucleotide exchange factor activity				0		all_cancers(49;9.23e-07)|all_epithelial(84;0.000315)|Breast(177;0.00122)|Ovarian(85;0.0202)|Medulloblastoma(188;0.0321)|all_neural(188;0.0762)		all cancers(45;4.45e-27)|Epithelial(43;2.94e-26)|OV - Ovarian serous cystadenocarcinoma(40;5.86e-21)|BRCA - Breast invasive adenocarcinoma(625;3.57e-05)|Lung(200;0.105)|LUSC - Lung squamous cell carcinoma(625;0.122)														---	---	---	---
ATHL1	80162	broad.mit.edu	37	11	293736	293736	+	Intron	SNP	C	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:293736C>A	uc010qvu.1	+						ATHL1_uc001lor.3_Intron|ATHL1_uc001lou.3_Intron|ATHL1_uc001lov.3_5'Flank	NM_025092	NP_079368			ATH1, acid trehalase-like 1						carbohydrate metabolic process		hydrolase activity, acting on glycosyl bonds			liver(1)|central_nervous_system(1)|skin(1)	3		all_cancers(49;1.12e-06)|all_epithelial(84;0.000375)|Breast(177;0.00122)|Ovarian(85;0.0228)|Medulloblastoma(188;0.0321)|all_neural(188;0.0762)		all cancers(45;5.38e-28)|Epithelial(43;3.25e-27)|OV - Ovarian serous cystadenocarcinoma(40;1.11e-20)|BRCA - Breast invasive adenocarcinoma(625;3.56e-05)|Lung(200;0.0327)|LUSC - Lung squamous cell carcinoma(625;0.122)														---	---	---	---
ATHL1	80162	broad.mit.edu	37	11	294457	294457	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:294457T>C	uc010qvu.1	+	13	2114	c.1999T>C	c.(1999-2001)TCC>CCC	p.S667P	ATHL1_uc001lor.3_Missense_Mutation_p.S419P|ATHL1_uc001lou.3_Missense_Mutation_p.S242P|ATHL1_uc001lov.3_Missense_Mutation_p.S128P	NM_025092	NP_079368	Q32M88	ATHL1_HUMAN	ATH1, acid trehalase-like 1	667					carbohydrate metabolic process		hydrolase activity, acting on glycosyl bonds			liver(1)|central_nervous_system(1)|skin(1)	3		all_cancers(49;1.12e-06)|all_epithelial(84;0.000375)|Breast(177;0.00122)|Ovarian(85;0.0228)|Medulloblastoma(188;0.0321)|all_neural(188;0.0762)		all cancers(45;5.38e-28)|Epithelial(43;3.25e-27)|OV - Ovarian serous cystadenocarcinoma(40;1.11e-20)|BRCA - Breast invasive adenocarcinoma(625;3.56e-05)|Lung(200;0.0327)|LUSC - Lung squamous cell carcinoma(625;0.122)														---	---	---	---
PKP3	11187	broad.mit.edu	37	11	396607	396607	+	Splice_Site	SNP	G	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:396607G>T	uc001lpc.2	+	2	309	c.233_splice	c.e2-1	p.G78_splice		NM_007183	NP_009114			plakophilin 3						cell adhesion	desmosome|nucleus	binding			skin(1)	1		all_cancers(49;3.02e-09)|all_epithelial(84;2.09e-06)|Breast(177;0.000162)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.0538)|all_lung(207;0.0713)		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	608104	608104	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:608104C>T	uc001lqe.2	+	14	2779	c.2648C>T	c.(2647-2649)ACG>ATG	p.T883M	PHRF1_uc010qwc.1_Missense_Mutation_p.T882M|PHRF1_uc010qwd.1_Missense_Mutation_p.T881M|PHRF1_uc010qwe.1_Missense_Mutation_p.T879M|PHRF1_uc009ybz.1_Missense_Mutation_p.T673M|PHRF1_uc009yca.1_RNA	NM_020901	NP_065952	Q9P1Y6	PHRF1_HUMAN	PHD and ring finger domains 1	883							RNA polymerase binding|zinc ion binding				0																		---	---	---	---
MUC5B	727897	broad.mit.edu	37	11	1213642	1213642	+	Intron	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:1213642G>A	uc009ycr.1	+						uc001lsz.2_RNA	NM_017511	NP_059981			SubName: Full=Mucin 5AC, oligomeric mucus/gel-forming;						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	1247906	1247906	+	Silent	SNP	C	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:1247906C>A	uc009ycr.1	+	20	2355	c.2229C>A	c.(2227-2229)ACC>ACA	p.T743T	MUC5B_uc009yct.1_Silent_p.T87T|MUC5B_uc001ltb.2_Silent_p.T87T|MUC5B_uc001lta.2_5'Flank	NM_017511	NP_059981	Q9HC84	MUC5B_HUMAN	SubName: Full=Mucin 5AC, oligomeric mucus/gel-forming;	87	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	1262799	1262799	+	Silent	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:1262799G>A	uc009ycr.1	+	47	6894	c.6768G>A	c.(6766-6768)GGG>GGA	p.G2256G	MUC5B_uc001ltb.2_Silent_p.G1566G	NM_017511	NP_059981	Q9HC84	MUC5B_HUMAN	SubName: Full=Mucin 5AC, oligomeric mucus/gel-forming;	1563	7 X Cys-rich subdomain repeats.|Cys-rich subdomain 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)														---	---	---	---
MUC5B	727897	broad.mit.edu	37	11	1267057	1267057	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:1267057C>T	uc009ycr.1	+	49	10822	c.10696C>T	c.(10696-10698)CCC>TCC	p.P3566S	MUC5B_uc001ltb.2_Missense_Mutation_p.P2986S	NM_017511	NP_059981	Q9HC84	MUC5B_HUMAN	SubName: Full=Mucin 5AC, oligomeric mucus/gel-forming;	2983	7 X Cys-rich subdomain repeats.|Thr-rich.|17 X approximate tandem repeats, Ser/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	1272925	1272925	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:1272925T>C	uc009ycr.1	+	52	15907	c.15781T>C	c.(15781-15783)TTC>CTC	p.F5261L	MUC5B_uc001ltb.2_Missense_Mutation_p.F4942L	NM_017511	NP_059981	Q9HC84	MUC5B_HUMAN	SubName: Full=Mucin 5AC, oligomeric mucus/gel-forming;	4939					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)														---	---	---	---
MOB2	81532	broad.mit.edu	37	11	1491524	1491524	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:1491524C>T	uc010qwz.1	-	5	875	c.685G>A	c.(685-687)GCC>ACC	p.A229T	MOB2_uc001lto.1_Missense_Mutation_p.A113T|MOB2_uc001ltp.1_5'UTR|MOB2_uc001ltq.1_Missense_Mutation_p.A192T|MOB2_uc010qwy.1_Missense_Mutation_p.A113T	NM_053005	NP_443731	Q70IA6	MOB2_HUMAN	HCCA2 protein	198						nucleus|perinuclear region of cytoplasm	metal ion binding				0																		---	---	---	---
KCNQ1	3784	broad.mit.edu	37	11	2610078	2610078	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:2610078A>G	uc001lwn.2	+	10	1495	c.1387A>G	c.(1387-1389)AGT>GGT	p.S463G	KCNQ1_uc009ydp.1_Missense_Mutation_p.S247G|KCNQ1_uc001lwo.2_Missense_Mutation_p.S336G	NM_000218	NP_000209	P51787	KCNQ1_HUMAN	potassium voltage-gated channel, KQT-like	463	Cytoplasmic (Potential).				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)													---	---	---	---
OR52I1	390037	broad.mit.edu	37	11	4615723	4615723	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:4615723T>C	uc010qyi.1	+	1	455	c.455T>C	c.(454-456)GTC>GCC	p.V152A		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)														---	---	---	---
TRIM68	55128	broad.mit.edu	37	11	4623443	4623443	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:4623443A>G	uc001lzf.1	-	4	960	c.722T>C	c.(721-723)CTG>CCG	p.L241P	TRIM68_uc001lzg.1_Missense_Mutation_p.L18P|TRIM68_uc010qyj.1_Intron|TRIM68_uc009yek.1_Missense_Mutation_p.L241P	NM_018073	NP_060543	Q6AZZ1	TRI68_HUMAN	ring finger protein 137	241					protein autoubiquitination|regulation of androgen receptor signaling pathway	Golgi apparatus|nucleolus|perinuclear region of cytoplasm	androgen receptor binding|histone acetyltransferase binding|ubiquitin-protein ligase activity|zinc ion binding			ovary(1)	1		Medulloblastoma(188;0.0025)|Breast(177;0.0101)|all_neural(188;0.0227)		Epithelial(150;9.49e-12)|BRCA - Breast invasive adenocarcinoma(625;0.0288)|LUSC - Lung squamous cell carcinoma(625;0.192)														---	---	---	---
OR51L1	119682	broad.mit.edu	37	11	5020940	5020940	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:5020940G>A	uc010qyu.1	+	1	728	c.728G>A	c.(727-729)TGT>TAT	p.C243Y		NM_001004755	NP_001004755	Q8NGJ5	O51L1_HUMAN	olfactory receptor, family 51, subfamily L,	243	Helical; Name=6; (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)														---	---	---	---
HBG2	3048	broad.mit.edu	37	11	5275590	5275590	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:5275590T>C	uc001mai.1	-	2	684	c.247A>G	c.(247-249)AAG>GAG	p.K83E	HBG2_uc001mak.1_RNA|HBG2_uc001maj.1_Missense_Mutation_p.K83E	NM_000559	NP_000550	P69892	HBG2_HUMAN	A-gamma globin	83					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)														---	---	---	---
TRIM6-TRIM34	445372	broad.mit.edu	37	11	5655886	5655886	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:5655886G>T	uc001mbf.2	+	10	1851	c.1607G>T	c.(1606-1608)AGG>ATG	p.R536M	HBG2_uc001mak.1_Intron|TRIM34_uc001mbh.2_Missense_Mutation_p.R182M|TRIM34_uc009yeq.2_Translation_Start_Site|TRIM34_uc001mbi.2_Missense_Mutation_p.R182M|TRIM34_uc001mbj.2_Missense_Mutation_p.R182M	NM_001003819	NP_001003819	B2RNG4	B2RNG4_HUMAN	tripartite motif-containing 6 and tripartite	536						intracellular	zinc ion binding			ovary(1)	1		Medulloblastoma(188;0.00225)|Breast(177;0.0204)|all_neural(188;0.0212)		Epithelial(150;1.01e-08)|BRCA - Breast invasive adenocarcinoma(625;0.145)														---	---	---	---
FAM160A2	84067	broad.mit.edu	37	11	6244041	6244041	+	Silent	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:6244041C>T	uc001mcl.3	-	5	1382	c.1023G>A	c.(1021-1023)AAG>AAA	p.K341K	FAM160A2_uc001mck.3_Silent_p.K341K|FAM160A2_uc001mcm.2_Silent_p.K341K	NM_001098794	NP_001092264	Q8N612	F16A2_HUMAN	hypothetical protein LOC84067 isoform 2	341					early endosome to late endosome transport|endosome organization|endosome to lysosome transport|lysosome organization|protein transport	FHF complex	protein binding			skin(2)	2																		---	---	---	---
ILK	3611	broad.mit.edu	37	11	6631463	6631463	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:6631463G>A	uc001mee.2	+	12	1298	c.1163G>A	c.(1162-1164)CGG>CAG	p.R388Q	ILK_uc001mef.2_Missense_Mutation_p.R388Q|ILK_uc010rap.1_Missense_Mutation_p.R254Q|ILK_uc010raq.1_Missense_Mutation_p.R327Q|ILK_uc001meg.2_Missense_Mutation_p.R234Q|ILK_uc001meh.2_Missense_Mutation_p.R388Q|ILK_uc001mei.2_Missense_Mutation_p.R14Q	NM_001014794	NP_001014794	Q13418	ILK_HUMAN	integrin-linked kinase	388	Protein 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	6704450	6704450	+	Silent	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:6704450G>A	uc001men.2	-	1	183	c.78C>T	c.(76-78)ATC>ATT	p.I26I		NM_022061	NP_071344	Q9NRX2	RM17_HUMAN	mitochondrial ribosomal protein L17 precursor	26					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)														---	---	---	---
OR2AG1	144125	broad.mit.edu	37	11	6806517	6806517	+	Silent	SNP	G	A	A	rs144825471		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:6806517G>A	uc001mer.1	+	1	249	c.249G>A	c.(247-249)GCG>GCA	p.A83A		NM_001004489	NP_001004489	Q9H205	O2AG1_HUMAN	olfactory receptor, family 2, subfamily AG,	83	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			central_nervous_system(1)	1		Medulloblastoma(188;0.00776)|all_neural(188;0.0652)		Epithelial(150;2.19e-08)|BRCA - Breast invasive adenocarcinoma(625;0.129)														---	---	---	---
OR6A2	8590	broad.mit.edu	37	11	6816805	6816805	+	Silent	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:6816805G>A	uc001mes.1	-	1	335	c.135C>T	c.(133-135)CTC>CTT	p.L45L		NM_003696	NP_003687	O95222	OR6A2_HUMAN	olfactory receptor, family 6, subfamily A,	45	Helical; Name=1; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(3)|central_nervous_system(1)|pancreas(1)	5		Medulloblastoma(188;0.0523)|all_neural(188;0.236)		Epithelial(150;4.78e-08)|BRCA - Breast invasive adenocarcinoma(625;0.129)														---	---	---	---
ZNF214	7761	broad.mit.edu	37	11	7021812	7021812	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:7021812T>C	uc001mfa.2	-	3	1405	c.1102A>G	c.(1102-1104)AAT>GAT	p.N368D	ZNF214_uc010ray.1_Missense_Mutation_p.N368D|ZNF214_uc009yfh.1_Missense_Mutation_p.N368D	NM_013249	NP_037381	Q9UL59	ZN214_HUMAN	zinc finger protein 214	368	C2H2-type 4.				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)														---	---	---	---
NLRP14	338323	broad.mit.edu	37	11	7081200	7081200	+	Silent	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:7081200G>A	uc001mfb.1	+	9	3032	c.2709G>A	c.(2707-2709)ACG>ACA	p.T903T		NM_176822	NP_789792	Q86W24	NAL14_HUMAN	NLR family, pyrin domain containing 14	903	LRR 7.				cell differentiation|multicellular organismal development|spermatogenesis		ATP binding			ovary(3)|breast(2)|pancreas(1)|lung(1)|skin(1)	8				Epithelial(150;4.62e-08)|BRCA - Breast invasive adenocarcinoma(625;0.0871)														---	---	---	---
OVCH2	341277	broad.mit.edu	37	11	7722004	7722004	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:7722004C>T	uc010rbf.1	-	7	740	c.740G>A	c.(739-741)CGG>CAG	p.R247Q		NM_198185	NP_937828			ovochymase 2 precursor												0				Epithelial(150;7.9e-08)|BRCA - Breast invasive adenocarcinoma(625;0.197)														---	---	---	---
OVCH2	341277	broad.mit.edu	37	11	7727880	7727880	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:7727880T>C	uc010rbf.1	-	1	62	c.62A>G	c.(61-63)AAA>AGA	p.K21R		NM_198185	NP_937828			ovochymase 2 precursor												0				Epithelial(150;7.9e-08)|BRCA - Breast invasive adenocarcinoma(625;0.197)														---	---	---	---
OR10A6	390093	broad.mit.edu	37	11	7949442	7949442	+	Silent	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:7949442A>G	uc010rbh.1	-	1	768	c.768T>C	c.(766-768)AGT>AGC	p.S256S		NM_001004461	NP_001004461	Q8NH74	O10A6_HUMAN	olfactory receptor, family 10, subfamily A,	256	Helical; Name=6; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)|skin(1)	2				Epithelial(150;1.38e-07)|BRCA - Breast invasive adenocarcinoma(625;0.189)														---	---	---	---
NLRP10	338322	broad.mit.edu	37	11	7982613	7982613	+	Silent	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:7982613G>A	uc001mfv.1	-	2	563	c.546C>T	c.(544-546)CTC>CTT	p.L182L		NM_176821	NP_789791	Q86W26	NAL10_HUMAN	NLR family, pyrin domain containing 10	182	NACHT.						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	8111204	8111204	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:8111204G>A	uc001mga.2	+	2	235	c.86G>A	c.(85-87)CGG>CAG	p.R29Q	TUB_uc010rbk.1_Missense_Mutation_p.R35Q|TUB_uc001mfy.2_Missense_Mutation_p.R84Q	NM_177972	NP_813977	P50607	TUB_HUMAN	tubby isoform b	29					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)														---	---	---	---
RPL27A	6157	broad.mit.edu	37	11	8707334	8707334	+	Missense_Mutation	SNP	C	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:8707334C>G	uc001mgs.3	+	5	794	c.428C>G	c.(427-429)GCC>GGC	p.A143G		NM_000990	NP_000981	P46776	RL27A_HUMAN	ribosomal protein L27a	143					endocrine pancreas development|translational elongation|translational termination|viral transcription	cytosolic large ribosomal subunit	protein binding|RNA binding|structural constituent of ribosome				0				Epithelial(150;3.24e-07)|BRCA - Breast invasive adenocarcinoma(625;0.189)														---	---	---	---
SCUBE2	57758	broad.mit.edu	37	11	9088332	9088332	+	Silent	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:9088332G>A	uc001mhh.1	-	6	752	c.672C>T	c.(670-672)TGC>TGT	p.C224C	SCUBE2_uc001mhi.1_Silent_p.C224C|SCUBE2_uc001mhj.1_Silent_p.C224C	NM_020974	NP_066025	Q9NQ36	SCUB2_HUMAN	CEGP1 protein precursor	224	EGF-like 5 (Potential).					extracellular region	calcium ion binding			ovary(1)|skin(1)	2				all cancers(16;8.57e-09)|Epithelial(150;4.42e-08)|BRCA - Breast invasive adenocarcinoma(625;0.0116)														---	---	---	---
WEE1	7465	broad.mit.edu	37	11	9598736	9598736	+	Missense_Mutation	SNP	A	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:9598736A>C	uc001mhs.2	+	5	1320	c.1067A>C	c.(1066-1068)CAT>CCT	p.H356P	WEE1_uc001mht.2_Missense_Mutation_p.H142P|WEE1_uc001mhu.2_Missense_Mutation_p.H142P	NM_003390	NP_003381	P30291	WEE1_HUMAN	WEE1 tyrosine kinase isoform 1	356	Protein kinase.				blood coagulation|cell cycle checkpoint|cell division|G1/S transition of mitotic cell cycle|G2/M transition of mitotic cell cycle|mitosis|S phase of mitotic cell cycle	nucleoplasm	ATP binding|magnesium ion binding|non-membrane spanning protein tyrosine kinase activity|protein binding|protein serine/threonine kinase activity			central_nervous_system(2)|ovary(1)|breast(1)|skin(1)	5				all cancers(16;4.59e-09)|Epithelial(150;3.15e-08)|BRCA - Breast invasive adenocarcinoma(625;0.0484)														---	---	---	---
LYVE1	10894	broad.mit.edu	37	11	10580752	10580752	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:10580752T>C	uc001miv.2	-	6	1161	c.875A>G	c.(874-876)AAC>AGC	p.N292S	uc001miu.2_Intron|LYVE1_uc010rca.1_Missense_Mutation_p.N188S	NM_006691	NP_006682	Q9Y5Y7	LYVE1_HUMAN	lymphatic vessel endothelial hyaluronan receptor	292	Cytoplasmic (Potential).				anatomical structure morphogenesis|cell-matrix adhesion|cellular component movement|response to wounding|transport	integral to plasma membrane|membrane fraction				central_nervous_system(1)|skin(1)	2				all cancers(16;7.22e-08)|Epithelial(150;1.03e-07)|BRCA - Breast invasive adenocarcinoma(625;0.0609)														---	---	---	---
USP47	55031	broad.mit.edu	37	11	11964494	11964494	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:11964494A>G	uc001mjq.1	+	21	3749	c.2986A>G	c.(2986-2988)ACG>GCG	p.T996A	USP47_uc001mjr.2_Missense_Mutation_p.T908A|USP47_uc001mjs.2_Missense_Mutation_p.T976A|USP47_uc001mjt.1_Missense_Mutation_p.T282A	NM_017944	NP_060414	Q96K76	UBP47_HUMAN	ubiquitin specific protease 47	996					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)														---	---	---	---
TEAD1	7003	broad.mit.edu	37	11	12923510	12923510	+	Silent	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:12923510C>T	uc001mkj.3	+	10	1343	c.678C>T	c.(676-678)CAC>CAT	p.H226H	TEAD1_uc001mkk.3_Silent_p.H145H|TEAD1_uc009ygl.2_Intron	NM_021961	NP_068780	P28347	TEAD1_HUMAN	TEA domain family member 1	241	Transcriptional activation (Potential).				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)														---	---	---	---
PDE3B	5140	broad.mit.edu	37	11	14882890	14882890	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:14882890T>C	uc001mln.2	+	14	3217	c.2864T>C	c.(2863-2865)ATT>ACT	p.I955T	PDE3B_uc010rcr.1_Missense_Mutation_p.I904T	NM_000922	NP_000913	Q13370	PDE3B_HUMAN	phosphodiesterase 3B	955	Catalytic (By similarity).				cAMP catabolic process|insulin receptor signaling pathway|negative regulation of lipid catabolic process|platelet activation	cytosol|endoplasmic reticulum|Golgi apparatus|guanyl-nucleotide exchange factor complex|integral to membrane|microsome	3',5'-cyclic-AMP phosphodiesterase activity|3',5'-cyclic-GMP phosphodiesterase activity|cGMP-inhibited cyclic-nucleotide phosphodiesterase activity|metal ion binding|protein kinase B binding				0																		---	---	---	---
SOX6	55553	broad.mit.edu	37	11	16117554	16117554	+	Silent	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:16117554G>A	uc001mme.2	-	9	1161	c.1128C>T	c.(1126-1128)CAC>CAT	p.H376H	SOX6_uc001mmd.2_Intron|SOX6_uc001mmf.2_Intron|SOX6_uc001mmg.2_Silent_p.H363H	NM_001145819	NP_001139291	P35712	SOX6_HUMAN	SRY (sex determining region Y)-box 6 isoform 4	363					muscle organ development	nucleus	sequence-specific DNA binding transcription factor activity			ovary(3)	3																		---	---	---	---
NUCB2	4925	broad.mit.edu	37	11	17351801	17351801	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:17351801G>A	uc001mmw.2	+	12	1375	c.1130G>A	c.(1129-1131)CGT>CAT	p.R377H	NUCB2_uc009ygz.2_Missense_Mutation_p.R347H|NUCB2_uc009yha.2_RNA|NUCB2_uc001mmx.3_RNA|uc001mmy.1_5'Flank	NM_005013	NP_005004	P80303	NUCB2_HUMAN	nucleobindin 2 precursor	377	Binds to necdin (By similarity).					cytosol|ER-Golgi intermediate compartment|extracellular space|Golgi apparatus|plasma membrane	calcium ion binding|DNA binding				0																		---	---	---	---
NELL1	4745	broad.mit.edu	37	11	21592478	21592478	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:21592478C>T	uc001mqe.2	+	18	2302	c.2149C>T	c.(2149-2151)CGG>TGG	p.R717W	NELL1_uc001mqf.2_Missense_Mutation_p.R670W|NELL1_uc009yid.2_Missense_Mutation_p.R745W|NELL1_uc010rdo.1_Missense_Mutation_p.R660W|NELL1_uc010rdp.1_Missense_Mutation_p.R430W|NELL1_uc001mqh.2_Missense_Mutation_p.R262W	NM_006157	NP_006148	Q92832	NELL1_HUMAN	nel-like 1 isoform 1 precursor	717	VWFC 4.				cell adhesion|nervous system development	extracellular region	calcium ion binding|structural molecule activity			ovary(2)|large_intestine(1)	3																		---	---	---	---
FANCF	2188	broad.mit.edu	37	11	22646570	22646570	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:22646570C>T	uc001mql.1	-	1	818	c.787G>A	c.(787-789)GTG>ATG	p.V263M		NM_022725	NP_073562	Q9NPI8	FANCF_HUMAN	Fanconi anemia, complementation group F	263					DNA repair	nucleoplasm	protein binding			skin(1)	1								N|F			AML|leukemia		Direct_reversal_of_damage|Involved_in_tolerance_or_repair_of_DNA_crosslinks	Fanconi_Anemia		OREG0020844	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
LUZP2	338645	broad.mit.edu	37	11	25098960	25098960	+	Intron	SNP	T	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:25098960T>A	uc001mqs.2	+						LUZP2_uc009yif.2_Intron|LUZP2_uc009yig.2_Intron	NM_001009909	NP_001009909			leucine zipper protein 2 precursor							extracellular region				ovary(1)|skin(1)	2																		---	---	---	---
LGR4	55366	broad.mit.edu	37	11	27401878	27401878	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:27401878C>T	uc001mrj.3	-	10	1396	c.911G>A	c.(910-912)CGT>CAT	p.R304H	LGR4_uc001mrk.3_Missense_Mutation_p.R280H	NM_018490	NP_060960	Q9BXB1	LGR4_HUMAN	leucine-rich repeat-containing G protein-coupled	304	Extracellular (Potential).					integral to membrane|plasma membrane	protein-hormone receptor activity			ovary(1)	1																		---	---	---	---
MPPED2	744	broad.mit.edu	37	11	30433131	30433131	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:30433131A>G	uc001msr.2	-	6	889	c.769T>C	c.(769-771)TAT>CAT	p.Y257H	MPPED2_uc001msq.3_Intron|MPPED2_uc009yji.2_Missense_Mutation_p.Y131H	NM_001584	NP_001575	Q15777	MPPD2_HUMAN	metallophosphoesterase domain containing 2	257					nervous system development		hydrolase activity|metal ion binding			skin(1)	1																		---	---	---	---
QSER1	79832	broad.mit.edu	37	11	32954153	32954153	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:32954153C>T	uc001mty.2	+	4	1229	c.962C>T	c.(961-963)TCG>TTG	p.S321L	QSER1_uc001mtz.1_Intron|QSER1_uc001mua.2_5'Flank	NM_001076786	NP_001070254	Q2KHR3	QSER1_HUMAN	glutamine and serine rich 1	321	Ser-rich.									ovary(3)|central_nervous_system(2)|skin(1)	6	Breast(20;0.158)																	---	---	---	---
QSER1	79832	broad.mit.edu	37	11	32956875	32956875	+	Silent	SNP	A	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:32956875A>T	uc001mty.2	+	4	3951	c.3684A>T	c.(3682-3684)TCA>TCT	p.S1228S	QSER1_uc001mtz.1_Silent_p.S989S|QSER1_uc001mua.2_Silent_p.S733S	NM_001076786	NP_001070254	Q2KHR3	QSER1_HUMAN	glutamine and serine rich 1	1228										ovary(3)|central_nervous_system(2)|skin(1)	6	Breast(20;0.158)																	---	---	---	---
C11orf41	25758	broad.mit.edu	37	11	33565580	33565580	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:33565580C>T	uc001mup.3	+	1	1704	c.1580C>T	c.(1579-1581)ACA>ATA	p.T527I	C11orf41_uc001mun.1_Missense_Mutation_p.T527I	NM_012194	NP_036326	Q6ZVL6	CK041_HUMAN	hypothetical protein LOC25758	527						integral to membrane				ovary(2)	2																		---	---	---	---
C11orf41	25758	broad.mit.edu	37	11	33596308	33596308	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:33596308C>A	uc001mup.3	+	9	3542	c.3418C>A	c.(3418-3420)CTG>ATG	p.L1140M	C11orf41_uc001mun.1_Missense_Mutation_p.L1140M	NM_012194	NP_036326	Q6ZVL6	CK041_HUMAN	hypothetical protein LOC25758	1134						integral to membrane				ovary(2)	2																		---	---	---	---
C11orf41	25758	broad.mit.edu	37	11	33689575	33689575	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:33689575G>A	uc001mup.3	+	20	5567	c.5443G>A	c.(5443-5445)GCA>ACA	p.A1815T		NM_012194	NP_036326	Q6ZVL6	CK041_HUMAN	hypothetical protein LOC25758	1809						integral to membrane				ovary(2)	2																		---	---	---	---
ABTB2	25841	broad.mit.edu	37	11	34189531	34189531	+	Silent	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:34189531C>T	uc001mvl.1	-	6	1244	c.1014G>A	c.(1012-1014)ACG>ACA	p.T338T		NM_145804	NP_665803	Q8N961	ABTB2_HUMAN	ankyrin repeat and BTB (POZ) domain containing	338							DNA binding			central_nervous_system(1)|skin(1)	2		Acute lymphoblastic leukemia(5;0.0508)|all_hematologic(20;0.0691)																---	---	---	---
RAG1	5896	broad.mit.edu	37	11	36595309	36595309	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:36595309C>T	uc001mwu.3	+	2	579	c.455C>T	c.(454-456)CCG>CTG	p.P152L	RAG1_uc001mwt.2_RNA	NM_000448	NP_000439	P15918	RAG1_HUMAN	recombination activating gene 1	152	Interaction with importin alpha-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				---	---	---	---
TTC17	55761	broad.mit.edu	37	11	43427496	43427496	+	Nonsense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:43427496C>T	uc001mxi.2	+	13	1770	c.1756C>T	c.(1756-1758)CGA>TGA	p.R586*	TTC17_uc001mxh.2_Nonsense_Mutation_p.R586*|TTC17_uc010rfj.1_Nonsense_Mutation_p.R529*|TTC17_uc001mxj.2_Nonsense_Mutation_p.R356*	NM_018259	NP_060729	Q96AE7	TTC17_HUMAN	tetratricopeptide repeat domain 17	586							binding			ovary(5)	5																		---	---	---	---
EXT2	2132	broad.mit.edu	37	11	44219391	44219391	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:44219391G>A	uc001mxz.2	+	9	1652	c.1318G>A	c.(1318-1320)GTG>ATG	p.V440M	EXT2_uc010rfo.1_Missense_Mutation_p.V468M|EXT2_uc001mxy.2_Missense_Mutation_p.V453M|EXT2_uc009ykt.2_Missense_Mutation_p.V450M|EXT2_uc001mya.2_Missense_Mutation_p.V473M	NM_207122	NP_997005	Q93063	EXT2_HUMAN	exostosin 2 isoform 2	440	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	44228411	44228411	+	Missense_Mutation	SNP	C	T	T	rs145507609		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:44228411C>T	uc001mxz.2	+	10	1898	c.1564C>T	c.(1564-1566)CGT>TGT	p.R522C	EXT2_uc010rfo.1_Missense_Mutation_p.R550C|EXT2_uc001mxy.2_Missense_Mutation_p.R535C|EXT2_uc009ykt.2_Missense_Mutation_p.R532C|EXT2_uc001mya.2_Missense_Mutation_p.R555C	NM_207122	NP_997005	Q93063	EXT2_HUMAN	exostosin 2 isoform 2	522	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				---	---	---	---
TP53I11	9537	broad.mit.edu	37	11	44956503	44956503	+	Missense_Mutation	SNP	G	A	A	rs150540503		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:44956503G>A	uc001myi.2	-	10	1107	c.502C>T	c.(502-504)CGC>TGC	p.R168C	TP53I11_uc001myf.1_Intron|TP53I11_uc001myj.2_Missense_Mutation_p.R168C|TP53I11_uc001myk.2_Missense_Mutation_p.R168C|TP53I11_uc001myl.2_Missense_Mutation_p.R168C|TP53I11_uc001mym.2_Missense_Mutation_p.R115C	NM_006034	NP_006025	O14683	P5I11_HUMAN	p53-induced protein	168	Helical; (Potential).				negative regulation of cell proliferation|response to stress	integral to membrane				ovary(1)	1																		---	---	---	---
CREB3L1	90993	broad.mit.edu	37	11	46338978	46338978	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:46338978G>A	uc001ncf.2	+	10	1633	c.1198G>A	c.(1198-1200)GGC>AGC	p.G400S	CREB3L1_uc001ncg.2_Missense_Mutation_p.G34S	NM_052854	NP_443086	Q96BA8	CR3L1_HUMAN	cAMP responsive element binding protein 3-like	400	Lumenal (Potential).				response to unfolded protein	endoplasmic reticulum membrane|integral to membrane|nucleus	protein dimerization activity|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity		FUS/CREB3L1(6)	soft_tissue(6)|ovary(2)	8				GBM - Glioblastoma multiforme(35;0.0285)				T	FUS	myxofibrosarcoma								---	---	---	---
F2	2147	broad.mit.edu	37	11	46747700	46747700	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:46747700G>A	uc001ndf.3	+	7	894	c.851G>A	c.(850-852)GGG>GAG	p.G284E	F2_uc001ndg.3_RNA	NM_000506	NP_000497	P00734	THRB_HUMAN	coagulation factor II preproprotein	284	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	46774258	46774258	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:46774258G>A	uc001ndi.1	-	38	5170	c.5060C>T	c.(5059-5061)GCC>GTC	p.A1687V	CKAP5_uc009ylg.1_Missense_Mutation_p.A1573V|CKAP5_uc001ndj.1_Missense_Mutation_p.A1627V|CKAP5_uc001ndh.1_Missense_Mutation_p.A616V	NM_001008938	NP_001008938	Q14008	CKAP5_HUMAN	colonic and hepatic tumor over-expressed protein	1687					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																		---	---	---	---
DDB2	1643	broad.mit.edu	37	11	47236683	47236683	+	5'UTR	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:47236683A>G	uc001neb.2	+	1					DDB2_uc001nec.2_RNA|DDB2_uc009yli.1_5'UTR|DDB2_uc001ned.2_RNA|DDB2_uc001nee.2_5'UTR|DDB2_uc001nef.2_5'UTR|DDB2_uc001neg.2_5'Flank|DDB2_uc001neh.2_5'Flank	NM_000107	NP_000098			damage-specific DNA binding protein 2						nucleotide-excision repair, DNA damage removal|protein autoubiquitination|protein polyubiquitination|response to UV	nucleoplasm|protein complex	damaged DNA binding|protein binding			kidney(2)|ovary(1)	3								Mis|N			skin basal cell|skin squamous cell|melanoma		Direct_reversal_of_damage|NER	Xeroderma_Pigmentosum				---	---	---	---
MYBPC3	4607	broad.mit.edu	37	11	47360063	47360063	+	Intron	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:47360063G>A	uc001nfa.3	-						MYBPC3_uc010rhl.1_Intron	NM_000256	NP_000247			myosin binding protein C, cardiac						cardiac muscle contraction|cell adhesion|muscle filament sliding|regulation of muscle filament sliding|regulation of striated muscle contraction|ventricular cardiac muscle tissue morphogenesis	C zone|cytosol|striated muscle myosin thick filament	actin binding|ATPase activator activity|metal ion binding|myosin heavy chain binding|structural constituent of muscle|titin binding			ovary(2)|central_nervous_system(1)	3				Lung(87;0.176)														---	---	---	---
SPI1	6688	broad.mit.edu	37	11	47381454	47381454	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:47381454G>A	uc001nfc.1	-	3	503	c.280C>T	c.(280-282)CAC>TAC	p.H94Y	SPI1_uc001nfb.1_Missense_Mutation_p.H95Y|SLC39A13_uc001nfd.2_Intron|SPI1_uc009ylp.1_Missense_Mutation_p.H88Y	NM_003120	NP_003111	P17947	SPI1_HUMAN	hematopoietic transcription factor PU.1 isoform	94					negative regulation of transcription from RNA polymerase II promoter|positive regulation of transcription, DNA-dependent|regulation of erythrocyte differentiation	nucleus	protein binding|RNA binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			lung(1)|central_nervous_system(1)	2				Lung(87;0.0967)														---	---	---	---
PTPMT1	114971	broad.mit.edu	37	11	47593072	47593072	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:47593072G>A	uc001nfs.3	+	4	690	c.497G>A	c.(496-498)CGG>CAG	p.R166Q	PTPMT1_uc001nfv.3_Silent_p.P138P|PTPMT1_uc009ylt.2_Missense_Mutation_p.R102Q|PTPMT1_uc001nfu.3_3'UTR|NDUFS3_uc001nft.3_5'UTR	NM_175732	NP_783859	Q8WUK0	PTPM1_HUMAN	protein tyrosine phosphatase, mitochondrial 1	166	Tyrosine-protein phosphatase.				inositol phosphate dephosphorylation	mitochondrial inner membrane	phosphatidylinositol-4,5-bisphosphate 5-phosphatase activity|protein tyrosine phosphatase activity|protein tyrosine/serine/threonine phosphatase activity			skin(1)	1																		---	---	---	---
OR4X1	390113	broad.mit.edu	37	11	48286016	48286016	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:48286016G>A	uc010rht.1	+	1	604	c.604G>A	c.(604-606)GGC>AGC	p.G202S		NM_001004726	NP_001004726	Q8NH49	OR4X1_HUMAN	olfactory receptor, family 4, subfamily X,	202	Helical; Name=5; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)|pancreas(1)|skin(1)	3																		---	---	---	---
OR4C13	283092	broad.mit.edu	37	11	49974741	49974741	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:49974741A>G	uc010rhz.1	+	1	767	c.767A>G	c.(766-768)TAC>TGC	p.Y256C		NM_001001955	NP_001001955	Q8NGP0	OR4CD_HUMAN	olfactory receptor, family 4, subfamily C,	256	Helical; Name=6; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			skin(3)|ovary(1)	4																		---	---	---	---
TRIM48	79097	broad.mit.edu	37	11	55035844	55035844	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-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																		---	---	---	---
OR4A15	81328	broad.mit.edu	37	11	55135410	55135410	+	Silent	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:55135410T>C	uc010rif.1	+	1	51	c.51T>C	c.(49-51)TGT>TGC	p.C17C		NM_001005275	NP_001005275	Q8NGL6	O4A15_HUMAN	olfactory receptor, family 4, subfamily A,	17	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)|skin(1)	2																		---	---	---	---
OR4A15	81328	broad.mit.edu	37	11	55136023	55136023	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:55136023G>A	uc010rif.1	+	1	664	c.664G>A	c.(664-666)GTC>ATC	p.V222I		NM_001005275	NP_001005275	Q8NGL6	O4A15_HUMAN	olfactory receptor, family 4, subfamily A,	222	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)|skin(1)	2																		---	---	---	---
OR4C11	219429	broad.mit.edu	37	11	55371132	55371132	+	Missense_Mutation	SNP	A	G	G	rs7114415	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:55371132A>G	uc010rii.1	-	1	718	c.718T>C	c.(718-720)TCT>CCT	p.S240P		NM_001004700	NP_001004700	Q6IEV9	OR4CB_HUMAN	olfactory receptor, family 4, subfamily C,	240	Helical; Name=6; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)	1																		---	---	---	---
OR5I1	10798	broad.mit.edu	37	11	55703610	55703610	+	Silent	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:55703610C>T	uc010ris.1	-	1	267	c.267G>A	c.(265-267)TCG>TCA	p.S89S		NM_006637	NP_006628	Q13606	OR5I1_HUMAN	olfactory receptor, family 5, subfamily I,	89	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)	1																		---	---	---	---
OR5F1	338674	broad.mit.edu	37	11	55761730	55761730	+	Silent	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:55761730C>T	uc010riv.1	-	1	372	c.372G>A	c.(370-372)GCG>GCA	p.A124A		NM_003697	NP_003688	O95221	OR5F1_HUMAN	olfactory receptor, family 5, subfamily F,	124	Cytoplasmic (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)|pancreas(1)	2	Esophageal squamous(21;0.00448)																	---	---	---	---
OR8I2	120586	broad.mit.edu	37	11	55861145	55861145	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:55861145A>G	uc010rix.1	+	1	362	c.362A>G	c.(361-363)AAT>AGT	p.N121S		NM_001003750	NP_001003750	Q8N0Y5	OR8I2_HUMAN	olfactory receptor, family 8, subfamily I,	121	Cytoplasmic (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			breast(1)	1	Esophageal squamous(21;0.00693)																	---	---	---	---
OR5AR1	219493	broad.mit.edu	37	11	56431654	56431654	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:56431654A>G	uc010rjm.1	+	1	493	c.493A>G	c.(493-495)AGC>GGC	p.S165G		NM_001004730	NP_001004730	Q8NGP9	O5AR1_HUMAN	olfactory receptor, family 5, subfamily AR,	165	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity				0																		---	---	---	---
P2RX3	5024	broad.mit.edu	37	11	57137410	57137410	+	Silent	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:57137410C>T	uc001nju.2	+	12	1210	c.1134C>T	c.(1132-1134)AGC>AGT	p.S378S		NM_002559	NP_002550	P56373	P2RX3_HUMAN	purinergic receptor P2X3	378	Cytoplasmic (Potential).				positive regulation of calcium ion transport into cytosol|positive regulation of calcium-mediated signaling	integral to plasma membrane	ATP binding|extracellular ATP-gated cation channel activity|purinergic nucleotide receptor activity				0																		---	---	---	---
SERPING1	710	broad.mit.edu	37	11	57373489	57373489	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:57373489C>T	uc001nkp.1	+	5	883	c.692C>T	c.(691-693)GCC>GTC	p.A231V	SERPING1_uc001nkq.1_Missense_Mutation_p.A231V|SERPING1_uc010rju.1_Missense_Mutation_p.A179V|SERPING1_uc010rjv.1_Missense_Mutation_p.A236V|SERPING1_uc001nkr.1_Missense_Mutation_p.A231V|SERPING1_uc009ymi.1_Missense_Mutation_p.A231V|SERPING1_uc009ymj.1_Missense_Mutation_p.A231V|SERPING1_uc001nks.1_5'UTR	NM_000062	NP_000053	P05155	IC1_HUMAN	serpin peptidase inhibitor, clade G, member 1	231					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	57428454	57428454	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:57428454G>A	uc001nkw.2	+	3	963	c.824G>A	c.(823-825)CGC>CAC	p.R275H	CLP1_uc010rjw.1_Missense_Mutation_p.R211H|CLP1_uc009yml.2_Missense_Mutation_p.R275H	NM_006831	NP_006822	Q92989	CLP1_HUMAN	ATP/GTP-binding protein isoform 1	275					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																		---	---	---	---
ZDHHC5	25921	broad.mit.edu	37	11	57460110	57460110	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:57460110A>G	uc001nkx.1	+	7	1944	c.688A>G	c.(688-690)AAC>GAC	p.N230D	ZDHHC5_uc001nky.1_Missense_Mutation_p.N177D|ZDHHC5_uc001nkz.1_Missense_Mutation_p.N44D	NM_015457	NP_056272	Q9C0B5	ZDHC5_HUMAN	zinc finger, DHHC domain containing 5	230						integral to membrane	acyltransferase activity|zinc ion binding			skin(1)	1																		---	---	---	---
CTNND1	1500	broad.mit.edu	37	11	57571132	57571132	+	Missense_Mutation	SNP	T	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:57571132T>A	uc001nmc.3	+	8	2031	c.1460T>A	c.(1459-1461)ATG>AAG	p.M487K	CTNND1_uc001nlh.1_Missense_Mutation_p.M487K|CTNND1_uc001nlu.3_Missense_Mutation_p.M386K|CTNND1_uc001nlt.3_Missense_Mutation_p.M386K|CTNND1_uc001nls.3_Missense_Mutation_p.M386K|CTNND1_uc001nlw.3_Missense_Mutation_p.M386K|CTNND1_uc001nmf.3_Missense_Mutation_p.M487K|CTNND1_uc001nmd.3_Missense_Mutation_p.M433K|CTNND1_uc001nlk.3_Missense_Mutation_p.M433K|CTNND1_uc001nme.3_Missense_Mutation_p.M487K|CTNND1_uc001nll.3_Missense_Mutation_p.M433K|CTNND1_uc001nmg.3_Missense_Mutation_p.M433K|CTNND1_uc001nlj.3_Missense_Mutation_p.M433K|CTNND1_uc001nlr.3_Missense_Mutation_p.M433K|CTNND1_uc001nlp.3_Missense_Mutation_p.M433K|CTNND1_uc001nlx.3_Missense_Mutation_p.M164K|CTNND1_uc001nlz.3_Missense_Mutation_p.M164K|CTNND1_uc009ymn.2_Missense_Mutation_p.M164K|CTNND1_uc001nlm.3_Missense_Mutation_p.M487K|CTNND1_uc001nly.3_Missense_Mutation_p.M164K|CTNND1_uc001nmb.3_Missense_Mutation_p.M164K|CTNND1_uc001nma.3_Missense_Mutation_p.M164K|CTNND1_uc001nmi.3_Missense_Mutation_p.M386K|CTNND1_uc001nmh.3_Missense_Mutation_p.M487K|CTNND1_uc001nlq.3_Missense_Mutation_p.M386K|CTNND1_uc001nln.3_Missense_Mutation_p.M487K|CTNND1_uc001nli.3_Missense_Mutation_p.M487K|CTNND1_uc001nlo.3_Missense_Mutation_p.M386K|CTNND1_uc001nlv.3_Missense_Mutation_p.M386K	NM_001085458	NP_001078927	O60716	CTND1_HUMAN	catenin, delta 1 isoform 1ABC	487	ARM 4.				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)																---	---	---	---
OR5B21	219968	broad.mit.edu	37	11	58275007	58275007	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:58275007C>T	uc010rki.1	-	1	572	c.572G>A	c.(571-573)CGC>CAC	p.R191H		NM_001005218	NP_001005218	A6NL26	OR5BL_HUMAN	olfactory receptor, family 5, subfamily B,	191	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(3)	3	Esophageal squamous(5;0.0027)	Breast(21;0.0778)																---	---	---	---
OR4D6	219983	broad.mit.edu	37	11	59225156	59225156	+	Silent	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:59225156G>A	uc010rku.1	+	1	723	c.723G>A	c.(721-723)ACG>ACA	p.T241T		NM_001004708	NP_001004708	Q8NGJ1	OR4D6_HUMAN	olfactory receptor, family 4, subfamily D,	241	Helical; Name=6; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)	1																		---	---	---	---
PATL1	219988	broad.mit.edu	37	11	59420040	59420040	+	Silent	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:59420040C>T	uc001noe.3	-	11	1466	c.1323G>A	c.(1321-1323)GAG>GAA	p.E441E	PATL1_uc009yms.1_Silent_p.E411E|PATL1_uc010rkw.1_Silent_p.E146E	NM_152716	NP_689929	Q86TB9	PATL1_HUMAN	protein associated with topoisomerase II homolog	441	Region H.				cytoplasmic mRNA processing body assembly|deadenylation-dependent decapping of nuclear-transcribed mRNA	cytoplasmic mRNA processing body	protein binding|RNA binding			ovary(1)	1																		---	---	---	---
MS4A7	58475	broad.mit.edu	37	11	60150701	60150701	+	Silent	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:60150701C>T	uc001npe.2	+	2	232	c.87C>T	c.(85-87)CAC>CAT	p.H29H	MS4A7_uc001npf.2_Silent_p.H29H|MS4A7_uc001npg.2_Silent_p.H29H|MS4A7_uc001nph.2_Silent_p.H29H|MS4A14_uc001npi.2_Intron|MS4A7_uc009ymx.1_Silent_p.H29H	NM_206939	NP_996822	Q9GZW8	MS4A7_HUMAN	membrane-spanning 4-domains, subfamily A, member	29	Cytoplasmic (Potential).					integral to membrane	receptor activity			ovary(1)|central_nervous_system(1)	2																		---	---	---	---
TMEM132A	54972	broad.mit.edu	37	11	60699224	60699224	+	Silent	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:60699224C>T	uc001nqj.2	+	6	1273	c.1080C>T	c.(1078-1080)GGC>GGT	p.G360G	TMEM132A_uc001nqi.2_Silent_p.G361G|TMEM132A_uc001nqk.2_Silent_p.G373G|TMEM132A_uc001nql.1_Silent_p.G373G|TMEM132A_uc001nqm.2_5'Flank	NM_178031	NP_821174	Q24JP5	T132A_HUMAN	transmembrane protein 132A isoform b	360	Extracellular (Potential).					endoplasmic reticulum membrane|Golgi membrane|integral to membrane				skin(1)	1																		---	---	---	---
CD5	921	broad.mit.edu	37	11	60887023	60887023	+	Nonsense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:60887023C>T	uc009ynk.2	+	5	884	c.781C>T	c.(781-783)CGA>TGA	p.R261*		NM_014207	NP_055022	P06127	CD5_HUMAN	CD5 molecule precursor	261	Extracellular (Potential).|SRCR 2.				cell proliferation|cell recognition	integral to plasma membrane	scavenger receptor activity			ovary(1)	1		all_lung(304;5.94e-05)|Lung NSC(402;7.26e-05)		BRCA - Breast invasive adenocarcinoma(625;0.000946)|Lung(977;0.0086)|LUSC - Lung squamous cell carcinoma(625;0.0528)														---	---	---	---
VWCE	220001	broad.mit.edu	37	11	61053835	61053835	+	Silent	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:61053835G>A	uc001nra.2	-	5	771	c.492C>T	c.(490-492)TGC>TGT	p.C164C	VWCE_uc001nrb.2_RNA	NM_152718	NP_689931	Q96DN2	VWCE_HUMAN	von Willebrand factor C and EGF domains	164	EGF-like 2; calcium-binding (Potential).					extracellular region	calcium ion binding			ovary(1)	1																		---	---	---	---
DAGLA	747	broad.mit.edu	37	11	61511714	61511714	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:61511714G>A	uc001nsa.2	+	20	2993	c.2882G>A	c.(2881-2883)CGT>CAT	p.R961H		NM_006133	NP_006124	Q9Y4D2	DGLA_HUMAN	neural stem cell-derived dendrite regulator	961	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)														---	---	---	---
FADS2	9415	broad.mit.edu	37	11	61630475	61630475	+	Missense_Mutation	SNP	G	A	A	rs145442804		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:61630475G>A	uc001nsl.1	+	8	1064	c.914G>A	c.(913-915)CGG>CAG	p.R305Q	FADS2_uc001nsj.2_Missense_Mutation_p.R283Q|FADS2_uc010rlo.1_Missense_Mutation_p.R274Q|FADS2_uc001nsk.2_Missense_Mutation_p.R305Q	NM_004265	NP_004256	O95864	FADS2_HUMAN	fatty acid desaturase 2	305	Lumenal (Potential).				electron transport chain|transport|unsaturated fatty acid biosynthetic process	endoplasmic reticulum membrane|integral to plasma membrane|membrane fraction	heme binding			ovary(1)|pancreas(1)	2					Alpha-Linolenic Acid(DB00132)													---	---	---	---
AHNAK	79026	broad.mit.edu	37	11	62285884	62285884	+	Silent	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:62285884A>G	uc001ntl.2	-	5	16305	c.16005T>C	c.(16003-16005)GGT>GGC	p.G5335G	AHNAK_uc001ntk.1_Intron	NM_001620	NP_001611	Q09666	AHNK_HUMAN	AHNAK nucleoprotein isoform 1	5335					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	62286327	62286327	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:62286327C>T	uc001ntl.2	-	5	15862	c.15562G>A	c.(15562-15564)GGC>AGC	p.G5188S	AHNAK_uc001ntk.1_Intron	NM_001620	NP_001611	Q09666	AHNK_HUMAN	AHNAK nucleoprotein isoform 1	5188					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	62290976	62290976	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:62290976A>G	uc001ntl.2	-	5	11213	c.10913T>C	c.(10912-10914)GTA>GCA	p.V3638A	AHNAK_uc001ntk.1_Intron	NM_001620	NP_001611	Q09666	AHNK_HUMAN	AHNAK nucleoprotein isoform 1	3638					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	62292417	62292417	+	Missense_Mutation	SNP	T	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:62292417T>A	uc001ntl.2	-	5	9772	c.9472A>T	c.(9472-9474)ATC>TTC	p.I3158F	AHNAK_uc001ntk.1_Intron	NM_001620	NP_001611	Q09666	AHNK_HUMAN	AHNAK nucleoprotein isoform 1	3158					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	62292802	62292802	+	Silent	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:62292802T>C	uc001ntl.2	-	5	9387	c.9087A>G	c.(9085-9087)AAA>AAG	p.K3029K	AHNAK_uc001ntk.1_Intron	NM_001620	NP_001611	Q09666	AHNK_HUMAN	AHNAK nucleoprotein isoform 1	3029					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	62334427	62334427	+	Silent	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:62334427A>G	uc001ntm.1	-	7	854	c.708T>C	c.(706-708)GGT>GGC	p.G236G	EEF1G_uc010rlw.1_Silent_p.G286G|EEF1G_uc001ntn.1_Silent_p.G116G	NM_001404	NP_001395	P26641	EF1G_HUMAN	eukaryotic translation elongation factor 1	236					response to virus	cytosol|eukaryotic translation elongation factor 1 complex	protein binding|translation elongation factor activity				0																		---	---	---	---
BSCL2	26580	broad.mit.edu	37	11	62457868	62457868	+	Nonsense_Mutation	SNP	G	A	A	rs138515091		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:62457868G>A	uc001nuo.1	-	11	1592	c.1168C>T	c.(1168-1170)CGA>TGA	p.R390*	LRRN4CL_uc001nun.2_5'Flank|BSCL2_uc009yoc.1_3'UTR|BSCL2_uc001nup.2_Nonsense_Mutation_p.R390*|BSCL2_uc001nuq.1_Nonsense_Mutation_p.R390*|BSCL2_uc001nur.3_Nonsense_Mutation_p.R454*|BSCL2_uc009yod.2_Nonsense_Mutation_p.R454*|BSCL2_uc001nut.3_Nonsense_Mutation_p.R456*|HNRNPUL2_uc001nuu.1_RNA	NM_032667	NP_116056	Q96G97	BSCL2_HUMAN	seipin isoform 2	390	Cytoplasmic (Potential).				cell death	integral to endoplasmic reticulum membrane					0																		---	---	---	---
NXF1	10482	broad.mit.edu	37	11	62564672	62564672	+	Silent	SNP	G	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:62564672G>T	uc001nvf.1	-	13	1297	c.1161C>A	c.(1159-1161)GTC>GTA	p.V387V	NXF1_uc001nvg.1_3'UTR|NXF1_uc009yog.1_Silent_p.V430V	NM_006362	NP_006353	Q9UBU9	NXF1_HUMAN	nuclear RNA export factor 1 isoform 1	387	NTF2.				gene expression|interspecies interaction between organisms	cytosol|nuclear speck	nucleotide binding|protein binding	p.V387V(1)		skin(3)	3																		---	---	---	---
NXF1	10482	broad.mit.edu	37	11	62569503	62569503	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:62569503T>C	uc001nvf.1	-	5	605	c.469A>G	c.(469-471)ACA>GCA	p.T157A	NXF1_uc001nvg.1_Missense_Mutation_p.T157A|NXF1_uc009yog.1_Missense_Mutation_p.T200A|NXF1_uc010rmh.1_Missense_Mutation_p.T20A	NM_006362	NP_006353	Q9UBU9	NXF1_HUMAN	nuclear RNA export factor 1 isoform 1	157	Interaction with THOC4.|RRM.				gene expression|interspecies interaction between organisms	cytosol|nuclear speck	nucleotide binding|protein binding			skin(3)	3																		---	---	---	---
SLC3A2	6520	broad.mit.edu	37	11	62655872	62655872	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:62655872C>T	uc001nwd.2	+	12	1824	c.1600C>T	c.(1600-1602)CGC>TGC	p.R534C	SLC3A2_uc001nwb.2_Missense_Mutation_p.R565C|SLC3A2_uc001nwc.2_Missense_Mutation_p.R535C|SLC3A2_uc001nwe.2_Missense_Mutation_p.R503C|SLC3A2_uc001nwf.2_Missense_Mutation_p.R472C|SLC3A2_uc001nwg.2_Missense_Mutation_p.R433C	NM_002394	NP_002385	P08195	4F2_HUMAN	solute carrier family 3, member 2 isoform c	534	Extracellular (Potential).				blood coagulation|carbohydrate metabolic process|cell growth|cellular nitrogen compound metabolic process|leucine import|leukocyte migration|tryptophan transport	apical plasma membrane|cell surface|integral to membrane|melanosome	calcium:sodium antiporter activity|catalytic activity|cation binding|neutral amino acid transmembrane transporter activity|protein binding				0																		---	---	---	---
FLRT1	23769	broad.mit.edu	37	11	63885401	63885401	+	Silent	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:63885401G>A	uc001nyi.1	+	2	2003	c.1662G>A	c.(1660-1662)GCG>GCA	p.A554A	MACROD1_uc001nyh.2_Intron	NM_013280	NP_037412	Q9NZU1	FLRT1_HUMAN	fibronectin leucine rich transmembrane protein	526	Helical; (Potential).				cell adhesion	integral to plasma membrane|proteinaceous extracellular matrix	protein binding, bridging|receptor signaling protein activity				0																		---	---	---	---
TRPT1	83707	broad.mit.edu	37	11	63992140	63992140	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:63992140G>A	uc001nyo.2	-	5	591	c.377C>T	c.(376-378)CCG>CTG	p.P126L	TRPT1_uc010rnc.1_Missense_Mutation_p.P126L|TRPT1_uc010rnd.1_Missense_Mutation_p.P128L|TRPT1_uc001nyn.2_Missense_Mutation_p.P77L|TRPT1_uc010rne.1_Missense_Mutation_p.P126L|TRPT1_uc010rnf.1_Missense_Mutation_p.P126L|NUDT22_uc009ypd.2_5'Flank|NUDT22_uc001nyp.3_5'Flank|NUDT22_uc009ype.2_5'Flank|NUDT22_uc001nyq.3_5'Flank|NUDT22_uc010rng.1_5'Flank	NM_001033678	NP_001028850	Q86TN4	TRPT1_HUMAN	tRNA phosphotransferase 1 isoform 1	126							tRNA 2'-phosphotransferase activity				0																		---	---	---	---
PLCB3	5331	broad.mit.edu	37	11	64030184	64030184	+	Silent	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:64030184C>T	uc001nzb.2	+	19	2259	c.2259C>T	c.(2257-2259)GGC>GGT	p.G753G	PLCB3_uc009ypg.1_Silent_p.G753G|PLCB3_uc009yph.1_Silent_p.G686G|PLCB3_uc009ypi.2_Silent_p.G753G	NM_000932	NP_000923	Q01970	PLCB3_HUMAN	phospholipase C beta 3	753	C2.				intracellular signal transduction|lipid catabolic process|synaptic transmission	cytosol	calcium ion binding|calmodulin binding|phosphatidylinositol phospholipase C activity|signal transducer activity			ovary(1)|pancreas(1)	2																		---	---	---	---
PLCB3	5331	broad.mit.edu	37	11	64031183	64031183	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:64031183C>T	uc001nzb.2	+	21	2476	c.2476C>T	c.(2476-2478)CGG>TGG	p.R826W	PLCB3_uc009ypg.1_Missense_Mutation_p.R826W|PLCB3_uc009yph.1_Missense_Mutation_p.R759W|PLCB3_uc009ypi.2_Missense_Mutation_p.R826W	NM_000932	NP_000923	Q01970	PLCB3_HUMAN	phospholipase C beta 3	826					intracellular signal transduction|lipid catabolic process|synaptic transmission	cytosol	calcium ion binding|calmodulin binding|phosphatidylinositol phospholipase C activity|signal transducer activity			ovary(1)|pancreas(1)	2																		---	---	---	---
PYGM	5837	broad.mit.edu	37	11	64522259	64522259	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:64522259G>A	uc001oax.3	-	8	1722	c.905C>T	c.(904-906)GCT>GTT	p.A302V	PYGM_uc001oay.3_Missense_Mutation_p.A214V	NM_005609	NP_005600	P11217	PYGM_HUMAN	muscle glycogen phosphorylase isoform 1	302					glucose metabolic process|glycogen catabolic process	cytosol	glycogen phosphorylase activity|protein binding			ovary(2)	2					Pyridoxal Phosphate(DB00114)													---	---	---	---
CDC42BPG	55561	broad.mit.edu	37	11	64599067	64599067	+	Missense_Mutation	SNP	G	A	A	rs56324326		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:64599067G>A	uc001obs.3	-	28	3214	c.3214C>T	c.(3214-3216)CGG>TGG	p.R1072W		NM_017525	NP_059995	Q6DT37	MRCKG_HUMAN	CDC42 binding protein kinase gamma (DMPK-like)	1072					actin cytoskeleton reorganization|intracellular signal transduction	cell leading edge|centrosome	ATP binding|magnesium ion binding|protein binding|protein serine/threonine kinase activity|small GTPase regulator activity			lung(3)|central_nervous_system(1)	4																OREG0004016	type=REGULATORY REGION|Gene=CDC42BPG|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay	---	---	---	---
ATG2A	23130	broad.mit.edu	37	11	64678652	64678652	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:64678652A>G	uc001obx.2	-	10	1439	c.1324T>C	c.(1324-1326)TCT>CCT	p.S442P		NM_015104	NP_055919	Q2TAZ0	ATG2A_HUMAN	autophagy related 2A	442							protein binding			ovary(1)|central_nervous_system(1)	2																		---	---	---	---
PPP2R5B	5526	broad.mit.edu	37	11	64695377	64695377	+	Splice_Site	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:64695377T>C	uc001oby.2	+	4	1083	c.498_splice	c.e4+2	p.Q166_splice	PPP2R5B_uc001obz.2_Splice_Site_p.Q166_splice	NM_006244	NP_006235			beta isoform of regulatory subunit B56, protein						signal transduction	cytoplasm|protein phosphatase type 2A complex	protein binding|protein phosphatase type 2A regulator activity			ovary(2)	2																		---	---	---	---
ZFPL1	7542	broad.mit.edu	37	11	64854011	64854011	+	Silent	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:64854011C>T	uc001ocq.1	+	4	504	c.339C>T	c.(337-339)CCC>CCT	p.P113P	CDCA5_uc001ocp.2_5'Flank	NM_006782	NP_006773	O95159	ZFPL1_HUMAN	zinc finger protein-like 1	113	Cytoplasmic (Potential).				regulation of transcription, DNA-dependent|vesicle-mediated transport	Golgi apparatus|integral to membrane|nucleus	DNA binding|zinc ion binding			ovary(1)	1																		---	---	---	---
TIGD3	220359	broad.mit.edu	37	11	65123908	65123908	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:65123908G>A	uc001odo.3	+	2	792	c.629G>A	c.(628-630)CGG>CAG	p.R210Q		NM_145719	NP_663771	Q6B0B8	TIGD3_HUMAN	tigger transposable element derived 3	210	DDE.				regulation of transcription, DNA-dependent	chromosome, centromeric region|nucleus	DNA binding				0																		---	---	---	---
SF3B2	10992	broad.mit.edu	37	11	65826347	65826347	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:65826347G>A	uc001ogy.1	+	10	1053	c.1013G>A	c.(1012-1014)CGG>CAG	p.R338Q		NM_006842	NP_006833	Q13435	SF3B2_HUMAN	splicing factor 3B subunit 2	338					interspecies interaction between organisms	catalytic step 2 spliceosome|nucleoplasm|U12-type spliceosomal complex	nucleic acid binding|protein binding			ovary(2)|breast(1)	3																		---	---	---	---
PACS1	55690	broad.mit.edu	37	11	66002844	66002844	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:66002844C>T	uc001oha.1	+	18	2311	c.2177C>T	c.(2176-2178)GCC>GTC	p.A726V	PACS1_uc010rou.1_Missense_Mutation_p.A262V	NM_018026	NP_060496	Q6VY07	PACS1_HUMAN	phosphofurin acidic cluster sorting protein 1	726					interspecies interaction between organisms|regulation of defense response to virus by virus|viral reproduction	cytosol	protein binding			ovary(6)	6																		---	---	---	---
CD248	57124	broad.mit.edu	37	11	66083068	66083068	+	Silent	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:66083068G>A	uc001ohm.1	-	1	1448	c.1431C>T	c.(1429-1431)TCC>TCT	p.S477S		NM_020404	NP_065137	Q9HCU0	CD248_HUMAN	tumor endothelial marker 1 precursor	477	Pro-rich.|Extracellular (Potential).					integral to membrane|proteinaceous extracellular matrix	calcium ion binding|sugar binding			large_intestine(3)	3					Cefalotin(DB00456)													---	---	---	---
PELI3	246330	broad.mit.edu	37	11	66240839	66240839	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:66240839G>A	uc001oic.3	+	6	748	c.584G>A	c.(583-585)CGC>CAC	p.R195H	PELI3_uc001oib.2_Missense_Mutation_p.R195H|PELI3_uc001oid.3_Missense_Mutation_p.R171H|PELI3_uc001oie.3_Missense_Mutation_p.R46H|PELI3_uc010rpd.1_Missense_Mutation_p.R36H	NM_145065	NP_659502	Q8N2H9	PELI3_HUMAN	pellino 3 alpha isoform 1	195						cytosol	protein binding			ovary(1)	1																		---	---	---	---
DPP3	10072	broad.mit.edu	37	11	66272255	66272255	+	Intron	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:66272255T>C	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																		---	---	---	---
SSH3	54961	broad.mit.edu	37	11	67076941	67076941	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:67076941C>T	uc001okj.2	+	11	1313	c.1135C>T	c.(1135-1137)CGC>TGC	p.R379C	SSH3_uc001okk.2_RNA|SSH3_uc001okl.2_Missense_Mutation_p.R233C	NM_017857	NP_060327	Q8TE77	SSH3_HUMAN	slingshot homolog 3	379	Tyrosine-protein phosphatase.				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	67166284	67166284	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:67166284A>G	uc001okw.1	-	6	914	c.791T>C	c.(790-792)GTG>GCG	p.V264A	PPP1CA_uc009yro.1_Missense_Mutation_p.V82A|PPP1CA_uc001okt.1_Missense_Mutation_p.V269A|PPP1CA_uc001oku.1_Missense_Mutation_p.V275A|PPP1CA_uc001okv.1_Missense_Mutation_p.V220A|PPP1CA_uc001okx.1_Missense_Mutation_p.V352A|PPP1CA_uc001oky.2_Missense_Mutation_p.V264A	NM_002708	NP_002699	P62136	PP1A_HUMAN	protein phosphatase 1, catalytic subunit, alpha	264					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	67225107	67225107	+	Missense_Mutation	SNP	C	T	T	rs150929930	byFrequency	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:67225107C>T	uc001olo.2	+	4	682	c.605C>T	c.(604-606)ACG>ATG	p.T202M	CABP4_uc001oln.2_Missense_Mutation_p.T97M	NM_145200	NP_660201	P57796	CABP4_HUMAN	calcium binding protein 4	202					visual perception	cytoplasm|extracellular region|terminal button	calcium ion binding				0			BRCA - Breast invasive adenocarcinoma(15;8.18e-06)															---	---	---	---
CABP2	51475	broad.mit.edu	37	11	67287301	67287301	+	Silent	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:67287301G>A	uc001omc.1	-	6	702	c.600C>T	c.(598-600)GAC>GAT	p.D200D	CABP2_uc001omd.1_Silent_p.D143D|CABP2_uc001ome.1_Silent_p.D206D	NM_016366	NP_057450	Q9NPB3	CABP2_HUMAN	calcium binding protein 2 isoform 1	200	EF-hand 4.				signal transduction	Golgi apparatus|perinuclear region of cytoplasm|plasma membrane	calcium ion binding			skin(1)	1																		---	---	---	---
UNC93B1	81622	broad.mit.edu	37	11	67766988	67766988	+	Splice_Site	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:67766988C>T	uc001omw.1	-	4	634	c.554_splice	c.e4+1	p.R185_splice		NM_030930	NP_112192			unc-93 homolog B1						innate immune response|intracellular protein transport|response to virus|toll-like receptor 3 signaling pathway|toll-like receptor 7 signaling pathway|toll-like receptor 9 signaling pathway	early phagosome|endoplasmic reticulum membrane|endosome|integral to membrane|lysosome					0																		---	---	---	---
ANO1	55107	broad.mit.edu	37	11	70007741	70007741	+	Silent	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:70007741G>A	uc001opj.2	+	18	2099	c.1794G>A	c.(1792-1794)ACG>ACA	p.T598T	ANO1_uc001opk.1_Silent_p.T540T|ANO1_uc001opl.1_RNA|ANO1_uc010rqk.1_Silent_p.T307T	NM_018043	NP_060513	Q5XXA6	ANO1_HUMAN	anoctamin 1, calcium activated chloride channel	598	Cytoplasmic (Potential).				multicellular organismal development	chloride channel complex|cytoplasm|plasma membrane	intracellular calcium activated chloride channel activity			ovary(1)|pancreas(1)	2																		---	---	---	---
MIR548K	100302272	broad.mit.edu	37	11	70130164	70130164	+	RNA	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:70130164T>C	hsa-mir-548k|MI0006354	+			c.104T>C			PPFIA1_uc001opn.1_Intron|PPFIA1_uc001opo.2_Intron|PPFIA1_uc001opp.2_Intron																	0																		---	---	---	---
NUMA1	4926	broad.mit.edu	37	11	71724556	71724556	+	Silent	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:71724556C>T	uc001orl.1	-	15	4165	c.3993G>A	c.(3991-3993)GCG>GCA	p.A1331A	NUMA1_uc009ysw.1_Silent_p.A894A|NUMA1_uc001ork.1_Intron|NUMA1_uc001orm.1_Silent_p.A1331A|NUMA1_uc001orn.2_Silent_p.A894A|NUMA1_uc009ysx.1_Silent_p.A1331A|NUMA1_uc001oro.1_Silent_p.A1331A	NM_006185	NP_006176	Q14980	NUMA1_HUMAN	nuclear mitotic apparatus protein 1	1331	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	71725583	71725583	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:71725583A>G	uc001orl.1	-	15	3138	c.2966T>C	c.(2965-2967)ATG>ACG	p.M989T	NUMA1_uc009ysw.1_Missense_Mutation_p.M552T|NUMA1_uc001ork.1_Intron|NUMA1_uc001orm.1_Missense_Mutation_p.M989T|NUMA1_uc001orn.2_Missense_Mutation_p.M552T|NUMA1_uc009ysx.1_Missense_Mutation_p.M989T|NUMA1_uc001oro.1_Missense_Mutation_p.M989T	NM_006185	NP_006176	Q14980	NUMA1_HUMAN	nuclear mitotic apparatus protein 1	989	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								---	---	---	---
FOLR2	2350	broad.mit.edu	37	11	71932674	71932674	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:71932674G>T	uc009ytd.2	+	5	805	c.636G>T	c.(634-636)CAG>CAT	p.Q212H	FOLR2_uc009yte.2_Missense_Mutation_p.Q212H|FOLR2_uc001ose.3_Missense_Mutation_p.Q212H|FOLR2_uc009ytf.2_Missense_Mutation_p.Q212H	NM_001113534	NP_001107006	P14207	FOLR2_HUMAN	folate receptor 2 precursor	212					folic acid transport	anchored to membrane|extracellular region|membrane fraction|plasma membrane	folic acid binding|receptor activity			breast(2)|ovary(1)	3					Folic Acid(DB00158)													---	---	---	---
P2RY2	5029	broad.mit.edu	37	11	72945998	72945998	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:72945998G>A	uc001otj.2	+	3	1127	c.794G>A	c.(793-795)CGC>CAC	p.R265H	P2RY2_uc001otk.2_Missense_Mutation_p.R265H|P2RY2_uc001otl.2_Missense_Mutation_p.R265H	NM_002564	NP_002555	P41231	P2RY2_HUMAN	purinergic receptor P2Y2	265	Helical; Name=6; (Potential).				activation of phospholipase C activity by G-protein coupled receptor protein signaling pathway coupled to IP3 second messenger	integral to plasma membrane	purinergic nucleotide receptor activity, G-protein coupled			ovary(2)|lung(1)|skin(1)	4					Suramin(DB04786)													---	---	---	---
PLEKHB1	58473	broad.mit.edu	37	11	73361679	73361679	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:73361679C>T	uc001oua.2	+	3	607	c.176C>T	c.(175-177)GCG>GTG	p.A59V	PLEKHB1_uc001oub.2_Missense_Mutation_p.A59V|PLEKHB1_uc010rrh.1_Missense_Mutation_p.A40V|PLEKHB1_uc001ouc.2_Missense_Mutation_p.A40V|PLEKHB1_uc001oud.2_Missense_Mutation_p.A40V|PLEKHB1_uc009ytq.2_Missense_Mutation_p.A40V	NM_021200	NP_067023	Q9UF11	PKHB1_HUMAN	pleckstrin homology domain containing, family B	59	PH.				multicellular organismal development|phototransduction	cytoplasm|integral to membrane	signal transducer activity			ovary(1)|lung(1)	2																		---	---	---	---
C2CD3	26005	broad.mit.edu	37	11	73872446	73872446	+	Nonsense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:73872446G>A	uc001ouu.2	-	3	708	c.481C>T	c.(481-483)CAG>TAG	p.Q161*	C2CD3_uc001ouv.2_Nonsense_Mutation_p.Q161*	NM_015531	NP_056346	Q4AC94	C2CD3_HUMAN	C2 calcium-dependent domain containing 3	161						centrosome				ovary(4)|pancreas(2)|skin(1)	7	Breast(11;4.16e-06)																	---	---	---	---
SLCO2B1	11309	broad.mit.edu	37	11	74914480	74914480	+	Intron	SNP	C	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:74914480C>A	uc001owb.2	+						SLCO2B1_uc010rrr.1_Intron|SLCO2B1_uc010rrs.1_Intron|SLCO2B1_uc001owc.2_Intron|SLCO2B1_uc001owd.2_Intron	NM_007256	NP_009187			solute carrier organic anion transporter family,						sodium-independent organic anion transport	integral to membrane	sodium-independent organic anion transmembrane transporter activity			ovary(1)|breast(1)	2					Ergoloid mesylate(DB01049)													---	---	---	---
C11orf30	56946	broad.mit.edu	37	11	76255556	76255556	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:76255556A>G	uc001oxl.2	+	19	3106	c.2963A>G	c.(2962-2964)CAG>CGG	p.Q988R	C11orf30_uc001oxm.2_Missense_Mutation_p.Q890R|C11orf30_uc010rsb.1_Missense_Mutation_p.Q1003R|C11orf30_uc010rsc.1_Missense_Mutation_p.Q989R|C11orf30_uc001oxn.2_Missense_Mutation_p.Q989R|C11orf30_uc010rsd.1_Missense_Mutation_p.Q897R|C11orf30_uc001oxo.1_Missense_Mutation_p.Q342R|C11orf30_uc010rse.1_Missense_Mutation_p.Q235R|C11orf30_uc001oxp.2_Missense_Mutation_p.Q88R	NM_020193	NP_064578	Q7Z589	EMSY_HUMAN	EMSY protein	988	Gln-rich.				chromatin modification|DNA repair|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus				ovary(5)|skin(1)	6																		---	---	---	---
TSKU	25987	broad.mit.edu	37	11	76507479	76507479	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:76507479G>T	uc001oxt.2	+	2	991	c.819G>T	c.(817-819)GAG>GAT	p.E273D		NM_015516	NP_056331	Q8WUA8	TSK_HUMAN	tsukushin precursor	273	LRR 9.					extracellular region					0	Ovarian(111;0.112)																	---	---	---	---
INTS4	92105	broad.mit.edu	37	11	77635944	77635944	+	Intron	SNP	A	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:77635944A>T	uc001oys.2	-						INTS4_uc001oyt.2_Intron|INTS4_uc001oyu.1_Intron	NM_033547	NP_291025			integrator complex subunit 4						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)															---	---	---	---
KCTD14	65987	broad.mit.edu	37	11	77727979	77727979	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:77727979G>A	uc001oyw.3	-	2	453	c.428C>T	c.(427-429)CCG>CTG	p.P143L		NM_023930	NP_076419	Q9BQ13	KCD14_HUMAN	potassium channel tetramerisation domain	143						voltage-gated potassium channel complex	voltage-gated potassium channel activity			ovary(2)	2	all_cancers(14;4.53e-19)|all_epithelial(13;1.73e-21)|Breast(9;2.71e-16)|Ovarian(111;0.152)		OV - Ovarian serous cystadenocarcinoma(8;1e-24)															---	---	---	---
NARS2	79731	broad.mit.edu	37	11	78176923	78176923	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:78176923G>A	uc001ozi.2	-	11	1539	c.1163C>T	c.(1162-1164)ACG>ATG	p.T388M	NARS2_uc010rsq.1_Missense_Mutation_p.T161M	NM_024678	NP_078954	Q96I59	SYNM_HUMAN	asparaginyl-tRNA synthetase 2, mitochondrial	388					asparaginyl-tRNA aminoacylation	mitochondrial matrix	asparagine-tRNA ligase activity|ATP binding|nucleic acid binding			ovary(2)	2	all_cancers(14;2.63e-17)|all_epithelial(13;1.85e-19)				L-Asparagine(DB00174)													---	---	---	---
ODZ4	26011	broad.mit.edu	37	11	78381279	78381279	+	Silent	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:78381279C>T	uc001ozl.3	-	32	6574	c.6111G>A	c.(6109-6111)ACG>ACA	p.T2037T	ODZ4_uc001ozk.3_Silent_p.T262T|ODZ4_uc009yvb.1_Silent_p.T621T	NM_001098816	NP_001092286	Q6N022	TEN4_HUMAN	odz, odd Oz/ten-m homolog 4	2037	Extracellular (Potential).|YD 11.				signal transduction	integral to membrane				ovary(2)|pancreas(2)	4																		---	---	---	---
PCF11	51585	broad.mit.edu	37	11	82880646	82880646	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:82880646T>C	uc001ozx.3	+	8	3614	c.3269T>C	c.(3268-3270)GTA>GCA	p.V1090A	PCF11_uc010rsu.1_Missense_Mutation_p.V1221A	NM_015885	NP_056969	O94913	PCF11_HUMAN	pre-mRNA cleavage complex II protein Pcf11	1090					mRNA 3'-end processing|mRNA cleavage|nuclear mRNA splicing, via spliceosome|termination of RNA polymerase II transcription	mRNA cleavage factor complex				ovary(1)	1																		---	---	---	---
CCDC81	60494	broad.mit.edu	37	11	86086264	86086264	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:86086264T>G	uc001pbx.1	+	1	487	c.59T>G	c.(58-60)CTG>CGG	p.L20R	CCDC81_uc001pbw.1_Missense_Mutation_p.L20R	NM_001156474	NP_001149946	Q6ZN84	CCD81_HUMAN	coiled-coil domain containing 81 isoform 1	20										skin(1)	1		Acute lymphoblastic leukemia(157;5.51e-06)|all_hematologic(158;0.00535)																---	---	---	---
ME3	10873	broad.mit.edu	37	11	86176128	86176128	+	Intron	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:86176128C>T	uc001pbz.2	-						ME3_uc001pca.2_Intron|ME3_uc009yvk.2_Intron|ME3_uc010rtr.1_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)													---	---	---	---
ME3	10873	broad.mit.edu	37	11	86198437	86198437	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:86198437C>T	uc001pbz.2	-	6	1005	c.751G>A	c.(751-753)GTG>ATG	p.V251M	ME3_uc001pca.2_Missense_Mutation_p.V251M|ME3_uc009yvk.2_Missense_Mutation_p.V251M|ME3_uc010rtr.1_RNA	NM_001014811	NP_001014811	Q16798	MAON_HUMAN	mitochondrial malic enzyme 3 precursor	251					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)													---	---	---	---
NAALAD2	10003	broad.mit.edu	37	11	89883677	89883677	+	Missense_Mutation	SNP	C	T	T	rs147884512		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:89883677C>T	uc001pdf.3	+	5	620	c.511C>T	c.(511-513)CGC>TGC	p.R171C	NAALAD2_uc009yvx.2_Missense_Mutation_p.R171C|NAALAD2_uc009yvy.2_Missense_Mutation_p.R171C|NAALAD2_uc001pdd.2_Missense_Mutation_p.R171C|NAALAD2_uc001pde.2_Missense_Mutation_p.R171C	NM_005467	NP_005458	Q9Y3Q0	NALD2_HUMAN	N-acetylated alpha-linked acidic dipeptidase 2	171	Extracellular (Potential).				proteolysis	integral to membrane	carboxypeptidase activity|dipeptidase activity|dipeptidyl-peptidase activity|metal ion binding|metallopeptidase activity|serine-type peptidase activity			pancreas(1)|skin(1)	2		Acute lymphoblastic leukemia(157;2.31e-05)|all_hematologic(158;0.00556)																---	---	---	---
FAT3	120114	broad.mit.edu	37	11	92577614	92577614	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:92577614C>T	uc001pdj.3	+	18	11098	c.11081C>T	c.(11080-11082)GCA>GTA	p.A3694V	FAT3_uc001pdi.3_Missense_Mutation_p.A134V	NM_001008781	NP_001008781	Q8TDW7	FAT3_HUMAN	FAT tumor suppressor homolog 3	3694	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)			---	---	---	---
GPR83	10888	broad.mit.edu	37	11	94134284	94134284	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:94134284A>G	uc001pet.2	-	1	302	c.130T>C	c.(130-132)TGG>CGG	p.W44R		NM_016540	NP_057624	Q9NYM4	GPR83_HUMAN	G protein-coupled receptor 83 precursor	44	Extracellular (Potential).					integral to membrane|plasma membrane	neuropeptide Y receptor activity			central_nervous_system(2)|ovary(1)	3		Acute lymphoblastic leukemia(157;2.26e-05)|all_hematologic(158;0.0123)																---	---	---	---
PIWIL4	143689	broad.mit.edu	37	11	94349674	94349674	+	Silent	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:94349674T>C	uc001pfa.2	+	16	2170	c.1959T>C	c.(1957-1959)TGT>TGC	p.C653C	PIWIL4_uc010rue.1_RNA|PIWIL4_uc009ywk.1_RNA	NM_152431	NP_689644	Q7Z3Z4	PIWL4_HUMAN	piwi-like 4	653	Piwi.				cell differentiation|DNA methylation involved in gamete generation|gene silencing by RNA|meiosis|multicellular organismal development|piRNA metabolic process|regulation of translation|spermatogenesis	nucleus|piP-body	piRNA binding			skin(1)	1		Acute lymphoblastic leukemia(157;2.26e-05)|all_hematologic(158;0.0123)																---	---	---	---
CNTN5	53942	broad.mit.edu	37	11	99690425	99690425	+	Nonsense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:99690425G>A	uc001pga.2	+	4	545	c.206G>A	c.(205-207)TGG>TAG	p.W69*	CNTN5_uc009ywv.1_Nonsense_Mutation_p.W69*|CNTN5_uc001pfz.2_Nonsense_Mutation_p.W69*|CNTN5_uc001pgb.2_Intron	NM_014361	NP_055176	O94779	CNTN5_HUMAN	contactin 5 isoform long	69					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	99827662	99827662	+	Silent	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:99827662C>T	uc001pga.2	+	8	1137	c.798C>T	c.(796-798)AGC>AGT	p.S266S	CNTN5_uc009ywv.1_Silent_p.S266S|CNTN5_uc001pfz.2_Silent_p.S266S|CNTN5_uc001pgb.2_Silent_p.S192S	NM_014361	NP_055176	O94779	CNTN5_HUMAN	contactin 5 isoform long	266	Ig-like C2-type 2.				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)														---	---	---	---
ANGPTL5	253935	broad.mit.edu	37	11	101778583	101778583	+	Nonsense_Mutation	SNP	C	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:101778583C>A	uc001pgl.2	-	2	654	c.58G>T	c.(58-60)GGA>TGA	p.G20*		NM_178127	NP_835228	Q86XS5	ANGL5_HUMAN	angiopoietin-like 5 precursor	20					signal transduction	extracellular space	receptor binding			ovary(1)	1		Acute lymphoblastic leukemia(157;0.000966)|all_hematologic(158;0.043)		BRCA - Breast invasive adenocarcinoma(274;0.0328)														---	---	---	---
C11orf70	85016	broad.mit.edu	37	11	101946776	101946776	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:101946776G>T	uc001pgp.2	+	5	636	c.608G>T	c.(607-609)AGT>ATT	p.S203I	C11orf70_uc001pgo.2_3'UTR|C11orf70_uc001pgq.2_Missense_Mutation_p.S165I	NM_032930	NP_116319	Q9BRQ4	CK070_HUMAN	hypothetical protein LOC85016	203										skin(1)	1	all_epithelial(12;0.0137)	Acute lymphoblastic leukemia(157;0.000966)|all_hematologic(158;0.0137)	Lung(13;0.245)	BRCA - Breast invasive adenocarcinoma(274;0.0335)														---	---	---	---
MMP20	9313	broad.mit.edu	37	11	102464176	102464176	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:102464176T>C	uc001phc.2	-	8	1254	c.1241A>G	c.(1240-1242)TAC>TGC	p.Y414C		NM_004771	NP_004762	O60882	MMP20_HUMAN	matrix metalloproteinase 20 preproprotein	414	Hemopexin-like 3.				proteolysis|regulation of enamel mineralization	extracellular space|proteinaceous extracellular matrix	calcium ion binding|metalloendopeptidase activity|protein binding|zinc ion binding			urinary_tract(1)|skin(1)	2	all_cancers(8;8.95e-05)|all_epithelial(12;0.00227)|Lung NSC(15;0.139)	Acute lymphoblastic leukemia(157;0.000967)|all_hematologic(158;0.0033)	Epithelial(9;0.0216)|Lung(13;0.0711)|all cancers(10;0.0889)|LUSC - Lung squamous cell carcinoma(19;0.13)	BRCA - Breast invasive adenocarcinoma(274;0.0161)														---	---	---	---
DYNC2H1	79659	broad.mit.edu	37	11	103014125	103014125	+	Splice_Site	SNP	G	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:103014125G>C	uc001pho.2	+	18	2846	c.2702_splice	c.e18+1	p.S901_splice	DYNC2H1_uc001phn.1_Splice_Site_p.S901_splice|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	103182637	103182637	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:103182637C>T	uc001pho.2	+	79	11668	c.11524C>T	c.(11524-11526)CGT>TGT	p.R3842C	DYNC2H1_uc001phn.1_Missense_Mutation_p.R3849C|DYNC2H1_uc009yxe.1_Intron	NM_001080463	NP_001073932	Q8NCM8	DYHC2_HUMAN	dynein, cytoplasmic 2, heavy chain 1	3842	AAA 6 (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)														---	---	---	---
PDGFD	80310	broad.mit.edu	37	11	103814332	103814332	+	Missense_Mutation	SNP	G	A	A	rs141538106		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:103814332G>A	uc001phq.2	-	5	992	c.620C>T	c.(619-621)GCG>GTG	p.A207V	PDGFD_uc001php.2_Missense_Mutation_p.A201V	NM_025208	NP_079484	Q9GZP0	PDGFD_HUMAN	platelet derived growth factor D isoform 1	207					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)														---	---	---	---
CASP5	838	broad.mit.edu	37	11	104872816	104872816	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:104872816A>G	uc010rva.1	-	5	688	c.656T>C	c.(655-657)ATG>ACG	p.M219T	CASP5_uc010ruz.1_Missense_Mutation_p.M232T|CASP5_uc010rvb.1_Missense_Mutation_p.M161T|CASP5_uc010rvc.1_Missense_Mutation_p.M77T|CASP5_uc009yxh.2_Missense_Mutation_p.M1T|CASP5_uc010rvd.1_Missense_Mutation_p.M1T	NM_004347	NP_004338	P51878	CASP5_HUMAN	caspase 5 isoform a precursor	219					apoptosis|cellular response to mechanical stimulus|proteolysis|regulation of apoptosis	intracellular	cysteine-type endopeptidase activity|protein binding			ovary(2)|lung(1)	3		Acute lymphoblastic leukemia(157;0.000967)|all_hematologic(158;0.0017)|Melanoma(852;0.0047)		BRCA - Breast invasive adenocarcinoma(274;0.000943)|Epithelial(105;0.0104)|all cancers(92;0.042)														---	---	---	---
ACAT1	38	broad.mit.edu	37	11	108018115	108018115	+	Nonstop_Mutation	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:108018115T>C	uc001pjy.2	+	12	1358	c.1282T>C	c.(1282-1284)TAG>CAG	p.*428Q		NM_000019	NP_000010	P24752	THIL_HUMAN	acetyl-Coenzyme A acetyltransferase 1 precursor	428					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)													---	---	---	---
FDX1	2230	broad.mit.edu	37	11	110333133	110333133	+	Nonsense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:110333133C>T	uc001pkx.2	+	4	747	c.496C>T	c.(496-498)CGA>TGA	p.R166*		NM_004109	NP_004100	P10109	ADX_HUMAN	ferredoxin 1 precursor	166	2Fe-2S ferredoxin-type.				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)													---	---	---	---
ARHGAP20	57569	broad.mit.edu	37	11	110450082	110450082	+	3'UTR	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:110450082T>C	uc001pkz.1	-	16					ARHGAP20_uc001pky.1_3'UTR|ARHGAP20_uc009yyb.1_3'UTR|ARHGAP20_uc001pla.1_3'UTR|ARHGAP20_uc001plb.2_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)														---	---	---	---
MIR34C	407042	broad.mit.edu	37	11	111384206	111384206	+	RNA	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:111384206A>G	hsa-mir-34c|MI0000743	+			c.43A>G			BTG4_uc001plj.2_5'Flank|BTG4_uc001plk.2_5'Flank|uc001pll.2_RNA|C11orf88_uc009yyd.2_5'Flank|C11orf88_uc001pln.3_5'Flank|C11orf88_uc001plo.1_5'Flank																	0																		---	---	---	---
CRYAB	1410	broad.mit.edu	37	11	111779547	111779547	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:111779547G>A	uc001pmf.1	-	3	494	c.469C>T	c.(469-471)CGC>TGC	p.R157C		NM_001885	NP_001876	P02511	CRYAB_HUMAN	crystallin, alpha B	157					anti-apoptosis|muscle contraction|negative regulation of intracellular transport|protein folding|protein homooligomerization|response to heat	cytoplasm|nucleus	protein homodimerization activity|structural constituent of eye lens|unfolded protein binding				0		all_cancers(61;1.26e-15)|all_epithelial(67;9.52e-10)|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;3.57e-07)|BRCA - Breast invasive adenocarcinoma(274;1.1e-06)|all cancers(92;6.57e-06)|OV - Ovarian serous cystadenocarcinoma(223;0.051)														---	---	---	---
SIDT2	51092	broad.mit.edu	37	11	117063357	117063357	+	Silent	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:117063357G>A	uc001pqh.1	+	21	2090	c.2049G>A	c.(2047-2049)CCG>CCA	p.P683P	SIDT2_uc010rxe.1_Silent_p.P683P|SIDT2_uc001pqg.2_Silent_p.P704P|SIDT2_uc001pqi.1_Silent_p.P680P|SIDT2_uc001pqj.1_5'UTR	NM_001040455	NP_001035545	Q8NBJ9	SIDT2_HUMAN	SID1 transmembrane family, member 2 precursor	683	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)														---	---	---	---
CEP164	22897	broad.mit.edu	37	11	117266805	117266805	+	Missense_Mutation	SNP	T	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:117266805T>A	uc001prc.2	+	25	3272	c.3125T>A	c.(3124-3126)CTG>CAG	p.L1042Q	CEP164_uc001prb.2_Missense_Mutation_p.L1045Q|CEP164_uc010rxk.1_Missense_Mutation_p.L1016Q|CEP164_uc001prf.2_Intron|CEP164_uc009yzp.1_RNA|CEP164_uc001prg.1_Missense_Mutation_p.L475Q	NM_014956	NP_055771	Q9UPV0	CE164_HUMAN	centrosomal protein 164kDa	1042					cell division|DNA repair|G2/M transition of mitotic cell cycle|mitosis	centriole|cytosol|nucleus				ovary(1)|central_nervous_system(1)	2	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;4e-05)|Epithelial(105;0.0008)														---	---	---	---
DSCAML1	57453	broad.mit.edu	37	11	117329506	117329506	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:117329506G>A	uc001prh.1	-	19	3714	c.3712C>T	c.(3712-3714)CGC>TGC	p.R1238C		NM_020693	NP_065744	Q8TD84	DSCL1_HUMAN	Down syndrome cell adhesion molecule like 1	1178	Fibronectin type-III 3.|Extracellular (Potential).				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	117352775	117352775	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:117352775C>T	uc001prh.1	-	12	2644	c.2642G>A	c.(2641-2643)CGC>CAC	p.R881H		NM_020693	NP_065744	Q8TD84	DSCL1_HUMAN	Down syndrome cell adhesion molecule like 1	821	Extracellular (Potential).|Ig-like C2-type 9.				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)														---	---	---	---
IL10RA	3587	broad.mit.edu	37	11	117869935	117869935	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:117869935C>T	uc001prv.2	+	7	1393	c.1316C>T	c.(1315-1317)GCT>GTT	p.A439V	IL10RA_uc010rxl.1_Missense_Mutation_p.A419V|IL10RA_uc010rxm.1_Missense_Mutation_p.A419V|IL10RA_uc010rxn.1_Missense_Mutation_p.A290V|IL10RA_uc001prw.2_Missense_Mutation_p.A290V	NM_001558	NP_001549	Q13651	I10R1_HUMAN	interleukin 10 receptor, alpha precursor	439	Cytoplasmic (Potential).					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)														---	---	---	---
UBE4A	9354	broad.mit.edu	37	11	118260453	118260453	+	Silent	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:118260453C>T	uc001psw.2	+	17	2730	c.2601C>T	c.(2599-2601)CTC>CTT	p.L867L	UBE4A_uc001psv.2_Silent_p.L874L	NM_004788	NP_004779	Q14139	UBE4A_HUMAN	ubiquitination factor E4A	867					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	118344254	118344254	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:118344254C>T	uc001pta.2	+	3	2403	c.2380C>T	c.(2380-2382)CCA>TCA	p.P794S	MLL_uc001ptb.2_Missense_Mutation_p.P794S|MLL_uc001psz.1_Missense_Mutation_p.P827S|MLL_uc001ptd.1_Intron	NM_005933	NP_005924	Q03164	MLL1_HUMAN	myeloid/lymphoid or mixed-lineage leukemia	794					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	118390753	118390753	+	Silent	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:118390753G>A	uc001pta.2	+	33	11417	c.11394G>A	c.(11392-11394)GAG>GAA	p.E3798E	MLL_uc001ptb.2_Silent_p.E3801E	NM_005933	NP_005924	Q03164	MLL1_HUMAN	myeloid/lymphoid or mixed-lineage leukemia	3798					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								---	---	---	---
UPK2	7379	broad.mit.edu	37	11	118827695	118827695	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:118827695T>G	uc001puh.2	+	2	214	c.179T>G	c.(178-180)CTG>CGG	p.L60R		NM_006760	NP_006751	O00526	UPK2_HUMAN	uroplakin 2 precursor	60					cellular membrane organization|epithelial cell differentiation|multicellular organismal development	integral to endoplasmic reticulum membrane|integral to plasma membrane				skin(1)	1	all_hematologic(175;0.0839)	Medulloblastoma(222;0.0523)|all_hematologic(192;0.122)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;7.47e-05)												OREG0021391	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	119045928	119045928	+	Missense_Mutation	SNP	T	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:119045928T>A	uc001pvu.2	+	6	1831	c.1616T>A	c.(1615-1617)ATC>AAC	p.I539N	NLRX1_uc010rzc.1_Missense_Mutation_p.I361N|NLRX1_uc001pvv.2_Missense_Mutation_p.I539N|NLRX1_uc001pvw.2_Missense_Mutation_p.I539N|NLRX1_uc001pvx.2_Missense_Mutation_p.I539N	NM_024618	NP_078894	Q86UT6	NLRX1_HUMAN	NLR family member X1 isoform 1	539	Required for interaction with MAVS.				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)														---	---	---	---
PDZD3	79849	broad.mit.edu	37	11	119059560	119059560	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:119059560G>A	uc001pwb.2	+	7	1993	c.1469G>A	c.(1468-1470)CGT>CAT	p.R490H	PDZD3_uc001pvy.2_Missense_Mutation_p.R410H|PDZD3_uc001pvz.2_Missense_Mutation_p.R424H|PDZD3_uc010rzd.1_Missense_Mutation_p.R411H|PDZD3_uc001pwa.2_Missense_Mutation_p.R120H			Q86UT5	NHRF4_HUMAN	RecName: Full=Na(+)/H(+) exchange regulatory cofactor NHE-RF4;          Short=NHERF-4; AltName: Full=PDZ domain-containing protein 3; AltName: Full=PDZ domain-containing protein 2; AltName: Full=Intestinal and kidney-enriched PDZ protein; AltName: Full=Sodium-hydrogen exchanger regulatory factor 4;	490	PDZ 4.				cGMP-mediated signaling|ion transport|negative regulation of cGMP biosynthetic process|response to toxin|water transport	apical part of cell|brush border|cytosol|membrane fraction|subapical complex	guanylate cyclase inhibitor activity|ion channel inhibitor activity|protein C-terminus binding			breast(1)	1	all_hematologic(175;0.0977)	Medulloblastoma(222;0.0523)|Breast(348;0.174)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;7.52e-05)														---	---	---	---
PVRL1	5818	broad.mit.edu	37	11	119535483	119535483	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:119535483T>C	uc001pwv.2	-	6	1700	c.1528A>G	c.(1528-1530)ATT>GTT	p.I510V	PVRL1_uc001pwu.1_Intron	NM_002855	NP_002846	Q15223	PVRL1_HUMAN	poliovirus receptor-related 1 isoform 1	510	Cytoplasmic (Potential).				adherens junction organization|cell junction assembly|entry of virus into host cell|heterophilic cell-cell adhesion|homophilic cell adhesion|immune response	cell-cell adherens junction|extracellular region|integral to membrane	cell adhesion molecule binding|coreceptor activity|protein homodimerization activity				0		Breast(348;0.037)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;4.29e-05)														---	---	---	---
TRIM29	23650	broad.mit.edu	37	11	120008075	120008075	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:120008075G>A	uc001pwz.2	-	1	789	c.665C>T	c.(664-666)GCC>GTC	p.A222V	TRIM29_uc001pxa.2_RNA	NM_012101	NP_036233	Q14134	TRI29_HUMAN	tripartite motif protein TRIM29	222	B box-type.				transcription from RNA polymerase II promoter	cytoplasm	protein binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(1)|breast(1)|kidney(1)|skin(1)	4		Breast(109;0.00117)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;5.37e-06)														---	---	---	---
ARHGEF12	23365	broad.mit.edu	37	11	120336012	120336012	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:120336012G>A	uc001pxl.1	+	28	2687	c.2680G>A	c.(2680-2682)GCC>ACC	p.A894T	ARHGEF12_uc009zat.2_Missense_Mutation_p.A875T|ARHGEF12_uc010rzn.1_Missense_Mutation_p.A791T|ARHGEF12_uc009zau.1_Missense_Mutation_p.A791T	NM_015313	NP_056128	Q9NZN5	ARHGC_HUMAN	Rho guanine nucleotide exchange factor (GEF) 12	894	DH.				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	120337898	120337898	+	Intron	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:120337898T>C	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								---	---	---	---
ARHGEF12	23365	broad.mit.edu	37	11	120348897	120348897	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:120348897T>C	uc001pxl.1	+	37	3572	c.3565T>C	c.(3565-3567)TCG>CCG	p.S1189P	ARHGEF12_uc009zat.2_Missense_Mutation_p.S1170P|ARHGEF12_uc009zau.1_Missense_Mutation_p.S1086P	NM_015313	NP_056128	Q9NZN5	ARHGC_HUMAN	Rho guanine nucleotide exchange factor (GEF) 12	1189					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	120831733	120831733	+	Missense_Mutation	SNP	G	A	A	rs139636929	byFrequency	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:120831733G>A	uc001pxn.2	+	17	2277	c.1990G>A	c.(1990-1992)GCC>ACC	p.A664T	GRIK4_uc009zav.1_Missense_Mutation_p.A664T|GRIK4_uc009zaw.1_Missense_Mutation_p.A664T|GRIK4_uc009zax.1_Missense_Mutation_p.A664T	NM_014619	NP_055434	Q16099	GRIK4_HUMAN	glutamate receptor KA1 precursor	664	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)													---	---	---	---
TECTA	7007	broad.mit.edu	37	11	120998618	120998618	+	Silent	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:120998618C>T	uc010rzo.1	+	8	1932	c.1932C>T	c.(1930-1932)TGC>TGT	p.C644C		NM_005422	NP_005413	O75443	TECTA_HUMAN	tectorin alpha precursor	644	TIL 1.				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)														---	---	---	---
SORL1	6653	broad.mit.edu	37	11	121424711	121424711	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:121424711G>A	uc001pxx.2	+	17	2412	c.2332G>A	c.(2332-2334)GCC>ACC	p.A778T		NM_003105	NP_003096	Q92673	SORL_HUMAN	sortilin-related receptor containing LDLR class	778	Extracellular (Potential).				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)														---	---	---	---
HSPA8	3312	broad.mit.edu	37	11	122928638	122928638	+	Intron	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:122928638G>A	uc001pyo.2	-						HSPA8_uc009zbc.2_Intron|HSPA8_uc001pyp.2_Intron|HSPA8_uc010rzu.1_Intron	NM_006597	NP_006588			heat shock 70kDa protein 8 isoform 1						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)														---	---	---	---
HSPA8	3312	broad.mit.edu	37	11	122929811	122929811	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:122929811T>C	uc001pyo.2	-	6	1357	c.1279A>G	c.(1279-1281)ACC>GCC	p.T427A	HSPA8_uc009zbc.2_Missense_Mutation_p.T191A|HSPA8_uc001pyp.2_Missense_Mutation_p.T427A|HSPA8_uc010rzu.1_Missense_Mutation_p.T350A	NM_006597	NP_006588	P11142	HSP7C_HUMAN	heat shock 70kDa protein 8 isoform 1	427					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	123477380	123477380	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:123477380G>A	uc001pyx.2	+	10	1287	c.958G>A	c.(958-960)GCC>ACC	p.A320T	GRAMD1B_uc001pyw.2_Missense_Mutation_p.A327T|GRAMD1B_uc010rzw.1_Missense_Mutation_p.A280T|GRAMD1B_uc010rzx.1_Missense_Mutation_p.A280T|GRAMD1B_uc009zbe.1_Missense_Mutation_p.A316T|GRAMD1B_uc001pyy.2_5'Flank	NM_020716	NP_065767	Q3KR37	GRM1B_HUMAN	GRAM domain containing 1B	320						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	123597301	123597301	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:123597301C>T	uc001pzd.1	-	9	1751	c.1351G>A	c.(1351-1353)GCG>ACG	p.A451T	ZNF202_uc001pzc.1_Missense_Mutation_p.A227T|ZNF202_uc001pze.1_Missense_Mutation_p.A451T|ZNF202_uc001pzf.1_Missense_Mutation_p.A451T	NM_003455	NP_003446	O95125	ZN202_HUMAN	zinc finger protein 202	451					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)														---	---	---	---
OR4D5	219875	broad.mit.edu	37	11	123811104	123811104	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:123811104C>T	uc001pzk.1	+	1	781	c.781C>T	c.(781-783)CCT>TCT	p.P261S		NM_001001965	NP_001001965	Q8NGN0	OR4D5_HUMAN	olfactory receptor, family 4, subfamily D,	261	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)	1		Breast(109;0.00867)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.22)		BRCA - Breast invasive adenocarcinoma(274;4.88e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0399)														---	---	---	---
OR10G7	390265	broad.mit.edu	37	11	123909171	123909171	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:123909171C>T	uc001pzq.1	-	1	538	c.538G>A	c.(538-540)GCA>ACA	p.A180T		NM_001004463	NP_001004463	Q8NGN6	O10G7_HUMAN	olfactory receptor, family 10, subfamily G,	180	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(2)	2		Breast(109;0.00867)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.22)		BRCA - Breast invasive adenocarcinoma(274;4.88e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0521)														---	---	---	---
OR8B8	26493	broad.mit.edu	37	11	124310904	124310904	+	Silent	SNP	G	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:124310904G>T	uc010sal.1	-	1	78	c.78C>A	c.(76-78)CCC>CCA	p.P26P		NM_012378	NP_036510	Q15620	OR8B8_HUMAN	olfactory receptor, family 8, subfamily B,	26	Helical; Name=1; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)	1		Breast(109;0.0115)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;1.49e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0277)														---	---	---	---
OR8A1	390275	broad.mit.edu	37	11	124440263	124440263	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:124440263T>C	uc010san.1	+	1	299	c.299T>C	c.(298-300)GTG>GCG	p.V100A		NM_001005194	NP_001005194	Q8NGG7	OR8A1_HUMAN	olfactory receptor, family 8, subfamily A,	100	Helical; Name=2; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)	1		Breast(109;0.0115)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;1.49e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0214)														---	---	---	---
TBRG1	84897	broad.mit.edu	37	11	124501197	124501197	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:124501197G>T	uc001qak.3	+	8	1212	c.974G>T	c.(973-975)TGC>TTC	p.C325F	TBRG1_uc001qaj.3_Missense_Mutation_p.C174F|TBRG1_uc001qal.3_Missense_Mutation_p.C101F|TBRG1_uc001qam.3_RNA|TBRG1_uc009zbf.2_RNA|TBRG1_uc009zbg.2_Intron|TBRG1_uc009zbh.2_Missense_Mutation_p.C101F	NM_032811	NP_116200	Q3YBR2	TBRG1_HUMAN	transforming growth factor beta regulator 1	325					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)														---	---	---	---
SIAE	54414	broad.mit.edu	37	11	124519603	124519603	+	Missense_Mutation	SNP	C	T	T	rs149466359		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:124519603C>T	uc001qan.2	-	5	747	c.634G>A	c.(634-636)GGG>AGG	p.G212R		NM_170601	NP_733746	Q9HAT2	SIAE_HUMAN	sialate O-acetylesterase precursor	212			G -> R (in AIS6; defective enzyme secretion and activity).			extracellular region|lysosome	carboxylesterase activity|sialate O-acetylesterase activity				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;1.63e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0243)														---	---	---	---
C11orf61	79684	broad.mit.edu	37	11	124637290	124637290	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:124637290A>G	uc001qba.1	-	4	1485	c.1462T>C	c.(1462-1464)TGC>CGC	p.C488R	C11orf61_uc001qaz.1_Missense_Mutation_p.C436R|C11orf61_uc010sap.1_Missense_Mutation_p.C208R|C11orf61_uc001qay.1_Missense_Mutation_p.C258R	NM_024631	NP_078907	Q6P1R3	CK061_HUMAN	hypothetical protein LOC79684	488											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)														---	---	---	---
STT3A	3703	broad.mit.edu	37	11	125484299	125484299	+	Silent	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:125484299C>T	uc001qcd.2	+	15	1862	c.1752C>T	c.(1750-1752)GGC>GGT	p.G584G	STT3A_uc001qce.2_Silent_p.G584G|STT3A_uc010sbg.1_Silent_p.G492G|STT3A_uc009zbn.2_Silent_p.G306G	NM_152713	NP_689926	P46977	STT3A_HUMAN	integral membrane protein 1	584	Lumenal (Potential).				post-translational protein modification|protein N-linked glycosylation via asparagine	integral to membrane|oligosaccharyltransferase complex	dolichyl-diphosphooligosaccharide-protein glycotransferase activity				0	all_hematologic(175;0.228)	Breast(109;0.0115)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.0919)|all_lung(97;0.0994)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;1.13e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0996)														---	---	---	---
PUS3	83480	broad.mit.edu	37	11	125765988	125765988	+	Silent	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:125765988G>A	uc001qcy.2	-	2	290	c.192C>T	c.(190-192)CAC>CAT	p.H64H	HYLS1_uc009zbv.2_Intron|HYLS1_uc001qcx.3_Intron	NM_031307	NP_112597	Q9BZE2	PUS3_HUMAN	pseudouridylate synthase 3	64						nucleus	RNA binding			ovary(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;1.1e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.043)														---	---	---	---
ST3GAL4	6484	broad.mit.edu	37	11	126283551	126283551	+	Intron	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:126283551C>T	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)														---	---	---	---
ARHGAP32	9743	broad.mit.edu	37	11	128843147	128843147	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:128843147T>C	uc009zcp.2	-	21	3212	c.3212A>G	c.(3211-3213)AAT>AGT	p.N1071S	ARHGAP32_uc009zcq.1_3'UTR|ARHGAP32_uc009zco.2_Missense_Mutation_p.N30S|ARHGAP32_uc001qez.2_Missense_Mutation_p.N722S	NM_001142685	NP_001136157	A7KAX9	RHG32_HUMAN	Rho GTPase-activating protein isoform 1	1071					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																		---	---	---	---
TMEM45B	120224	broad.mit.edu	37	11	129727331	129727331	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:129727331G>A	uc001qfe.1	+	5	755	c.694G>A	c.(694-696)GTC>ATC	p.V232I	TMEM45B_uc001qff.1_Missense_Mutation_p.V232I	NM_138788	NP_620143	Q96B21	TM45B_HUMAN	transmembrane protein 45B	232	Helical; (Potential).					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)														---	---	---	---
APLP2	334	broad.mit.edu	37	11	129999940	129999940	+	Missense_Mutation	SNP	G	A	A	rs144823565	byFrequency	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:129999940G>A	uc010sby.1	+	11	1620	c.1463G>A	c.(1462-1464)CGC>CAC	p.R488H	APLP2_uc001qfp.2_Missense_Mutation_p.R488H|APLP2_uc001qfq.2_Missense_Mutation_p.R432H|APLP2_uc010sbz.1_Missense_Mutation_p.R276H|APLP2_uc001qfr.2_Missense_Mutation_p.R254H|APLP2_uc001qfs.2_Missense_Mutation_p.R259H|APLP2_uc001qfv.2_Missense_Mutation_p.R379H	NM_001642	NP_001633	Q06481	APLP2_HUMAN	amyloid beta (A4) precursor-like protein 2	488	Extracellular (Potential).				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)														---	---	---	---
SNX19	399979	broad.mit.edu	37	11	130776508	130776508	+	Intron	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:130776508T>C	uc001qgk.3	-						SNX19_uc009zcw.2_Intron|SNX19_uc010sce.1_Intron|SNX19_uc010scf.1_Intron|SNX19_uc010scg.1_Intron|SNX19_uc001qgl.3_Intron|SNX19_uc009zcx.1_Intron	NM_014758	NP_055573			sorting nexin 19						cell communication|protein transport	cytoplasmic vesicle membrane	phosphatidylinositol binding|protein binding			ovary(2)|lung(2)	4	all_hematologic(175;0.0597)	Lung NSC(97;0.000272)|all_lung(97;0.000608)|Breast(109;0.000962)|all_neural(223;0.0298)|Medulloblastoma(222;0.0425)		OV - Ovarian serous cystadenocarcinoma(99;0.0195)|Lung(977;0.233)														---	---	---	---
OPCML	4978	broad.mit.edu	37	11	132527047	132527047	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:132527047G>A	uc001qgs.2	-	2	385	c.335C>T	c.(334-336)CCG>CTG	p.P112L	OPCML_uc001qgu.2_Missense_Mutation_p.P105L|OPCML_uc010sck.1_Missense_Mutation_p.P112L|OPCML_uc001qgt.2_Missense_Mutation_p.P112L|OPCML_uc010scl.1_Missense_Mutation_p.P71L	NM_002545	NP_002536	Q14982	OPCM_HUMAN	opioid binding protein/cell adhesion	112	Ig-like C2-type 1.				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)														---	---	---	---
IGSF9B	22997	broad.mit.edu	37	11	133794713	133794713	+	Splice_Site	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:133794713A>G	uc001qgx.3	-	15	2350	c.2119_splice	c.e15+1	p.D707_splice	IGSF9B_uc001qgy.1_Splice_Site_p.D549_splice	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)														---	---	---	---
GLB1L2	89944	broad.mit.edu	37	11	134238551	134238551	+	Silent	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:134238551C>T	uc001qhp.2	+	10	1091	c.903C>T	c.(901-903)ACC>ACT	p.T301T	GLB1L2_uc009zdg.1_RNA	NM_138342	NP_612351	Q8IW92	GLBL2_HUMAN	galactosidase, beta 1-like 2 precursor	301					carbohydrate metabolic process	extracellular region	cation binding|hydrolase activity, hydrolyzing O-glycosyl compounds			ovary(1)|pancreas(1)|skin(1)	3	all_hematologic(175;0.127)	all_cancers(12;2.85e-18)|all_epithelial(12;1.21e-12)|all_lung(97;0.000276)|Lung NSC(97;0.000518)|Breast(109;0.00122)|Medulloblastoma(222;0.0399)|all_neural(223;0.0412)|Esophageal squamous(93;0.0844)		Epithelial(10;1.37e-11)|all cancers(11;2.2e-10)|BRCA - Breast invasive adenocarcinoma(10;3.09e-10)|OV - Ovarian serous cystadenocarcinoma(99;0.000885)|Lung(977;0.223)														---	---	---	---
KDM5A	5927	broad.mit.edu	37	12	432867	432867	+	Silent	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:432867A>G	uc001qif.1	-	15	2412	c.2049T>C	c.(2047-2049)TGT>TGC	p.C683C	KDM5A_uc001qie.1_Silent_p.C683C|KDM5A_uc010sdn.1_Silent_p.C642C|KDM5A_uc010sdo.1_Silent_p.C302C	NM_001042603	NP_001036068	P29375	KDM5A_HUMAN	retinoblastoma binding protein 2 isoform 1	683					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								---	---	---	---
CACNA2D4	93589	broad.mit.edu	37	12	2017137	2017137	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:2017137C>T	uc001qjp.2	-	5	784	c.553G>A	c.(553-555)GCC>ACC	p.A185T	CACNA2D4_uc009zds.1_RNA|CACNA2D4_uc009zdt.1_Missense_Mutation_p.A185T	NM_172364	NP_758952	Q7Z3S7	CA2D4_HUMAN	voltage-gated calcium channel alpha(2)delta-4	185	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)														---	---	---	---
KCNA5	3741	broad.mit.edu	37	12	5154042	5154042	+	Silent	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:5154042G>A	uc001qni.2	+	1	958	c.729G>A	c.(727-729)CCG>CCA	p.P243P		NM_002234	NP_002225	P22460	KCNA5_HUMAN	potassium voltage-gated channel, shaker-related	243						Golgi apparatus|voltage-gated potassium channel complex	delayed rectifier potassium channel activity			ovary(2)|breast(2)	4																		---	---	---	---
NTF3	4908	broad.mit.edu	37	12	5541481	5541481	+	5'UTR	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:5541481C>T	uc001qnk.3	+	1						NM_001102654	NP_001096124			neurotrophin 3 isoform 1 preproprotein						signal transduction	extracellular region	growth factor activity|neurotrophin receptor binding			pancreas(1)	1																		---	---	---	---
VWF	7450	broad.mit.edu	37	12	6128047	6128047	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:6128047C>T	uc001qnn.1	-	28	4787	c.4537G>A	c.(4537-4539)GAC>AAC	p.D1513N	VWF_uc010set.1_Intron	NM_000552	NP_000543	P04275	VWF_HUMAN	von Willebrand factor preproprotein	1513	VWFA 2.				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	6182857	6182857	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:6182857C>T	uc001qnn.1	-	8	1175	c.925G>A	c.(925-927)GCC>ACC	p.A309T	VWF_uc010set.1_Missense_Mutation_p.A309T	NM_000552	NP_000543	P04275	VWF_HUMAN	von Willebrand factor preproprotein	309	TIL 1.				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)													---	---	---	---
IFFO1	25900	broad.mit.edu	37	12	6664512	6664512	+	Silent	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:6664512G>A	uc001qpd.1	-	1	718	c.684C>T	c.(682-684)GGC>GGT	p.G228G	IFFO1_uc001qpe.1_RNA|IFFO1_uc010sfe.1_Silent_p.G228G|IFFO1_uc001qpf.1_Silent_p.G228G|IFFO1_uc001qpc.1_Silent_p.G228G	NM_080730	NP_542768	Q0D2I5	IFFO1_HUMAN	intermediate filament family orphan isoform 2	228						intermediate filament					0																		---	---	---	---
CD4	920	broad.mit.edu	37	12	6927642	6927642	+	Silent	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:6927642C>T	uc001qqv.1	+	8	1457	c.1212C>T	c.(1210-1212)GGC>GGT	p.G404G	CD4_uc010sfj.1_Silent_p.G131G|CD4_uc009zfc.1_Silent_p.G225G|CD4_uc010sfk.1_Silent_p.G131G|CD4_uc010sfl.1_Silent_p.G131G|CD4_uc010sfm.1_Silent_p.G131G	NM_000616	NP_000607	P01730	CD4_HUMAN	CD4 antigen precursor	404	Helical; (Potential).				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)																---	---	---	---
ATN1	1822	broad.mit.edu	37	12	7046020	7046020	+	Silent	SNP	C	T	T	rs140073846		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:7046020C>T	uc001qrw.1	+	5	1827	c.1590C>T	c.(1588-1590)TAC>TAT	p.Y530Y	ATN1_uc001qrx.1_Silent_p.Y530Y	NM_001007026	NP_001007027	P54259	ATN1_HUMAN	atrophin-1	530	Involved in binding BAIAP2.				cell death|central nervous system development	cytoplasm|nucleus	protein domain specific binding			ovary(2)|breast(2)|pancreas(1)|skin(1)	6																		---	---	---	---
ATN1	1822	broad.mit.edu	37	12	7046098	7046098	+	Silent	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:7046098G>A	uc001qrw.1	+	5	1905	c.1668G>A	c.(1666-1668)GTG>GTA	p.V556V	ATN1_uc001qrx.1_Silent_p.V556V	NM_001007026	NP_001007027	P54259	ATN1_HUMAN	atrophin-1	556	Involved in binding BAIAP2.				cell death|central nervous system development	cytoplasm|nucleus	protein domain specific binding			ovary(2)|breast(2)|pancreas(1)|skin(1)	6																		---	---	---	---
C1S	716	broad.mit.edu	37	12	7172560	7172560	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:7172560T>C	uc001qsj.2	+	9	1393	c.674T>C	c.(673-675)GTG>GCG	p.V225A	C1S_uc001qsk.2_Missense_Mutation_p.V225A|C1S_uc001qsl.2_Missense_Mutation_p.V225A|C1S_uc009zfr.2_Missense_Mutation_p.V58A|C1S_uc009zfs.2_RNA	NM_201442	NP_958850	P09871	C1S_HUMAN	complement component 1, s subcomponent	225	CUB 2.				complement activation, classical pathway|innate immune response|proteolysis	extracellular region	calcium ion binding|serine-type endopeptidase activity			skin(1)	1					Abciximab(DB00054)|Adalimumab(DB00051)|Basiliximab(DB00074)|Cetuximab(DB00002)|Etanercept(DB00005)|Gemtuzumab ozogamicin(DB00056)|Ibritumomab(DB00078)|Immune globulin(DB00028)|Muromonab(DB00075)|Rituximab(DB00073)|Trastuzumab(DB00072)													---	---	---	---
ACSM4	341392	broad.mit.edu	37	12	7469878	7469878	+	Splice_Site	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:7469878T>C	uc001qsx.1	+	4	764	c.764_splice	c.e4+2	p.R255_splice		NM_001080454	NP_001073923			acyl-CoA synthetase medium-chain family member 4						fatty acid metabolic process	mitochondrial matrix	ATP binding|butyrate-CoA ligase activity|metal ion binding				0																		---	---	---	---
M6PR	4074	broad.mit.edu	37	12	9098067	9098067	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:9098067T>C	uc001qvf.2	-	3	460	c.290A>G	c.(289-291)AAT>AGT	p.N97S		NM_002355	NP_002346	P20645	MPRD_HUMAN	cation-dependent mannose-6-phosphate receptor	97	Lumenal (Potential).				endosome to lysosome transport|receptor-mediated endocytosis	cell surface|endosome|integral to plasma membrane|lysosomal membrane	mannose binding|mannose transmembrane transporter activity|transmembrane receptor activity				0		Hepatocellular(102;0.137)		BRCA - Breast invasive adenocarcinoma(232;0.0146)														---	---	---	---
A2M	2	broad.mit.edu	37	12	9223083	9223083	+	Splice_Site	SNP	C	G	G	rs111851042		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:9223083C>G	uc001qvk.1	-	32	4307	c.4194_splice	c.e32+1	p.M1398_splice	A2M_uc001qvj.1_Splice_Site_p.M440_splice|A2M_uc009zgk.1_Splice_Site_p.M1248_splice	NM_000014	NP_000005			alpha-2-macroglobulin precursor						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)													---	---	---	---
PZP	5858	broad.mit.edu	37	12	9318692	9318692	+	Silent	SNP	T	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:9318692T>A	uc001qvl.2	-	18	2243	c.2214A>T	c.(2212-2214)CGA>CGT	p.R738R	PZP_uc009zgl.2_Silent_p.R607R|PZP_uc010sgo.1_RNA|PZP_uc009zgm.1_Silent_p.R70R	NM_002864	NP_002855			pregnancy-zone protein precursor											ovary(3)|upper_aerodigestive_tract(1)|large_intestine(1)	5																		---	---	---	---
OLR1	4973	broad.mit.edu	37	12	10321685	10321685	+	Silent	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:10321685G>A	uc001qxo.1	-	2	280	c.166C>T	c.(166-168)CTG>TTG	p.L56L	OLR1_uc010sgz.1_5'Flank|OLR1_uc010sha.1_Silent_p.L56L	NM_002543	NP_002534	P78380	OLR1_HUMAN	oxidized low density lipoprotein (lectin-like)	56	Helical; Signal-anchor for type II membrane protein; (Potential).				blood circulation|blood coagulation|inflammatory response|leukocyte migration|proteolysis	extracellular region|integral to plasma membrane|membrane fraction	sugar binding			ovary(1)	1																		---	---	---	---
PRR4	11272	broad.mit.edu	37	12	11001963	11001963	+	Intron	SNP	A	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:11001963A>T	uc001qyz.3	-						PRR4_uc009zhp.2_Intron|PRH1_uc001qzb.3_Intron|PRR4_uc001qza.3_Intron|PRR4_uc009zhq.1_Intron	NM_007244	NP_009175			proline rich 4 (lacrimal) isoform 2						visual perception	extracellular space					0																		---	---	---	---
TAS2R50	259296	broad.mit.edu	37	12	11139175	11139175	+	Silent	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:11139175G>A	uc001qzl.2	-	1	337	c.285C>T	c.(283-285)AGC>AGT	p.S95S	PRR4_uc009zhp.2_Intron|PRH1_uc001qzb.3_Intron|PRH1_uc001qzc.2_Intron|PRB4_uc001qzf.1_Intron|PRH1_uc001qzj.2_Intron	NM_176890	NP_795371	P59544	T2R50_HUMAN	taste receptor, type 2, member 50	95	Helical; Name=3; (Potential).				sensory perception of taste	integral to membrane	G-protein coupled receptor activity			ovary(2)	2																		---	---	---	---
TAS2R46	259292	broad.mit.edu	37	12	11214068	11214068	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:11214068G>T	uc001qzp.1	-	1	826	c.826C>A	c.(826-828)CCA>ACA	p.P276T	PRR4_uc009zhp.2_Intron|PRH1_uc001qzb.3_Intron|PRH1_uc001qzc.2_Intron|PRB4_uc001qzf.1_Intron|PRH1_uc001qzj.2_Intron	NM_176887	NP_795368	P59540	T2R46_HUMAN	taste receptor, type 2, member 46	276	Helical; Name=7; (Potential).				sensory perception of taste	cilium membrane|integral to membrane	G-protein coupled receptor activity			ovary(1)	1			OV - Ovarian serous cystadenocarcinoma(49;0.0344)	BRCA - Breast invasive adenocarcinoma(232;0.196)														---	---	---	---
PRB3	5544	broad.mit.edu	37	12	11420257	11420257	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:11420257G>T	uc001qzs.2	-	4	837	c.799C>A	c.(799-801)CAA>AAA	p.Q267K	PRB4_uc001qzf.1_Intron	NM_006249	NP_006240	Q04118	PRB3_HUMAN	proline-rich protein BstNI subfamily 3	267	Pro-rich.					extracellular region	Gram-negative bacterial cell surface binding			skin(1)	1			OV - Ovarian serous cystadenocarcinoma(49;0.201)															---	---	---	---
BCL2L14	79370	broad.mit.edu	37	12	12232553	12232553	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:12232553C>T	uc001rac.2	+	2	515	c.314C>T	c.(313-315)TCG>TTG	p.S105L	ETV6_uc001raa.1_Intron|BCL2L14_uc001raf.1_RNA|BCL2L14_uc001rad.2_Missense_Mutation_p.S105L|BCL2L14_uc001rae.2_Missense_Mutation_p.S105L	NM_138723	NP_620049	Q9BZR8	B2L14_HUMAN	BCL2-like 14 isoform 1	105					apoptosis|regulation of apoptosis	cytosol|endomembrane system|intracellular organelle|membrane	protein binding			skin(1)	1		Prostate(47;0.0872)		BRCA - Breast invasive adenocarcinoma(232;0.154)														---	---	---	---
LRP6	4040	broad.mit.edu	37	12	12279734	12279734	+	Silent	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:12279734A>G	uc001rah.3	-	20	4345	c.4203T>C	c.(4201-4203)CGT>CGC	p.R1401R	BCL2L14_uc001raf.1_Intron|LRP6_uc010shl.1_Silent_p.R1356R	NM_002336	NP_002327	O75581	LRP6_HUMAN	low density lipoprotein receptor-related protein	1401	Cytoplasmic (Potential).				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)																---	---	---	---
DDX47	51202	broad.mit.edu	37	12	12975657	12975657	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:12975657G>A	uc001rav.2	+	9	1222	c.624G>A	c.(622-624)ATG>ATA	p.M208I	DDX47_uc009zhw.1_Missense_Mutation_p.M208I|DDX47_uc001rax.2_Missense_Mutation_p.M208I|DDX47_uc001ray.2_Missense_Mutation_p.M208I	NM_016355	NP_057439	Q9H0S4	DDX47_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 47	208	Helicase ATP-binding.					nucleolus|nucleolus	ATP binding|ATP-dependent helicase activity|protein binding|RNA binding				0		Prostate(47;0.0526)		BRCA - Breast invasive adenocarcinoma(232;0.0354)														---	---	---	---
HEBP1	50865	broad.mit.edu	37	12	13140152	13140152	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:13140152T>C	uc001rbd.2	-	3	505	c.332A>G	c.(331-333)GAC>GGC	p.D111G	HEBP1_uc001rbf.2_Missense_Mutation_p.D111G	NM_015987	NP_057071	Q9NRV9	HEBP1_HUMAN	heme binding protein 1	111					circadian rhythm	extracellular region				breast(1)	1		Prostate(47;0.183)		BRCA - Breast invasive adenocarcinoma(232;0.153)														---	---	---	---
GRIN2B	2904	broad.mit.edu	37	12	13716636	13716636	+	Missense_Mutation	SNP	A	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:13716636A>T	uc001rbt.2	-	13	3715	c.3536T>A	c.(3535-3537)ATC>AAC	p.I1179N		NM_000834	NP_000825	Q13224	NMDE2_HUMAN	N-methyl-D-aspartate receptor subunit 2B	1179	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	13724803	13724803	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:13724803C>T	uc001rbt.2	-	10	2285	c.2106G>A	c.(2104-2106)ATG>ATA	p.M702I		NM_000834	NP_000825	Q13224	NMDE2_HUMAN	N-methyl-D-aspartate receptor subunit 2B	702	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)													---	---	---	---
PDE3A	5139	broad.mit.edu	37	12	20807149	20807149	+	Intron	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:20807149A>G	uc001reh.1	+							NM_000921	NP_000912			phosphodiesterase 3A						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)													---	---	---	---
ABCC9	10060	broad.mit.edu	37	12	21960379	21960379	+	Silent	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:21960379G>A	uc001rfi.1	-	36	4370	c.4350C>T	c.(4348-4350)AGC>AGT	p.S1450S	ABCC9_uc001rfh.2_Silent_p.S1450S|ABCC9_uc001rfj.1_Silent_p.S1414S|ABCC9_uc001rfg.2_5'UTR	NM_005691	NP_005682	O60706	ABCC9_HUMAN	ATP-binding cassette, sub-family C, member 9	1450	Cytoplasmic (Potential).|ABC transporter 2.				defense response to virus|potassium ion import	ATP-sensitive potassium channel complex	ATP binding|ATPase activity, coupled to transmembrane movement of substances|potassium channel regulator activity|sulfonylurea receptor activity			ovary(4)|skin(2)	6					Adenosine triphosphate(DB00171)|Glibenclamide(DB01016)													---	---	---	---
ABCC9	10060	broad.mit.edu	37	12	21970196	21970196	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:21970196C>T	uc001rfi.1	-	31	3837	c.3817G>A	c.(3817-3819)GAG>AAG	p.E1273K	ABCC9_uc001rfh.2_Missense_Mutation_p.E1273K|ABCC9_uc001rfj.1_Missense_Mutation_p.E1237K	NM_005691	NP_005682	O60706	ABCC9_HUMAN	ATP-binding cassette, sub-family C, member 9	1273	Cytoplasmic (Potential).|ABC transmembrane type-1 2.				defense response to virus|potassium ion import	ATP-sensitive potassium channel complex	ATP binding|ATPase activity, coupled to transmembrane movement of substances|potassium channel regulator activity|sulfonylurea receptor activity			ovary(4)|skin(2)	6					Adenosine triphosphate(DB00171)|Glibenclamide(DB01016)													---	---	---	---
ABCC9	10060	broad.mit.edu	37	12	21997762	21997762	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:21997762G>A	uc001rfi.1	-	25	3204	c.3184C>T	c.(3184-3186)CTC>TTC	p.L1062F	ABCC9_uc001rfh.2_Missense_Mutation_p.L1062F|ABCC9_uc001rfj.1_Missense_Mutation_p.L1026F	NM_005691	NP_005682	O60706	ABCC9_HUMAN	ATP-binding cassette, sub-family C, member 9	1062	ABC transmembrane type-1 2.|Cytoplasmic (Potential).				defense response to virus|potassium ion import	ATP-sensitive potassium channel complex	ATP binding|ATPase activity, coupled to transmembrane movement of substances|potassium channel regulator activity|sulfonylurea receptor activity			ovary(4)|skin(2)	6					Adenosine triphosphate(DB00171)|Glibenclamide(DB01016)													---	---	---	---
KRAS	3845	broad.mit.edu	37	12	25362833	25362833	+	3'UTR	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:25362833C>T	uc001rgp.1	-	6					KRAS_uc001rgq.1_Missense_Mutation_p.A155T	NM_033360	NP_203524			c-K-ras2 protein isoform a precursor						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			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)				119	Mis		pancreatic|colorectal|lung|thyroid|AML|others				Cardiofaciocutaneous_syndrome|Noonan_syndrome	TSP Lung(1;<1E-08)|Multiple Myeloma(2;<1E-6)			---	---	---	---
KRAS	3845	broad.mit.edu	37	12	25378603	25378603	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:25378603T>C	uc001rgp.1	-	4	576	c.395A>G	c.(394-396)GAC>GGC	p.D132G	KRAS_uc001rgq.1_Missense_Mutation_p.D132G	NM_033360	NP_203524	P01116	RASK_HUMAN	c-K-ras2 protein isoform a precursor	132					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			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)				119	Mis		pancreatic|colorectal|lung|thyroid|AML|others				Cardiofaciocutaneous_syndrome|Noonan_syndrome	TSP Lung(1;<1E-08)|Multiple Myeloma(2;<1E-6)			---	---	---	---
STK38L	23012	broad.mit.edu	37	12	27472310	27472310	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:27472310A>G	uc001rhr.2	+	12	1328	c.1129A>G	c.(1129-1131)ATA>GTA	p.I377V	STK38L_uc001rhs.2_RNA|STK38L_uc010sjm.1_Missense_Mutation_p.I284V|STK38L_uc010sjn.1_Missense_Mutation_p.I115V|STK38L_uc010sjo.1_Missense_Mutation_p.I42V	NM_015000	NP_055815	Q9Y2H1	ST38L_HUMAN	serine/threonine kinase 38 like	377	Protein kinase.				intracellular protein kinase cascade|regulation of cellular component organization	actin cytoskeleton|cytoplasm	actin binding|ATP binding|magnesium ion binding|protein serine/threonine kinase activity			ovary(2)|haematopoietic_and_lymphoid_tissue(1)|lung(1)|kidney(1)	5	Colorectal(261;0.0847)																	---	---	---	---
CCDC91	55297	broad.mit.edu	37	12	28544293	28544293	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:28544293T>G	uc001riq.2	+	7	727	c.711T>G	c.(709-711)ATT>ATG	p.I237M	CCDC91_uc001rio.2_Missense_Mutation_p.I207M|CCDC91_uc009zjk.2_RNA|CCDC91_uc001rip.1_Missense_Mutation_p.I237M|CCDC91_uc001rir.2_Missense_Mutation_p.I75M|CCDC91_uc009zjl.2_Intron	NM_018318	NP_060788	Q7Z6B0	CCD91_HUMAN	GGA binding partner	237	Homodimerization.				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)																	---	---	---	---
TMTC1	83857	broad.mit.edu	37	12	29709910	29709910	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:29709910G>A	uc001rjb.2	-	10	1706	c.1232C>T	c.(1231-1233)GCG>GTG	p.A411V	TMTC1_uc001riz.2_Missense_Mutation_p.A168V|TMTC1_uc001rja.2_Missense_Mutation_p.A255V|TMTC1_uc001rjc.1_Missense_Mutation_p.A473V	NM_175861	NP_787057	Q8IUR5	TMTC1_HUMAN	transmembrane and tetratricopeptide repeat	519	TPR 2.					integral to membrane	binding				0	Lung NSC(12;7.61e-10)|Acute lymphoblastic leukemia(23;0.0122)|all_hematologic(23;0.032)																	---	---	---	---
IPO8	10526	broad.mit.edu	37	12	30815376	30815376	+	Missense_Mutation	SNP	A	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:30815376A>C	uc001rjd.2	-	15	1810	c.1640T>G	c.(1639-1641)CTG>CGG	p.L547R	IPO8_uc001rje.1_Missense_Mutation_p.L36R|IPO8_uc010sjt.1_Missense_Mutation_p.L342R	NM_006390	NP_006381	O15397	IPO8_HUMAN	importin 8	547					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)																	---	---	---	---
TSPAN11	441631	broad.mit.edu	37	12	31116840	31116840	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:31116840G>A	uc010sju.1	+	3	544	c.164G>A	c.(163-165)AGC>AAC	p.S55N	TSPAN11_uc001rjp.2_Missense_Mutation_p.S55N|TSPAN11_uc010sjv.1_Missense_Mutation_p.S45N	NM_001080509	NP_001073978	A1L157	TSN11_HUMAN	tetraspanin 11	55						integral to membrane					0	all_lung(12;3.11e-10)|Lung NSC(12;5.24e-08)|Acute lymphoblastic leukemia(23;0.0122)|all_hematologic(23;0.0429)|Lung SC(12;0.0592)|Esophageal squamous(101;0.233)																	---	---	---	---
C12orf35	55196	broad.mit.edu	37	12	32137042	32137042	+	Silent	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:32137042A>G	uc001rks.2	+	4	3567	c.3153A>G	c.(3151-3153)CTA>CTG	p.L1051L		NM_018169	NP_060639	Q9HCM1	CL035_HUMAN	hypothetical protein LOC55196	1051										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	33021955	33021955	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:33021955A>G	uc001rlj.3	-	4	1191	c.1076T>C	c.(1075-1077)ATG>ACG	p.M359T	PKP2_uc001rlk.3_Missense_Mutation_p.M359T|PKP2_uc010skj.1_Missense_Mutation_p.M359T	NM_004572	NP_004563	Q99959	PKP2_HUMAN	plakophilin 2 isoform 2b	359	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)																	---	---	---	---
ALG10B	144245	broad.mit.edu	37	12	38710828	38710828	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:38710828G>A	uc001rln.3	+	1	272	c.133G>A	c.(133-135)GCG>ACG	p.A45T	ALG10B_uc001rlo.3_5'UTR|ALG10B_uc010skk.1_5'UTR	NM_001013620	NP_001013642	Q5I7T1	AG10B_HUMAN	asparagine-linked glycosylation 10 homolog B	45	Extracellular (Potential).				dolichol-linked oligosaccharide biosynthetic process|post-translational protein modification|protein N-linked glycosylation via asparagine	endoplasmic reticulum membrane|integral to membrane|plasma membrane	dolichyl-phosphate-glucose-glycolipid alpha-glucosyltransferase activity			ovary(2)|skin(1)	3	Esophageal squamous(101;0.187)	Lung NSC(34;0.204)|all_lung(34;0.235)																---	---	---	---
C12orf40	283461	broad.mit.edu	37	12	40040214	40040214	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:40040214T>C	uc001rmc.2	+	4	453	c.286T>C	c.(286-288)TCG>CCG	p.S96P	C12orf40_uc009zjv.1_RNA	NM_001031748	NP_001026918	Q86WS4	CL040_HUMAN	hypothetical protein LOC283461	96										ovary(6)	6																		---	---	---	---
C12orf40	283461	broad.mit.edu	37	12	40077227	40077227	+	Silent	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:40077227A>G	uc001rmc.2	+	9	1394	c.1227A>G	c.(1225-1227)GAA>GAG	p.E409E	C12orf40_uc009zjv.1_RNA	NM_001031748	NP_001026918	Q86WS4	CL040_HUMAN	hypothetical protein LOC283461	409										ovary(6)	6																		---	---	---	---
SLC2A13	114134	broad.mit.edu	37	12	40158575	40158575	+	Missense_Mutation	SNP	G	T	T	rs138801535		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:40158575G>T	uc010skm.1	-	8	1582	c.1531C>A	c.(1531-1533)CTG>ATG	p.L511M	C12orf40_uc009zjv.1_RNA	NM_052885	NP_443117	Q96QE2	MYCT_HUMAN	solute carrier family 2 (facilitated glucose	511	Helical; Name=10; (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)			---	---	---	---
ADAMTS20	80070	broad.mit.edu	37	12	43777417	43777417	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:43777417T>C	uc010skx.1	-	31	4741	c.4741A>G	c.(4741-4743)AAG>GAG	p.K1581E		NM_025003	NP_079279	P59510	ATS20_HUMAN	a disintegrin-like and metalloprotease with	1581	TSP type-1 13.					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	44693379	44693379	+	Silent	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:44693379C>T	uc001rod.2	+	6	691	c.625C>T	c.(625-627)CTG>TTG	p.L209L	TMEM117_uc001roe.2_Silent_p.L105L|TMEM117_uc009zkc.2_Silent_p.L209L	NM_032256	NP_115632	Q9H0C3	TM117_HUMAN	transmembrane protein 117	209	Helical; (Potential).					endoplasmic reticulum|integral to membrane					0	Lung SC(27;0.192)			GBM - Glioblastoma multiforme(48;0.124)														---	---	---	---
ANO6	196527	broad.mit.edu	37	12	45815023	45815023	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:45815023C>T	uc001roo.2	+	18	2722	c.2387C>T	c.(2386-2388)CCG>CTG	p.P796L	ANO6_uc010sld.1_Missense_Mutation_p.P796L|ANO6_uc010sle.1_Missense_Mutation_p.P796L|ANO6_uc010slf.1_Missense_Mutation_p.P817L|ANO6_uc010slg.1_Missense_Mutation_p.P778L	NM_001025356	NP_001020527	Q4KMQ2	ANO6_HUMAN	anoctamin 6 isoform a	796	Extracellular (Potential).				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																		---	---	---	---
ARID2	196528	broad.mit.edu	37	12	46246297	46246297	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:46246297G>A	uc001ros.1	+	15	4391	c.4391G>A	c.(4390-4392)CGC>CAC	p.R1464H	ARID2_uc001ror.2_Missense_Mutation_p.R1464H|ARID2_uc009zkg.1_Missense_Mutation_p.R920H|ARID2_uc009zkh.1_Missense_Mutation_p.R1091H|ARID2_uc001rou.1_Missense_Mutation_p.R798H	NM_152641	NP_689854	Q68CP9	ARID2_HUMAN	AT rich interactive domain 2 (ARID, RFX-like)	1464					chromatin modification|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|protein binding|zinc ion binding			ovary(6)|skin(3)|upper_aerodigestive_tract(1)	10	Lung SC(27;0.192)|Renal(347;0.236)	Lung NSC(34;0.106)|all_lung(34;0.22)	OV - Ovarian serous cystadenocarcinoma(5;0.00691)	GBM - Glioblastoma multiforme(48;0.0153)														---	---	---	---
SLC38A1	81539	broad.mit.edu	37	12	46591733	46591733	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:46591733T>C	uc001rpa.2	-	15	1491	c.1233A>G	c.(1231-1233)ATA>ATG	p.I411M	SLC38A1_uc001rpb.2_Missense_Mutation_p.I411M|SLC38A1_uc001rpc.2_Missense_Mutation_p.I411M|SLC38A1_uc001rpd.2_Missense_Mutation_p.I411M|SLC38A1_uc001rpe.2_Missense_Mutation_p.I411M|SLC38A1_uc009zkj.1_Missense_Mutation_p.I411M	NM_030674	NP_109599	Q9H2H9	S38A1_HUMAN	amino acid transporter system A1	411	Helical; (Potential).				cellular nitrogen compound metabolic process|neurotransmitter uptake	integral to membrane|plasma membrane	sodium:amino acid symporter activity			ovary(2)|skin(2)|central_nervous_system(1)	5	Lung SC(27;0.137)|Renal(347;0.236)		all cancers(1;0.00805)|OV - Ovarian serous cystadenocarcinoma(5;0.0106)|Epithelial(2;0.0344)															---	---	---	---
SLC38A1	81539	broad.mit.edu	37	12	46592460	46592460	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:46592460C>T	uc001rpa.2	-	14	1328	c.1070G>A	c.(1069-1071)CGG>CAG	p.R357Q	SLC38A1_uc001rpb.2_Missense_Mutation_p.R357Q|SLC38A1_uc001rpc.2_Missense_Mutation_p.R357Q|SLC38A1_uc001rpd.2_Missense_Mutation_p.R357Q|SLC38A1_uc001rpe.2_Missense_Mutation_p.R357Q|SLC38A1_uc009zkj.1_Missense_Mutation_p.R357Q	NM_030674	NP_109599	Q9H2H9	S38A1_HUMAN	amino acid transporter system A1	357	Helical; (Potential).				cellular nitrogen compound metabolic process|neurotransmitter uptake	integral to membrane|plasma membrane	sodium:amino acid symporter activity			ovary(2)|skin(2)|central_nervous_system(1)	5	Lung SC(27;0.137)|Renal(347;0.236)		all cancers(1;0.00805)|OV - Ovarian serous cystadenocarcinoma(5;0.0106)|Epithelial(2;0.0344)															---	---	---	---
SLC38A1	81539	broad.mit.edu	37	12	46622973	46622973	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:46622973C>T	uc001rpa.2	-	5	535	c.277G>A	c.(277-279)GCC>ACC	p.A93T	SLC38A1_uc001rpb.2_Missense_Mutation_p.A93T|SLC38A1_uc001rpc.2_Missense_Mutation_p.A93T|SLC38A1_uc001rpd.2_Missense_Mutation_p.A93T|SLC38A1_uc001rpe.2_Missense_Mutation_p.A93T|SLC38A1_uc010slh.1_Missense_Mutation_p.A66T|SLC38A1_uc009zkj.1_Missense_Mutation_p.A93T	NM_030674	NP_109599	Q9H2H9	S38A1_HUMAN	amino acid transporter system A1	93	Helical; (Potential).				cellular nitrogen compound metabolic process|neurotransmitter uptake	integral to membrane|plasma membrane	sodium:amino acid symporter activity			ovary(2)|skin(2)|central_nervous_system(1)	5	Lung SC(27;0.137)|Renal(347;0.236)		all cancers(1;0.00805)|OV - Ovarian serous cystadenocarcinoma(5;0.0106)|Epithelial(2;0.0344)															---	---	---	---
PFKM	5213	broad.mit.edu	37	12	48501882	48501882	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:48501882T>G	uc001rrb.1	+	3	334	c.110T>G	c.(109-111)CTC>CGC	p.L37R	SENP1_uc001rqw.2_5'Flank|SENP1_uc001rqx.2_5'Flank|SENP1_uc001rqy.2_5'Flank|SENP1_uc001rqz.2_5'Flank|SENP1_uc009zkx.2_5'Flank|PFKM_uc001rra.1_5'UTR	NM_000289	NP_000280	P08237	K6PF_HUMAN	phosphofructokinase, muscle	Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment					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																		---	---	---	---
CCNT1	904	broad.mit.edu	37	12	49086863	49086863	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:49086863G>A	uc001rse.1	-	9	2457	c.2134C>T	c.(2134-2136)CCT>TCT	p.P712S	LOC144438_uc001rsd.3_5'Flank|CCNT1_uc009zkz.1_Missense_Mutation_p.P427S	NM_001240	NP_001231	O60563	CCNT1_HUMAN	cyclin T1	712	Pro-rich.				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																		---	---	---	---
MLL2	8085	broad.mit.edu	37	12	49420661	49420661	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:49420661G>A	uc001rta.3	-	48	15088	c.15088C>T	c.(15088-15090)CGT>TGT	p.R5030C		NM_003482	NP_003473	O14686	MLL2_HUMAN	myeloid/lymphoid or mixed-lineage leukemia 2	5030					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)			---	---	---	---
MLL2	8085	broad.mit.edu	37	12	49446122	49446122	+	Silent	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:49446122G>A	uc001rta.3	-	10	1344	c.1344C>T	c.(1342-1344)CCC>CCT	p.P448P		NM_003482	NP_003473	O14686	MLL2_HUMAN	myeloid/lymphoid or mixed-lineage leukemia 2	448	15 X 5 AA repeats of S/P-P-P-E/P-E/A.|Pro-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)			---	---	---	---
NCKAP5L	57701	broad.mit.edu	37	12	50190076	50190076	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:50190076G>A	uc009zlk.2	-	8	1769	c.1567C>T	c.(1567-1569)CCT>TCT	p.P523S	NCKAP5L_uc001rvc.3_5'Flank|NCKAP5L_uc001rvb.2_Missense_Mutation_p.P116S	NM_001037806	NP_001032895	Q9HCH0	NCK5L_HUMAN	NCK-associated protein 5-like	519	Pro-rich.									central_nervous_system(1)	1																		---	---	---	---
LARP4	113251	broad.mit.edu	37	12	50855106	50855106	+	Missense_Mutation	SNP	A	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:50855106A>C	uc001rwp.1	+	11	1454	c.1310A>C	c.(1309-1311)CAG>CCG	p.Q437P	LARP4_uc001rwo.1_Missense_Mutation_p.Q443P|LARP4_uc001rwq.1_Missense_Mutation_p.Q366P|LARP4_uc001rwr.1_Intron|LARP4_uc001rws.1_Missense_Mutation_p.Q436P|LARP4_uc009zlr.1_Missense_Mutation_p.Q256P|LARP4_uc001rwt.1_Intron|LARP4_uc001rwm.2_Missense_Mutation_p.Q437P|LARP4_uc001rwn.2_Missense_Mutation_p.Q367P	NM_052879	NP_443111	Q71RC2	LARP4_HUMAN	c-Mpl binding protein isoform a	437							nucleotide binding|RNA binding			ovary(1)	1																		---	---	---	---
DIP2B	57609	broad.mit.edu	37	12	51115108	51115108	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:51115108G>T	uc001rwv.2	+	26	3251	c.3095G>T	c.(3094-3096)AGG>ATG	p.R1032M	DIP2B_uc009zlt.2_Missense_Mutation_p.R462M	NM_173602	NP_775873	Q9P265	DIP2B_HUMAN	DIP2 disco-interacting protein 2 homolog B	1032						nucleus	catalytic activity|transcription factor binding			ovary(4)|breast(1)|pancreas(1)	6																		---	---	---	---
METTL7A	25840	broad.mit.edu	37	12	51323842	51323842	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:51323842C>T	uc001rxb.2	+	2	932	c.644C>T	c.(643-645)GCC>GTC	p.A215V	METTL7A_uc010smv.1_3'UTR	NM_014033	NP_054752	Q9H8H3	MET7A_HUMAN	methyltransferase like 7A precursor	215						endoplasmic reticulum|lipid particle|membrane	methyltransferase activity				0																		---	---	---	---
SCN8A	6334	broad.mit.edu	37	12	52094994	52094994	+	Intron	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:52094994A>G	uc001ryw.2	+						SCN8A_uc010snl.1_Intron|SCN8A_uc001ryx.1_Intron|SCN8A_uc001ryz.1_Intron|SCN8A_uc001ryy.2_Intron	NM_014191	NP_055006			sodium channel, voltage gated, type VIII, alpha						axon guidance|myelination|peripheral nervous system development	cytoplasmic membrane-bounded vesicle|node of Ranvier	ATP binding|voltage-gated sodium channel activity			ovary(7)	7				BRCA - Breast invasive adenocarcinoma(357;0.181)	Lamotrigine(DB00555)													---	---	---	---
ACVR1B	91	broad.mit.edu	37	12	52370136	52370136	+	Silent	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:52370136G>A	uc001rzn.2	+	3	399	c.357G>A	c.(355-357)CCG>CCA	p.P119P	ACVR1B_uc001rzl.2_Silent_p.P119P|ACVR1B_uc001rzm.2_Silent_p.P119P|ACVR1B_uc010snn.1_Silent_p.P119P	NM_004302	NP_004293	P36896	ACV1B_HUMAN	activin A receptor, type IB isoform a precursor	119	Extracellular (Potential).				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)													---	---	---	---
ACVR1B	91	broad.mit.edu	37	12	52387816	52387816	+	Silent	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:52387816C>T	uc001rzn.2	+	9	1482	c.1440C>T	c.(1438-1440)AAC>AAT	p.N480N	ACVR1B_uc010snn.1_Silent_p.N521N	NM_004302	NP_004293	P36896	ACV1B_HUMAN	activin A receptor, type IB isoform a precursor	480	Protein kinase.|Cytoplasmic (Potential).				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)													---	---	---	---
KRT84	3890	broad.mit.edu	37	12	52779237	52779237	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:52779237G>A	uc001sah.1	-	1	181	c.133C>T	c.(133-135)CGG>TGG	p.R45W		NM_033045	NP_149034	Q9NSB2	KRT84_HUMAN	keratin, hair, basic, 4	45	Head.					keratin filament	structural constituent of epidermis			skin(1)	1	all_hematologic(5;0.12)			BRCA - Breast invasive adenocarcinoma(357;0.189)														---	---	---	---
KRT71	112802	broad.mit.edu	37	12	52946672	52946672	+	Missense_Mutation	SNP	C	T	T	rs144702886		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:52946672C>T	uc001sao.2	-	1	260	c.190G>A	c.(190-192)GGG>AGG	p.G64R		NM_033448	NP_258259	Q3SY84	K2C71_HUMAN	keratin 71	64	Head.|Gly-rich.						structural molecule activity			ovary(1)|skin(1)	2				BRCA - Breast invasive adenocarcinoma(357;0.194)														---	---	---	---
C12orf10	60314	broad.mit.edu	37	12	53700508	53700508	+	Silent	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:53700508T>C	uc001scp.3	+	6	862	c.810T>C	c.(808-810)TGT>TGC	p.C270C	C12orf10_uc009zmx.2_Silent_p.C219C|C12orf10_uc001scq.3_Silent_p.C155C	NM_021640	NP_067653	Q86UA3	Q86UA3_HUMAN	MYG1 protein precursor	270										ovary(2)	2																		---	---	---	---
C12orf10	60314	broad.mit.edu	37	12	53700841	53700841	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:53700841G>A	uc001scp.3	+	7	1091	c.1039G>A	c.(1039-1041)GGC>AGC	p.G347S	C12orf10_uc009zmx.2_Missense_Mutation_p.G296S|C12orf10_uc001scq.3_Missense_Mutation_p.G232S	NM_021640	NP_067653	Q86UA3	Q86UA3_HUMAN	MYG1 protein precursor	347										ovary(2)	2																		---	---	---	---
ATF7	11016	broad.mit.edu	37	12	53910963	53910963	+	Silent	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:53910963C>T	uc001sdy.2	-	11	1464	c.1443G>A	c.(1441-1443)TCG>TCA	p.S481S	ATF7_uc010sok.1_RNA|ATF7_uc001sdz.2_Silent_p.S470S|ATF7_uc010sol.1_Silent_p.S449S|uc001sdx.2_RNA	NM_001130059	NP_001123531	P17544	ATF7_HUMAN	activating transcription factor 7 isoform 1	481	Essential for binding adenovirus 2 E1A.				interspecies interaction between organisms	cytoplasm|nuclear periphery|nucleoplasm	protein dimerization activity|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(1)|lung(1)	2																		---	---	---	---
HOXC6	3223	broad.mit.edu	37	12	54422562	54422562	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:54422562A>G	uc001sev.2	+	1	369	c.257A>G	c.(256-258)AAC>AGC	p.N86S	HOXC6_uc001ses.2_Missense_Mutation_p.N4S|HOXC5_uc001set.2_Intron|HOXC4_uc001seu.2_Intron	NM_004503	NP_004494	P09630	HXC6_HUMAN	homeobox C6 isoform 1	86					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																		---	---	---	---
HOXC5	3222	broad.mit.edu	37	12	54428092	54428092	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:54428092A>G	uc001sew.2	+	2	560	c.485A>G	c.(484-486)TAC>TGC	p.Y162C	HOXC5_uc001set.2_RNA|HOXC4_uc001seu.2_Intron	NM_018953	NP_061826	Q00444	HXC5_HUMAN	homeobox C5	162	Homeobox.				regulation of transcription from RNA polymerase II promoter	cell junction|nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity				0																		---	---	---	---
NEUROD4	58158	broad.mit.edu	37	12	55421190	55421190	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:55421190A>G	uc001sgp.3	+	2	1345	c.967A>G	c.(967-969)ACC>GCC	p.T323A		NM_021191	NP_067014	Q9HD90	NDF4_HUMAN	neurogenic differentiation 4	323					amacrine cell differentiation|positive regulation of cell differentiation|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding			ovary(3)|skin(1)	4																		---	---	---	---
OR10A7	121364	broad.mit.edu	37	12	55615217	55615217	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:55615217A>G	uc010spf.1	+	1	409	c.409A>G	c.(409-411)AAC>GAC	p.N137D		NM_001005280	NP_001005280	Q8NGE5	O10A7_HUMAN	olfactory receptor, family 10, subfamily A,	137	Cytoplasmic (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(4)	4																		---	---	---	---
OR6C1	390321	broad.mit.edu	37	12	55715110	55715110	+	Missense_Mutation	SNP	A	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:55715110A>C	uc010spi.1	+	1	727	c.727A>C	c.(727-729)ATG>CTG	p.M243L		NM_001005182	NP_001005182	Q96RD1	OR6C1_HUMAN	olfactory receptor, family 6, subfamily C,	243	Helical; Name=6; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			large_intestine(1)|ovary(1)	2																		---	---	---	---
OR6C2	341416	broad.mit.edu	37	12	55846437	55846437	+	Nonsense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:55846437G>A	uc001sgz.1	+	1	440	c.440G>A	c.(439-441)TGG>TAG	p.W147*		NM_054105	NP_473446	Q9NZP2	OR6C2_HUMAN	olfactory receptor, family 6, subfamily C,	147	Helical; Name=4; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			skin(2)	2																		---	---	---	---
DGKA	1606	broad.mit.edu	37	12	56346601	56346601	+	Silent	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:56346601C>T	uc001sij.2	+	21	2091	c.1827C>T	c.(1825-1827)TCC>TCT	p.S609S	DGKA_uc009zod.1_Silent_p.S528S|DGKA_uc001sik.2_Silent_p.S609S|DGKA_uc001sil.2_Silent_p.S609S|DGKA_uc001sim.2_Silent_p.S609S|DGKA_uc001sin.2_Silent_p.S609S|DGKA_uc009zof.2_Silent_p.S255S|DGKA_uc001sio.2_Silent_p.S351S	NM_001345	NP_001336	P23743	DGKA_HUMAN	diacylglycerol kinase, alpha 80kDa	609					activation of protein kinase C activity by G-protein coupled receptor protein signaling pathway|intracellular signal transduction|platelet activation	plasma membrane	ATP binding|calcium ion binding|diacylglycerol kinase activity			ovary(3)|pancreas(1)	4					Vitamin E(DB00163)													---	---	---	---
SILV	6490	broad.mit.edu	37	12	56355493	56355493	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:56355493C>A	uc001sip.2	-	2	131	c.100G>T	c.(100-102)GGT>TGT	p.G34C	SILV_uc001siq.2_Missense_Mutation_p.G34C|SILV_uc010spx.1_Intron|SILV_uc001sir.2_Missense_Mutation_p.G34C	NM_006928	NP_008859	P40967	PMEL_HUMAN	silver homolog	34					melanin biosynthetic process|melanosome organization	endoplasmic reticulum membrane|extracellular region|Golgi apparatus|integral to membrane|melanosome|multivesicular body membrane|plasma membrane	protein binding				0																		---	---	---	---
ERBB3	2065	broad.mit.edu	37	12	56482387	56482387	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:56482387T>C	uc001sjh.2	+	8	1128	c.935T>C	c.(934-936)GTA>GCA	p.V312A	ERBB3_uc009zoj.2_RNA|ERBB3_uc010sqb.1_Intron|ERBB3_uc010sqc.1_Missense_Mutation_p.V253A|ERBB3_uc001sji.2_Missense_Mutation_p.V3A	NM_001982	NP_001973	P21860	ERBB3_HUMAN	erbB-3 isoform 1 precursor	312	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)															---	---	---	---
PAN2	9924	broad.mit.edu	37	12	56717879	56717879	+	Silent	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:56717879G>A	uc001skx.2	-	13	2392	c.2019C>T	c.(2017-2019)ACC>ACT	p.T673T	PAN2_uc001skw.2_5'UTR|PAN2_uc001skz.2_Silent_p.T672T|PAN2_uc001sky.2_Silent_p.T673T	NM_001127460	NP_001120932	Q504Q3	PAN2_HUMAN	PAN2 polyA specific ribonuclease subunit homolog	673					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																		---	---	---	---
TIMELESS	8914	broad.mit.edu	37	12	56817581	56817581	+	Missense_Mutation	SNP	G	A	A	rs146499318		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:56817581G>A	uc001slf.2	-	16	2134	c.1966C>T	c.(1966-1968)CGG>TGG	p.R656W		NM_003920	NP_003911	Q9UNS1	TIM_HUMAN	timeless homolog	656					cell division|circadian rhythm|detection of abiotic stimulus|mitosis|morphogenesis of an epithelium|negative regulation of transcription, DNA-dependent|regulation of S phase|response to DNA damage stimulus|transcription, DNA-dependent	nuclear chromatin				ovary(5)|breast(2)|pancreas(1)	8																		---	---	---	---
MYO1A	4640	broad.mit.edu	37	12	57435017	57435017	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:57435017A>G	uc001smw.3	-	14	1463	c.1220T>C	c.(1219-1221)GTG>GCG	p.V407A	MYO1A_uc010sqz.1_Missense_Mutation_p.V245A|MYO1A_uc009zpd.2_Missense_Mutation_p.V407A	NM_005379	NP_005370	Q9UBC5	MYO1A_HUMAN	myosin IA	407	Myosin head-like.				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																		---	---	---	---
MYO1A	4640	broad.mit.edu	37	12	57437652	57437652	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:57437652G>T	uc001smw.3	-	10	1123	c.880C>A	c.(880-882)CGT>AGT	p.R294S	MYO1A_uc010sqz.1_Missense_Mutation_p.R132S|MYO1A_uc009zpd.2_Missense_Mutation_p.R294S	NM_005379	NP_005370	Q9UBC5	MYO1A_HUMAN	myosin IA	294	Myosin head-like.				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																		---	---	---	---
SHMT2	6472	broad.mit.edu	37	12	57627569	57627569	+	Silent	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:57627569G>A	uc001snf.1	+	10	1171	c.1161G>A	c.(1159-1161)CGG>CGA	p.R387R	SHMT2_uc001sng.1_Silent_p.R283R|SHMT2_uc001snh.1_Silent_p.R226R|SHMT2_uc009zpk.1_Silent_p.R377R|SHMT2_uc001sni.1_Silent_p.R366R|SHMT2_uc010srg.1_Silent_p.R396R|SHMT2_uc001snj.1_Silent_p.R291R|SHMT2_uc010srh.1_Silent_p.R366R|SHMT2_uc001snk.1_Silent_p.R291R|SHMT2_uc010sri.1_Silent_p.R366R|SHMT2_uc001snl.2_Silent_p.R291R|SHMT2_uc010srj.1_Silent_p.R42R	NM_005412	NP_005403	P34897	GLYM_HUMAN	serine hydroxymethyltransferase 2	387						microtubule cytoskeleton|mitochondrial nucleoid	glycine hydroxymethyltransferase activity|methyltransferase activity			ovary(1)|central_nervous_system(1)	2					Glycine(DB00145)|Pyridoxal Phosphate(DB00114)|Tetrahydrofolic acid(DB00116)													---	---	---	---
SHMT2	6472	broad.mit.edu	37	12	57627850	57627850	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:57627850A>G	uc001snf.1	+	11	1354	c.1344A>G	c.(1342-1344)ATA>ATG	p.I448M	SHMT2_uc001sng.1_Missense_Mutation_p.I344M|SHMT2_uc001snh.1_Missense_Mutation_p.I287M|SHMT2_uc009zpk.1_Missense_Mutation_p.I438M|SHMT2_uc001sni.1_Missense_Mutation_p.I427M|SHMT2_uc010srg.1_Missense_Mutation_p.I457M|SHMT2_uc001snj.1_Missense_Mutation_p.I352M|SHMT2_uc010srh.1_Missense_Mutation_p.I427M|SHMT2_uc001snk.1_Missense_Mutation_p.I352M|SHMT2_uc010sri.1_Missense_Mutation_p.I427M|SHMT2_uc001snl.2_Missense_Mutation_p.I352M|SHMT2_uc010srj.1_Missense_Mutation_p.I103M	NM_005412	NP_005403	P34897	GLYM_HUMAN	serine hydroxymethyltransferase 2	448						microtubule cytoskeleton|mitochondrial nucleoid	glycine hydroxymethyltransferase activity|methyltransferase activity			ovary(1)|central_nervous_system(1)	2					Glycine(DB00145)|Pyridoxal Phosphate(DB00114)|Tetrahydrofolic acid(DB00116)													---	---	---	---
GLI1	2735	broad.mit.edu	37	12	57860034	57860034	+	Silent	SNP	C	T	T	rs150321991	byFrequency	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:57860034C>T	uc001snx.2	+	8	852	c.774C>T	c.(772-774)AGC>AGT	p.S258S	GLI1_uc009zpq.2_Silent_p.S130S	NM_005269	NP_005260	P08151	GLI1_HUMAN	GLI family zinc finger 1 isoform 1	258	C2H2-type 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)															---	---	---	---
GLI1	2735	broad.mit.edu	37	12	57861782	57861782	+	Silent	SNP	G	A	A	rs146290478		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:57861782G>A	uc001snx.2	+	10	1161	c.1083G>A	c.(1081-1083)CCG>CCA	p.P361P	GLI1_uc009zpq.2_Silent_p.P233P	NM_005269	NP_005260	P08151	GLI1_HUMAN	GLI family zinc finger 1 isoform 1	361					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)															---	---	---	---
MBD6	114785	broad.mit.edu	37	12	57920864	57920864	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:57920864G>A	uc001soj.1	+	7	2160	c.1936G>A	c.(1936-1938)GGG>AGG	p.G646R	MBD6_uc001sok.1_Missense_Mutation_p.G513R|MBD6_uc001sol.1_RNA	NM_052897	NP_443129	Q96DN6	MBD6_HUMAN	methyl-CpG binding domain protein 6	646	Pro-rich.					chromosome|nucleus	chromatin binding|DNA binding			central_nervous_system(3)|ovary(1)	4																		---	---	---	---
KIF5A	3798	broad.mit.edu	37	12	57963919	57963919	+	Missense_Mutation	SNP	C	T	T	rs140917012		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:57963919C>T	uc001sor.1	+	12	1475	c.1267C>T	c.(1267-1269)CGT>TGT	p.R423C	KIF5A_uc010srr.1_Missense_Mutation_p.R334C	NM_004984	NP_004975	Q12840	KIF5A_HUMAN	kinesin family member 5A	423					blood coagulation|cell death|microtubule-based movement|synaptic transmission	cytosol|kinesin complex|membrane fraction|microtubule|perinuclear region of cytoplasm	ATP binding|microtubule motor activity			ovary(2)|skin(1)	3																		---	---	---	---
PIP4K2C	79837	broad.mit.edu	37	12	57994761	57994761	+	Silent	SNP	C	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:57994761C>A	uc001sou.2	+	8	1112	c.981C>A	c.(979-981)ACC>ACA	p.T327T	PIP4K2C_uc001sot.2_Silent_p.T327T|PIP4K2C_uc010srs.1_Silent_p.T309T|PIP4K2C_uc010srt.1_Silent_p.T279T	NM_001146258	NP_001139730	Q8TBX8	PI42C_HUMAN	phosphatidylinositol-5-phosphate 4-kinase, type	327	PIPK.					cytoplasm|membrane	1-phosphatidylinositol-5-phosphate 4-kinase activity|ATP binding|identical protein binding			central_nervous_system(2)|lung(1)	3	Melanoma(17;0.122)																	---	---	---	---
GEFT	115557	broad.mit.edu	37	12	58007142	58007142	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:58007142G>T	uc001spb.2	+	3	868	c.408G>T	c.(406-408)CAG>CAT	p.Q136H	GEFT_uc009zpy.2_Missense_Mutation_p.Q175H|GEFT_uc001soz.1_Intron|GEFT_uc001spa.2_Missense_Mutation_p.Q30H|uc001spc.2_RNA|GEFT_uc001spd.2_5'Flank	NM_182947	NP_891992	Q86VW2	ARHGP_HUMAN	RhoA/RAC/CDC42 exchange factor isoform 1	136					regulation of Rho protein signal transduction	cytosol|plasma membrane|sarcomere	Rho guanyl-nucleotide exchange factor activity				0	Melanoma(17;0.122)																	---	---	---	---
OS9	10956	broad.mit.edu	37	12	58088008	58088008	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:58088008G>A	uc001spj.2	+	1	123	c.64G>A	c.(64-66)GCA>ACA	p.A22T	OS9_uc010srx.1_Missense_Mutation_p.A22T|OS9_uc001spk.2_Missense_Mutation_p.A22T|OS9_uc001spl.2_Missense_Mutation_p.A22T|OS9_uc001spm.2_Missense_Mutation_p.A22T|OS9_uc001spn.2_Missense_Mutation_p.A22T|OS9_uc010sry.1_Missense_Mutation_p.A22T|OS9_uc010srz.1_Missense_Mutation_p.A22T	NM_006812	NP_006803	Q13438	OS9_HUMAN	osteosarcoma amplified 9, endoplasmic reticulum	22					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)															---	---	---	---
XPOT	11260	broad.mit.edu	37	12	64812808	64812808	+	Silent	SNP	C	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:64812808C>G	uc001ssb.2	+	6	849	c.423C>G	c.(421-423)CTC>CTG	p.L141L	XPOT_uc009zqm.1_Silent_p.L51L	NM_007235	NP_009166	O43592	XPOT_HUMAN	tRNA exportin	141	Necessary for interaction with Ran, nuclear localization and nuclear import.				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	64827277	64827277	+	Missense_Mutation	SNP	A	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:64827277A>T	uc001ssb.2	+	19	2772	c.2346A>T	c.(2344-2346)GAA>GAT	p.E782D		NM_007235	NP_009166	O43592	XPOT_HUMAN	tRNA exportin	782	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)														---	---	---	---
GRIP1	23426	broad.mit.edu	37	12	66786216	66786216	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:66786216T>C	uc001stk.2	-	18	2421	c.2180A>G	c.(2179-2181)GAG>GGG	p.E727G	GRIP1_uc010sta.1_Missense_Mutation_p.E671G|GRIP1_uc001stj.2_Missense_Mutation_p.E509G|GRIP1_uc001stl.1_Missense_Mutation_p.E619G|GRIP1_uc001stm.2_Missense_Mutation_p.E727G	NM_021150	NP_066973	Q9Y3R0	GRIP1_HUMAN	glutamate receptor interacting protein 1	779					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	67691189	67691189	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:67691189A>G	uc001stn.2	+	5	931	c.494A>G	c.(493-495)CAA>CGA	p.Q165R	CAND1_uc001sto.2_5'Flank	NM_018448	NP_060918	Q86VP6	CAND1_HUMAN	TIP120 protein	165	HEAT 4.				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)														---	---	---	---
CAND1	55832	broad.mit.edu	37	12	67703742	67703742	+	Silent	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:67703742A>G	uc001stn.2	+	12	3524	c.3087A>G	c.(3085-3087)ACA>ACG	p.T1029T	CAND1_uc001sto.2_Silent_p.T539T	NM_018448	NP_060918	Q86VP6	CAND1_HUMAN	TIP120 protein	1029	HEAT 24.				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)														---	---	---	---
DYRK2	8445	broad.mit.edu	37	12	68051258	68051258	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:68051258C>T	uc001str.3	+	3	973	c.571C>T	c.(571-573)CGC>TGC	p.R191C	DYRK2_uc001sts.3_Missense_Mutation_p.R118C	NM_006482	NP_006473	Q92630	DYRK2_HUMAN	dual-specificity tyrosine-(Y)-phosphorylation	191					apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|positive regulation of glycogen biosynthetic process|smoothened signaling pathway	cytoplasm|nucleus	ATP binding|magnesium ion binding|manganese ion binding|protein serine/threonine kinase activity|protein tyrosine kinase activity			ovary(2)|breast(1)|central_nervous_system(1)	4			Lung(24;6.81e-05)|LUAD - Lung adenocarcinoma(15;0.00107)|LUSC - Lung squamous cell carcinoma(43;0.196)	GBM - Glioblastoma multiforme(7;0.000573)														---	---	---	---
RAP1B	5908	broad.mit.edu	37	12	69045809	69045809	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:69045809A>G	uc001sub.2	+	4	324	c.161A>G	c.(160-162)GAA>GGA	p.E54G	RAP1B_uc010ste.1_Intron|RAP1B_uc001suc.2_Missense_Mutation_p.E54G|RAP1B_uc010stf.1_Intron|RAP1B_uc010stg.1_Intron|RAP1B_uc010sth.1_Intron|RAP1B_uc010sti.1_Missense_Mutation_p.E54G	NM_001089704	NP_001083173	P61224	RAP1B_HUMAN	SubName: Full=Ras-related protein Rap-1A; SubName: Full=cDNA FLJ75985, highly similar to Homo sapiens RAP1A, member of RAS oncogene family (RAP1A), transcript variant 2, mRNA; SubName: Full=RAP1A, member of RAS oncogene family;	54					blood coagulation|energy reserve metabolic process|regulation of establishment of cell polarity|regulation of insulin secretion	cell-cell junction|cytosol	GDP binding|GTP binding|GTPase activity|protein binding				0	Breast(13;1.24e-05)		Lung(24;0.000131)|LUAD - Lung adenocarcinoma(15;0.00107)|STAD - Stomach adenocarcinoma(21;0.00694)	GBM - Glioblastoma multiforme(7;0.000306)														---	---	---	---
YEATS4	8089	broad.mit.edu	37	12	69784036	69784036	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:69784036A>G	uc001sux.2	+	7	845	c.624A>G	c.(622-624)ATA>ATG	p.I208M		NM_006530	NP_006521	O95619	YETS4_HUMAN	glioma-amplified sequence-41	208	Interaction with MLLT10.|Potential.|Interaction with TACC1.				histone H2A acetylation|histone H4 acetylation|mitosis|positive regulation of transcription, DNA-dependent|regulation of growth	NuA4 histone acetyltransferase complex|nuclear matrix	DNA binding|protein C-terminus binding|sequence-specific DNA binding transcription factor activity|structural constituent of cytoskeleton				0	all_epithelial(5;9.25e-35)|Breast(13;9.83e-07)|Esophageal squamous(21;0.187)		Epithelial(6;6.89e-18)|BRCA - Breast invasive adenocarcinoma(5;3.14e-09)|Lung(24;9.68e-05)|LUAD - Lung adenocarcinoma(15;0.00107)|OV - Ovarian serous cystadenocarcinoma(12;0.00691)|STAD - Stomach adenocarcinoma(21;0.0151)|LUSC - Lung squamous cell carcinoma(43;0.24)|Kidney(9;0.241)															---	---	---	---
PTPRR	5801	broad.mit.edu	37	12	71078482	71078482	+	Splice_Site	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:71078482A>G	uc001swi.1	-	9	1775	c.1359_splice	c.e9+1	p.R453_splice	PTPRR_uc001swh.1_Splice_Site_p.R208_splice|PTPRR_uc009zrs.2_Splice_Site_p.R302_splice|PTPRR_uc010stq.1_Splice_Site_p.R341_splice|PTPRR_uc010str.1_Splice_Site_p.R302_splice	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)														---	---	---	---
TRHDE	29953	broad.mit.edu	37	12	72667268	72667268	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:72667268A>G	uc001sxa.2	+	1	740	c.710A>G	c.(709-711)TAC>TGC	p.Y237C	LOC283392_uc010stv.1_5'UTR	NM_013381	NP_037513	Q9UKU6	TRHDE_HUMAN	thyrotropin-releasing hormone degrading enzyme	237	Extracellular (Potential).				cell-cell signaling|proteolysis|signal transduction	integral to plasma membrane	aminopeptidase activity|metallopeptidase activity|zinc ion binding			ovary(2)|skin(1)	3																		---	---	---	---
OSBPL8	114882	broad.mit.edu	37	12	76784299	76784299	+	Missense_Mutation	SNP	A	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:76784299A>T	uc001sye.1	-	11	1548	c.1068T>A	c.(1066-1068)GAT>GAA	p.D356E	OSBPL8_uc001syf.1_Missense_Mutation_p.D314E|OSBPL8_uc001syg.1_Missense_Mutation_p.D314E|OSBPL8_uc001syh.1_Missense_Mutation_p.D331E	NM_020841	NP_065892	Q9BZF1	OSBL8_HUMAN	oxysterol-binding protein-like protein 8 isoform	356					lipid transport		lipid binding			ovary(1)	1																		---	---	---	---
OSBPL8	114882	broad.mit.edu	37	12	76791508	76791508	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:76791508A>G	uc001sye.1	-	8	1118	c.638T>C	c.(637-639)TTC>TCC	p.F213S	OSBPL8_uc001syf.1_Missense_Mutation_p.F171S|OSBPL8_uc001syg.1_Missense_Mutation_p.F171S|OSBPL8_uc001syh.1_Missense_Mutation_p.F188S	NM_020841	NP_065892	Q9BZF1	OSBL8_HUMAN	oxysterol-binding protein-like protein 8 isoform	213	PH.				lipid transport		lipid binding			ovary(1)	1																		---	---	---	---
E2F7	144455	broad.mit.edu	37	12	77417803	77417803	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:77417803C>T	uc001sym.3	-	13	2964	c.2728G>A	c.(2728-2730)GCT>ACT	p.A910T	E2F7_uc009zse.2_3'UTR	NM_203394	NP_976328	Q96AV8	E2F7_HUMAN	E2F transcription factor 7	910					cell cycle	transcription factor complex	DNA binding|identical protein binding			upper_aerodigestive_tract(1)|ovary(1)|kidney(1)	3																		---	---	---	---
NAV3	89795	broad.mit.edu	37	12	78553059	78553059	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:78553059A>G	uc001syp.2	+	23	5035	c.4862A>G	c.(4861-4863)GAA>GGA	p.E1621G	NAV3_uc001syo.2_Missense_Mutation_p.E1621G|NAV3_uc010sub.1_Missense_Mutation_p.E1107G|NAV3_uc009zsf.2_Missense_Mutation_p.E452G	NM_014903	NP_055718	Q8IVL0	NAV3_HUMAN	neuron navigator 3	1621	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	78583982	78583982	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:78583982G>A	uc001syp.2	+	34	6447	c.6274G>A	c.(6274-6276)GAC>AAC	p.D2092N	NAV3_uc001syo.2_Missense_Mutation_p.D2070N|NAV3_uc010sub.1_Missense_Mutation_p.D1549N|NAV3_uc009zsf.2_Missense_Mutation_p.D901N	NM_014903	NP_055718	Q8IVL0	NAV3_HUMAN	neuron navigator 3	2092						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	78594360	78594360	+	Nonsense_Mutation	SNP	G	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:78594360G>T	uc001syp.2	+	38	6996	c.6823G>T	c.(6823-6825)GAG>TAG	p.E2275*	NAV3_uc001syo.2_Nonsense_Mutation_p.E2253*|NAV3_uc010sub.1_Nonsense_Mutation_p.E1732*|NAV3_uc009zsf.2_Nonsense_Mutation_p.E1084*	NM_014903	NP_055718	Q8IVL0	NAV3_HUMAN	neuron navigator 3	2275						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)			---	---	---	---
C12orf29	91298	broad.mit.edu	37	12	88433914	88433914	+	Intron	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:88433914C>T	uc001tao.2	+						C12orf29_uc001tap.2_Intron|C12orf29_uc009zsk.2_Intron	NM_001009894	NP_001009894			hypothetical protein LOC91298												0																		---	---	---	---
KERA	11081	broad.mit.edu	37	12	91449339	91449339	+	Silent	SNP	G	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:91449339G>T	uc001tbl.2	-	2	1339	c.720C>A	c.(718-720)GCC>GCA	p.A240A		NM_007035	NP_008966	O60938	KERA_HUMAN	keratocan precursor	240	LRR 8.				response to stimulus|visual perception	proteinaceous extracellular matrix				skin(1)	1																		---	---	---	---
CCDC41	51134	broad.mit.edu	37	12	94706683	94706683	+	Intron	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:94706683A>G	uc001tdd.2	-						CCDC41_uc001tde.2_Intron|CCDC41_uc009zsw.1_Intron	NM_016122	NP_057206			NY-REN-58 antigen												0																		---	---	---	---
CCDC41	51134	broad.mit.edu	37	12	94806201	94806201	+	Silent	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:94806201A>G	uc001tdd.2	-	3	652	c.66T>C	c.(64-66)AGT>AGC	p.S22S	CCDC41_uc001tde.2_Silent_p.S22S|CCDC41_uc009zsw.1_RNA|CCDC41_uc001tdf.2_Silent_p.S22S	NM_016122	NP_057206	Q9Y592	CCD41_HUMAN	NY-REN-58 antigen	14											0																		---	---	---	---
NR2C1	7181	broad.mit.edu	37	12	95442919	95442919	+	Silent	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:95442919T>C	uc001tdm.3	-	9	1312	c.1056A>G	c.(1054-1056)CTA>CTG	p.L352L	NR2C1_uc010suu.1_Silent_p.L352L|NR2C1_uc001tdo.3_Silent_p.L352L|NR2C1_uc001tdn.3_Silent_p.L352L	NM_003297	NP_003288	P13056	NR2C1_HUMAN	nuclear receptor subfamily 2, group C, member 1	352					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	95485481	95485481	+	Splice_Site	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:95485481A>G	uc001tdp.3	-	17	4074	c.3850_splice	c.e17+1	p.D1284_splice	FGD6_uc009zsx.2_Splice_Site_p.D417_splice|FGD6_uc001tdq.1_Splice_Site_p.D320_splice	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																		---	---	---	---
USP44	84101	broad.mit.edu	37	12	95922612	95922612	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:95922612C>T	uc001teg.2	-	3	1739	c.1595G>A	c.(1594-1596)GGA>GAA	p.G532E	USP44_uc001teh.2_Missense_Mutation_p.G532E|USP44_uc009zte.2_Missense_Mutation_p.G529E	NM_001042403	NP_001035862	Q9H0E7	UBP44_HUMAN	ubiquitin thiolesterase 44	532					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																		---	---	---	---
CCDC38	120935	broad.mit.edu	37	12	96273433	96273433	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:96273433T>C	uc001tek.1	-	12	1365	c.1131A>G	c.(1129-1131)ATA>ATG	p.I377M		NM_182496	NP_872302	Q502W7	CCD38_HUMAN	coiled-coil domain containing 38	377										skin(1)	1																		---	---	---	---
ELK3	2004	broad.mit.edu	37	12	96653595	96653595	+	Silent	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:96653595T>C	uc001teo.1	+	4	1368	c.1089T>C	c.(1087-1089)AGT>AGC	p.S363S		NM_005230	NP_005221	P41970	ELK3_HUMAN	ELK3 protein	363					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)																	---	---	---	---
NEDD1	121441	broad.mit.edu	37	12	97339612	97339612	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:97339612C>T	uc001teu.3	+	14	2135	c.1796C>T	c.(1795-1797)ACG>ATG	p.T599M	NEDD1_uc001tev.3_Missense_Mutation_p.T599M|NEDD1_uc010svc.1_Missense_Mutation_p.T510M|NEDD1_uc001tew.2_Missense_Mutation_p.T606M|NEDD1_uc001tex.2_Missense_Mutation_p.T510M	NM_152905	NP_690869	Q8NHV4	NEDD1_HUMAN	neural precursor cell expressed, developmentally	599					cell division|G2/M transition of mitotic cell cycle|mitosis	cytosol					0																		---	---	---	---
MYBPC1	4604	broad.mit.edu	37	12	102053557	102053557	+	Missense_Mutation	SNP	T	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:102053557T>A	uc001tii.2	+	17	1902	c.1800T>A	c.(1798-1800)AAT>AAA	p.N600K	MYBPC1_uc001tig.2_Missense_Mutation_p.N625K|MYBPC1_uc010svq.1_Missense_Mutation_p.N587K|MYBPC1_uc001tih.2_Missense_Mutation_p.N625K|MYBPC1_uc001tij.2_Missense_Mutation_p.N600K|MYBPC1_uc010svr.1_Missense_Mutation_p.N600K|MYBPC1_uc010svs.1_Missense_Mutation_p.N600K|MYBPC1_uc010svt.1_Missense_Mutation_p.N588K|MYBPC1_uc010svu.1_Missense_Mutation_p.N581K|MYBPC1_uc001tik.2_Missense_Mutation_p.N574K	NM_206820	NP_996556	Q00872	MYPC1_HUMAN	myosin binding protein C, slow type isoform 3	600	Ig-like C2-type 5.				cell adhesion|muscle filament sliding	cytosol|myofibril|myosin filament	actin binding|structural constituent of muscle|titin binding			ovary(2)|liver(1)|skin(1)	4																		---	---	---	---
PAH	5053	broad.mit.edu	37	12	103288534	103288534	+	Nonsense_Mutation	SNP	G	A	A	rs76296470		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:103288534G>A	uc001tjq.1	-	4	803	c.331C>T	c.(331-333)CGA>TGA	p.R111*	PAH_uc010swc.1_Nonsense_Mutation_p.R111*	NM_000277	NP_000268	P00439	PH4H_HUMAN	phenylalanine hydroxylase	111					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)													---	---	---	---
STAB2	55576	broad.mit.edu	37	12	104063393	104063393	+	Silent	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:104063393A>G	uc001tjw.2	+	21	2433	c.2247A>G	c.(2245-2247)TCA>TCG	p.S749S		NM_017564	NP_060034	Q8WWQ8	STAB2_HUMAN	stabilin 2 precursor	749	Extracellular (Potential).|EGF-like 6.				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	104121095	104121095	+	Silent	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:104121095A>G	uc001tjw.2	+	47	5088	c.4902A>G	c.(4900-4902)GCA>GCG	p.A1634A	STAB2_uc009zug.2_RNA	NM_017564	NP_060034	Q8WWQ8	STAB2_HUMAN	stabilin 2 precursor	1634	Extracellular (Potential).|FAS1 5.				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																		---	---	---	---
TDG	6996	broad.mit.edu	37	12	104373839	104373839	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:104373839G>T	uc001tkg.2	+	3	620	c.397G>T	c.(397-399)GAC>TAC	p.D133Y	TDG_uc010swh.1_Missense_Mutation_p.D133Y|TDG_uc009zuk.2_Missense_Mutation_p.D129Y|TDG_uc010swi.1_5'UTR|TDG_uc010swj.1_5'UTR	NM_003211	NP_003202	Q13569	TDG_HUMAN	thymine-DNA glycosylase	133					depyrimidination|mismatch repair	nucleoplasm	damaged DNA binding|mismatched DNA binding|protein binding|pyrimidine-specific mismatch base pair DNA N-glycosylase activity			ovary(3)|lung(3)	6				BRCA - Breast invasive adenocarcinoma(302;0.00114)									BER_DNA_glycosylases					---	---	---	---
HCFC2	29915	broad.mit.edu	37	12	104481776	104481776	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:104481776A>G	uc001tkj.3	+	9	1347	c.1244A>G	c.(1243-1245)GAC>GGC	p.D415G	HCFC2_uc009zul.2_Intron	NM_013320	NP_037452	Q9Y5Z7	HCFC2_HUMAN	host cell factor C2	415	Fibronectin type-III 1.				regulation of transcription from RNA polymerase II promoter|viral reproduction	cytoplasm|nucleus	transcription coactivator activity			ovary(2)|central_nervous_system(1)	3																		---	---	---	---
TXNRD1	7296	broad.mit.edu	37	12	104732986	104732986	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:104732986C>T	uc010swk.1	+	16	1838	c.1816C>T	c.(1816-1818)CTC>TTC	p.L606F	TXNRD1_uc010swl.1_Missense_Mutation_p.L456F|TXNRD1_uc010swm.1_Missense_Mutation_p.L508F|TXNRD1_uc010swn.1_Missense_Mutation_p.L456F|TXNRD1_uc010swo.1_Missense_Mutation_p.L456F|TXNRD1_uc010swp.1_Missense_Mutation_p.L418F|TXNRD1_uc010swq.1_Missense_Mutation_p.L506F|TXNRD1_uc001tku.2_RNA|TXNRD1_uc009zun.2_Missense_Mutation_p.L522F	NM_001093771	NP_001087240	Q16881	TRXR1_HUMAN	thioredoxin reductase 1 isoform 3	606					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																		---	---	---	---
KIAA1033	23325	broad.mit.edu	37	12	105534985	105534985	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:105534985T>C	uc001tld.2	+	18	1835	c.1748T>C	c.(1747-1749)GTC>GCC	p.V583A	KIAA1033_uc010swr.1_Missense_Mutation_p.V584A|KIAA1033_uc010sws.1_Missense_Mutation_p.V395A	NM_015275	NP_056090	Q2M389	WAHS7_HUMAN	hypothetical protein LOC23325	583					endosome transport	WASH complex				kidney(1)|central_nervous_system(1)	2																		---	---	---	---
KIAA1033	23325	broad.mit.edu	37	12	105536245	105536245	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:105536245G>A	uc001tld.2	+	19	1889	c.1802G>A	c.(1801-1803)TGT>TAT	p.C601Y	KIAA1033_uc010swr.1_Missense_Mutation_p.C602Y|KIAA1033_uc010sws.1_Missense_Mutation_p.C413Y	NM_015275	NP_056090	Q2M389	WAHS7_HUMAN	hypothetical protein LOC23325	601					endosome transport	WASH complex				kidney(1)|central_nervous_system(1)	2																		---	---	---	---
APPL2	55198	broad.mit.edu	37	12	105600945	105600945	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:105600945C>T	uc001tlf.1	-	8	733	c.515G>A	c.(514-516)CGG>CAG	p.R172Q	APPL2_uc010swt.1_Missense_Mutation_p.R129Q|APPL2_uc001tlg.1_5'UTR|APPL2_uc010swu.1_Missense_Mutation_p.R178Q|APPL2_uc009zuq.2_Missense_Mutation_p.R129Q	NM_018171	NP_060641	Q8NEU8	DP13B_HUMAN	adaptor protein, phosphotyrosine interaction, PH	172	Required for RAB5A binding (By similarity).				cell cycle|cell proliferation|signal transduction	early endosome membrane|nucleus	protein binding			upper_aerodigestive_tract(1)	1																		---	---	---	---
TCP11L2	255394	broad.mit.edu	37	12	106729579	106729579	+	Missense_Mutation	SNP	A	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:106729579A>T	uc001tln.2	+	7	1109	c.935A>T	c.(934-936)GAT>GTT	p.D312V		NM_152772	NP_689985	Q8N4U5	T11L2_HUMAN	t-complex 11 (mouse) like 2	312										ovary(3)	3																		---	---	---	---
RFX4	5992	broad.mit.edu	37	12	107048120	107048120	+	Silent	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:107048120C>T	uc001tlr.2	+	4	372	c.306C>T	c.(304-306)AGC>AGT	p.S102S	RFX4_uc010swv.1_RNA|RFX4_uc001tls.2_Silent_p.S111S|RFX4_uc001tlt.2_Silent_p.S111S	NM_213594	NP_998759	Q33E94	RFX4_HUMAN	regulatory factor X4 isoform c	102	|RFX-type winged-helix.				transcription, DNA-dependent	nucleus	DNA binding			upper_aerodigestive_tract(1)	1																		---	---	---	---
WSCD2	9671	broad.mit.edu	37	12	108600059	108600059	+	Intron	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:108600059C>T	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																		---	---	---	---
FICD	11153	broad.mit.edu	37	12	108912793	108912793	+	Silent	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:108912793C>T	uc001tmx.1	+	3	1064	c.918C>T	c.(916-918)GCC>GCT	p.A306A		NM_007076	NP_009007	Q9BVA6	FICD_HUMAN	Huntingtin interacting protein E	306	Fido.				negative regulation of Rho GTPase activity	integral to membrane	binding|protein adenylyltransferase activity				0																		---	---	---	---
ACACB	32	broad.mit.edu	37	12	109660633	109660633	+	Silent	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:109660633C>T	uc001tob.2	+	26	3827	c.3708C>T	c.(3706-3708)TAC>TAT	p.Y1236Y	ACACB_uc001toc.2_Silent_p.Y1236Y	NM_001093	NP_001084	O00763	ACACB_HUMAN	acetyl-Coenzyme A carboxylase beta	1236					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	109703054	109703054	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:109703054G>A	uc001tob.2	+	51	7201	c.7082G>A	c.(7081-7083)CGC>CAC	p.R2361H	ACACB_uc001toc.2_Missense_Mutation_p.R2361H|ACACB_uc001tod.2_RNA|ACACB_uc010sxm.1_Missense_Mutation_p.R1027H	NM_001093	NP_001084	O00763	ACACB_HUMAN	acetyl-Coenzyme A carboxylase beta	2361					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)													---	---	---	---
UBE3B	89910	broad.mit.edu	37	12	109921360	109921360	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:109921360T>C	uc001top.2	+	3	607	c.4T>C	c.(4-6)TTC>CTC	p.F2L	UBE3B_uc001toq.2_Missense_Mutation_p.F2L|UBE3B_uc001tol.1_Missense_Mutation_p.F2L|UBE3B_uc001tom.2_Missense_Mutation_p.F2L|UBE3B_uc001ton.2_Missense_Mutation_p.F2L|UBE3B_uc001too.1_RNA|UBE3B_uc009zvj.1_Missense_Mutation_p.F2L|UBE3B_uc001tor.2_Missense_Mutation_p.F2L	NM_130466	NP_569733	Q7Z3V4	UBE3B_HUMAN	ubiquitin protein ligase E3B	2					protein ubiquitination involved in ubiquitin-dependent protein catabolic process	intracellular	ubiquitin-protein ligase activity			ovary(2)|lung(2)	4																		---	---	---	---
TRPV4	59341	broad.mit.edu	37	12	110226500	110226500	+	Missense_Mutation	SNP	G	A	A	rs35058636	byFrequency	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:110226500G>A	uc001tpj.1	-	12	2008	c.1913C>T	c.(1912-1914)CCG>CTG	p.P638L	TRPV4_uc001tpg.1_Missense_Mutation_p.P604L|TRPV4_uc001tph.1_Missense_Mutation_p.P591L|TRPV4_uc001tpi.1_Missense_Mutation_p.P531L|TRPV4_uc001tpk.1_Missense_Mutation_p.P638L|TRPV4_uc001tpl.1_Missense_Mutation_p.P578L	NM_021625	NP_067638	Q9HBA0	TRPV4_HUMAN	transient receptor potential cation channel,	638					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																		---	---	---	---
GIT2	9815	broad.mit.edu	37	12	110429441	110429441	+	Silent	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:110429441T>C	uc001tps.2	-	2	342	c.177A>G	c.(175-177)ACA>ACG	p.T59T	GIT2_uc001tpq.2_Silent_p.T59T|GIT2_uc001tpv.2_Silent_p.T59T|GIT2_uc001tpu.2_Silent_p.T59T|GIT2_uc001tpt.2_Silent_p.T59T|GIT2_uc010sxu.1_Intron|GIT2_uc001tpw.2_Silent_p.T59T|GIT2_uc010sxv.1_Silent_p.T59T	NM_057169	NP_476510	Q14161	GIT2_HUMAN	G protein-coupled receptor kinase interacting	59	Arf-GAP.				regulation of ARF GTPase activity|regulation of G-protein coupled receptor protein signaling pathway	nucleoplasm	ARF GTPase activator activity|protein binding|zinc ion binding			central_nervous_system(1)	1																		---	---	---	---
ANAPC7	51434	broad.mit.edu	37	12	110812072	110812072	+	Silent	SNP	C	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:110812072C>A	uc001tqo.2	-	11	1678	c.1677G>T	c.(1675-1677)ACG>ACT	p.T559T		NM_016238	NP_057322	Q9UJX3	APC7_HUMAN	anaphase-promoting complex subunit 7 isoform a	559					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	protein phosphatase binding				0																		---	---	---	---
CUX2	23316	broad.mit.edu	37	12	111734353	111734353	+	Intron	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:111734353C>T	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																		---	---	---	---
ERP29	10961	broad.mit.edu	37	12	112460343	112460343	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:112460343G>A	uc001ttk.1	+	3	791	c.673G>A	c.(673-675)GCC>ACC	p.A225T	ERP29_uc001ttl.1_3'UTR	NM_006817	NP_006808	P30040	ERP29_HUMAN	endoplasmic reticulum protein 29 isoform 1	225					intracellular protein transport|protein folding|protein secretion	endoplasmic reticulum lumen|melanosome	protein disulfide isomerase activity				0																		---	---	---	---
OAS3	4940	broad.mit.edu	37	12	113407510	113407510	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:113407510C>A	uc001tug.2	+	15	3289	c.3202C>A	c.(3202-3204)CTG>ATG	p.L1068M		NM_006187	NP_006178	Q9Y6K5	OAS3_HUMAN	2'-5'oligoadenylate synthetase 3	1068	OAS domain 3.				interferon-gamma-mediated signaling pathway|nucleobase, nucleoside, nucleotide and nucleic acid metabolic process|type I interferon-mediated signaling pathway	microsome	ATP binding|nucleotidyltransferase activity|RNA binding			central_nervous_system(1)	1																		---	---	---	---
SDSL	113675	broad.mit.edu	37	12	113875889	113875889	+	3'UTR	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:113875889T>C	uc001tvi.2	+	9					SDSL_uc009zwh.2_3'UTR	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)													---	---	---	---
MED13L	23389	broad.mit.edu	37	12	116418721	116418721	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:116418721A>G	uc001tvw.2	-	23	5253	c.5198T>C	c.(5197-5199)CTG>CCG	p.L1733P		NM_015335	NP_056150	Q71F56	MD13L_HUMAN	mediator complex subunit 13-like	1733					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	116446340	116446340	+	Silent	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:116446340C>T	uc001tvw.2	-	10	1933	c.1878G>A	c.(1876-1878)CCG>CCA	p.P626P		NM_015335	NP_056150	Q71F56	MD13L_HUMAN	mediator complex subunit 13-like	626					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)														---	---	---	---
RNFT2	84900	broad.mit.edu	37	12	117187694	117187694	+	Silent	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:117187694C>T	uc009zwn.2	+	4	365	c.132C>T	c.(130-132)GGC>GGT	p.G44G	RNFT2_uc001twb.3_Silent_p.G44G|RNFT2_uc001twa.3_5'UTR	NM_001109903	NP_001103373	Q96EX2	RNFT2_HUMAN	transmembrane protein 118 isoform 1	44	Extracellular (Potential).					integral to membrane	zinc ion binding				0	all_neural(191;0.117)|Medulloblastoma(191;0.163)			BRCA - Breast invasive adenocarcinoma(302;0.034)														---	---	---	---
FBXW8	26259	broad.mit.edu	37	12	117402490	117402490	+	Intron	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:117402490G>A	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)														---	---	---	---
TAOK3	51347	broad.mit.edu	37	12	118610365	118610365	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:118610365T>C	uc001twx.2	-	17	2091	c.1796A>G	c.(1795-1797)CAC>CGC	p.H599R	TAOK3_uc001twv.2_Missense_Mutation_p.H139R|TAOK3_uc001tww.2_Missense_Mutation_p.H429R|TAOK3_uc001twy.3_Missense_Mutation_p.H599R	NM_016281	NP_057365	Q9H2K8	TAOK3_HUMAN	TAO kinase 3	599	Potential.				MAPKKK cascade|negative regulation of JNK cascade|positive regulation of JNK cascade|protein autophosphorylation	mitochondrion|plasma membrane	ATP binding|protein kinase inhibitor activity|protein serine/threonine kinase activity			lung(5)|central_nervous_system(1)	6	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)																	---	---	---	---
SFRS9	8683	broad.mit.edu	37	12	120901933	120901933	+	Intron	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:120901933T>C	uc001tyi.2	-							NM_003769	NP_003760			splicing factor, arginine/serine-rich 9						mRNA 3'-end processing|mRNA export from nucleus|mRNA splice site selection|termination of RNA polymerase II transcription	nucleoplasm	nucleotide binding|RNA binding				0	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)																	---	---	---	---
CAMKK2	10645	broad.mit.edu	37	12	121687598	121687598	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:121687598C>T	uc001tzu.2	-	13	1439	c.1315G>A	c.(1315-1317)GAA>AAA	p.E439K	CAMKK2_uc001tzt.2_Missense_Mutation_p.E439K|CAMKK2_uc001tzv.2_Missense_Mutation_p.E439K|CAMKK2_uc001tzw.2_Missense_Mutation_p.E439K|CAMKK2_uc001tzx.2_Missense_Mutation_p.E439K|CAMKK2_uc001tzy.2_Missense_Mutation_p.E439K|CAMKK2_uc001tzz.1_Missense_Mutation_p.E226K|CAMKK2_uc001uaa.1_Missense_Mutation_p.E439K|CAMKK2_uc001uab.2_Missense_Mutation_p.E439K|CAMKK2_uc001uac.2_Missense_Mutation_p.E439K	NM_006549	NP_006540	Q96RR4	KKCC2_HUMAN	calcium/calmodulin-dependent protein kinase	439	Protein kinase.				calcium-mediated signaling|MAPKKK cascade|positive regulation of transcription, DNA-dependent|protein autophosphorylation|regulation of protein kinase activity	cytoplasm	ATP binding|calcium ion binding|calmodulin binding|calmodulin-dependent protein kinase activity|protein tyrosine kinase activity			lung(1)|large_intestine(1)|stomach(1)	3	all_neural(191;0.0684)|Medulloblastoma(191;0.0922)																	---	---	---	---
VPS33A	65082	broad.mit.edu	37	12	122734469	122734469	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:122734469T>C	uc001ucd.2	-	6	837	c.724A>G	c.(724-726)ACT>GCT	p.T242A	VPS33A_uc001ucc.2_RNA	NM_022916	NP_075067	Q96AX1	VP33A_HUMAN	vacuolar protein sorting 33A	242					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)														---	---	---	---
GPR109B	8843	broad.mit.edu	37	12	123200725	123200725	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:123200725C>T	uc001ucy.3	-	1	715	c.560G>A	c.(559-561)CGG>CAG	p.R187Q	GPR81_uc001ucw.1_Intron	NM_006018	NP_006009	P49019	HCAR3_HUMAN	G protein-coupled receptor 109B	187	Extracellular (Potential).					integral to plasma membrane	purinergic nucleotide receptor activity, G-protein coupled			ovary(1)|skin(1)	2	all_neural(191;0.0837)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;2.12e-05)|Epithelial(86;3.19e-05)|BRCA - Breast invasive adenocarcinoma(302;0.196)	Mepenzolate(DB04843)|Niacin(DB00627)													---	---	---	---
PITPNM2	57605	broad.mit.edu	37	12	123481978	123481978	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:123481978A>G	uc001uej.1	-	10	1505	c.1366T>C	c.(1366-1368)TTC>CTC	p.F456L	PITPNM2_uc001uek.1_Missense_Mutation_p.F456L	NM_020845	NP_065896	Q9BZ72	PITM2_HUMAN	phosphatidylinositol transfer protein,	456					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)														---	---	---	---
SBNO1	55206	broad.mit.edu	37	12	123812252	123812252	+	Splice_Site	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:123812252A>G	uc010tap.1	-	11	1538	c.1538_splice	c.e11+1	p.R513_splice	SBNO1_uc010tao.1_Splice_Site_p.R512_splice|SBNO1_uc010taq.1_Intron|SBNO1_uc001uet.2_Splice_Site_p.R513_splice|SBNO1_uc001ueu.2_Splice_Site_p.R512_splice|SBNO1_uc001uev.2_Splice_Site_p.R511_splice|SBNO1_uc009zxy.1_Splice_Site_p.R478_splice	NM_018183	NP_060653			sno, strawberry notch homolog 1								ATP binding|DNA binding|hydrolase activity			breast(5)|skin(2)|ovary(1)|kidney(1)	9	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000701)|Epithelial(86;0.00197)														---	---	---	---
GTF2H3	2967	broad.mit.edu	37	12	124132585	124132585	+	Silent	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:124132585T>C	uc001ufo.1	+	4	302	c.276T>C	c.(274-276)AAT>AAC	p.N92N	GTF2H3_uc010tau.1_Silent_p.N51N	NM_001516	NP_001507	Q13889	TF2H3_HUMAN	general transcription factor IIH, polypeptide 3,	92					mRNA capping|nucleotide-excision repair, DNA damage removal|positive regulation of viral transcription|protein phosphorylation|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	core TFIIH complex|holo TFIIH complex	damaged DNA binding|metal ion binding|protein N-terminus binding|sequence-specific DNA binding transcription factor activity|translation factor activity, nucleic acid binding				0	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;7.1e-05)|Epithelial(86;0.000388)|all cancers(50;0.00362)									NER					---	---	---	---
DHX37	57647	broad.mit.edu	37	12	125434995	125434995	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:125434995G>A	uc001ugy.2	-	23	3184	c.3085C>T	c.(3085-3087)CGG>TGG	p.R1029W	DHX37_uc001ugz.1_Missense_Mutation_p.R116W	NM_032656	NP_116045	Q8IY37	DHX37_HUMAN	DEAH (Asp-Glu-Ala-His) box polypeptide 37	1029							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)														---	---	---	---
TMEM132B	114795	broad.mit.edu	37	12	126137105	126137105	+	Missense_Mutation	SNP	A	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:126137105A>C	uc001uhe.1	+	8	2026	c.2018A>C	c.(2017-2019)CAG>CCG	p.Q673P	TMEM132B_uc001uhf.1_Missense_Mutation_p.Q185P	NM_052907	NP_443139	Q14DG7	T132B_HUMAN	transmembrane protein 132B	673	Extracellular (Potential).					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)														---	---	---	---
PIWIL1	9271	broad.mit.edu	37	12	130830350	130830350	+	Silent	SNP	T	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:130830350T>A	uc001uik.2	+	4	333	c.243T>A	c.(241-243)GGT>GGA	p.G81G	PIWIL1_uc001uij.1_Silent_p.G81G	NM_004764	NP_004755	Q96J94	PIWL1_HUMAN	piwi-like 1	81					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	130890795	130890795	+	Intron	SNP	A	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:130890795A>C	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)														---	---	---	---
EP400	57634	broad.mit.edu	37	12	132504686	132504686	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:132504686C>T	uc001ujn.2	+	21	4405	c.4370C>T	c.(4369-4371)ACG>ATG	p.T1457M	EP400_uc001ujl.2_Missense_Mutation_p.T1456M|EP400_uc001ujm.2_Missense_Mutation_p.T1457M	NM_015409	NP_056224	Q96L91	EP400_HUMAN	E1A binding protein p400	1493					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	132510187	132510187	+	Intron	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:132510187G>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)														---	---	---	---
GOLGA3	2802	broad.mit.edu	37	12	133363046	133363046	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:133363046T>C	uc001ukz.1	-	15	3561	c.3002A>G	c.(3001-3003)AAC>AGC	p.N1001S	GOLGA3_uc001ula.1_Missense_Mutation_p.N1001S|GOLGA3_uc001ulb.2_Missense_Mutation_p.N1001S	NM_005895	NP_005886	Q08378	GOGA3_HUMAN	Golgi autoantigen, golgin subfamily a, 3	1001	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)														---	---	---	---
GOLGA3	2802	broad.mit.edu	37	12	133372686	133372686	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:133372686C>T	uc001ukz.1	-	11	2780	c.2221G>A	c.(2221-2223)GAT>AAT	p.D741N	GOLGA3_uc001ula.1_Missense_Mutation_p.D741N|GOLGA3_uc001ulb.2_Missense_Mutation_p.D741N	NM_005895	NP_005886	Q08378	GOGA3_HUMAN	Golgi autoantigen, golgin subfamily a, 3	741	Gln-rich.|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)														---	---	---	---
GOLGA3	2802	broad.mit.edu	37	12	133378448	133378448	+	Missense_Mutation	SNP	A	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:133378448A>T	uc001ukz.1	-	8	2264	c.1705T>A	c.(1705-1707)TCG>ACG	p.S569T	GOLGA3_uc001ula.1_Missense_Mutation_p.S569T|GOLGA3_uc001ulb.2_Missense_Mutation_p.S569T	NM_005895	NP_005886	Q08378	GOGA3_HUMAN	Golgi autoantigen, golgin subfamily a, 3	569	Gln-rich.|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)														---	---	---	---
GOLGA3	2802	broad.mit.edu	37	12	133393363	133393363	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:133393363T>C	uc001ukz.1	-	3	728	c.169A>G	c.(169-171)AGC>GGC	p.S57G	GOLGA3_uc001ula.1_Missense_Mutation_p.S57G|GOLGA3_uc001ulb.2_Missense_Mutation_p.S57G	NM_005895	NP_005886	Q08378	GOGA3_HUMAN	Golgi autoantigen, golgin subfamily a, 3	57	Pro-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)														---	---	---	---
MPHOSPH8	54737	broad.mit.edu	37	13	20220883	20220883	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:20220883A>G	uc001umh.2	+	3	679	c.670A>G	c.(670-672)ACA>GCA	p.T224A	MPHOSPH8_uc001umf.1_Missense_Mutation_p.T224A|MPHOSPH8_uc001umg.2_Missense_Mutation_p.T224A|MPHOSPH8_uc001umi.2_5'UTR	NM_017520	NP_059990	Q99549	MPP8_HUMAN	M-phase phosphoprotein 8	224	Lys-rich.				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)														---	---	---	---
MPHOSPH8	54737	broad.mit.edu	37	13	20235888	20235888	+	Silent	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:20235888C>T	uc001umh.2	+	8	1851	c.1842C>T	c.(1840-1842)GAC>GAT	p.D614D	MPHOSPH8_uc001umg.2_Silent_p.D614D	NM_017520	NP_059990	Q99549	MPP8_HUMAN	M-phase phosphoprotein 8	614	ANK 1.				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)														---	---	---	---
GJA3	2700	broad.mit.edu	37	13	20716728	20716728	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:20716728C>T	uc001umx.1	-	2	872	c.700G>A	c.(700-702)GTG>ATG	p.V234M		NM_021954	NP_068773	Q9Y6H8	CXA3_HUMAN	connexin 46	234	Cytoplasmic (Potential).				cell-cell signaling|visual perception	connexon complex|integral to membrane				pancreas(1)	1		all_cancers(29;1.4e-21)|all_epithelial(30;8.75e-19)|all_lung(29;1.28e-17)|Lung SC(185;0.0257)|Ovarian(182;0.0822)		all cancers(112;0.000554)|Epithelial(112;0.000872)|OV - Ovarian serous cystadenocarcinoma(117;0.0105)|Lung(94;0.0251)|LUSC - Lung squamous cell carcinoma(192;0.0784)														---	---	---	---
EFHA1	221154	broad.mit.edu	37	13	22084195	22084195	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:22084195G>A	uc001uof.2	-	8	731	c.709C>T	c.(709-711)CGT>TGT	p.R237C	EFHA1_uc010tct.1_Missense_Mutation_p.R27C	NM_152726	NP_689939	Q8IYU8	EFHA1_HUMAN	EF-hand domain family, member A1	237	EF-hand 2.						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)														---	---	---	---
PARP4	143	broad.mit.edu	37	13	25009283	25009283	+	Silent	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:25009283G>A	uc001upl.2	-	31	4102	c.3996C>T	c.(3994-3996)CGC>CGT	p.R1332R		NM_006437	NP_006428	Q9UKK3	PARP4_HUMAN	poly (ADP-ribose) polymerase family, member 4	1332					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)														---	---	---	---
ATP12A	479	broad.mit.edu	37	13	25284650	25284650	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:25284650T>C	uc001upp.2	+	20	3003	c.2816T>C	c.(2815-2817)GTT>GCT	p.V939A	ATP12A_uc010aaa.2_Missense_Mutation_p.V945A	NM_001676	NP_001667	P54707	AT12A_HUMAN	hydrogen/potassium-exchanging ATPase 12A	939	Helical; (Potential).				ATP biosynthetic process	hydrogen:potassium-exchanging ATPase complex	ATP binding|hydrogen:potassium-exchanging ATPase activity|metal ion binding			ovary(2)|central_nervous_system(2)|large_intestine(1)|breast(1)	6		Lung SC(185;0.0225)|Breast(139;0.077)		all cancers(112;0.0307)|Epithelial(112;0.086)|OV - Ovarian serous cystadenocarcinoma(117;0.228)	Esomeprazole(DB00736)|Pantoprazole(DB00213)													---	---	---	---
FAM123A	219287	broad.mit.edu	37	13	25744304	25744304	+	Missense_Mutation	SNP	G	A	A	rs61754943	byFrequency;by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:25744304G>A	uc001uqb.2	-	1	1554	c.1454C>T	c.(1453-1455)GCG>GTG	p.A485V	FAM123A_uc001uqa.2_Missense_Mutation_p.A366V|FAM123A_uc001uqc.2_Missense_Mutation_p.A366V	NM_152704	NP_689917	Q8N7J2	F123A_HUMAN	hypothetical protein LOC219287 isoform 1	485										ovary(2)|large_intestine(1)|lung(1)	4		Lung SC(185;0.0225)|Breast(139;0.0602)		all cancers(112;0.0071)|Epithelial(112;0.0398)|OV - Ovarian serous cystadenocarcinoma(117;0.151)|GBM - Glioblastoma multiforme(144;0.222)|Lung(94;0.241)														---	---	---	---
WASF3	10810	broad.mit.edu	37	13	27250705	27250705	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:27250705G>A	uc001uqv.2	+	7	785	c.560G>A	c.(559-561)GGC>GAC	p.G187D	WASF3_uc001uqw.2_Intron	NM_006646	NP_006637	Q9UPY6	WASF3_HUMAN	WAS protein family, member 3	187	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)														---	---	---	---
LNX2	222484	broad.mit.edu	37	13	28143269	28143269	+	Silent	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:28143269G>A	uc001url.3	-	3	861	c.552C>T	c.(550-552)GGC>GGT	p.G184G	LNX2_uc001urm.1_Silent_p.G184G	NM_153371	NP_699202	Q8N448	LNX2_HUMAN	ligand of numb-protein X 2	184							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)														---	---	---	---
PAN3	255967	broad.mit.edu	37	13	28854644	28854644	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:28854644T>C	uc001urz.2	+	15	1855	c.1847T>C	c.(1846-1848)ATG>ACG	p.M616T	PAN3_uc001ury.2_Missense_Mutation_p.M450T|PAN3_uc001urx.2_Missense_Mutation_p.M562T	NM_175854	NP_787050	Q58A45	PAN3_HUMAN	PABP1-dependent poly A-specific ribonuclease	762	Interaction with PAN2.				nuclear-transcribed mRNA catabolic process, nonsense-mediated decay|nuclear-transcribed mRNA poly(A) tail shortening	centrosome|cytosol	ATP binding|protein kinase activity			ovary(1)	1	Acute lymphoblastic leukemia(6;0.04)	Lung SC(185;0.0262)	Colorectal(13;0.000334)	all cancers(112;0.0102)|Epithelial(112;0.0803)|GBM - Glioblastoma multiforme(144;0.121)|OV - Ovarian serous cystadenocarcinoma(117;0.13)|Lung(94;0.174)														---	---	---	---
USPL1	10208	broad.mit.edu	37	13	31231887	31231887	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:31231887G>A	uc001utc.2	+	9	2105	c.1673G>A	c.(1672-1674)CGT>CAT	p.R558H	USPL1_uc001utd.2_Missense_Mutation_p.R229H|USPL1_uc001ute.1_Missense_Mutation_p.R229H	NM_005800	NP_005791	Q5W0Q7	USPL1_HUMAN	ubiquitin specific peptidase like 1	558					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)														---	---	---	---
ALOX5AP	241	broad.mit.edu	37	13	31309763	31309763	+	Silent	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:31309763C>T	uc001utf.1	+	1	95	c.21C>T	c.(19-21)GGC>GGT	p.G7G	ALOX5AP_uc010tdr.1_Silent_p.G64G	NM_001629	NP_001620	P20292	AL5AP_HUMAN	arachidonate 5-lipoxygenase-activating protein	7	Lumenal.				cellular response to calcium ion|leukotriene biosynthetic process|leukotriene production involved in inflammatory response|protein homotrimerization	endoplasmic reticulum membrane|integral to membrane|microsome|nuclear membrane	arachidonic acid binding|protein N-terminus binding				0		Lung SC(185;0.0257)|Breast(139;0.203)		all cancers(112;0.0187)|Epithelial(112;0.0803)|OV - Ovarian serous cystadenocarcinoma(117;0.0864)														---	---	---	---
N4BP2L2	10443	broad.mit.edu	37	13	33018125	33018125	+	Silent	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:33018125C>T	uc010abe.1	-	7	571	c.549G>A	c.(547-549)CCG>CCA	p.P183P	N4BP2L2_uc001uug.2_Silent_p.P66P|N4BP2L2_uc010abd.1_Silent_p.P96P|N4BP2L2_uc001uuh.2_Silent_p.P14P|N4BP2L2_uc001uuj.2_Intron|N4BP2L2_uc010tdz.1_Silent_p.P168P	NM_033111	NP_149102	Q92802	N42L2_HUMAN	phosphonoformate immuno-associated protein 5	Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment											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)														---	---	---	---
KL	9365	broad.mit.edu	37	13	33634834	33634834	+	Nonsense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:33634834C>T	uc001uus.2	+	4	1626	c.1618C>T	c.(1618-1620)CAG>TAG	p.Q540*	KL_uc001uur.1_3'UTR	NM_004795	NP_004786	Q9UEF7	KLOT_HUMAN	klotho precursor	540	Glycosyl hydrolase-1 2.|Extracellular (Potential).				aging|carbohydrate metabolic process|insulin receptor signaling pathway|positive regulation of bone mineralization	extracellular space|extracellular space|integral to membrane|integral to plasma membrane|membrane fraction|soluble fraction	beta-glucosidase activity|beta-glucuronidase activity|cation binding|fibroblast growth factor binding|hormone activity|signal transducer activity|vitamin D binding			large_intestine(1)|ovary(1)|skin(1)	3	all_epithelial(80;0.133)	Ovarian(182;1.78e-06)|Breast(139;4.08e-05)|Hepatocellular(188;0.00886)|Lung SC(185;0.0262)		GBM - Glioblastoma multiforme(144;7.13e-230)|all cancers(112;1.33e-165)|OV - Ovarian serous cystadenocarcinoma(117;1.09e-113)|Epithelial(112;3.79e-112)|Lung(94;8.52e-27)|LUSC - Lung squamous cell carcinoma(192;1.4e-13)|Kidney(163;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(186;5.63e-08)|BRCA - Breast invasive adenocarcinoma(63;1.41e-05)														---	---	---	---
STARD13	90627	broad.mit.edu	37	13	33741684	33741684	+	Intron	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:33741684G>A	uc001uuw.2	-						STARD13_uc001uuu.2_Intron|STARD13_uc001uuv.2_Intron|STARD13_uc001uux.2_Intron|STARD13_uc010tec.1_Intron|STARD13_uc010abh.1_Intron	NM_178006	NP_821074			StAR-related lipid transfer (START) domain						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)														---	---	---	---
NBEA	26960	broad.mit.edu	37	13	35745411	35745411	+	Silent	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:35745411G>A	uc001uvb.2	+	26	4451	c.4245G>A	c.(4243-4245)ACG>ACA	p.T1415T	NBEA_uc010abi.2_Silent_p.T103T	NM_015678	NP_056493	Q8NFP9	NBEA_HUMAN	neurobeachin	1415						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	35770120	35770120	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:35770120G>A	uc001uvb.2	+	31	5253	c.5047G>A	c.(5047-5049)GCT>ACT	p.A1683T	NBEA_uc010abi.2_Missense_Mutation_p.A339T	NM_015678	NP_056493	Q8NFP9	NBEA_HUMAN	neurobeachin	1683						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)														---	---	---	---
DCLK1	9201	broad.mit.edu	37	13	36402449	36402449	+	Intron	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:36402449G>A	uc001uvf.2	-						DCLK1_uc001uve.3_Intron|DCLK1_uc010teh.1_Intron|DCLK1_uc010abk.2_Intron	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)														---	---	---	---
POSTN	10631	broad.mit.edu	37	13	38161020	38161020	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:38161020C>A	uc001uwo.3	-	6	770	c.652G>T	c.(652-654)GCA>TCA	p.A218S	POSTN_uc001uwp.3_Missense_Mutation_p.A218S|POSTN_uc001uwr.2_Missense_Mutation_p.A218S|POSTN_uc001uwq.2_Missense_Mutation_p.A218S|POSTN_uc010teu.1_Missense_Mutation_p.A218S|POSTN_uc010tev.1_Missense_Mutation_p.A218S|POSTN_uc010tew.1_Missense_Mutation_p.A218S|POSTN_uc010tex.1_Missense_Mutation_p.A133S	NM_006475	NP_006466	Q15063	POSTN_HUMAN	periostin, osteoblast specific factor isoform 1	218	FAS1 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)														---	---	---	---
TRPC4	7223	broad.mit.edu	37	13	38211245	38211245	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:38211245T>C	uc001uws.2	-	11	2964	c.2729A>G	c.(2728-2730)GAC>GGC	p.D910G	TRPC4_uc010abv.2_Missense_Mutation_p.D490G|TRPC4_uc001uwt.2_Missense_Mutation_p.D826G|TRPC4_uc010tey.1_Missense_Mutation_p.D769G|TRPC4_uc010abw.2_Missense_Mutation_p.D737G|TRPC4_uc010abx.2_Missense_Mutation_p.D915G|TRPC4_uc010aby.2_Missense_Mutation_p.D761G	NM_016179	NP_057263	Q9UBN4	TRPC4_HUMAN	transient receptor potential cation channel,	910	Binds to ITPR1, ITPR2 and ITPR3.|Cytoplasmic (Potential).				axon guidance|calcium ion import	basolateral plasma membrane|calcium channel complex|cell surface|cortical cytoskeleton	beta-catenin binding|cadherin binding|store-operated calcium channel activity			ovary(3)|skin(2)|breast(1)	6				all cancers(112;1.92e-08)|Epithelial(112;5.04e-06)|OV - Ovarian serous cystadenocarcinoma(117;0.000677)|GBM - Glioblastoma multiforme(144;0.00623)|BRCA - Breast invasive adenocarcinoma(63;0.0126)														---	---	---	---
FREM2	341640	broad.mit.edu	37	13	39262627	39262627	+	Silent	SNP	C	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:39262627C>A	uc001uwv.2	+	1	1455	c.1146C>A	c.(1144-1146)TCC>TCA	p.S382S		NM_207361	NP_997244	Q5SZK8	FREM2_HUMAN	FRAS1-related extracellular matrix protein 2	382	CSPG 1.|Extracellular (Potential).				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)														---	---	---	---
FREM2	341640	broad.mit.edu	37	13	39262641	39262641	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:39262641A>G	uc001uwv.2	+	1	1469	c.1160A>G	c.(1159-1161)GAT>GGT	p.D387G		NM_207361	NP_997244	Q5SZK8	FREM2_HUMAN	FRAS1-related extracellular matrix protein 2	387	CSPG 1.|Extracellular (Potential).				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)														---	---	---	---
FREM2	341640	broad.mit.edu	37	13	39263697	39263697	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:39263697G>A	uc001uwv.2	+	1	2525	c.2216G>A	c.(2215-2217)CGT>CAT	p.R739H		NM_207361	NP_997244	Q5SZK8	FREM2_HUMAN	FRAS1-related extracellular matrix protein 2	739	CSPG 4.|Extracellular (Potential).				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)														---	---	---	---
FREM2	341640	broad.mit.edu	37	13	39265370	39265370	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:39265370A>G	uc001uwv.2	+	1	4198	c.3889A>G	c.(3889-3891)ATC>GTC	p.I1297V		NM_207361	NP_997244	Q5SZK8	FREM2_HUMAN	FRAS1-related extracellular matrix protein 2	1297	Extracellular (Potential).|CSPG 9.				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)														---	---	---	---
NHLRC3	387921	broad.mit.edu	37	13	39613274	39613274	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:39613274T>C	uc001uxc.2	+	2	408	c.86T>C	c.(85-87)GTT>GCT	p.V29A	C13orf23_uc001uwy.2_5'Flank|C13orf23_uc001uwz.2_5'Flank|NHLRC3_uc001uxa.1_Missense_Mutation_p.V29A|NHLRC3_uc001uxb.1_Missense_Mutation_p.V29A|NHLRC3_uc001uxd.2_Missense_Mutation_p.V29A|NHLRC3_uc001uxe.2_5'UTR	NM_001012754	NP_001012772	Q5JS37	NHLC3_HUMAN	NHL repeat containing 3 isoform a	29						extracellular region				skin(1)	1		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;2.37e-08)|Epithelial(112;3.14e-06)|OV - Ovarian serous cystadenocarcinoma(117;0.00101)|BRCA - Breast invasive adenocarcinoma(63;0.00335)|GBM - Glioblastoma multiforme(144;0.0128)														---	---	---	---
COG6	57511	broad.mit.edu	37	13	40293787	40293787	+	Intron	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:40293787T>C	uc001uxh.2	+						COG6_uc001uxi.2_Intron|COG6_uc010acb.2_Intron	NM_020751	NP_065802			component of oligomeric golgi complex 6 isoform						protein transport	Golgi membrane|Golgi transport complex				kidney(1)|skin(1)	2		Lung NSC(96;0.000124)|Breast(139;0.0199)|Prostate(109;0.0233)|Lung SC(185;0.0367)		all cancers(112;6.03e-09)|Epithelial(112;7e-07)|OV - Ovarian serous cystadenocarcinoma(117;0.00015)|BRCA - Breast invasive adenocarcinoma(63;0.00438)|GBM - Glioblastoma multiforme(144;0.0168)														---	---	---	---
MRPS31	10240	broad.mit.edu	37	13	41323384	41323384	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:41323384G>A	uc001uxm.3	-	6	923	c.848C>T	c.(847-849)GCT>GTT	p.A283V		NM_005830	NP_005821	Q92665	RT31_HUMAN	mitochondrial ribosomal protein S31 precursor	283						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)														---	---	---	---
ELF1	1997	broad.mit.edu	37	13	41507588	41507588	+	Silent	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:41507588G>A	uc001uxs.2	-	9	2206	c.1833C>T	c.(1831-1833)AAC>AAT	p.N611N	ELF1_uc010tfc.1_Silent_p.N587N|ELF1_uc010acd.2_Silent_p.N504N	NM_172373	NP_758961	P32519	ELF1_HUMAN	E74-like factor 1 (ets domain transcription	611					positive regulation of transcription from RNA polymerase II promoter	cytoplasm|nucleus	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			ovary(1)	1		Lung NSC(96;8.3e-05)|Prostate(109;0.0233)|Breast(139;0.0296)|Lung SC(185;0.0367)		all cancers(112;1.87e-08)|Epithelial(112;8.45e-06)|OV - Ovarian serous cystadenocarcinoma(117;0.000202)|GBM - Glioblastoma multiforme(144;0.00266)|BRCA - Breast invasive adenocarcinoma(63;0.072)														---	---	---	---
WBP4	11193	broad.mit.edu	37	13	41654797	41654797	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:41654797A>G	uc001uxt.2	+	9	885	c.772A>G	c.(772-774)AGT>GGT	p.S258G	WBP4_uc010tfd.1_Missense_Mutation_p.S237G	NM_007187	NP_009118	O75554	WBP4_HUMAN	WW domain-containing binding protein 4	258					nuclear mRNA cis splicing, via spliceosome	nuclear speck|spliceosomal complex	nucleic acid binding|proline-rich region binding|zinc ion binding			breast(2)|kidney(1)	3		Lung NSC(96;3.55e-06)|Breast(139;0.00123)|Prostate(109;0.0181)|Lung SC(185;0.0262)|Hepatocellular(98;0.114)		all cancers(112;3.11e-09)|Epithelial(112;3.37e-06)|OV - Ovarian serous cystadenocarcinoma(117;8.3e-05)|GBM - Glioblastoma multiforme(144;0.00102)|BRCA - Breast invasive adenocarcinoma(63;0.07)														---	---	---	---
DGKH	160851	broad.mit.edu	37	13	42740812	42740812	+	Splice_Site	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:42740812T>C	uc001uyl.1	+	9	1139	c.1118_splice	c.e9+2	p.G373_splice	DGKH_uc010tfh.1_Splice_Site_p.G373_splice|DGKH_uc001uym.1_Splice_Site_p.G373_splice|DGKH_uc010tfi.1_Splice_Site_p.G128_splice|DGKH_uc010tfj.1_Splice_Site_p.G228_splice|DGKH_uc001uyn.1_Splice_Site|DGKH_uc001uyo.1_Splice_Site_p.G228_splice|DGKH_uc001uyp.2_Splice_Site	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)														---	---	---	---
TNFSF11	8600	broad.mit.edu	37	13	43180998	43180998	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:43180998G>T	uc001uyu.2	+	5	1047	c.898G>T	c.(898-900)GAT>TAT	p.D300Y	TNFSF11_uc001uyt.2_Missense_Mutation_p.D227Y	NM_003701	NP_003692	O14788	TNF11_HUMAN	tumor necrosis factor ligand superfamily, member	300	Extracellular (Potential).				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)														---	---	---	---
TSC22D1	8848	broad.mit.edu	37	13	45150010	45150010	+	Silent	SNP	C	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:45150010C>G	uc001uzn.3	-	1	692	c.201G>C	c.(199-201)CCG>CCC	p.P67P	TSC22D1_uc001uzo.1_Silent_p.P67P	NM_183422	NP_904358	Q15714	T22D1_HUMAN	TSC22 domain family, member 1 isoform 1	67	Pro-rich.				transcription from RNA polymerase II promoter	cytoplasm|nucleus	protein binding|sequence-specific DNA binding transcription factor activity				0		all_hematologic(4;8.74e-08)|Acute lymphoblastic leukemia(4;1.78e-07)|Lung NSC(96;2.21e-05)|Breast(139;0.000625)|Prostate(109;0.000947)|Hepatocellular(98;0.0202)|Lung SC(185;0.0262)		GBM - Glioblastoma multiforme(144;0.000522)|BRCA - Breast invasive adenocarcinoma(63;0.118)														---	---	---	---
SPERT	220082	broad.mit.edu	37	13	46276606	46276606	+	Intron	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:46276606G>A	uc001van.1	+						SPERT_uc001vao.2_5'Flank	NM_152719	NP_689932			spermatid associated							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)														---	---	---	---
ZC3H13	23091	broad.mit.edu	37	13	46559531	46559531	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:46559531T>C	uc010tfw.1	-	9	1627	c.1621A>G	c.(1621-1623)ACG>GCG	p.T541A	ZC3H13_uc001vas.1_Missense_Mutation_p.T541A|ZC3H13_uc001vat.1_Missense_Mutation_p.T541A	NM_015070	NP_055885	Q5T200	ZC3HD_HUMAN	zinc finger CCCH-type containing 13	541	Arg/Ser-rich.						nucleic acid binding|zinc ion binding			ovary(1)|lung(1)	2		Lung NSC(96;7.26e-05)|Breast(56;0.000118)|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;4.18e-05)														---	---	---	---
ZC3H13	23091	broad.mit.edu	37	13	46577412	46577412	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:46577412G>T	uc010tfw.1	-	7	812	c.806C>A	c.(805-807)CCT>CAT	p.P269H	ZC3H13_uc001vas.1_Missense_Mutation_p.P269H|ZC3H13_uc001vat.1_Missense_Mutation_p.P269H	NM_015070	NP_055885	Q5T200	ZC3HD_HUMAN	zinc finger CCCH-type containing 13	269							nucleic acid binding|zinc ion binding			ovary(1)|lung(1)	2		Lung NSC(96;7.26e-05)|Breast(56;0.000118)|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;4.18e-05)														---	---	---	---
FNDC3A	22862	broad.mit.edu	37	13	49765467	49765467	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:49765467C>A	uc001vcm.2	+	19	2478	c.2173C>A	c.(2173-2175)CTT>ATT	p.L725I	FNDC3A_uc001vcn.2_Missense_Mutation_p.L725I|FNDC3A_uc001vco.2_RNA|FNDC3A_uc001vcq.2_Missense_Mutation_p.L669I	NM_001079673	NP_001073141	Q9Y2H6	FND3A_HUMAN	fibronectin type III domain containing 3A	725	Fibronectin type-III 5.					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)														---	---	---	---
MLNR	2862	broad.mit.edu	37	13	49796265	49796265	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:49796265T>C	uc010tgj.1	+	2	991	c.991T>C	c.(991-993)TAC>CAC	p.Y331H		NM_001507	NP_001498	O43193	MTLR_HUMAN	motilin receptor	331	Extracellular (Potential).				digestion	integral to plasma membrane	growth hormone-releasing hormone receptor activity				0		all_lung(13;8.31e-06)|Lung NSC(96;0.000251)|Breast(56;0.0008)|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;6.1e-09)														---	---	---	---
PHF11	51131	broad.mit.edu	37	13	50102662	50102662	+	Missense_Mutation	SNP	T	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:50102662T>A	uc001vdb.2	+	10	1194	c.857T>A	c.(856-858)ATT>AAT	p.I286N	PHF11_uc001vdc.2_Missense_Mutation_p.I247N|PHF11_uc001vdd.2_RNA	NM_001040443	NP_001035533	Q9UIL8	PHF11_HUMAN	PHD finger protein 11 isoform a	286					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	zinc ion binding				0		Lung NSC(96;2.1e-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;2.38e-09)														---	---	---	---
TRIM13	10206	broad.mit.edu	37	13	50586440	50586440	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:50586440G>A	uc001vdq.1	+	3	677	c.364G>A	c.(364-366)GAG>AAG	p.E122K	DLEU2_uc001vdn.1_Intron|DLEU2_uc001vdo.1_Intron|KCNRG_uc001vdt.2_5'Flank|KCNRG_uc001vdu.2_5'Flank|TRIM13_uc001vdp.1_Missense_Mutation_p.E125K|TRIM13_uc001vdr.1_Missense_Mutation_p.E122K|TRIM13_uc001vds.1_Missense_Mutation_p.E122K	NM_052811	NP_434698	O60858	TRI13_HUMAN	ret finger protein 2 isoform 1	122	B box-type.				anatomical structure morphogenesis|ER-associated protein catabolic process|positive regulation of I-kappaB kinase/NF-kappaB cascade|protein autoubiquitination	cytoplasm|endoplasmic reticulum membrane|integral to membrane	protein binding|signal transducer activity|ubiquitin-protein ligase activity|zinc ion binding			ovary(2)	2		Acute lymphoblastic leukemia(7;3.41e-06)|Lung NSC(96;3.08e-05)|Breast(56;9.7e-05)|Prostate(109;0.00174)|Hepatocellular(98;0.0207)|Myeloproliferative disorder(33;0.163)|Lung SC(185;0.187)|all_neural(104;0.19)		GBM - Glioblastoma multiforme(99;1.53e-10)|COAD - Colon adenocarcinoma(199;0.205)														---	---	---	---
MIR16-1	406950	broad.mit.edu	37	13	50623165	50623165	+	RNA	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:50623165C>T	hsa-mir-16-1|MI0000070	-			c.33C>T			DLEU2_uc001vdn.1_Intron|DLEU2_uc001vdo.1_Intron|DLEU2_uc001vdw.2_Intron|DLEU2_uc001vdx.2_Intron|DLEU2_uc001vdy.2_Intron|DLEU2_uc001vdz.2_Intron|uc001vea.1_RNA																	0																		---	---	---	---
SERPINE3	647174	broad.mit.edu	37	13	51922547	51922547	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:51922547G>T	uc001vfh.2	+	4	959	c.899G>T	c.(898-900)AGG>ATG	p.R300M	SERPINE3_uc010tgp.1_Missense_Mutation_p.R300M	NM_001101320	NP_001094790	A8MV23	SERP3_HUMAN	nexin-related serine protease inhibitor	300					regulation of proteolysis	extracellular region	serine-type endopeptidase inhibitor activity			ovary(2)	2																		---	---	---	---
INTS6	26512	broad.mit.edu	37	13	52026558	52026558	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:52026558A>G	uc001vfk.2	-	1	718	c.104T>C	c.(103-105)TTC>TCC	p.F35S	INTS6_uc001vfj.2_Missense_Mutation_p.F22S|INTS6_uc001vfl.2_5'UTR|INTS6_uc001vfm.2_Missense_Mutation_p.F35S|uc001vfn.2_5'Flank	NM_012141	NP_036273	Q9UL03	INT6_HUMAN	integrator complex subunit 6 isoform a	35	VWFA.				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)														---	---	---	---
UTP14C	9724	broad.mit.edu	37	13	52593285	52593285	+	Intron	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:52593285T>C	uc001vgb.2	+						UTP14C_uc001vga.2_Intron|UTP14C_uc001vgc.2_5'Flank	NM_021645	NP_067677			UTP14, U3 small nucleolar ribonucleoprotein,						cell differentiation|meiosis|multicellular organismal development|rRNA processing|spermatogenesis	nucleolus|small-subunit processome				ovary(3)|large_intestine(1)|breast(1)	5		Breast(56;0.00173)|Lung NSC(96;0.0108)|Prostate(109;0.0412)|Hepatocellular(98;0.152)|Glioma(44;0.236)		GBM - Glioblastoma multiforme(99;2.3e-08)														---	---	---	---
UTP14C	9724	broad.mit.edu	37	13	52603788	52603788	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:52603788A>G	uc001vgb.2	+	2	1383	c.848A>G	c.(847-849)GAA>GGA	p.E283G	UTP14C_uc001vga.2_3'UTR|UTP14C_uc001vgc.2_RNA	NM_021645	NP_067677	Q5TAP6	UT14C_HUMAN	UTP14, U3 small nucleolar ribonucleoprotein,	283					cell differentiation|meiosis|multicellular organismal development|rRNA processing|spermatogenesis	nucleolus|small-subunit processome				ovary(3)|large_intestine(1)|breast(1)	5		Breast(56;0.00173)|Lung NSC(96;0.0108)|Prostate(109;0.0412)|Hepatocellular(98;0.152)|Glioma(44;0.236)		GBM - Glioblastoma multiforme(99;2.3e-08)														---	---	---	---
HNRNPA1L2	144983	broad.mit.edu	37	13	53217073	53217073	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:53217073C>T	uc001vgx.1	+	7	1519	c.446C>T	c.(445-447)GCC>GTC	p.A149V	HNRNPA1L2_uc001vgy.1_Missense_Mutation_p.A149V|HNRNPA1L2_uc001vgz.1_Missense_Mutation_p.A149V	NM_001011724	NP_001011724	Q32P51	RA1L2_HUMAN	heterogeneous nuclear ribonucleoprotein A1-like	149	Globular B domain.|RRM 2.				mRNA processing|mRNA transport|RNA splicing	cytoplasm|spliceosomal complex	nucleotide binding|RNA binding				0																		---	---	---	---
HNRNPA1L2	144983	broad.mit.edu	37	13	53217101	53217101	+	Silent	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:53217101C>T	uc001vgx.1	+	7	1547	c.474C>T	c.(472-474)TCC>TCT	p.S158S	HNRNPA1L2_uc001vgy.1_Silent_p.S158S|HNRNPA1L2_uc001vgz.1_Silent_p.S158S	NM_001011724	NP_001011724	Q32P51	RA1L2_HUMAN	heterogeneous nuclear ribonucleoprotein A1-like	158	Globular B domain.|RRM 2.				mRNA processing|mRNA transport|RNA splicing	cytoplasm|spliceosomal complex	nucleotide binding|RNA binding				0																		---	---	---	---
LECT1	11061	broad.mit.edu	37	13	53286861	53286861	+	Silent	SNP	G	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:53286861G>T	uc001vhf.2	-	5	723	c.612C>A	c.(610-612)ACC>ACA	p.T204T	LECT1_uc001vhg.2_Silent_p.T204T|LECT1_uc001vhh.2_Silent_p.T193T	NM_007015	NP_008946	O75829	LECT1_HUMAN	leukocyte cell derived chemotaxin 1 isoform 1	204					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)														---	---	---	---
PCDH17	27253	broad.mit.edu	37	13	58299290	58299290	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:58299290G>A	uc001vhq.1	+	4	4234	c.3342G>A	c.(3340-3342)ATG>ATA	p.M1114I	PCDH17_uc010aec.1_Missense_Mutation_p.M1113I|PCDH17_uc001vhr.1_Missense_Mutation_p.M203I	NM_001040429	NP_001035519	O14917	PCD17_HUMAN	protocadherin 17 precursor	1114	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)														---	---	---	---
PCDH20	64881	broad.mit.edu	37	13	61985998	61985998	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:61985998G>T	uc001vid.3	-	2	2598	c.2234C>A	c.(2233-2235)CCT>CAT	p.P745H	PCDH20_uc010thj.1_Missense_Mutation_p.P745H	NM_022843	NP_073754	Q8N6Y1	PCD20_HUMAN	protocadherin 20	718	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	67802402	67802402	+	Silent	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:67802402C>T	uc001vik.2	-	2	863	c.171G>A	c.(169-171)GGG>GGA	p.G57G	PCDH9_uc001vil.2_Silent_p.G57G|PCDH9_uc010thl.1_Silent_p.G57G|PCDH9_uc001vin.3_Silent_p.G57G	NM_203487	NP_982354	Q9HC56	PCDH9_HUMAN	protocadherin 9 isoform 1 precursor	57	Extracellular (Potential).|Cadherin 1.				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)														---	---	---	---
UCHL3	7347	broad.mit.edu	37	13	76141460	76141460	+	Intron	SNP	C	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:76141460C>A	uc001vjq.2	+						UCHL3_uc001vjr.2_Intron	NM_006002	NP_005993			ubiquitin carboxyl-terminal esterase L3						ubiquitin-dependent protein catabolic process	cytoplasm	cysteine-type peptidase activity|ubiquitin binding|ubiquitin thiolesterase activity				0				GBM - Glioblastoma multiforme(99;0.0125)														---	---	---	---
LMO7	4008	broad.mit.edu	37	13	76210865	76210865	+	Intron	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:76210865G>A	uc010thv.1	+						LMO7_uc001vjt.1_Intron	NM_005358	NP_005349			LIM domain only 7 isoform 1							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)														---	---	---	---
LMO7	4008	broad.mit.edu	37	13	76432077	76432077	+	Silent	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:76432077T>C	uc001vjv.2	+	27	4846	c.4086T>C	c.(4084-4086)TGT>TGC	p.C1362C	LMO7_uc010thv.1_Nonstop_Mutation_p.*1350R|LMO7_uc010thw.1_Nonstop_Mutation_p.*1276R|LMO7_uc001vjx.1_RNA	NM_015842	NP_056667	Q8WWI1	LMO7_HUMAN	LIM domain only 7 isoform 2	Error:Variant_position_missing_in_Q8WWI1_after_alignment						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)														---	---	---	---
CLN5	1203	broad.mit.edu	37	13	77570239	77570239	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:77570239T>C	uc001vkc.2	+	3	717	c.689T>C	c.(688-690)TTA>TCA	p.L230S		NM_006493	NP_006484	O75503	CLN5_HUMAN	ceroid-lipofuscinosis, neuronal 5	181					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)														---	---	---	---
RNF219	79596	broad.mit.edu	37	13	79212986	79212986	+	Missense_Mutation	SNP	A	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:79212986A>C	uc001vkw.1	-	4	580	c.521T>G	c.(520-522)GTG>GGG	p.V174G	RNF219_uc010afb.1_5'UTR|RNF219_uc010afc.2_Missense_Mutation_p.V174G	NM_024546	NP_078822	Q5W0B1	RN219_HUMAN	ring finger protein 219	174	Potential.						zinc ion binding			large_intestine(2)	2		Acute lymphoblastic leukemia(28;0.0279)|Breast(118;0.0848)		GBM - Glioblastoma multiforme(99;0.0414)														---	---	---	---
SLITRK1	114798	broad.mit.edu	37	13	84453757	84453757	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:84453757A>G	uc001vlk.2	-	1	2772	c.1886T>C	c.(1885-1887)GTC>GCC	p.V629A		NM_052910	NP_443142	Q96PX8	SLIK1_HUMAN	slit and trk like 1 protein precursor	629	Helical; (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)														---	---	---	---
GPC5	2262	broad.mit.edu	37	13	92380883	92380883	+	Missense_Mutation	SNP	C	T	T	rs140775585		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:92380883C>T	uc010tif.1	+	4	1484	c.1118C>T	c.(1117-1119)ACA>ATA	p.T373I		NM_004466	NP_004457	P78333	GPC5_HUMAN	glypican 5 precursor	373						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)																---	---	---	---
GPC6	10082	broad.mit.edu	37	13	95034809	95034809	+	Intron	SNP	G	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:95034809G>T	uc001vlt.2	+							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)																---	---	---	---
UGGT2	55757	broad.mit.edu	37	13	96529989	96529989	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:96529989T>C	uc001vmt.2	-	28	3520	c.3350A>G	c.(3349-3351)AAA>AGA	p.K1117R	UGGT2_uc001vmu.1_Missense_Mutation_p.K204R	NM_020121	NP_064506	Q9NYU1	UGGG2_HUMAN	UDP-glucose ceramide glucosyltransferase-like 2	1117					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																		---	---	---	---
FARP1	10160	broad.mit.edu	37	13	99091401	99091401	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:99091401C>T	uc001vnj.2	+	21	2720	c.2384C>T	c.(2383-2385)GCC>GTC	p.A795V	FARP1_uc001vnh.2_Missense_Mutation_p.A826V	NM_005766	NP_005757	Q9Y4F1	FARP1_HUMAN	FERM, RhoGEF, and pleckstrin domain protein 1	795	PH 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	99109446	99109446	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:99109446G>A	uc001vnm.1	-	10	1506	c.1271C>T	c.(1270-1272)GCC>GTC	p.A424V	STK24_uc001vnn.1_Missense_Mutation_p.A412V|STK24_uc010tim.1_Missense_Mutation_p.A393V	NM_003576	NP_003567	Q9Y6E0	STK24_HUMAN	serine/threonine kinase 24 isoform a	424					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	99498191	99498191	+	Silent	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:99498191G>A	uc001vnt.2	-	38	4174	c.4119C>T	c.(4117-4119)CTC>CTT	p.L1373L	DOCK9_uc001vnw.2_Silent_p.L1372L|DOCK9_uc001vnv.1_RNA|DOCK9_uc010tir.1_Silent_p.L1373L|DOCK9_uc001vnq.2_5'UTR|DOCK9_uc001vnr.2_Silent_p.L16L|DOCK9_uc010tin.1_Silent_p.L16L|DOCK9_uc001vns.2_Intron|DOCK9_uc010tio.1_Silent_p.L65L|DOCK9_uc010tip.1_Silent_p.L83L|DOCK9_uc001vnu.1_5'UTR|DOCK9_uc010tiq.1_Silent_p.L351L	NM_015296	NP_056111	Q9BZ29	DOCK9_HUMAN	dedicator of cytokinesis 9 isoform a	1373					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)																	---	---	---	---
KDELC1	79070	broad.mit.edu	37	13	103441401	103441401	+	Silent	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:103441401C>T	uc001vpq.3	-	7	1638	c.1254G>A	c.(1252-1254)CTG>CTA	p.L418L	KDELC1_uc001vpr.3_Silent_p.L199L	NM_024089	NP_076994	Q6UW63	KDEL1_HUMAN	KDEL (Lys-Asp-Glu-Leu) containing 1 precursor	418						endoplasmic reticulum lumen				ovary(1)	1	all_neural(89;0.0438)|Medulloblastoma(90;0.163)|Lung SC(71;0.211)																	---	---	---	---
ERCC5	2073	broad.mit.edu	37	13	103506692	103506692	+	Silent	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:103506692T>C	uc001vpw.2	+	4	878	c.435T>C	c.(433-435)GTT>GTC	p.V145V	ERCC5_uc001vpu.1_Silent_p.V599V|ERCC5_uc010tjb.1_Silent_p.V145V|ERCC5_uc010tjc.1_RNA|ERCC5_uc010tjd.1_5'UTR	NM_000123	NP_000114	P28715	ERCC5_HUMAN	XPG-complementing protein	145					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				---	---	---	---
COL4A1	1282	broad.mit.edu	37	13	110862375	110862375	+	Silent	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:110862375C>T	uc001vqw.3	-	10	689	c.567G>A	c.(565-567)CTG>CTA	p.L189L	COL4A1_uc010agl.2_Silent_p.L189L	NM_001845	NP_001836	P02462	CO4A1_HUMAN	alpha 1 type IV collagen preproprotein	189	Triple-helical region.				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)															---	---	---	---
CARS2	79587	broad.mit.edu	37	13	111303435	111303435	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:111303435T>C	uc001vrd.2	-	10	1040	c.1000A>G	c.(1000-1002)ACC>GCC	p.T334A	CARS2_uc010tjm.1_RNA	NM_024537	NP_078813	Q9HA77	SYCM_HUMAN	cysteinyl-tRNA synthetase 2, mitochondrial	334					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)													---	---	---	---
ING1	3621	broad.mit.edu	37	13	111371944	111371944	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:111371944G>A	uc001vri.2	+	2	1366	c.934G>A	c.(934-936)GAC>AAC	p.D312N	ING1_uc001vrf.2_Missense_Mutation_p.D125N|ING1_uc001vrg.2_Missense_Mutation_p.D100N|ING1_uc001vrh.2_Missense_Mutation_p.D169N	NM_005537	NP_005528	Q9UK53	ING1_HUMAN	inhibitor of growth family, member 1 isoform D	312					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)															---	---	---	---
ATP11A	23250	broad.mit.edu	37	13	113478673	113478673	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:113478673C>T	uc001vsi.3	+	10	894	c.806C>T	c.(805-807)ACG>ATG	p.T269M	ATP11A_uc001vsj.3_Missense_Mutation_p.T269M|ATP11A_uc001vsm.1_Missense_Mutation_p.T145M	NM_015205	NP_056020	P98196	AT11A_HUMAN	ATPase, class VI, type 11A isoform a	269	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			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)																---	---	---	---
F10	2159	broad.mit.edu	37	13	113803660	113803660	+	Silent	SNP	C	T	T	rs139031355		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:113803660C>T	uc001vsx.2	+	8	1353	c.1296C>T	c.(1294-1296)TTC>TTT	p.F432F	F10_uc001vsy.2_3'UTR|F10_uc001vsz.2_3'UTR	NM_000504	NP_000495	P00742	FA10_HUMAN	coagulation factor X preproprotein	432	Peptidase S1.				blood coagulation, extrinsic pathway|blood coagulation, intrinsic pathway|peptidyl-glutamic acid carboxylation|positive regulation of cell migration|positive regulation of protein kinase B signaling cascade|post-translational protein modification|proteolysis	endoplasmic reticulum lumen|extracellular region|Golgi lumen	calcium ion binding|phospholipid binding|protein binding|serine-type endopeptidase activity			pancreas(1)	1	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;0.113)|all_lung(25;0.0364)|all_epithelial(44;0.0373)|Lung NSC(25;0.128)|Breast(118;0.188)	all cancers(43;0.0805)|Epithelial(84;0.231)		Alteplase(DB00009)|Anistreplase(DB00029)|Antihemophilic Factor(DB00025)|Coagulation Factor IX(DB00100)|Coagulation factor VIIa(DB00036)|Enoxaparin(DB01225)|Heparin(DB01109)|Menadione(DB00170)|Reteplase(DB00015)|Tenecteplase(DB00031)													---	---	---	---
LAMP1	3916	broad.mit.edu	37	13	113976698	113976698	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:113976698G>A	uc001vtm.1	+	9	1497	c.1216G>A	c.(1216-1218)GGC>AGC	p.G406S	LAMP1_uc010tka.1_Missense_Mutation_p.G353S	NM_005561	NP_005552	P11279	LAMP1_HUMAN	lysosomal-associated membrane protein 1	406	Cytoplasmic (Potential).					endosome membrane|integral to plasma membrane|lysosomal membrane|membrane fraction				central_nervous_system(2)	2	Lung NSC(43;0.0161)|all_neural(89;0.0804)|Hepatocellular(20;0.0877)|Medulloblastoma(90;0.163)|Lung SC(71;0.218)	all_cancers(25;0.0482)|all_epithelial(44;0.0148)|all_lung(25;0.0271)|Lung NSC(25;0.0977)|Breast(118;0.188)	all cancers(43;0.025)|GBM - Glioblastoma multiforme(44;0.206)|Epithelial(84;0.246)															---	---	---	---
OR4K2	390431	broad.mit.edu	37	14	20344748	20344748	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:20344748A>G	uc001vwh.1	+	1	322	c.322A>G	c.(322-324)ACT>GCT	p.T108A		NM_001005501	NP_001005501	Q8NGD2	OR4K2_HUMAN	olfactory receptor, family 4, subfamily K,	108	Helical; Name=3; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(2)|skin(2)	4	all_cancers(95;0.00108)		Epithelial(56;9.96e-07)|all cancers(55;2.95e-06)	GBM - Glioblastoma multiforme(265;0.00327)														---	---	---	---
TEP1	7011	broad.mit.edu	37	14	20849543	20849543	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:20849543A>G	uc001vxe.2	-	32	4616	c.4576T>C	c.(4576-4578)TGT>CGT	p.C1526R	TEP1_uc010ahk.2_Missense_Mutation_p.C869R|TEP1_uc010tlf.1_RNA|TEP1_uc010tlg.1_Missense_Mutation_p.C1418R|TEP1_uc010tlh.1_5'UTR	NM_007110	NP_009041	Q99973	TEP1_HUMAN	telomerase-associated protein 1	1526					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)														---	---	---	---
ZNF219	51222	broad.mit.edu	37	14	21561758	21561758	+	Translation_Start_Site	SNP	C	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:21561758C>A	uc001vzr.2	-	2	414	c.-7G>T	c.(-9--5)AAGGG>AATGG		ZNF219_uc001vzs.2_Translation_Start_Site|ZNF219_uc010aik.1_Translation_Start_Site	NM_016423	NP_057507			zinc finger protein 219						negative regulation of transcription, DNA-dependent	integral to membrane|nucleus	DNA binding|histamine receptor activity|protein binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			central_nervous_system(1)	1	all_cancers(95;0.00185)		OV - Ovarian serous cystadenocarcinoma(11;9.86e-11)|Epithelial(56;1.27e-08)|all cancers(55;6.06e-08)	GBM - Glioblastoma multiforme(265;0.0191)												OREG0022565	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
SUPT16H	11198	broad.mit.edu	37	14	21826136	21826136	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:21826136T>C	uc001wao.2	-	21	2779	c.2440A>G	c.(2440-2442)ACC>GCC	p.T814A	SUPT16H_uc001wan.2_5'UTR	NM_007192	NP_009123	Q9Y5B9	SP16H_HUMAN	chromatin-specific transcription elongation	814					DNA repair|DNA replication|nucleosome disassembly|positive regulation of transcription elongation, DNA-dependent|positive regulation of viral transcription|transcription elongation from RNA polymerase II promoter|viral reproduction	chromosome|nucleoplasm	GTP binding				0	all_cancers(95;0.00115)		Epithelial(56;1.62e-06)|all cancers(55;1.49e-05)	GBM - Glioblastoma multiforme(265;0.0159)														---	---	---	---
OR10G2	26534	broad.mit.edu	37	14	22102477	22102477	+	Nonsense_Mutation	SNP	A	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:22102477A>T	uc010tmc.1	-	1	522	c.522T>A	c.(520-522)TGT>TGA	p.C174*		NM_001005466	NP_001005466	Q8NGC3	O10G2_HUMAN	olfactory receptor, family 10, subfamily G,	174	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			skin(1)	1	all_cancers(95;0.00113)	Acute lymphoblastic leukemia(2;0.0279)		GBM - Glioblastoma multiforme(265;0.0142)														---	---	---	---
OR10G2	26534	broad.mit.edu	37	14	22102755	22102755	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:22102755T>C	uc010tmc.1	-	1	244	c.244A>G	c.(244-246)ACC>GCC	p.T82A		NM_001005466	NP_001005466	Q8NGC3	O10G2_HUMAN	olfactory receptor, family 10, subfamily G,	82	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			skin(1)	1	all_cancers(95;0.00113)	Acute lymphoblastic leukemia(2;0.0279)		GBM - Glioblastoma multiforme(265;0.0142)														---	---	---	---
Unknown	0	broad.mit.edu	37	14	22111231	22111231	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:22111231G>A	uc001wbk.3	+	1	123	c.90G>A	c.(88-90)ATG>ATA	p.M30I						SubName: Full=Putative uncharacterized protein ENSP00000374930;																														---	---	---	---
OR4E2	26686	broad.mit.edu	37	14	22133626	22133626	+	Silent	SNP	C	T	T	rs118047831	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:22133626C>T	uc010tmd.1	+	1	330	c.330C>T	c.(328-330)GCC>GCT	p.A110A		NM_001001912	NP_001001912	Q8NGC2	OR4E2_HUMAN	olfactory receptor, family 4, subfamily E,	110	Helical; Name=3; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(2)|pancreas(1)|skin(1)	4	all_cancers(95;0.00113)	Acute lymphoblastic leukemia(2;0.0279)		GBM - Glioblastoma multiforme(265;0.0137)														---	---	---	---
Unknown	0	broad.mit.edu	37	14	22236815	22236815	+	Intron	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:22236815T>C	uc010tmf.1	+						uc001wbt.1_Missense_Mutation_p.V27A					SubName: Full=Putative uncharacterized protein ENSP00000374943;																														---	---	---	---
Unknown	0	broad.mit.edu	37	14	22938043	22938043	+	Intron	SNP	A	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:22938043A>C	uc001wbw.2	+						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|uc001wcx.3_Intron|uc001wdd.2_Intron|uc010ajj.1_Intron|uc001wde.1_Intron|uc001wdf.2_Intron|uc010ajk.1_Intron|uc001wdg.1_Intron|uc010ajl.1_Intron|uc001wdj.2_Intron|uc010ajo.1_Intron|uc010ajp.1_Intron|uc001wds.1_Intron|uc001wdv.3_Intron|uc001web.1_Missense_Mutation_p.C111G					SubName: Full=Alpha-chain C region; Flags: Fragment;																														---	---	---	---
Unknown	0	broad.mit.edu	37	14	23011160	23011160	+	Intron	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:23011160A>G	uc001wbw.2	+						uc010aja.1_Intron|uc010tmk.1_Intron|uc001wco.2_Intron|uc010aje.1_Intron|uc001wcp.2_Intron|uc001wcr.1_Intron|uc001wcs.1_Intron|uc010ajf.1_Intron|uc001wcx.3_Intron|uc001wde.1_Intron|uc010ajk.1_Intron|uc001wdg.1_Intron|uc010ajo.1_Intron|uc010ajp.1_Intron|uc001wdv.3_Intron|uc001wec.2_Intron|uc001wee.3_Intron|uc010tmt.1_Intron|uc010ajv.1_Intron|uc001weg.2_Intron|uc001wei.2_Intron|uc001wej.2_Intron|uc001wek.2_Intron|uc001wel.2_Intron|uc001wem.3_Intron|uc001wen.1_Intron|uc001weo.2_Intron|uc001wep.2_Intron|uc001weq.2_Intron|uc001wer.2_Intron|uc001wet.2_Intron|uc001weu.2_Intron|uc001wev.2_Intron|uc001wew.2_Intron|uc010tmv.1_Intron|uc001wez.2_Intron|uc010ajx.1_Intron|uc001wfb.1_Intron|uc001wfd.1_Intron|uc001wfe.2_Intron|uc001wfg.2_Intron|uc001wfh.1_Intron|uc001wfi.2_Intron|uc001wfk.2_Intron|uc001wfl.2_Intron|uc010ajy.1_Intron|uc001wfn.2_Intron|uc001wfp.2_Intron|uc001wfq.1_Intron|uc001wfr.1_Intron|uc010ajz.1_Intron|uc001wfs.1_Intron|uc001wft.1_Intron|uc001wfu.2_Intron|uc001wfv.1_Intron|uc001wfw.1_Intron|uc001wfx.2_Intron|uc001wfy.1_Intron|uc001wfz.1_Intron|uc001wgc.2_Intron|uc001wgd.2_Intron|uc001wge.3_Intron|uc001wgf.2_Intron|uc010tmw.1_Intron|uc010tmx.1_Intron|uc001wgh.2_Intron|uc001wgi.1_Intron|uc001wgj.1_5'UTR|uc001wgk.2_5'Flank					SubName: Full=Alpha-chain C region; Flags: Fragment;																														---	---	---	---
ACIN1	22985	broad.mit.edu	37	14	23549824	23549824	+	Silent	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:23549824T>C	uc001wit.3	-	6	1222	c.894A>G	c.(892-894)GCA>GCG	p.A298A	ACIN1_uc001wis.3_5'UTR|ACIN1_uc010akg.2_Silent_p.A298A|ACIN1_uc010tnj.1_Silent_p.A258A	NM_014977	NP_055792	Q9UKV3	ACINU_HUMAN	apoptotic chromatin condensation inducer 1	298	Glu-rich.				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)														---	---	---	---
IL25	64806	broad.mit.edu	37	14	23844877	23844877	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:23844877G>A	uc001wjr.2	+	2	632	c.322G>A	c.(322-324)GCC>ACC	p.A108T	IL25_uc001wjq.2_Missense_Mutation_p.A92T|CMTM5_uc001wjs.2_5'Flank|CMTM5_uc001wjt.2_5'Flank|CMTM5_uc010akm.2_5'Flank|CMTM5_uc010akn.2_5'Flank|CMTM5_uc001wju.2_5'Flank|CMTM5_uc010ako.2_5'Flank	NM_022789	NP_073626	Q9H293	IL25_HUMAN	interleukin 25 isoform 1 precursor	108					inflammatory response	extracellular space|membrane	cytokine activity|interleukin-17E receptor binding			ovary(1)	1	all_cancers(95;2e-05)			GBM - Glioblastoma multiforme(265;0.00665)|READ - Rectum adenocarcinoma(4;0.0276)|Colorectal(4;0.0396)														---	---	---	---
LRRC16B	90668	broad.mit.edu	37	14	24531772	24531772	+	Missense_Mutation	SNP	G	T	T	rs144871552		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:24531772G>T	uc001wlj.2	+	28	2721	c.2564G>T	c.(2563-2565)AGC>ATC	p.S855I	LRRC16B_uc001wlk.2_5'UTR	NM_138360	NP_612369	Q8ND23	LR16B_HUMAN	leucine rich repeat containing 16B	855										ovary(2)|breast(2)|pancreas(1)	5				GBM - Glioblastoma multiforme(265;0.019)														---	---	---	---
PCK2	5106	broad.mit.edu	37	14	24572932	24572932	+	Missense_Mutation	SNP	G	T	T	rs111723834	byFrequency	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:24572932G>T	uc001wlt.2	+	10	1814	c.1682G>T	c.(1681-1683)CGG>CTG	p.R561L	NRL_uc001wlq.2_Intron|PCK2_uc001wlr.1_Intron|PCK2_uc010tnw.1_Missense_Mutation_p.R427L|PCK2_uc010tnx.1_Missense_Mutation_p.R427L|PCK2_uc001wlu.3_Missense_Mutation_p.R395L	NM_004563	NP_004554	Q16822	PCKGM_HUMAN	mitochondrial phosphoenolpyruvate carboxykinase	561					gluconeogenesis	mitochondrial matrix	GTP binding|metal ion binding|phosphoenolpyruvate carboxykinase (GTP) activity			ovary(1)	1				GBM - Glioblastoma multiforme(265;0.0184)														---	---	---	---
TGM1	7051	broad.mit.edu	37	14	24730980	24730980	+	Silent	SNP	G	A	A	rs144989372	byFrequency;by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:24730980G>A	uc001wod.2	-	3	553	c.429C>T	c.(427-429)CGC>CGT	p.R143R	TGM1_uc010tog.1_Intron	NM_000359	NP_000350	P22735	TGM1_HUMAN	transglutaminase 1	143			R -> H (in LI1).|R -> C (in LI1 and NCIE).		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	24737100	24737100	+	Silent	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:24737100G>A	uc001wof.2	-	12	1634	c.1212C>T	c.(1210-1212)ACC>ACT	p.T404T	RABGGTA_uc001woe.2_RNA|RABGGTA_uc001wog.2_Silent_p.T404T|RABGGTA_uc001woh.2_RNA|RABGGTA_uc001woi.2_RNA	NM_004581	NP_004572	Q92696	PGTA_HUMAN	Rab geranylgeranyltransferase alpha	404					visual perception		Rab geranylgeranyltransferase activity|zinc ion binding				0				GBM - Glioblastoma multiforme(265;0.0184)														---	---	---	---
C14orf21	161424	broad.mit.edu	37	14	24769710	24769710	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:24769710G>A	uc001wol.1	+	2	407	c.344G>A	c.(343-345)GGA>GAA	p.G115E	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	115	Pumilio 1.						RNA binding			breast(2)|central_nervous_system(1)|skin(1)	4				GBM - Glioblastoma multiforme(265;0.0185)														---	---	---	---
ADCY4	196883	broad.mit.edu	37	14	24800328	24800328	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:24800328A>G	uc001wov.2	-	6	832	c.826T>C	c.(826-828)TAT>CAT	p.Y276H	ADCY4_uc001wow.2_Missense_Mutation_p.Y276H|ADCY4_uc010toh.1_5'UTR|ADCY4_uc001wox.2_Missense_Mutation_p.Y276H|ADCY4_uc001woy.2_Missense_Mutation_p.Y276H	NM_139247	NP_640340	Q8NFM4	ADCY4_HUMAN	adenylate cyclase 4	276	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)														---	---	---	---
HEATR5A	25938	broad.mit.edu	37	14	31844141	31844141	+	Missense_Mutation	SNP	A	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:31844141A>T	uc001wrf.3	-	6	940	c.863T>A	c.(862-864)GTT>GAT	p.V288D	HEATR5A_uc010ami.2_Missense_Mutation_p.V186D|HEATR5A_uc001wrg.1_Missense_Mutation_p.V170D|HEATR5A_uc010tpk.1_Missense_Mutation_p.V581D	NM_015473	NP_056288	Q86XA9	HTR5A_HUMAN	HEAT repeat containing 5A	575							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)														---	---	---	---
AKAP6	9472	broad.mit.edu	37	14	33292946	33292946	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:33292946C>A	uc001wrq.2	+	13	6097	c.5927C>A	c.(5926-5928)GCC>GAC	p.A1976D		NM_004274	NP_004265	Q13023	AKAP6_HUMAN	A-kinase anchor protein 6	1976					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)														---	---	---	---
PSMA6	5687	broad.mit.edu	37	14	35779975	35779975	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:35779975C>T	uc001wtd.2	+	4	392	c.283C>T	c.(283-285)CGC>TGC	p.R95C	KIAA0391_uc001wta.2_RNA|PSMA6_uc010tpt.1_Missense_Mutation_p.R16C|PSMA6_uc010tpu.1_Missense_Mutation_p.R16C	NM_002791	NP_002782	P60900	PSA6_HUMAN	proteasome alpha 6 subunit	95					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 NF-kappaB transcription factor activity|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|nuclear matrix|polysome|proteasome core complex, alpha-subunit complex|sarcomere	NF-kappaB binding|purine ribonucleoside triphosphate binding|RNA binding|threonine-type endopeptidase activity				0	Breast(36;0.0519)|Hepatocellular(127;0.158)		Lung(238;3.81e-05)|LUAD - Lung adenocarcinoma(48;5.59e-05)|Epithelial(34;0.00342)|all cancers(34;0.00973)	GBM - Glioblastoma multiforme(112;0.0234)														---	---	---	---
MBIP	51562	broad.mit.edu	37	14	36783947	36783947	+	Nonsense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:36783947G>A	uc001wtm.2	-	3	512	c.424C>T	c.(424-426)CAG>TAG	p.Q142*	MBIP_uc001wto.2_Nonsense_Mutation_p.Q142*|MBIP_uc010tpy.1_Intron|MBIP_uc001wtn.2_Nonsense_Mutation_p.Q142*	NM_016586	NP_057670	Q9NS73	MBIP1_HUMAN	MAP3K12 binding inhibitory protein 1 isoform 1	142					histone H3 acetylation|inactivation of MAPK activity involved in osmosensory signaling pathway	Ada2/Gcn5/Ada3 transcription activator complex|cytoplasm|nucleolus	identical protein binding|protein kinase inhibitor activity				0	all_cancers(3;1.55e-52)|all_epithelial(1;2.69e-62)|Breast(36;0.0505)|Hepatocellular(127;0.158)|Esophageal squamous(585;0.164)		Lung(8;1.28e-07)|LUAD - Lung adenocarcinoma(9;3e-07)|Epithelial(34;0.0303)|all cancers(34;0.0781)	GBM - Glioblastoma multiforme(112;0.0191)														---	---	---	---
NKX2-1	7080	broad.mit.edu	37	14	36986996	36986996	+	Silent	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:36986996C>T	uc001wtt.2	-	2	944	c.603G>A	c.(601-603)ACG>ACA	p.T201T	SFTA3_uc001wts.2_Intron|NKX2-1_uc001wtu.2_Silent_p.T231T|NKX2-1_uc001wtv.2_Silent_p.T201T|uc001wtw.1_5'Flank	NM_003317	NP_003308	P43699	NKX21_HUMAN	thyroid transcription factor 1 isoform 2	201	Homeobox.				epithelial tube branching involved in lung morphogenesis|globus pallidus development|negative regulation of cell migration|negative regulation of epithelial to mesenchymal transition|negative regulation of transforming growth factor beta receptor signaling pathway|positive regulation of transcription from RNA polymerase II promoter|response to hormone stimulus|thyroid gland development		protein binding|transcription regulatory region DNA binding			skin(1)	1	all_cancers(3;4.47e-51)|Hepatocellular(127;0.158)|Esophageal squamous(585;0.164)|Breast(36;0.165)		Lung(8;1.8e-08)|LUAD - Lung adenocarcinoma(9;2.16e-07)|Epithelial(34;0.014)|all cancers(34;0.0366)|LUSC - Lung squamous cell carcinoma(13;0.132)	GBM - Glioblastoma multiforme(112;0.0171)				A		NSCLC								---	---	---	---
KLHL28	54813	broad.mit.edu	37	14	45415035	45415035	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:45415035C>T	uc001wvq.2	-	2	343	c.97G>A	c.(97-99)GAA>AAA	p.E33K	KLHL28_uc001wvr.2_Missense_Mutation_p.E33K|KLHL28_uc001wvt.3_Missense_Mutation_p.E33K	NM_017658	NP_060128	Q9NXS3	KLH28_HUMAN	BTB (POZ) domain containing 5	33										ovary(1)	1																		---	---	---	---
FAM179B	23116	broad.mit.edu	37	14	45473513	45473513	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:45473513G>A	uc001wvv.2	+	4	2797	c.2588G>A	c.(2587-2589)AGT>AAT	p.S863N	FAM179B_uc001wvw.2_Missense_Mutation_p.S863N|FAM179B_uc010anc.2_RNA|FAM179B_uc001wvu.2_Missense_Mutation_p.S863N	NM_015091	NP_055906	Q9Y4F4	F179B_HUMAN	hypothetical protein LOC23116	863							binding			skin(2)|upper_aerodigestive_tract(1)	3																		---	---	---	---
KLHDC2	23588	broad.mit.edu	37	14	50249284	50249284	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:50249284T>G	uc001wwx.2	+	12	1469	c.1069T>G	c.(1069-1071)TTT>GTT	p.F357V	SDCCAG1_uc010anj.1_Intron|KLHDC2_uc001wwy.2_Intron|KLHDC2_uc010anp.2_Intron	NM_014315	NP_055130	Q9Y2U9	KLDC2_HUMAN	kelch domain containing 2	357	Kelch 6.					nucleus	protein binding			ovary(1)	1	all_epithelial(31;0.000959)|Breast(41;0.0117)																	---	---	---	---
SDCCAG1	9147	broad.mit.edu	37	14	50255915	50255915	+	Silent	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:50255915A>G	uc001wxc.2	-	28	2912	c.2844T>C	c.(2842-2844)GTT>GTC	p.V948V	SDCCAG1_uc010anj.1_Silent_p.V948V|SDCCAG1_uc001wwz.2_Silent_p.V148V|SDCCAG1_uc001wxa.2_Silent_p.V228V|SDCCAG1_uc010tqi.1_Silent_p.V927V|SDCCAG1_uc001wxe.2_Silent_p.V906V	NM_004713	NP_004704	O60524	NEMF_HUMAN	serologically defined colon cancer antigen 1	948						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)														---	---	---	---
SOS2	6655	broad.mit.edu	37	14	50612211	50612211	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:50612211T>C	uc001wxs.3	-	15	2586	c.2488A>G	c.(2488-2490)ACC>GCC	p.T830A	SOS2_uc010tql.1_Missense_Mutation_p.T797A|SOS2_uc010tqm.1_RNA	NM_006939	NP_008870	Q07890	SOS2_HUMAN	son of sevenless homolog 2	830	Ras-GEF.				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)																	---	---	---	---
SOS2	6655	broad.mit.edu	37	14	50666423	50666423	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:50666423T>C	uc001wxs.3	-	4	594	c.496A>G	c.(496-498)ATG>GTG	p.M166V	SOS2_uc010tql.1_Missense_Mutation_p.M166V	NM_006939	NP_008870	Q07890	SOS2_HUMAN	son of sevenless homolog 2	166					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)																	---	---	---	---
CDKL1	8814	broad.mit.edu	37	14	50802771	50802771	+	Silent	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:50802771T>C	uc010anu.1	-	20	2922	c.2922A>G	c.(2920-2922)CCA>CCG	p.P974P	CDKL1_uc001wxz.2_Intron	NM_004196	NP_004187	Q00532	CDKL1_HUMAN	cyclin-dependent kinase-like 1	Error:Variant_position_missing_in_Q00532_after_alignment						cytoplasm|nucleus	ATP binding|cyclin-dependent protein kinase activity			ovary(1)|stomach(1)	2	all_epithelial(31;0.000746)|Breast(41;0.0102)																	---	---	---	---
MAP4K5	11183	broad.mit.edu	37	14	50929503	50929503	+	Intron	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:50929503A>G	uc001wya.2	-						MAP4K5_uc001wyb.2_Intron|MAP4K5_uc010anv.1_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)																	---	---	---	---
ERO1L	30001	broad.mit.edu	37	14	53112977	53112977	+	Missense_Mutation	SNP	A	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:53112977A>T	uc001wzv.2	-	15	1467	c.1241T>A	c.(1240-1242)ATC>AAC	p.I414N	ERO1L_uc001wzw.2_RNA|ERO1L_uc010aof.2_Intron	NM_014584	NP_055399	Q96HE7	ERO1A_HUMAN	ERO1-like precursor	414					chaperone mediated protein folding requiring cofactor|electron transport chain|protein thiol-disulfide exchange|response to temperature stimulus|transport	endoplasmic reticulum lumen|endoplasmic reticulum membrane|microsome	disulfide oxidoreductase activity|flavin adenine dinucleotide binding|oxidoreductase activity, acting on a sulfur group of donors, disulfide as acceptor				0	Breast(41;0.226)																	---	---	---	---
BMP4	652	broad.mit.edu	37	14	54418739	54418739	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:54418739G>A	uc001xal.3	-	2	389	c.202C>T	c.(202-204)CGC>TGC	p.R68C	BMP4_uc010aoh.2_Missense_Mutation_p.R68C|BMP4_uc001xao.3_Missense_Mutation_p.R68C|BMP4_uc001xan.3_Missense_Mutation_p.R68C	NM_130851	NP_570912	P12644	BMP4_HUMAN	bone morphogenetic protein 4 preproprotein	68					activation of MAPKK activity|blood vessel endothelial cell proliferation involved in sprouting angiogenesis|BMP signaling pathway involved in heart induction|BMP signaling pathway involved in nephric duct formation|branching involved in ureteric bud morphogenesis|bronchus development|bud dilation involved in lung branching|cardiac septum development|cartilage development|endocardial cushion development|epithelial cell proliferation involved in lung morphogenesis|intermediate mesodermal cell differentiation|lung alveolus development|lymphoid progenitor cell differentiation|mesenchymal to epithelial transition involved in metanephros morphogenesis|mesonephros development|negative regulation of branch elongation involved in ureteric bud branching by BMP signaling pathway|negative regulation of branching involved in ureteric bud morphogenesis|negative regulation of cell proliferation involved in heart morphogenesis|negative regulation of glomerular mesangial cell proliferation|negative regulation of glomerulus development|negative regulation of immature T cell proliferation in thymus|negative regulation of MAP kinase activity|negative regulation of metanephric comma-shaped body morphogenesis|negative regulation of metanephric S-shaped body morphogenesis|negative regulation of mitosis|negative regulation of myoblast differentiation|negative regulation of phosphorylation|negative regulation of striated muscle tissue development|negative regulation of thymocyte apoptosis|negative regulation of transcription from RNA polymerase II promoter|osteoblast differentiation|positive regulation of apoptosis|positive regulation of bone mineralization|positive regulation of cardiac muscle fiber development|positive regulation of cartilage development|positive regulation of collagen biosynthetic process|positive regulation of endothelial cell migration|positive regulation of endothelial cell proliferation|positive regulation of kidney development|positive regulation of osteoblast differentiation|positive regulation of pathway-restricted SMAD protein phosphorylation|positive regulation of SMAD protein import into nucleus|positive regulation of smooth muscle cell proliferation|positive regulation of transcription from RNA polymerase II promoter|post-embryonic development|protein localization to nucleus|pulmonary artery endothelial tube morphogenesis|secondary heart field specification|SMAD protein signal transduction|specification of ureteric bud anterior/posterior symmetry by BMP signaling pathway|steroid hormone mediated signaling pathway	extracellular space|proteinaceous extracellular matrix	BMP receptor binding|chemoattractant activity|cytokine activity|growth factor activity				0																		---	---	---	---
GMFB	2764	broad.mit.edu	37	14	54947660	54947660	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:54947660C>A	uc010tqz.1	-	5	314	c.215G>T	c.(214-216)AGT>ATT	p.S72I	GMFB_uc001xaw.1_Splice_Site	NM_004124	NP_004115	P60983	GMFB_HUMAN	glia maturation factor, beta	72	ADF-H.				nervous system development|protein phosphorylation	intracellular	actin binding|enzyme activator activity|growth factor activity|protein kinase inhibitor activity|signal transducer activity				0																		---	---	---	---
WDHD1	11169	broad.mit.edu	37	14	55462508	55462508	+	Silent	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:55462508A>G	uc001xbm.1	-	11	1044	c.966T>C	c.(964-966)GAT>GAC	p.D322D	WDHD1_uc001xbn.1_Silent_p.D199D	NM_007086	NP_009017	O75717	WDHD1_HUMAN	WD repeat and HMG-box DNA binding protein 1	322						cytoplasm|nucleoplasm	DNA binding			skin(1)	1																		---	---	---	---
KIAA0586	9786	broad.mit.edu	37	14	58896094	58896094	+	Silent	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:58896094A>G	uc001xdv.3	+	2	486	c.213A>G	c.(211-213)TTA>TTG	p.L71L	KIAA0586_uc010trr.1_Silent_p.L71L|KIAA0586_uc001xdt.3_5'UTR|KIAA0586_uc001xdu.3_Silent_p.L56L|KIAA0586_uc010trs.1_5'UTR|TIMM9_uc010aph.2_5'Flank|TIMM9_uc001xds.2_5'Flank|TIMM9_uc010api.2_5'Flank	NM_014749	NP_055564	E9PGW8	E9PGW8_HUMAN	talpid3 protein	71										ovary(1)	1																		---	---	---	---
C14orf39	317761	broad.mit.edu	37	14	60932746	60932746	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:60932746T>C	uc001xez.3	-	11	1033	c.923A>G	c.(922-924)CAG>CGG	p.Q308R	C14orf39_uc010apo.2_Missense_Mutation_p.Q19R	NM_174978	NP_777638	Q08AQ4	Q08AQ4_HUMAN	hypothetical protein LOC317761	308										ovary(2)|haematopoietic_and_lymphoid_tissue(1)|skin(1)	4				OV - Ovarian serous cystadenocarcinoma(108;0.0448)														---	---	---	---
HIF1A	3091	broad.mit.edu	37	14	62204920	62204920	+	Silent	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:62204920C>T	uc001xfq.2	+	10	1769	c.1365C>T	c.(1363-1365)ACC>ACT	p.T455T	HIF1A_uc001xfr.2_Silent_p.T455T|HIF1A_uc001xfs.2_Silent_p.T456T	NM_001530	NP_001521	Q16665	HIF1A_HUMAN	hypoxia-inducible factor 1, alpha subunit	455	ODD.				cellular response to hypoxia|collagen metabolic process|connective tissue replacement involved in inflammatory response wound healing|elastin metabolic process|epithelial to mesenchymal transition|oxygen homeostasis|positive regulation of chemokine production|positive regulation of epithelial cell migration|positive regulation of hormone biosynthetic process|positive regulation of nitric-oxide synthase activity|positive regulation of transcription from RNA polymerase II promoter|positive regulation vascular endothelial growth factor production|regulation of transcription from RNA polymerase II promoter in response to oxidative stress|regulation of transforming growth factor-beta2 production	cytoplasm|nucleolus|transcription factor complex	histone acetyltransferase binding|Hsp90 protein binding|protein heterodimerization activity|sequence-specific enhancer binding RNA polymerase II transcription factor activity|signal transducer activity|transcription factor binding|transcription regulatory region DNA binding			kidney(3)|lung(1)	4				OV - Ovarian serous cystadenocarcinoma(108;1.62e-09)|BRCA - Breast invasive adenocarcinoma(234;0.189)														---	---	---	---
SYT16	83851	broad.mit.edu	37	14	62567320	62567320	+	Silent	SNP	C	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:62567320C>A	uc001xfu.1	+	6	2030	c.1833C>A	c.(1831-1833)GCC>GCA	p.A611A	SYT16_uc010tse.1_Silent_p.A169A	NM_031914	NP_114120	Q17RD7	SYT16_HUMAN	synaptotagmin XIV-like	611	C2 2.									central_nervous_system(1)	1				OV - Ovarian serous cystadenocarcinoma(108;0.0438)|BRCA - Breast invasive adenocarcinoma(234;0.118)														---	---	---	---
SYNE2	23224	broad.mit.edu	37	14	64491082	64491082	+	Silent	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:64491082T>C	uc001xgm.2	+	39	5975	c.5745T>C	c.(5743-5745)AGT>AGC	p.S1915S	SYNE2_uc001xgl.2_Silent_p.S1915S	NM_015180	NP_055995	Q8WXH0	SYNE2_HUMAN	spectrin repeat containing, nuclear envelope 2	1915	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)														---	---	---	---
SYNE2	23224	broad.mit.edu	37	14	64669601	64669601	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:64669601A>G	uc001xgm.2	+	100	18351	c.18121A>G	c.(18121-18123)ATT>GTT	p.I6041V	SYNE2_uc001xgl.2_Missense_Mutation_p.I6041V|SYNE2_uc010apy.2_Missense_Mutation_p.I2426V|SYNE2_uc001xgn.2_Missense_Mutation_p.I1003V|SYNE2_uc001xgo.2_RNA|SYNE2_uc010aqa.2_Missense_Mutation_p.I11V|SYNE2_uc001xgq.2_Missense_Mutation_p.I406V	NM_015180	NP_055995	Q8WXH0	SYNE2_HUMAN	spectrin repeat containing, nuclear envelope 2	6041	Cytoplasmic (Potential).|Spectrin 6.				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)														---	---	---	---
SYNE2	23224	broad.mit.edu	37	14	64687230	64687230	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:64687230A>G	uc001xgm.2	+	110	20097	c.19867A>G	c.(19867-19869)ACC>GCC	p.T6623A	SYNE2_uc001xgl.2_Missense_Mutation_p.T6646A|SYNE2_uc010apy.2_Missense_Mutation_p.T3008A|SYNE2_uc001xgn.2_Missense_Mutation_p.T1585A|SYNE2_uc001xgo.2_RNA|SYNE2_uc010aqa.2_Missense_Mutation_p.T593A|SYNE2_uc001xgq.2_Missense_Mutation_p.T988A|SYNE2_uc001xgr.2_Missense_Mutation_p.T406A|SYNE2_uc010tsi.1_Missense_Mutation_p.T280A|SYNE2_uc001xgs.2_Missense_Mutation_p.T280A|SYNE2_uc001xgt.2_Missense_Mutation_p.T154A	NM_015180	NP_055995	Q8WXH0	SYNE2_HUMAN	spectrin repeat containing, nuclear envelope 2	6623	Cytoplasmic (Potential).|Spectrin 9.				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)														---	---	---	---
MTHFD1	4522	broad.mit.edu	37	14	64877835	64877835	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:64877835T>C	uc001xhb.2	+	3	541	c.154T>C	c.(154-156)TAT>CAT	p.Y52H	MTHFD1_uc010aqe.2_Intron|MTHFD1_uc010aqf.2_Missense_Mutation_p.Y108H	NM_005956	NP_005947	P11586	C1TC_HUMAN	methylenetetrahydrofolate dehydrogenase 1	52	Methylenetetrahydrofolate dehydrogenase and cyclohydrolase.|Substrate binding.			Y->A,S: Reduces dehydrogenase activity by 99%. Reduces cyclohydrolase activity by 70%. No effect on Km for NADP and for 5,10-methenyltetrahydrofolate.|Y->F: Slightly reduces dehydrogenase and cyclohydrolase activity. Increase of Km for NADP and for 5,10- methenyltetrahydrofolate.	folic acid metabolic process|folic acid-containing compound biosynthetic process|histidine biosynthetic process|methionine biosynthetic process|one-carbon metabolic process|purine nucleotide biosynthetic process	cytosol|mitochondrion	ATP binding|formate-tetrahydrofolate ligase activity|methenyltetrahydrofolate cyclohydrolase activity|methylenetetrahydrofolate dehydrogenase (NADP+) activity|methylenetetrahydrofolate dehydrogenase|protein binding			ovary(2)	2				OV - Ovarian serous cystadenocarcinoma(108;8.7e-12)|all cancers(60;3.29e-11)|BRCA - Breast invasive adenocarcinoma(234;0.0488)	NADH(DB00157)|Tetrahydrofolic acid(DB00116)													---	---	---	---
PLEKHG3	26030	broad.mit.edu	37	14	65197639	65197639	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:65197639G>A	uc001xho.1	+	6	958	c.689G>A	c.(688-690)CGC>CAC	p.R230H	PLEKHG3_uc001xhn.1_Missense_Mutation_p.R174H|PLEKHG3_uc001xhp.2_Missense_Mutation_p.R230H|PLEKHG3_uc010aqh.1_5'UTR	NM_015549	NP_056364	A1L390	PKHG3_HUMAN	pleckstrin homology domain containing, family G,	230	DH.				regulation of Rho protein signal transduction	intracellular	Rho guanyl-nucleotide exchange factor activity			skin(1)	1				all cancers(60;0.00802)|OV - Ovarian serous cystadenocarcinoma(108;0.0109)|BRCA - Breast invasive adenocarcinoma(234;0.0485)														---	---	---	---
SPTB	6710	broad.mit.edu	37	14	65218952	65218952	+	Silent	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:65218952T>C	uc010aqi.2	-	15	2682	c.2667A>G	c.(2665-2667)GAA>GAG	p.E889E	SPTB_uc001xhr.2_Intron|SPTB_uc001xhs.2_Intron	NM_001024858	NP_001020029	P11277	SPTB1_HUMAN	spectrin beta isoform a	Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment					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	65233527	65233527	+	Intron	SNP	A	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:65233527A>T	uc001xht.2	-						SPTB_uc001xhr.2_Intron|SPTB_uc001xhs.2_Intron|SPTB_uc001xhu.2_Intron|SPTB_uc010aqi.2_Intron	NM_000347	NP_000338			spectrin beta isoform b						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)														---	---	---	---
FUT8	2530	broad.mit.edu	37	14	66188717	66188717	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:66188717G>T	uc001xin.2	+	8	2257	c.1060G>T	c.(1060-1062)GGC>TGC	p.G354C	FUT8_uc001xio.2_Missense_Mutation_p.G354C|FUT8_uc010tsp.1_Missense_Mutation_p.G191C|FUT8_uc001xir.3_Intron|FUT8_uc001xip.2_Missense_Mutation_p.G354C|FUT8_uc001xiq.2_Missense_Mutation_p.G225C|FUT8_uc001xis.2_Intron	NM_178155	NP_835368	Q9BYC5	FUT8_HUMAN	fucosyltransferase 8 isoform a	354	Lumenal (Potential).				in utero embryonic development|L-fucose catabolic process|N-glycan processing|oligosaccharide biosynthetic process|post-translational protein modification|protein glycosylation in Golgi|protein N-linked glycosylation via asparagine	Golgi cisterna membrane|integral to membrane	glycoprotein 6-alpha-L-fucosyltransferase activity|SH3 domain binding			ovary(1)	1				all cancers(60;0.00109)|OV - Ovarian serous cystadenocarcinoma(108;0.00242)|BRCA - Breast invasive adenocarcinoma(234;0.0114)														---	---	---	---
RAD51L1	5890	broad.mit.edu	37	14	68331838	68331838	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:68331838C>T	uc001xkf.1	+	5	498	c.434C>T	c.(433-435)TCT>TTT	p.S145F	RAD51L1_uc010aqq.2_Missense_Mutation_p.S145F|RAD51L1_uc001xkd.2_Missense_Mutation_p.S145F|RAD51L1_uc010aqr.2_Missense_Mutation_p.S26F|RAD51L1_uc001xke.2_Missense_Mutation_p.S145F|RAD51L1_uc010aqs.1_Missense_Mutation_p.S145F|RAD51L1_uc001xkg.1_Missense_Mutation_p.S145F	NM_133509	NP_598193	O15315	RA51B_HUMAN	RAD51-like 1 isoform 3	145					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					---	---	---	---
SMOC1	64093	broad.mit.edu	37	14	70420183	70420183	+	Silent	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:70420183G>A	uc001xls.1	+	3	565	c.312G>A	c.(310-312)GAG>GAA	p.E104E	SMOC1_uc001xlt.1_Silent_p.E104E	NM_022137	NP_071420	Q9H4F8	SMOC1_HUMAN	secreted modular calcium-binding protein 1	104	Thyroglobulin type-1 1.				cell differentiation|eye development|limb development|regulation of osteoblast differentiation|signal transduction	basement membrane	calcium ion binding			upper_aerodigestive_tract(1)|pancreas(1)	2				all cancers(60;0.00417)|BRCA - Breast invasive adenocarcinoma(234;0.0119)|OV - Ovarian serous cystadenocarcinoma(108;0.028)														---	---	---	---
ADAM20	8748	broad.mit.edu	37	14	70989860	70989860	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:70989860T>C	uc001xme.2	-	2	2010	c.1765A>G	c.(1765-1767)AAC>GAC	p.N589D		NM_003814	NP_003805	O43506	ADA20_HUMAN	ADAM metallopeptidase domain 20 preproprotein	539	Cys-rich.|Extracellular (Potential).				proteolysis|single fertilization	integral to membrane	metalloendopeptidase activity|zinc ion binding			skin(1)	1			KIRC - Kidney renal clear cell carcinoma(12;0.133)|Kidney(31;0.188)	all cancers(60;0.00294)|BRCA - Breast invasive adenocarcinoma(234;0.00668)|OV - Ovarian serous cystadenocarcinoma(108;0.0344)														---	---	---	---
TTC9	23508	broad.mit.edu	37	14	71137786	71137786	+	Intron	SNP	C	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:71137786C>A	uc001xmi.2	+							NM_015351	NP_056166			tetratricopeptide repeat domain 9								binding				0				all cancers(60;0.00545)|BRCA - Breast invasive adenocarcinoma(234;0.00747)|OV - Ovarian serous cystadenocarcinoma(108;0.0538)														---	---	---	---
PCNX	22990	broad.mit.edu	37	14	71445269	71445269	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:71445269C>T	uc001xmo.2	+	6	2661	c.2215C>T	c.(2215-2217)CGG>TGG	p.R739W	PCNX_uc001xmn.3_Missense_Mutation_p.R739W|PCNX_uc010are.1_Missense_Mutation_p.R739W	NM_014982	NP_055797	Q96RV3	PCX1_HUMAN	pecanex-like 1	739						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)														---	---	---	---
PCNX	22990	broad.mit.edu	37	14	71502788	71502788	+	Nonsense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:71502788C>T	uc001xmo.2	+	19	4227	c.3781C>T	c.(3781-3783)CGA>TGA	p.R1261*	PCNX_uc010are.1_Nonsense_Mutation_p.R1150*|PCNX_uc010arf.1_Nonsense_Mutation_p.R121*	NM_014982	NP_055797	Q96RV3	PCX1_HUMAN	pecanex-like 1	1261						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)														---	---	---	---
C14orf169	79697	broad.mit.edu	37	14	73957853	73957853	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:73957853G>A	uc001xok.1	+	1	210	c.131G>A	c.(130-132)CGA>CAA	p.R44Q	HEATR4_uc010tua.1_Intron	NM_024644	NP_078920	Q9H6W3	NO66_HUMAN	chromosome 14 open reading frame 169	44					negative regulation of osteoblast differentiation|negative regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleolus|nucleoplasm	histone demethylase activity (H3-K36 specific)|histone demethylase activity (H3-K4 specific)|iron ion binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen				0				BRCA - Breast invasive adenocarcinoma(234;0.0033)|OV - Ovarian serous cystadenocarcinoma(108;0.215)														---	---	---	---
ABCD4	5826	broad.mit.edu	37	14	74754524	74754524	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:74754524G>A	uc001xpr.2	-	17	1777	c.1625C>T	c.(1624-1626)CCG>CTG	p.P542L	ABCD4_uc001xps.2_Missense_Mutation_p.P383L|ABCD4_uc001xpt.2_Missense_Mutation_p.P383L|ABCD4_uc010tur.1_Missense_Mutation_p.P438L	NM_005050	NP_005041	O14678	ABCD4_HUMAN	ATP-binding cassette, sub-family D, member 4	542	ABC transporter.					ATP-binding cassette (ABC) transporter complex|integral to membrane|peroxisomal membrane	ATP binding|ATPase activity, coupled to transmembrane movement of substances			upper_aerodigestive_tract(2)|large_intestine(1)|ovary(1)	4				BRCA - Breast invasive adenocarcinoma(234;0.00153)														---	---	---	---
LTBP2	4053	broad.mit.edu	37	14	74995341	74995341	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:74995341C>T	uc001xqa.2	-	12	2600	c.2213G>A	c.(2212-2214)CGC>CAC	p.R738H		NM_000428	NP_000419	Q14767	LTBP2_HUMAN	latent transforming growth factor beta binding	738					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	75142904	75142904	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:75142904A>G	uc001xqb.2	-	7	1277	c.772T>C	c.(772-774)TGC>CGC	p.C258R	KIAA0317_uc010tut.1_Missense_Mutation_p.C97R|KIAA0317_uc001xqc.2_Missense_Mutation_p.C258R	NM_001039479	NP_001034568	O15033	K0317_HUMAN	hypothetical protein LOC9870	258					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	75264366	75264366	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:75264366G>A	uc001xqj.3	+	5	2490	c.2366G>A	c.(2365-2367)CGC>CAC	p.R789H	YLPM1_uc001xql.3_RNA	NM_019589	NP_062535	P49750	YLPM1_HUMAN	YLP motif containing 1	594					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)														---	---	---	---
DLST	1743	broad.mit.edu	37	14	75352347	75352347	+	Intron	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:75352347A>G	uc001xqv.2	+						DLST_uc001xqu.2_Intron|DLST_uc001xqt.2_Intron|DLST_uc010tuw.1_Intron|DLST_uc010tuu.1_Intron|DLST_uc001xqs.2_Intron|DLST_uc010tuv.1_Intron	NM_001933	NP_001924			dihydrolipoamide S-succinyltransferase (E2						lysine catabolic process|tricarboxylic acid cycle	mitochondrial matrix|nucleus	dihydrolipoyllysine-residue succinyltransferase activity			ovary(1)	1				BRCA - Breast invasive adenocarcinoma(234;0.00698)														---	---	---	---
NEK9	91754	broad.mit.edu	37	14	75580049	75580049	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:75580049G>A	uc001xrl.2	-	8	1085	c.931C>T	c.(931-933)CGC>TGC	p.R311C	NEK9_uc001xrk.2_Translation_Start_Site	NM_033116	NP_149107	Q8TD19	NEK9_HUMAN	NIMA-related kinase 9	311					cell division|mitosis	mitochondrion|nucleus	ATP binding|metal ion binding|protein kinase binding|protein serine/threonine kinase activity			lung(2)|stomach(2)|ovary(1)	5				BRCA - Breast invasive adenocarcinoma(234;0.00718)														---	---	---	---
TGFB3	7043	broad.mit.edu	37	14	76447190	76447190	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:76447190T>C	uc001xsc.2	-	1	903	c.47A>G	c.(46-48)AAC>AGC	p.N16S	TGFB3_uc001xsd.2_Missense_Mutation_p.N14S	NM_003239	NP_003230	P10600	TGFB3_HUMAN	transforming growth factor, beta 3 precursor	16					cell growth|cell-cell junction organization|detection of hypoxia|face morphogenesis|in utero embryonic development|induction of apoptosis|lung alveolus development|mammary gland development|menstrual cycle phase|negative regulation of cell proliferation|negative regulation of DNA replication|negative regulation of macrophage cytokine production|negative regulation of neuron apoptosis|odontogenesis|ossification involved in bone remodeling|palate development|platelet activation|platelet degranulation|positive regulation of bone mineralization|positive regulation of cell division|positive regulation of collagen biosynthetic process|positive regulation of DNA replication|positive regulation of epithelial to mesenchymal transition|positive regulation of filopodium assembly|positive regulation of pathway-restricted SMAD protein phosphorylation|positive regulation of protein secretion|positive regulation of SMAD protein import into nucleus|positive regulation of transcription from RNA polymerase II promoter|response to progesterone stimulus|salivary gland morphogenesis|transforming growth factor beta receptor signaling pathway	extracellular matrix|platelet alpha granule lumen	growth factor activity|identical protein binding|transforming growth factor beta binding|type I transforming growth factor beta receptor binding|type II transforming growth factor beta receptor binding			breast(1)|skin(1)	2				BRCA - Breast invasive adenocarcinoma(234;0.0169)														---	---	---	---
ESRRB	2103	broad.mit.edu	37	14	76905709	76905709	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:76905709G>A	uc001xsq.1	+	2	80	c.13G>A	c.(13-15)GAC>AAC	p.D5N	ESRRB_uc001xsr.2_Missense_Mutation_p.D5N|ESRRB_uc001xso.2_RNA	NM_004452	NP_004443	A2VDJ2	A2VDJ2_HUMAN	estrogen-related receptor beta	5						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)														---	---	---	---
TMEM63C	57156	broad.mit.edu	37	14	77718125	77718125	+	Intron	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:77718125T>C	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)														---	---	---	---
TSHR	7253	broad.mit.edu	37	14	81610521	81610521	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:81610521C>T	uc001xvd.1	+	10	2275	c.2119C>T	c.(2119-2121)CGG>TGG	p.R707W		NM_000369	NP_000360	P16473	TSHR_HUMAN	thyroid stimulating hormone receptor isoform 1	707	Cytoplasmic (Potential).				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 						---	---	---	---
STON2	85439	broad.mit.edu	37	14	81737056	81737056	+	Silent	SNP	G	A	A	rs142313733		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:81737056G>A	uc010tvu.1	-	5	2772	c.2571C>T	c.(2569-2571)GAC>GAT	p.D857D	STON2_uc001xvk.1_Silent_p.D857D|STON2_uc010tvt.1_Silent_p.D654D	NM_033104	NP_149095	Q8WXE9	STON2_HUMAN	stonin 2	857	MHD.				endocytosis|intracellular protein transport|regulation of endocytosis	clathrin adaptor complex|nucleolus	protein binding			skin(3)|pancreas(2)	5				BRCA - Breast invasive adenocarcinoma(234;0.0348)														---	---	---	---
SEL1L	6400	broad.mit.edu	37	14	81952795	81952795	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:81952795A>G	uc010tvv.1	-	17	1753	c.1636T>C	c.(1636-1638)TTT>CTT	p.F546L		NM_005065	NP_005056	Q9UBV2	SE1L1_HUMAN	sel-1 suppressor of lin-12-like precursor	546	Lumenal (Potential).|Interaction with ERLEC1, OS9 and SYVN1.|Sel1-like 9.				Notch signaling pathway	endoplasmic reticulum membrane|integral to membrane	protein binding			ovary(1)	1				BRCA - Breast invasive adenocarcinoma(234;0.0299)														---	---	---	---
PTPN21	11099	broad.mit.edu	37	14	88934524	88934524	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:88934524T>C	uc001xwv.3	-	19	3813	c.3482A>G	c.(3481-3483)TAC>TGC	p.Y1161C	PTPN21_uc010twc.1_Missense_Mutation_p.Y957C	NM_007039	NP_008970	Q16825	PTN21_HUMAN	protein tyrosine phosphatase, non-receptor type	1161	Tyrosine-protein phosphatase.					cytoplasm|cytoskeleton	binding|protein tyrosine phosphatase activity			ovary(3)|skin(1)	4																		---	---	---	---
ZC3H14	79882	broad.mit.edu	37	14	89039284	89039284	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:89039284T>C	uc001xww.2	+	6	1019	c.794T>C	c.(793-795)GTG>GCG	p.V265A	ZC3H14_uc010twd.1_Missense_Mutation_p.V265A|ZC3H14_uc010twe.1_Missense_Mutation_p.V265A|ZC3H14_uc001xwx.2_Missense_Mutation_p.V265A|ZC3H14_uc010twf.1_Missense_Mutation_p.V110A|ZC3H14_uc001xwy.2_Missense_Mutation_p.V231A|ZC3H14_uc010twg.1_Missense_Mutation_p.V110A|ZC3H14_uc001xxa.2_5'Flank	NM_024824	NP_079100	Q6PJT7	ZC3HE_HUMAN	zinc finger CCCH-type containing 14 isoform 1	265						cytoplasm|cytoplasm|nuclear speck	protein binding|RNA binding|zinc ion binding			ovary(2)|skin(1)	3																		---	---	---	---
EML5	161436	broad.mit.edu	37	14	89087460	89087460	+	Silent	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:89087460A>G	uc001xxg.2	-	38	5385	c.5199T>C	c.(5197-5199)GAT>GAC	p.D1733D	EML5_uc001xxf.2_Silent_p.D520D|EML5_uc001xxd.2_5'Flank|EML5_uc001xxe.2_Silent_p.D82D	NM_183387	NP_899243	Q05BV3	EMAL5_HUMAN	echinoderm microtubule associated protein like	1725	WD 25.					cytoplasm|microtubule				ovary(3)	3																		---	---	---	---
GPR68	8111	broad.mit.edu	37	14	91701139	91701139	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:91701139T>C	uc001xzg.2	-	2	597	c.256A>G	c.(256-258)AAC>GAC	p.N86D	GPR68_uc001xzh.2_Missense_Mutation_p.N96D	NM_003485	NP_003476	Q15743	OGR1_HUMAN	G protein-coupled receptor 68	86	Extracellular (Potential).				inflammatory response	integral to plasma membrane	G-protein coupled receptor activity			kidney(1)	1		all_cancers(154;0.0555)		COAD - Colon adenocarcinoma(157;0.21)														---	---	---	---
SMEK1	55671	broad.mit.edu	37	14	91942746	91942746	+	Intron	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:91942746A>G	uc001xzn.2	-						SMEK1_uc001xzm.2_Intron|SMEK1_uc001xzo.2_Intron|SMEK1_uc010atz.2_Intron|SMEK1_uc001xzp.1_Intron|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)														---	---	---	---
FBLN5	10516	broad.mit.edu	37	14	92336583	92336583	+	Silent	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:92336583C>T	uc001xzx.3	-	11	1805	c.1332G>A	c.(1330-1332)TCG>TCA	p.S444S	TC2N_uc001xzv.3_5'Flank|FBLN5_uc010aud.2_Silent_p.S449S|FBLN5_uc010aue.2_Silent_p.S485S|FBLN5_uc001xzw.2_RNA	NM_006329	NP_006320	Q9UBX5	FBLN5_HUMAN	fibulin 5 precursor	444					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)																---	---	---	---
CPSF2	53981	broad.mit.edu	37	14	92601838	92601838	+	Silent	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:92601838G>A	uc001yah.1	+	6	780	c.543G>A	c.(541-543)GAG>GAA	p.E181E		NM_017437	NP_059133	Q9P2I0	CPSF2_HUMAN	cleavage and polyadenylation specific factor 2	181					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)														---	---	---	---
SLC24A4	123041	broad.mit.edu	37	14	92959881	92959881	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:92959881T>C	uc001yak.2	+	17	1751	c.1727T>C	c.(1726-1728)GTT>GCT	p.V576A	SLC24A4_uc001yai.2_Missense_Mutation_p.V529A|SLC24A4_uc010twm.1_Missense_Mutation_p.V574A|SLC24A4_uc001yaj.2_Missense_Mutation_p.V557A|SLC24A4_uc010auj.2_3'UTR|SLC24A4_uc010twn.1_Missense_Mutation_p.V349A|SLC24A4_uc001yan.2_Missense_Mutation_p.V287A	NM_153646	NP_705932	Q8NFF2	NCKX4_HUMAN	solute carrier family 24 member 4 isoform 1	593	Helical; (Potential).					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)														---	---	---	---
LGMN	5641	broad.mit.edu	37	14	93171040	93171040	+	Silent	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:93171040A>G	uc001yav.2	-	14	1530	c.1204T>C	c.(1204-1206)TTG>CTG	p.L402L	LGMN_uc001yat.2_Silent_p.L345L|LGMN_uc001yau.2_Intron|LGMN_uc001yaw.2_Silent_p.L402L|LGMN_uc010aul.2_Silent_p.L283L|LGMN_uc001yax.2_Silent_p.L345L|LGMN_uc001yay.2_Intron	NM_001008530	NP_001008530	Q99538	LGMN_HUMAN	legumain preproprotein	402					hormone biosynthetic process|negative regulation of neuron apoptosis|vitamin D metabolic process	lysosome	cysteine-type endopeptidase activity|protein serine/threonine kinase activity			skin(1)	1		all_cancers(154;0.0706)		COAD - Colon adenocarcinoma(157;0.224)														---	---	---	---
KIAA1409	57578	broad.mit.edu	37	14	94120193	94120193	+	Silent	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:94120193G>A	uc001ybv.1	+	35	5924	c.5841G>A	c.(5839-5841)ACG>ACA	p.T1947T	KIAA1409_uc001ybs.1_Silent_p.T1925T	NM_020818	NP_065869	Q9P2D8	UNC79_HUMAN	hypothetical protein LOC57578	2102						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)														---	---	---	---
SERPINA5	5104	broad.mit.edu	37	14	95054284	95054284	+	Silent	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:95054284G>A	uc001ydm.2	+	3	795	c.585G>A	c.(583-585)GCG>GCA	p.A195A	SERPINA5_uc010ave.2_Silent_p.A195A|SERPINA5_uc001ydn.1_Silent_p.A195A	NM_000624	NP_000615	P05154	IPSP_HUMAN	serine (or cysteine) proteinase inhibitor, clade	195					fusion of sperm to egg plasma membrane|regulation of proteolysis|spermatogenesis	extracellular region|membrane|protein complex	acrosin binding|heparin binding|protease binding|serine-type endopeptidase inhibitor activity			ovary(2)	2				COAD - Colon adenocarcinoma(157;0.21)	Drotrecogin alfa(DB00055)|Urokinase(DB00013)													---	---	---	---
DICER1	23405	broad.mit.edu	37	14	95570058	95570058	+	Silent	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:95570058G>A	uc001ydw.2	-	22	3857	c.3675C>T	c.(3673-3675)TAC>TAT	p.Y1225Y	DICER1_uc010avh.1_Silent_p.Y123Y|DICER1_uc001ydv.2_Silent_p.Y1215Y|DICER1_uc001ydx.2_Silent_p.Y1225Y|DICER1_uc001ydy.1_Silent_p.Y77Y	NM_030621	NP_085124	Q9UPY3	DICER_HUMAN	dicer1	1225					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_				---	---	---	---
C14orf49	161176	broad.mit.edu	37	14	95884357	95884357	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:95884357G>A	uc001yei.3	-	17	2749	c.2734C>T	c.(2734-2736)CGG>TGG	p.R912W	C14orf49_uc010avi.2_Missense_Mutation_p.R907W	NM_152592	NP_689805	Q6ZMZ3	SYNE3_HUMAN	nesprin-3	912	Cytoplasmic (Potential).				cytoskeletal anchoring at nuclear membrane	integral to membrane|nuclear outer membrane|SUN-KASH complex	actin binding			central_nervous_system(1)	1		all_cancers(154;0.0937)		COAD - Colon adenocarcinoma(157;0.245)														---	---	---	---
SETD3	84193	broad.mit.edu	37	14	99865138	99865138	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:99865138C>A	uc001ygc.2	-	13	1833	c.1663G>T	c.(1663-1665)GGT>TGT	p.G555C		NM_032233	NP_115609	Q86TU7	SETD3_HUMAN	SET domain containing 3 isoform a	555					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)																---	---	---	---
DIO3	1735	broad.mit.edu	37	14	102028520	102028520	+	Silent	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:102028520G>A	uc010txq.1	+	2	833	c.609G>A	c.(607-609)GCG>GCA	p.A203A	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	203	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)																---	---	---	---
TECPR2	9895	broad.mit.edu	37	14	102901040	102901040	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:102901040A>G	uc001ylw.1	+	9	2034	c.1886A>G	c.(1885-1887)GAC>GGC	p.D629G	TECPR2_uc010awl.2_Missense_Mutation_p.D629G|TECPR2_uc010txx.1_Intron	NM_014844	NP_055659	O15040	TCPR2_HUMAN	tectonin beta-propeller repeat containing 2	629							protein binding			lung(1)|central_nervous_system(1)|skin(1)	3																		---	---	---	---
CDC42BPB	9578	broad.mit.edu	37	14	103416115	103416115	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:103416115C>T	uc001ymi.1	-	26	3668	c.3436G>A	c.(3436-3438)GTC>ATC	p.V1146I	CDC42BPB_uc001ymj.1_Missense_Mutation_p.V248I	NM_006035	NP_006026	Q9Y5S2	MRCKB_HUMAN	CDC42-binding protein kinase beta	1146	PH.				actin cytoskeleton reorganization|establishment or maintenance of cell polarity|intracellular signal transduction	cell leading edge|cell-cell junction|cytoplasm|cytoskeleton	ATP binding|magnesium ion binding|protein serine/threonine kinase activity|small GTPase regulator activity			large_intestine(3)|skin(3)|lung(2)|stomach(1)|breast(1)|ovary(1)	11		Melanoma(154;0.155)		Colorectal(3;0.0129)|READ - Rectum adenocarcinoma(2;0.0419)|Epithelial(152;0.0474)|all cancers(159;0.199)														---	---	---	---
MARK3	4140	broad.mit.edu	37	14	103932781	103932781	+	Splice_Site	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:103932781T>C	uc001ymz.3	+	10	1663	c.997_splice	c.e10+2	p.D333_splice	MARK3_uc001ymx.3_Splice_Site_p.D333_splice|MARK3_uc001ymw.3_Splice_Site_p.D333_splice|MARK3_uc001yna.3_Splice_Site_p.D333_splice|MARK3_uc001ymy.3_Splice_Site_p.D254_splice|MARK3_uc010awp.2_Splice_Site_p.D356_splice|MARK3_uc010tyb.1_Splice_Site_p.D144_splice	NM_001128918	NP_001122390			MAP/microtubule affinity-regulating kinase 3								ATP binding|protein binding|protein serine/threonine kinase activity			central_nervous_system(2)|ovary(1)|stomach(1)	4		Melanoma(154;0.155)	Epithelial(46;0.241)															---	---	---	---
C14orf153	84334	broad.mit.edu	37	14	104056564	104056564	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:104056564G>A	uc010tyc.1	+	5	563	c.562G>A	c.(562-564)GTG>ATG	p.V188M	KLC1_uc010tyd.1_Intron|C14orf153_uc001ynl.3_RNA	NM_032374	NP_115750	Q96IL0	CN153_HUMAN	chromosome 14 open reading frame 153	175											0		Melanoma(154;0.226)																---	---	---	---
KLC1	3831	broad.mit.edu	37	14	104136622	104136622	+	Splice_Site	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:104136622T>C	uc001yno.2	+	7	1295	c.987_splice	c.e7+2	p.K329_splice	KLC1_uc010tyd.1_Splice_Site_p.K488_splice|KLC1_uc010tye.1_Splice_Site_p.K325_splice|KLC1_uc001ynm.1_Splice_Site_p.K329_splice|KLC1_uc001ynn.1_Splice_Site_p.K323_splice|KLC1_uc010tyf.1_Splice_Site_p.K329_splice	NM_182923	NP_891553			kinesin light chain 1 isoform 2						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)																---	---	---	---
AKT1	207	broad.mit.edu	37	14	105239690	105239690	+	Silent	SNP	G	A	A	rs149484260		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:105239690G>A	uc001ypk.2	-	10	1409	c.855C>T	c.(853-855)GAC>GAT	p.D285D	INF2_uc010tyi.1_Intron|AKT1_uc001ypl.2_Silent_p.D285D|AKT1_uc010axa.2_Silent_p.D285D|AKT1_uc001ypm.2_Silent_p.D285D|AKT1_uc001ypn.2_Silent_p.D285D|AKT1_uc001ypj.2_5'Flank|AKT1_uc010tyk.1_Silent_p.D223D	NM_005163	NP_005154	P31749	AKT1_HUMAN	AKT1 kinase	285	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								---	---	---	---
INF2	64423	broad.mit.edu	37	14	105241551	105241551	+	Intron	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:105241551G>A	uc010tyi.1	+						AKT1_uc001ypk.2_Intron|AKT1_uc001ypl.2_Intron|AKT1_uc010axa.2_Intron|AKT1_uc001ypm.2_Intron|AKT1_uc001ypn.2_Intron|AKT1_uc010tyk.1_Intron	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)														---	---	---	---
AHNAK2	113146	broad.mit.edu	37	14	105411302	105411302	+	Silent	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:105411302G>A	uc010axc.1	-	7	10606	c.10486C>T	c.(10486-10488)CTG>TTG	p.L3496L	AHNAK2_uc001ypx.2_Silent_p.L3396L	NM_138420	NP_612429	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	3496						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	105415817	105415817	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:105415817G>A	uc010axc.1	-	7	6091	c.5971C>T	c.(5971-5973)CCC>TCC	p.P1991S	AHNAK2_uc001ypx.2_Missense_Mutation_p.P1891S	NM_138420	NP_612429	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	1991						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)															---	---	---	---
MTA1	9112	broad.mit.edu	37	14	105924661	105924661	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:105924661A>G	uc001yqx.2	+	8	792	c.605A>G	c.(604-606)CAC>CGC	p.H202R	MTA1_uc001yqy.2_RNA|MTA1_uc001yqz.1_Missense_Mutation_p.H116R|MTA1_uc001yra.1_Missense_Mutation_p.H116R|MTA1_uc001yrb.2_5'UTR	NM_004689	NP_004680	Q13330	MTA1_HUMAN	metastasis associated protein	202	ELM2.				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	106237654	106237654	+	RNA	SNP	C	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:106237654C>A	uc010tyt.1	-	3611		c.57229G>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	106791002	106791002	+	RNA	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:106791002G>A	uc010tyt.1	-	386		c.14616C>T								Parts of antibodies, mostly variable regions.												0																		---	---	---	---
ADAM6	8755	broad.mit.edu	37	14	106815719	106815719	+	RNA	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:106815719G>A	uc010tyt.1	-	342		c.13440C>T								Parts of antibodies, mostly variable regions.												0																		---	---	---	---
ADAM6	8755	broad.mit.edu	37	14	107048776	107048776	+	RNA	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:107048776C>T	uc010tyt.1	-	144		c.6814G>A								Parts of antibodies, mostly variable regions.												0																		---	---	---	---
ADAM6	8755	broad.mit.edu	37	14	107131137	107131137	+	RNA	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:107131137C>T	uc010tyt.1	-	63		c.3373G>A								Parts of antibodies, mostly variable regions.												0																		---	---	---	---
GOLGA6L1	283767	broad.mit.edu	37	15	22743190	22743190	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:22743190A>G	uc010tzx.1	+	8	1666	c.1575A>G	c.(1573-1575)ATA>ATG	p.I525M	uc010tzy.1_5'Flank	NM_001001413	NP_001001413			golgi autoantigen, golgin subfamily a, 6-like 1												0																		---	---	---	---
CYFIP1	23191	broad.mit.edu	37	15	22969368	22969368	+	Intron	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:22969368C>T	uc001yus.2	+						CYFIP1_uc001yut.2_Intron|CYFIP1_uc010aya.1_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)														---	---	---	---
C15orf2	23742	broad.mit.edu	37	15	24921535	24921535	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:24921535A>G	uc001ywo.2	+	1	995	c.521A>G	c.(520-522)GAC>GGC	p.D174G		NM_018958	NP_061831	Q9NZP6	CO002_HUMAN	hypothetical protein LOC23742	174					cell differentiation|multicellular organismal development|spermatogenesis			p.D174D(1)		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)														---	---	---	---
C15orf2	23742	broad.mit.edu	37	15	24922950	24922950	+	Nonsense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:24922950C>T	uc001ywo.2	+	1	2410	c.1936C>T	c.(1936-1938)CAG>TAG	p.Q646*		NM_018958	NP_061831	Q9NZP6	CO002_HUMAN	hypothetical protein LOC23742	646					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)														---	---	---	---
SNORD116-4	100033416	broad.mit.edu	37	15	25330551	25330551	+	Intron	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:25330551T>C	uc001yxh.1	+						SNORD116-4_uc001yxm.1_Intron|IPW_uc001yxn.3_Intron|SNORD116-28_uc001yxy.2_Intron|IPW_uc001yyb.3_Intron|uc001yyd.2_Intron|SNORD116-18_uc010ayk.2_RNA|SNORD116-19_uc001yye.1_5'Flank|SNORD116-20_uc001yyf.2_5'Flank					Homo sapiens clone kid4 SNURF-SNRPN mRNA, downstream untranslated exons, alternatively spliced.												0																		---	---	---	---
SNORD116-4	100033416	broad.mit.edu	37	15	25344654	25344654	+	Intron	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:25344654G>A	uc001yxh.1	+						SNORD116-4_uc001yxm.1_Intron|IPW_uc001yxn.3_Intron|SNORD116-28_uc001yxy.2_Intron|IPW_uc001yyb.3_Intron|uc001yyd.2_Intron|SNORD116-26_uc001yyl.2_RNA|SNORD116-27_uc001yym.2_5'Flank					Homo sapiens clone kid4 SNURF-SNRPN mRNA, downstream untranslated exons, alternatively spliced.												0																		---	---	---	---
SNORD116-4	100033416	broad.mit.edu	37	15	25349791	25349791	+	Intron	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:25349791A>G	uc001yxh.1	+						SNORD116-4_uc001yxm.1_Intron|IPW_uc001yxn.3_Intron|SNORD116-28_uc001yxy.2_RNA|IPW_uc001yyb.3_Intron|uc001yyd.2_Intron|SNORD116-28_uc001yyn.3_RNA|SNORD116-29_uc001yyo.2_5'Flank					Homo sapiens clone kid4 SNURF-SNRPN mRNA, downstream untranslated exons, alternatively spliced.												0																		---	---	---	---
UBE3A	7337	broad.mit.edu	37	15	25620906	25620906	+	Nonsense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:25620906G>A	uc001zaq.2	-	3	76	c.76C>T	c.(76-78)CGA>TGA	p.R26*	UBE3A_uc001zar.2_Nonsense_Mutation_p.R3*|UBE3A_uc001zas.2_Nonsense_Mutation_p.R23*|UBE3A_uc001zat.2_Nonsense_Mutation_p.R3*	NM_000462	NP_000453	Q05086	UBE3A_HUMAN	ubiquitin protein ligase E3A isoform 2	26					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)														---	---	---	---
OCA2	4948	broad.mit.edu	37	15	28228487	28228487	+	Intron	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:28228487G>A	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	28414756	28414756	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:28414756C>T	uc001zbj.2	-	66	10209	c.10103G>A	c.(10102-10104)AGT>AAT	p.S3368N		NM_004667	NP_004658	O95714	HERC2_HUMAN	hect domain and RLD 2	3368					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	28482215	28482215	+	Silent	SNP	A	G	G	rs4035908		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:28482215A>G	uc001zbj.2	-	26	4003	c.3897T>C	c.(3895-3897)TCT>TCC	p.S1299S		NM_004667	NP_004658	O95714	HERC2_HUMAN	hect domain and RLD 2	1299					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	29346080	29346080	+	Translation_Start_Site	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:29346080C>T	uc001zck.2	+	3	200	c.-7C>T	c.(-9--5)AACGA>AATGA		APBA2_uc010azj.2_Translation_Start_Site|APBA2_uc010uat.1_Translation_Start_Site|APBA2_uc001zcl.2_Translation_Start_Site|APBA2_uc010uas.1_Translation_Start_Site	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)														---	---	---	---
APBA2	321	broad.mit.edu	37	15	29385267	29385267	+	Intron	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:29385267C>T	uc001zck.2	+						APBA2_uc010azj.2_Intron|APBA2_uc010uat.1_Intron|APBA2_uc001zcl.2_Intron|APBA2_uc001zcm.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)														---	---	---	---
TRPM1	4308	broad.mit.edu	37	15	31294403	31294403	+	Silent	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:31294403C>T	uc001zfm.2	-	27	4562	c.4434G>A	c.(4432-4434)ACG>ACA	p.T1478T	TRPM1_uc010azy.2_Silent_p.T1385T|TRPM1_uc001zfl.2_RNA	NM_002420	NP_002411	Q7Z4N2	TRPM1_HUMAN	transient receptor potential cation channel,	1478	Cytoplasmic (Potential).				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	31318358	31318358	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:31318358G>A	uc001zfm.2	-	26	3675	c.3547C>T	c.(3547-3549)CGG>TGG	p.R1183W	TRPM1_uc010azy.2_Missense_Mutation_p.R1090W|TRPM1_uc001zfl.2_RNA	NM_002420	NP_002411	Q7Z4N2	TRPM1_HUMAN	transient receptor potential cation channel,	1183	Potential.|Cytoplasmic (Potential).				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)														---	---	---	---
OTUD7A	161725	broad.mit.edu	37	15	31862241	31862241	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:31862241C>A	uc001zfq.2	-	2	404	c.311G>T	c.(310-312)AGG>ATG	p.R104M	OTUD7A_uc001zfr.2_Missense_Mutation_p.R104M|OTUD7A_uc001zfs.1_RNA|OTUD7A_uc010baa.1_Missense_Mutation_p.R104M	NM_130901	NP_570971	Q8TE49	OTU7A_HUMAN	OTU domain containing 7A	104						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)														---	---	---	---
RYR3	6263	broad.mit.edu	37	15	33954529	33954529	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:33954529G>A	uc001zhi.2	+	35	4868	c.4798G>A	c.(4798-4800)GGC>AGC	p.G1600S	RYR3_uc010bar.2_Missense_Mutation_p.G1600S	NM_001036	NP_001027	Q15413	RYR3_HUMAN	ryanodine receptor 3	1600	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)														---	---	---	---
RYR3	6263	broad.mit.edu	37	15	34105155	34105155	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:34105155G>A	uc001zhi.2	+	73	10419	c.10349G>A	c.(10348-10350)CGT>CAT	p.R3450H	RYR3_uc010bar.2_Missense_Mutation_p.R3445H	NM_001036	NP_001027	Q15413	RYR3_HUMAN	ryanodine receptor 3	3450					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	34127172	34127172	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:34127172C>A	uc001zhi.2	+	87	11537	c.11467C>A	c.(11467-11469)CCT>ACT	p.P3823T	RYR3_uc010bar.2_Missense_Mutation_p.P3818T	NM_001036	NP_001027	Q15413	RYR3_HUMAN	ryanodine receptor 3	3823					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)														---	---	---	---
C15orf24	56851	broad.mit.edu	37	15	34388111	34388111	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:34388111G>A	uc001zhm.2	-	2	354	c.341C>T	c.(340-342)TCG>TTG	p.S114L	C15orf24_uc001zhn.2_5'UTR	NM_020154	NP_064539	Q9NPA0	CO024_HUMAN	chromosome 15 open reading frame 24 precursor	114	Extracellular (Potential).					cytoplasm|integral to membrane	carbohydrate binding|carboxypeptidase activity|purine nucleotide binding				0		all_lung(180;1.76e-08)		all cancers(64;2.02e-17)|GBM - Glioblastoma multiforme(113;2.15e-06)|BRCA - Breast invasive adenocarcinoma(123;0.0252)														---	---	---	---
SLC12A6	9990	broad.mit.edu	37	15	34537475	34537475	+	Intron	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:34537475C>T	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_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)													---	---	---	---
THBS1	7057	broad.mit.edu	37	15	39881253	39881253	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:39881253G>A	uc001zkh.2	+	11	1918	c.1739G>A	c.(1738-1740)AGT>AAT	p.S580N	THBS1_uc010bbi.2_Missense_Mutation_p.S52N	NM_003246	NP_003237	P07996	TSP1_HUMAN	thrombospondin 1 precursor	580	EGF-like 1.				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)													---	---	---	---
THBS1	7057	broad.mit.edu	37	15	39886493	39886493	+	Intron	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:39886493T>C	uc001zkh.2	+						THBS1_uc010bbi.2_Intron	NM_003246	NP_003237			thrombospondin 1 precursor						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	40231740	40231740	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:40231740A>G	uc001zkm.1	+	2	229	c.179A>G	c.(178-180)TAC>TGC	p.Y60C	EIF2AK4_uc001zkl.2_Missense_Mutation_p.Y60C	NM_001013703	NP_001013725	Q9P2K8	E2AK4_HUMAN	eukaryotic translation initiation factor 2 alpha	60	RWD.				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)														---	---	---	---
SRP14	6727	broad.mit.edu	37	15	40328526	40328526	+	3'UTR	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:40328526T>C	uc001zkq.2	-	5					SRP14_uc001zkr.2_3'UTR|uc001zks.1_5'Flank	NM_003134	NP_003125			signal recognition particle 14kDa (homologous						negative regulation of translational elongation|response to drug|SRP-dependent cotranslational protein targeting to membrane	cytosol|signal recognition particle, endoplasmic reticulum targeting	7S RNA binding|endoplasmic reticulum signal peptide binding|protein binding				0		all_cancers(109;7.56e-18)|all_epithelial(112;4.02e-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;1.84e-07)|BRCA - Breast invasive adenocarcinoma(123;0.0505)														---	---	---	---
C15orf57	90416	broad.mit.edu	37	15	40849575	40849575	+	Intron	SNP	G	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:40849575G>T	uc001zmc.1	-						uc001zlx.1_RNA|C15orf57_uc001zly.2_Intron|C15orf57_uc001zma.1_Intron|C15orf57_uc001zmb.1_Intron|C15orf57_uc010bbr.2_Intron	NM_001080792	NP_001074261			coiled-coil domain containing 32 isoform a											ovary(1)	1																		---	---	---	---
CASC5	57082	broad.mit.edu	37	15	40915927	40915927	+	Silent	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:40915927A>G	uc010bbs.1	+	11	3704	c.3543A>G	c.(3541-3543)GTA>GTG	p.V1181V	CASC5_uc010ucq.1_Silent_p.V1005V|CASC5_uc001zme.2_Silent_p.V1155V|CASC5_uc010bbt.1_Silent_p.V1155V	NM_170589	NP_733468	Q8NG31	CASC5_HUMAN	cancer susceptibility candidate 5 isoform 1	1181	2.|2 X 104 AA approximate repeats.				acrosome assembly|attachment of spindle microtubules to kinetochore|cell division|CenH3-containing nucleosome assembly at centromere|mitotic prometaphase|spindle assembly checkpoint	acrosomal vesicle|condensed chromosome kinetochore|cytosol|nucleoplasm	protein binding			breast(3)|central_nervous_system(1)|skin(1)	5		all_cancers(109;2.03e-18)|all_epithelial(112;4.26e-15)|Lung NSC(122;1.12e-10)|all_lung(180;2.59e-09)|Melanoma(134;0.0574)|Ovarian(310;0.0822)|Colorectal(260;0.0946)		GBM - Glioblastoma multiforme(113;4.99e-05)|BRCA - Breast invasive adenocarcinoma(123;0.0861)|COAD - Colon adenocarcinoma(120;0.211)														---	---	---	---
RHOV	171177	broad.mit.edu	37	15	41165603	41165603	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:41165603T>C	uc001znd.2	-	3	514	c.364A>G	c.(364-366)ACA>GCA	p.T122A		NM_133639	NP_598378	Q96L33	RHOV_HUMAN	ras homolog gene family, member V	122					regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol|endosome membrane|plasma membrane	GTP binding|metal ion binding				0		all_cancers(109;1.42e-13)|all_epithelial(112;1.48e-11)|Lung NSC(122;5.77e-09)|all_lung(180;1.08e-07)|Melanoma(134;0.091)|Colorectal(260;0.175)|Ovarian(310;0.243)		GBM - Glioblastoma multiforme(113;2.58e-05)|COAD - Colon adenocarcinoma(120;0.149)|BRCA - Breast invasive adenocarcinoma(123;0.163)														---	---	---	---
RHOV	171177	broad.mit.edu	37	15	41165872	41165872	+	Intron	SNP	A	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:41165872A>C	uc001znd.2	-							NM_133639	NP_598378			ras homolog gene family, member V						regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol|endosome membrane|plasma membrane	GTP binding|metal ion binding				0		all_cancers(109;1.42e-13)|all_epithelial(112;1.48e-11)|Lung NSC(122;5.77e-09)|all_lung(180;1.08e-07)|Melanoma(134;0.091)|Colorectal(260;0.175)|Ovarian(310;0.243)		GBM - Glioblastoma multiforme(113;2.58e-05)|COAD - Colon adenocarcinoma(120;0.149)|BRCA - Breast invasive adenocarcinoma(123;0.163)														---	---	---	---
VPS18	57617	broad.mit.edu	37	15	41192463	41192463	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:41192463G>A	uc001zne.2	+	4	1786	c.1447G>A	c.(1447-1449)GCC>ACC	p.A483T		NM_020857	NP_065908	Q9P253	VPS18_HUMAN	vacuolar protein sorting 18	483					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)														---	---	---	---
RPAP1	26015	broad.mit.edu	37	15	41814290	41814290	+	Intron	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:41814290A>G	uc001zod.2	-						RPAP1_uc001zoc.2_Intron	NM_015540	NP_056355			RNA polymerase II associated protein 1							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)														---	---	---	---
MAPKBP1	23005	broad.mit.edu	37	15	42105267	42105267	+	Nonsense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:42105267C>T	uc001zok.3	+	8	1073	c.787C>T	c.(787-789)CGA>TGA	p.R263*	MAPKBP1_uc001zoj.3_Nonsense_Mutation_p.R263*|MAPKBP1_uc010bcj.2_5'UTR|MAPKBP1_uc010bci.2_Nonsense_Mutation_p.R263*|MAPKBP1_uc010udb.1_Nonsense_Mutation_p.R151*|MAPKBP1_uc010bck.2_5'UTR|MAPKBP1_uc010bcl.2_5'UTR	NM_001128608	NP_001122080	O60336	MABP1_HUMAN	mitogen-activated protein kinase binding protein	263										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)														---	---	---	---
MAPKBP1	23005	broad.mit.edu	37	15	42109219	42109219	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:42109219C>A	uc001zok.3	+	15	2001	c.1715C>A	c.(1714-1716)GCT>GAT	p.A572D	MAPKBP1_uc001zoj.3_Missense_Mutation_p.A566D|MAPKBP1_uc010bcj.2_Missense_Mutation_p.A73D|MAPKBP1_uc010bci.2_Missense_Mutation_p.A566D|MAPKBP1_uc010udb.1_Missense_Mutation_p.A405D|MAPKBP1_uc010bck.2_Translation_Start_Site|MAPKBP1_uc010bcl.2_Missense_Mutation_p.A73D	NM_001128608	NP_001122080	O60336	MABP1_HUMAN	mitogen-activated protein kinase binding protein	572	WD 9.									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	42135893	42135893	+	Nonsense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:42135893C>T	uc010bco.2	+	11	864	c.763C>T	c.(763-765)CGA>TGA	p.R255*	JMJD7-PLA2G4B_uc001zoo.3_Nonsense_Mutation_p.R486*|JMJD7-PLA2G4B_uc010bcn.2_Nonsense_Mutation_p.R486*|JMJD7-PLA2G4B_uc001zoq.3_5'UTR|JMJD7-PLA2G4B_uc001zor.1_5'UTR	NM_001114633	NP_001108105	P0C869	PA24B_HUMAN	phospholipase A2, group IVB	255	PLA2c.				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																		---	---	---	---
CDAN1	146059	broad.mit.edu	37	15	43020879	43020879	+	Silent	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:43020879G>A	uc001zql.2	-	20	2892	c.2775C>T	c.(2773-2775)CAC>CAT	p.H925H	CDAN1_uc001zqj.2_RNA|CDAN1_uc001zqk.2_Silent_p.H251H	NM_138477	NP_612486	Q8IWY9	CDAN1_HUMAN	codanin 1	925						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	43094352	43094352	+	Intron	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:43094352C>T	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	43299462	43299462	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:43299462T>C	uc001zqq.2	-	30	3296	c.3230A>G	c.(3229-3231)TAC>TGC	p.Y1077C		NM_174916	NP_777576	Q8IWV7	UBR1_HUMAN	ubiquitin protein ligase E3 component n-recognin	1077					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)														---	---	---	---
LCMT2	9836	broad.mit.edu	37	15	43621169	43621169	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:43621169C>T	uc001zrg.2	-	1	1723	c.1519G>A	c.(1519-1521)GTA>ATA	p.V507I	LCMT2_uc010udn.1_Missense_Mutation_p.V86I|ADAL_uc001zrh.2_5'Flank|ADAL_uc010udo.1_5'Flank	NM_014793	NP_055608	O60294	LCMT2_HUMAN	leucine carboxyl methyltransferase 2	507					tRNA processing		methyltransferase activity|protein binding				0		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;8.1e-07)	L-Leucine(DB00149)													---	---	---	---
TP53BP1	7158	broad.mit.edu	37	15	43720290	43720290	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:43720290A>G	uc001zrs.2	-	18	3885	c.3737T>C	c.(3736-3738)GTA>GCA	p.V1246A	TP53BP1_uc010udp.1_Missense_Mutation_p.V1246A|TP53BP1_uc001zrq.3_Missense_Mutation_p.V1251A|TP53BP1_uc001zrr.3_Missense_Mutation_p.V1251A|TP53BP1_uc010udq.1_Missense_Mutation_p.V1251A	NM_005657	NP_005648	Q12888	TP53B_HUMAN	tumor protein p53 binding protein 1 isoform 3	1246					double-strand break repair via homologous recombination|positive regulation of transcription from RNA polymerase II promoter	condensed chromosome kinetochore|cytoplasm|nucleoplasm	p53 binding|RNA polymerase II activating transcription factor binding|RNA polymerase II transcription cofactor activity			ovary(2)|skin(2)|large_intestine(1)|pancreas(1)|kidney(1)	7		all_cancers(109;6.94e-11)|all_epithelial(112;2.69e-09)|Lung NSC(122;7.86e-07)|all_lung(180;7.84e-06)|Melanoma(134;0.0728)		GBM - Glioblastoma multiforme(94;1.59e-06)									Direct_reversal_of_damage|Other_conserved_DNA_damage_response_genes					---	---	---	---
MAP1A	4130	broad.mit.edu	37	15	43820487	43820487	+	Silent	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:43820487G>A	uc001zrt.2	+	4	7283	c.6816G>A	c.(6814-6816)GCG>GCA	p.A2272A		NM_002373	NP_002364	P78559	MAP1A_HUMAN	microtubule-associated protein 1A	2272						cytoplasm|microtubule|microtubule associated complex	protein binding|structural molecule activity			ovary(3)|breast(3)|pancreas(2)|skin(1)	9		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;3.05e-06)	Estramustine(DB01196)													---	---	---	---
TRIM69	140691	broad.mit.edu	37	15	45059494	45059494	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:45059494A>G	uc001zuf.2	+	8	1922	c.1027A>G	c.(1027-1029)ACC>GCC	p.T343A	TRIM69_uc001zui.1_Missense_Mutation_p.T139A|TRIM69_uc010bdy.1_Missense_Mutation_p.T122A|TRIM69_uc001zug.1_Missense_Mutation_p.T343A|TRIM69_uc001zuh.1_Missense_Mutation_p.T184A	NM_182985	NP_892030	Q86WT6	TRI69_HUMAN	tripartite motif-containing 69 isoform a	343	B30.2/SPRY.				apoptosis	nuclear speck	zinc ion binding				0		all_cancers(109;2.47e-13)|all_epithelial(112;2.84e-11)|Lung NSC(122;2.23e-07)|all_lung(180;1.81e-06)|Melanoma(134;0.0122)		all cancers(107;5.5e-19)|GBM - Glioblastoma multiforme(94;1.07e-06)|Colorectal(105;0.138)|COAD - Colon adenocarcinoma(120;0.141)														---	---	---	---
CEP152	22995	broad.mit.edu	37	15	49085560	49085560	+	Missense_Mutation	SNP	G	A	A	rs146482586	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:49085560G>A	uc001zwy.2	-	7	824	c.790C>T	c.(790-792)CGT>TGT	p.R264C	CEP152_uc001zwz.2_Missense_Mutation_p.R264C|CEP152_uc001zxa.1_Missense_Mutation_p.R171C	NM_014985	NP_055800	O94986	CE152_HUMAN	centrosomal protein 152kDa	264	Potential.				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)														---	---	---	---
GALK2	2585	broad.mit.edu	37	15	49528040	49528040	+	Intron	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:49528040C>T	uc001zxj.1	+						GALK2_uc001zxi.1_Intron|GALK2_uc010ufb.1_Intron|GALK2_uc001zxk.2_Intron|GALK2_uc010ufc.1_Intron	NM_002044	NP_002035			galactokinase 2 isoform 1						galactose metabolic process	cytoplasm	ATP binding|galactokinase activity|N-acetylgalactosamine kinase activity			breast(1)	1		all_lung(180;0.000325)		all cancers(107;3.71e-08)|GBM - Glioblastoma multiforme(94;7e-05)														---	---	---	---
DMXL2	23312	broad.mit.edu	37	15	51773819	51773819	+	Silent	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:51773819A>G	uc002abf.2	-	24	5709	c.5484T>C	c.(5482-5484)GTT>GTC	p.V1828V	DMXL2_uc002abd.2_5'UTR|DMXL2_uc010ufy.1_Silent_p.V1828V|DMXL2_uc010bfa.2_Silent_p.V1192V	NM_015263	NP_056078	Q8TDJ6	DMXL2_HUMAN	Dmx-like 2	1828						cell junction|synaptic vesicle membrane	Rab GTPase binding			ovary(6)|skin(3)	9				all cancers(107;0.00494)														---	---	---	---
DMXL2	23312	broad.mit.edu	37	15	51787282	51787282	+	Silent	SNP	G	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:51787282G>C	uc002abf.2	-	19	4947	c.4722C>G	c.(4720-4722)CGC>CGG	p.R1574R	DMXL2_uc010ufy.1_Silent_p.R1574R|DMXL2_uc010bfa.2_Silent_p.R938R	NM_015263	NP_056078	Q8TDJ6	DMXL2_HUMAN	Dmx-like 2	1574						cell junction|synaptic vesicle membrane	Rab GTPase binding			ovary(6)|skin(3)	9				all cancers(107;0.00494)														---	---	---	---
TMOD3	29766	broad.mit.edu	37	15	52155105	52155105	+	Missense_Mutation	SNP	C	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:52155105C>G	uc002abm.2	+	2	243	c.24C>G	c.(22-24)GAC>GAG	p.D8E		NM_014547	NP_055362	Q9NYL9	TMOD3_HUMAN	tropomodulin 3 (ubiquitous)	8						cytoplasm|cytoskeleton	actin binding|tropomyosin binding			ovary(1)	1				all cancers(107;0.00194)														---	---	---	---
MYO5C	55930	broad.mit.edu	37	15	52497128	52497128	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:52497128G>A	uc010bff.2	-	38	4891	c.4754C>T	c.(4753-4755)GCG>GTG	p.A1585V	MYO5C_uc010uga.1_RNA|uc002abv.2_RNA	NM_018728	NP_061198	Q9NQX4	MYO5C_HUMAN	myosin VC	1585	Dilute.					myosin complex	actin binding|ATP binding|calmodulin binding|motor activity			ovary(7)|central_nervous_system(3)|large_intestine(2)|skin(2)	14				all cancers(107;0.0137)														---	---	---	---
UNC13C	440279	broad.mit.edu	37	15	54592541	54592541	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:54592541A>G	uc002ack.2	+	11	4238	c.4238A>G	c.(4237-4239)TAT>TGT	p.Y1413C	UNC13C_uc002acl.2_Missense_Mutation_p.Y243C	NM_001080534	NP_001074003	Q8NB66	UN13C_HUMAN	unc-13 homolog C	1413					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)														---	---	---	---
PYGO1	26108	broad.mit.edu	37	15	55841108	55841108	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:55841108C>A	uc010bfl.1	-	2	191	c.135G>T	c.(133-135)CAG>CAT	p.Q45H	PYGO1_uc002adf.1_Missense_Mutation_p.Q45H	NM_015617	NP_056432	Q9Y3Y4	PYGO1_HUMAN	pygopus homolog 1	45					Wnt receptor signaling pathway	nucleus	zinc ion binding			ovary(1)|skin(1)	2				all cancers(107;0.0131)|GBM - Glioblastoma multiforme(80;0.18)														---	---	---	---
RFX7	64864	broad.mit.edu	37	15	56386542	56386542	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:56386542C>A	uc010bfn.2	-	9	3384	c.3384G>T	c.(3382-3384)CAG>CAT	p.Q1128H	RFX7_uc010ugk.1_RNA|RFX7_uc002adn.1_Missense_Mutation_p.Q942H	NM_022841	NP_073752	Q2KHR2	RFX7_HUMAN	regulatory factor X domain containing 2	1031					regulation of transcription, DNA-dependent	nucleus	DNA binding				0																		---	---	---	---
RNF111	54778	broad.mit.edu	37	15	59323537	59323537	+	Silent	SNP	T	C	C	rs143083683	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:59323537T>C	uc002afv.2	+	2	795	c.516T>C	c.(514-516)GCT>GCC	p.A172A	RNF111_uc002afs.2_Silent_p.A172A|RNF111_uc002aft.2_Silent_p.A172A|RNF111_uc002afu.2_Silent_p.A172A|RNF111_uc002afw.2_Silent_p.A172A	NM_017610	NP_060080	Q6ZNA4	RN111_HUMAN	ring finger protein 111	172					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)														---	---	---	---
RNF111	54778	broad.mit.edu	37	15	59383264	59383264	+	Missense_Mutation	SNP	A	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:59383264A>T	uc002afv.2	+	12	2929	c.2650A>T	c.(2650-2652)ATT>TTT	p.I884F	RNF111_uc002afs.2_Missense_Mutation_p.I884F|RNF111_uc002aft.2_Missense_Mutation_p.I893F|RNF111_uc002afu.2_Missense_Mutation_p.I883F|RNF111_uc002afw.2_Missense_Mutation_p.I893F|RNF111_uc002afx.2_Missense_Mutation_p.I410F|RNF111_uc002afy.2_Missense_Mutation_p.I35F	NM_017610	NP_060080	Q6ZNA4	RN111_HUMAN	ring finger protein 111	884					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)														---	---	---	---
TLN2	83660	broad.mit.edu	37	15	62989956	62989956	+	Silent	SNP	C	T	T	rs61730198	byFrequency	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:62989956C>T	uc002alb.3	+	12	1362	c.1362C>T	c.(1360-1362)GCC>GCT	p.A454A		NM_015059	NP_055874	Q9Y4G6	TLN2_HUMAN	talin 2	454					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	63017208	63017208	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:63017208T>C	uc002alb.3	+	24	3160	c.3160T>C	c.(3160-3162)TCA>CCA	p.S1054P		NM_015059	NP_055874	Q9Y4G6	TLN2_HUMAN	talin 2	1054	Ala-rich.				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	63901323	63901323	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:63901323G>A	uc002amp.2	-	78	14691	c.14543C>T	c.(14542-14544)TCG>TTG	p.S4848L	HERC1_uc002amo.2_RNA	NM_003922	NP_003913	Q15751	HERC1_HUMAN	hect domain and RCC1-like domain 1	4848	HECT.				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																		---	---	---	---
HERC1	8925	broad.mit.edu	37	15	63942057	63942057	+	Silent	SNP	C	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:63942057C>A	uc002amp.2	-	54	10762	c.10614G>T	c.(10612-10614)CCG>CCT	p.P3538P		NM_003922	NP_003913	Q15751	HERC1_HUMAN	hect domain and RCC1-like domain 1	3538	WD 6.				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																		---	---	---	---
SNX22	79856	broad.mit.edu	37	15	64445448	64445448	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:64445448T>C	uc002anc.1	+	4	328	c.269T>C	c.(268-270)ATC>ACC	p.I90T	SNX22_uc002amz.1_Missense_Mutation_p.I62T|SNX22_uc002ana.1_3'UTR|SNX22_uc002anb.1_RNA	NM_024798	NP_079074	Q96L94	SNX22_HUMAN	sorting nexin 22	90	PX.				cell communication|protein transport	cytoplasmic vesicle membrane	phosphatidylinositol binding				0																		---	---	---	---
PIF1	80119	broad.mit.edu	37	15	65110491	65110491	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:65110491C>T	uc002ant.2	-	10	1559	c.1493G>A	c.(1492-1494)CGA>CAA	p.R498Q	PIF1_uc002anr.2_Missense_Mutation_p.R46Q|PIF1_uc002ans.2_Missense_Mutation_p.R189Q|PIF1_uc010uiq.1_Missense_Mutation_p.R498Q	NM_025049	NP_079325	Q9H611	PIF1_HUMAN	DNA helicase homolog PIF1	498	Hydrolyzes ATP in the presence of both magnesium and single-stranded DNA; weak activity in the presence of RNA or double-stranded DNA; No unwinding activity.				negative regulation of telomerase activity|regulation of telomere maintenance|viral genome replication	nuclear chromosome, telomeric region	ATP binding|ATP-dependent 5'-3' DNA helicase activity|ATP-dependent 5'-3' DNA/RNA helicase activity|magnesium ion binding|single-stranded DNA-dependent ATP-dependent DNA helicase activity|telomeric DNA binding				0																		---	---	---	---
CLPX	10845	broad.mit.edu	37	15	65444840	65444840	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:65444840G>T	uc002aom.2	-	13	1811	c.1739C>A	c.(1738-1740)CCT>CAT	p.P580H	CLPX_uc010uiu.1_RNA	NM_006660	NP_006651	O76031	CLPX_HUMAN	ClpX caseinolytic protease X homolog precursor	580					protein folding|proteolysis involved in cellular protein catabolic process	mitochondrial endopeptidase Clp complex|mitochondrial inner membrane|mitochondrial nucleoid	ATP binding|ATPase activity|metal ion binding|peptidase activator activity|unfolded protein binding				0																		---	---	---	---
CILP	8483	broad.mit.edu	37	15	65499319	65499319	+	Silent	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:65499319G>A	uc002aon.2	-	4	406	c.225C>T	c.(223-225)GAC>GAT	p.D75D		NM_003613	NP_003604	O75339	CILP1_HUMAN	cartilage intermediate layer protein	75					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																		---	---	---	---
IGDCC3	9543	broad.mit.edu	37	15	65621401	65621401	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:65621401G>A	uc002aos.2	-	14	2543	c.2291C>T	c.(2290-2292)ACG>ATG	p.T764M	IGDCC3_uc002aor.1_Missense_Mutation_p.T50M	NM_004884	NP_004875	Q8IVU1	IGDC3_HUMAN	putative neuronal cell adhesion molecule	764	Cytoplasmic (Potential).									ovary(3)	3																		---	---	---	---
DIS3L	115752	broad.mit.edu	37	15	66621623	66621623	+	Silent	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:66621623A>G	uc010ujm.1	+	14	2436	c.2421A>G	c.(2419-2421)GTA>GTG	p.V807V	DIS3L_uc002app.2_Silent_p.V724V|DIS3L_uc010bho.2_Silent_p.V673V	NM_001143688	NP_001137160	Q8TF46	DI3L1_HUMAN	DIS3 mitotic control homolog (S.	807					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	66729156	66729156	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:66729156A>G	uc010bhq.2	+	3	839	c.364A>G	c.(364-366)AAC>GAC	p.N122D	MAP2K1_uc010ujp.1_Missense_Mutation_p.N100D	NM_002755	NP_002746	Q02750	MP2K1_HUMAN	mitogen-activated protein kinase kinase 1	122	Protein kinase.				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				---	---	---	---
RPL4	6124	broad.mit.edu	37	15	66795168	66795168	+	Intron	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:66795168G>A	uc002apv.2	-						RPL4_uc010bhr.2_Intron|RPL4_uc002apw.2_Translation_Start_Site|RPL4_uc002apx.2_Intron|RPL4_uc010ujq.1_Intron|SNORD18C_uc010bhs.1_5'Flank|SNORD18B_uc002apy.1_5'Flank|SNORD16_uc010bht.2_RNA|ZWILCH_uc010bhu.1_5'Flank|ZWILCH_uc002aqb.2_5'Flank|ZWILCH_uc002aqa.2_5'Flank|ZWILCH_uc010bhv.2_5'Flank	NM_000968	NP_000959			ribosomal protein L4						endocrine pancreas development|translational elongation|translational termination|viral transcription	cytosolic large ribosomal subunit|nucleolus	protein binding|RNA binding|structural constituent of ribosome				0																		---	---	---	---
IQCH	64799	broad.mit.edu	37	15	67553646	67553646	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:67553646A>G	uc002aqo.1	+	2	135	c.88A>G	c.(88-90)ACA>GCA	p.T30A	IQCH_uc010ujv.1_5'UTR|IQCH_uc002aqn.1_5'UTR|IQCH_uc002aqq.1_5'UTR|IQCH_uc002aqp.1_5'UTR|IQCH_uc002aqm.2_Missense_Mutation_p.T30A	NM_001031715	NP_001026885	Q86VS3	IQCH_HUMAN	IQ motif containing H isoform 1	30										skin(3)|ovary(1)	4				Colorectal(3;0.0856)														---	---	---	---
KIF23	9493	broad.mit.edu	37	15	69727909	69727909	+	Intron	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:69727909G>A	uc002asb.2	+						KIF23_uc002asc.2_Intron|KIF23_uc010bii.2_Intron|KIF23_uc010ukc.1_Intron|KIF23_uc010bih.1_Intron	NM_138555	NP_612565			kinesin family member 23 isoform 1						blood coagulation|cytokinesis|microtubule-based movement|mitosis|mitotic spindle elongation	cytosol|kinesin complex|microtubule|midbody|nucleoplasm|spindle	ATP binding|microtubule motor activity|protein binding				0																		---	---	---	---
HEXA	3073	broad.mit.edu	37	15	72646032	72646032	+	Silent	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:72646032T>C	uc002aun.3	-	4	666	c.459A>G	c.(457-459)ACA>ACG	p.T153T	CELF6_uc002auk.3_Intron|HEXA_uc010ukn.1_Silent_p.T164T|HEXA_uc002auo.3_Intron|HEXA_uc010bix.2_Silent_p.T153T|HEXA_uc010biy.2_Intron|HEXA_uc010uko.1_Intron|HEXA_uc010biz.1_RNA	NM_000520	NP_000511	P06865	HEXA_HUMAN	hexosaminidase A preproprotein	153					cell death	lysosome	beta-N-acetylhexosaminidase activity|cation binding|protein heterodimerization activity			ovary(3)|upper_aerodigestive_tract(1)	4																		---	---	---	---
HCN4	10021	broad.mit.edu	37	15	73617662	73617662	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:73617662C>T	uc002avp.2	-	5	2708	c.1714G>A	c.(1714-1716)GAG>AAG	p.E572K		NM_005477	NP_005468	Q9Y3Q4	HCN4_HUMAN	hyperpolarization activated cyclic	572	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	74290533	74290533	+	Silent	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:74290533C>T	uc002awv.2	+	2	458	c.318C>T	c.(316-318)AAC>AAT	p.N106N	PML_uc002awm.2_Silent_p.N106N|PML_uc002awl.2_Silent_p.N106N|PML_uc002awj.1_Silent_p.N106N|PML_uc002awk.2_Silent_p.N106N|PML_uc002awn.2_Silent_p.N106N|PML_uc002awo.2_Silent_p.N106N|PML_uc002awp.2_Silent_p.N106N|PML_uc002awq.2_Silent_p.N106N|PML_uc002awr.2_Silent_p.N106N|PML_uc002aws.2_Silent_p.N106N|PML_uc002awt.2_Silent_p.N106N|PML_uc002awu.2_Silent_p.N106N|PML_uc010ule.1_Intron|PML_uc002aww.1_Silent_p.N21N	NM_033238	NP_150241	P29590	PML_HUMAN	promyelocytic leukemia protein isoform 1	106					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	74425358	74425358	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:74425358G>A	uc002axd.2	+	4	1032	c.263G>A	c.(262-264)CGC>CAC	p.R88H	ISLR2_uc002axe.2_Missense_Mutation_p.R88H|ISLR2_uc010bjg.2_Missense_Mutation_p.R88H|ISLR2_uc010bjf.2_Missense_Mutation_p.R88H	NM_001130136	NP_001123608	Q6UXK2	ISLR2_HUMAN	immunoglobulin superfamily containing	88	Extracellular (Potential).|LRR 2.				positive regulation of axon extension	cell surface|integral to membrane|plasma membrane					0																		---	---	---	---
STRA6	64220	broad.mit.edu	37	15	74472489	74472489	+	Silent	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:74472489G>A	uc002axk.2	-	19	2118	c.1936C>T	c.(1936-1938)CTG>TTG	p.L646L	STRA6_uc002axi.2_Silent_p.L455L|STRA6_uc010ulh.1_Silent_p.L684L|STRA6_uc002axj.2_Silent_p.L685L|STRA6_uc010bji.2_Silent_p.L646L|STRA6_uc002axl.2_Silent_p.L578L|STRA6_uc002axm.2_Silent_p.L646L|STRA6_uc002axn.2_Silent_p.L637L|STRA6_uc010uli.1_Silent_p.L683L	NM_022369	NP_071764	Q9BX79	STRA6_HUMAN	stimulated by retinoic acid gene 6 homolog	646	Cytoplasmic (Potential).				adrenal gland development|alveolar primary septum development|developmental growth|diaphragm development|digestive tract morphogenesis|ear development|embryonic camera-type eye formation|embryonic digestive tract development|eyelid development in camera-type eye|face morphogenesis|feeding behavior|female genitalia development|kidney development|lung vasculature development|neuromuscular process|nose morphogenesis|paramesonephric duct development|positive regulation of behavior|pulmonary artery morphogenesis|pulmonary valve morphogenesis|smooth muscle tissue development|transport|uterus morphogenesis|ventricular septum development|vocal learning	integral to membrane|plasma membrane|protein complex	receptor activity			central_nervous_system(1)	1																		---	---	---	---
CYP11A1	1583	broad.mit.edu	37	15	74630906	74630906	+	Intron	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:74630906A>G	uc002axt.2	-						CYP11A1_uc002axs.2_Intron|CYP11A1_uc010bjm.1_Intron|CYP11A1_uc010bjn.1_Intron|CYP11A1_uc010bjo.1_Intron	NM_000781	NP_000772			cytochrome P450, family 11, subfamily A,						C21-steroid hormone biosynthetic process|cholesterol metabolic process|vitamin D metabolic process|xenobiotic metabolic process	mitochondrial matrix	cholesterol monooxygenase (side-chain-cleaving) activity|electron carrier activity|heme binding			ovary(2)	2					Aminoglutethimide(DB00357)|Cholecalciferol(DB00169)|Cimetidine(DB00501)|Clotrimazole(DB00257)|Digitoxin(DB01396)|Digoxin(DB00390)|Medroxyprogesterone(DB00603)|Ouabain(DB01092)|Progesterone(DB00396)|Testosterone(DB00624)|Trilostane(DB01108)													---	---	---	---
SEMA7A	8482	broad.mit.edu	37	15	74703167	74703167	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:74703167A>G	uc002axv.2	-	14	1839	c.1799T>C	c.(1798-1800)ATC>ACC	p.I600T	SEMA7A_uc010ulk.1_Missense_Mutation_p.I435T|SEMA7A_uc010ull.1_Missense_Mutation_p.I586T	NM_003612	NP_003603	O75326	SEM7A_HUMAN	semaphorin 7A isoform 1 preproprotein	600	Ig-like C2-type.				axon guidance|immune response|inflammatory response|integrin-mediated signaling pathway|positive regulation of axon extension|positive regulation of ERK1 and ERK2 cascade|positive regulation of macrophage cytokine production|regulation of inflammatory response	anchored to membrane|external side of plasma membrane	receptor activity			breast(1)|central_nervous_system(1)	2																		---	---	---	---
ARID3B	10620	broad.mit.edu	37	15	74882287	74882287	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:74882287C>T	uc002aye.2	+	5	1025	c.824C>T	c.(823-825)ACC>ATC	p.T275I	ARID3B_uc002ayd.2_Missense_Mutation_p.T275I|ARID3B_uc010bjs.1_5'Flank	NM_006465	NP_006456	Q8IVW6	ARI3B_HUMAN	AT rich interactive domain 3B	275	ARID.|Interaction with RB1.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding				0																		---	---	---	---
ULK3	25989	broad.mit.edu	37	15	75132646	75132646	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:75132646C>T	uc010bkf.1	-	6	731	c.625G>A	c.(625-627)GGG>AGG	p.G209R	ULK3_uc010ulp.1_Missense_Mutation_p.G119R|ULK3_uc010ulq.1_Missense_Mutation_p.G220R|ULK3_uc010ulr.1_Missense_Mutation_p.G92R|ULK3_uc002ayv.2_Missense_Mutation_p.G209R|ULK3_uc010uls.1_Missense_Mutation_p.G92R|ULK3_uc010ult.1_3'UTR|ULK3_uc010ulu.1_3'UTR	NM_001099436	NP_001092906	Q6PHR2	ULK3_HUMAN	unc-51-like kinase 3	209	Protein kinase.					cytoplasm	ATP binding|protein serine/threonine kinase activity			breast(2)	2																		---	---	---	---
C15orf39	56905	broad.mit.edu	37	15	75498562	75498562	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:75498562C>T	uc002azp.3	+	2	493	c.173C>T	c.(172-174)GCC>GTC	p.A58V	C15orf39_uc002azq.3_Missense_Mutation_p.A58V|C15orf39_uc002azr.3_5'Flank	NM_015492	NP_056307	Q6ZRI6	CO039_HUMAN	hypothetical protein LOC56905	58											0																		---	---	---	---
C15orf39	56905	broad.mit.edu	37	15	75499633	75499633	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:75499633G>T	uc002azp.3	+	2	1564	c.1244G>T	c.(1243-1245)AGG>ATG	p.R415M	C15orf39_uc002azq.3_Missense_Mutation_p.R415M|C15orf39_uc002azr.3_5'Flank	NM_015492	NP_056307	Q6ZRI6	CO039_HUMAN	hypothetical protein LOC56905	415											0																		---	---	---	---
COMMD4	54939	broad.mit.edu	37	15	75630462	75630462	+	Silent	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:75630462G>A	uc002azy.2	+	2	120	c.63G>A	c.(61-63)ACG>ACA	p.T21T	COMMD4_uc010umf.1_Silent_p.T21T|COMMD4_uc002azz.2_Silent_p.T21T|COMMD4_uc002baa.2_Silent_p.T21T|COMMD4_uc010umg.1_Silent_p.T21T|COMMD4_uc010umh.1_RNA	NM_017828	NP_060298	Q9H0A8	COMD4_HUMAN	COMM domain containing 4	21						cytoplasm	protein binding				0																		---	---	---	---
SGK269	79834	broad.mit.edu	37	15	77407377	77407377	+	Silent	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:77407377C>T	uc002bcm.2	-	6	4670	c.4362G>A	c.(4360-4362)AAG>AAA	p.K1454K		NM_024776	NP_079052	Q9H792	PEAK1_HUMAN	NKF3 kinase family member	1454	Protein kinase.				cell migration|protein autophosphorylation|substrate adhesion-dependent cell spreading	actin cytoskeleton|cytoplasm|focal adhesion	ATP binding|non-membrane spanning protein tyrosine kinase activity|protein binding				0				STAD - Stomach adenocarcinoma(199;0.124)														---	---	---	---
HMG20A	10363	broad.mit.edu	37	15	77770758	77770758	+	Silent	SNP	G	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:77770758G>T	uc002bcr.2	+	9	1014	c.813G>T	c.(811-813)GTG>GTT	p.V271V	HMG20A_uc002bcs.2_Silent_p.V271V	NM_018200	NP_060670	Q9NP66	HM20A_HUMAN	high-mobility group 20A	271	Potential.				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																		---	---	---	---
IREB2	3658	broad.mit.edu	37	15	78790398	78790398	+	Silent	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:78790398C>T	uc002bdr.2	+	22	2967	c.2805C>T	c.(2803-2805)AGC>AGT	p.S935S	IREB2_uc010unb.1_Silent_p.S685S	NM_004136	NP_004127	P48200	IREB2_HUMAN	iron-responsive element binding protein 2	935							4 iron, 4 sulfur cluster binding|metal ion binding|protein binding				0				UCEC - Uterine corpus endometrioid carcinoma (272;0.232)														---	---	---	---
IL16	3603	broad.mit.edu	37	15	81585206	81585206	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:81585206C>T	uc002bgh.3	+	12	2106	c.1730C>T	c.(1729-1731)CCG>CTG	p.P577L	IL16_uc002bgc.2_RNA|IL16_uc010blq.1_Missense_Mutation_p.P577L|IL16_uc002bge.3_RNA|IL16_uc010unp.1_Missense_Mutation_p.P619L|IL16_uc002bgg.2_Missense_Mutation_p.P577L|IL16_uc002bgi.1_5'UTR|IL16_uc002bgj.2_Missense_Mutation_p.P71L|IL16_uc002bgk.2_5'Flank	NM_172217	NP_757366	Q14005	IL16_HUMAN	interleukin 16 isoform 2	577					immune response|interspecies interaction between organisms|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|extracellular space|nucleus|plasma membrane	cytokine activity			ovary(2)|lung(1)|skin(1)	4																		---	---	---	---
AP3B2	8120	broad.mit.edu	37	15	83349617	83349617	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:83349617C>T	uc010uoh.1	-	7	920	c.743G>A	c.(742-744)CGC>CAC	p.R248H	AP3B2_uc010uoi.1_Missense_Mutation_p.R248H|AP3B2_uc010uoj.1_Missense_Mutation_p.R216H|AP3B2_uc010uog.1_5'Flank	NM_004644	NP_004635	Q13367	AP3B2_HUMAN	adaptor-related protein complex 3, beta 2	248					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)															---	---	---	---
BNC1	646	broad.mit.edu	37	15	83933481	83933481	+	Silent	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:83933481T>C	uc002bjt.1	-	4	610	c.522A>G	c.(520-522)GGA>GGG	p.G174G	BNC1_uc010uos.1_Silent_p.G162G	NM_001717	NP_001708	Q01954	BNC1_HUMAN	basonuclin 1	174					epidermis development|positive regulation of cell proliferation	cytoplasm|nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(3)	3																		---	---	---	---
ALPK3	57538	broad.mit.edu	37	15	85411385	85411385	+	Silent	SNP	C	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:85411385C>A	uc002ble.2	+	14	5589	c.5422C>A	c.(5422-5424)CGG>AGG	p.R1808R	ALPK3_uc010upc.1_Silent_p.R109R	NM_020778	NP_065829	Q96L96	ALPK3_HUMAN	alpha-kinase 3	1808	Alpha-type protein kinase.				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	86273806	86273806	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:86273806C>T	uc002blv.1	+	30	7320	c.7150C>T	c.(7150-7152)CGG>TGG	p.R2384W	AKAP13_uc002blu.1_Missense_Mutation_p.R2388W|AKAP13_uc002blw.1_Missense_Mutation_p.R849W|AKAP13_uc002blx.1_Missense_Mutation_p.R629W	NM_007200	NP_009131	Q12802	AKP13_HUMAN	A-kinase anchor protein 13 isoform 2	2384	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																OREG0023425	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
DET1	55070	broad.mit.edu	37	15	89074505	89074505	+	Silent	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:89074505A>G	uc002bmr.2	-	2	584	c.432T>C	c.(430-432)TGT>TGC	p.C144C	DET1_uc002bmp.3_RNA|DET1_uc010bnk.2_RNA|DET1_uc002bmq.2_Silent_p.C155C	NM_001144074	NP_001137546	Q7L5Y6	DET1_HUMAN	de-etiolated 1 isoform 2	144						nucleus				lung(1)|pancreas(1)	2	Lung NSC(78;0.105)|all_lung(78;0.182)		BRCA - Breast invasive adenocarcinoma(143;0.188)															---	---	---	---
HAPLN3	145864	broad.mit.edu	37	15	89421319	89421319	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:89421319C>T	uc002bnc.2	-	5	1093	c.965G>A	c.(964-966)CGC>CAC	p.R322H	HAPLN3_uc002bne.2_RNA|HAPLN3_uc002bnd.2_Missense_Mutation_p.R384H	NM_178232	NP_839946	Q96S86	HPLN3_HUMAN	hyaluronan and proteoglycan link protein 3	322	Link 2.				cell adhesion	proteinaceous extracellular matrix	hyaluronic acid binding				0	Lung NSC(78;0.0392)|all_lung(78;0.077)																	---	---	---	---
FANCI	55215	broad.mit.edu	37	15	89859683	89859683	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:89859683A>G	uc010bnp.1	+	38	4070	c.3980A>G	c.(3979-3981)AAA>AGA	p.K1327R	FANCI_uc002bnm.1_Missense_Mutation_p.K1267R|FANCI_uc002bnn.1_RNA|FANCI_uc002bnp.1_Missense_Mutation_p.K1087R|FANCI_uc002bnq.1_Missense_Mutation_p.K740R|POLG_uc002bns.3_3'UTR|POLG_uc002bnr.3_3'UTR	NM_001113378	NP_001106849	Q9NVI1	FANCI_HUMAN	Fanconi anemia, complementation group I isoform	1327					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				---	---	---	---
TTLL13	440307	broad.mit.edu	37	15	90801972	90801972	+	Intron	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:90801972C>T	uc002bpd.1	+						TTLL13_uc002bpe.1_Intron	NM_001029964	NP_001025135			tubulin tyrosine ligase-like family, member 13						protein modification process		ATP binding|tubulin-tyrosine ligase activity				0	Melanoma(11;0.00551)|Lung NSC(78;0.0178)|all_lung(78;0.0378)		KIRC - Kidney renal clear cell carcinoma(17;0.0286)|BRCA - Breast invasive adenocarcinoma(143;0.0323)|Kidney(142;0.0514)															---	---	---	---
ZNF774	342132	broad.mit.edu	37	15	90903819	90903819	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:90903819G>A	uc002bpk.3	+	4	942	c.756G>A	c.(754-756)ATG>ATA	p.M252I		NM_001004309	NP_001004309	Q6NX45	ZN774_HUMAN	zinc finger protein 774	252	C2H2-type 4.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0	Melanoma(11;0.00551)|Lung NSC(78;0.0158)|all_lung(78;0.0331)		BRCA - Breast invasive adenocarcinoma(143;0.0224)|KIRC - Kidney renal clear cell carcinoma(17;0.138)|Kidney(142;0.194)															---	---	---	---
VPS33B	26276	broad.mit.edu	37	15	91557622	91557622	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:91557622T>C	uc002bqp.1	-	4	635	c.281A>G	c.(280-282)TAC>TGC	p.Y94C	VPS33B_uc002bqq.1_Missense_Mutation_p.Y3C|VPS33B_uc010uqu.1_Missense_Mutation_p.Y67C	NM_018668	NP_061138	Q9H267	VP33B_HUMAN	vacuolar protein sorting 33B (yeast homolog))	94					cellular membrane fusion|lysosome localization|melanosome localization|platelet alpha granule organization|protein transport|vesicle docking involved in exocytosis	late endosome membrane|lysosomal membrane|perinuclear region of cytoplasm|platelet alpha granule	protein binding			ovary(2)	2	Lung NSC(78;0.0987)|all_lung(78;0.175)																	---	---	---	---
MCTP2	55784	broad.mit.edu	37	15	94841650	94841650	+	Silent	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:94841650G>A	uc002btj.2	+	1	221	c.156G>A	c.(154-156)GTG>GTA	p.V52V	MCTP2_uc010urg.1_Silent_p.V52V|MCTP2_uc002bti.2_Silent_p.V52V|MCTP2_uc010boj.2_5'UTR|MCTP2_uc010bok.2_Silent_p.V52V|MCTP2_uc002btg.3_Silent_p.V52V|MCTP2_uc002bth.3_Silent_p.V52V	NM_018349	NP_060819	Q6DN12	MCTP2_HUMAN	multiple C2 domains, transmembrane 2 isoform 1	52					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)															---	---	---	---
TTC23	64927	broad.mit.edu	37	15	99696449	99696449	+	Silent	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:99696449G>A	uc002bur.2	-	11	1578	c.1047C>T	c.(1045-1047)GGC>GGT	p.G349G	TTC23_uc002bus.2_Silent_p.G349G|TTC23_uc002but.2_Silent_p.G349G|TTC23_uc002buu.2_Silent_p.G349G|TTC23_uc002buv.2_Silent_p.G349G|TTC23_uc002bux.2_Silent_p.G349G|TTC23_uc002buw.2_Silent_p.G349G|TTC23_uc010boq.2_RNA|TTC23_uc002buy.2_Silent_p.G349G|TTC23_uc010bor.2_Silent_p.G349G|TTC23_uc002buz.2_Silent_p.G349G	NM_022905	NP_075056	Q5W5X9	TTC23_HUMAN	tetratricopeptide repeat domain 23	349							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)															---	---	---	---
LYSMD4	145748	broad.mit.edu	37	15	100271573	100271573	+	Intron	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:100271573C>T	uc002bvk.2	-						LYSMD4_uc002bvj.1_Intron|LYSMD4_uc010bou.1_Intron|LYSMD4_uc002bvl.2_Silent_p.P83P|LYSMD4_uc002bvm.2_Intron|LYSMD4_uc010bov.2_Intron					SubName: Full=cDNA FLJ77040, highly similar to Homo sapiens LysM, putative peptidoglycan-binding, domain containing 4, mRNA; SubName: Full=LysM, putative peptidoglycan-binding, domain containing 4, isoform CRA_c;						cell wall macromolecule catabolic process	integral to membrane					0	Lung NSC(78;0.00335)|all_lung(78;0.00659)|Melanoma(26;0.00778)|Medulloblastoma(229;0.163)		OV - Ovarian serous cystadenocarcinoma(32;0.00162)|LUSC - Lung squamous cell carcinoma(107;0.17)|Lung(145;0.208)															---	---	---	---
C15orf51	196968	broad.mit.edu	37	15	100339865	100339865	+	RNA	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:100339865C>T	uc010urx.1	-	4		c.1062G>A			C15orf51_uc010ury.1_RNA|uc002bvp.2_5'Flank|C15orf51_uc010urz.1_RNA|uc002bvq.2_5'Flank|uc002bvt.1_5'Flank	NR_003260				Homo sapiens cDNA FLJ43799 fis, clone TESTI4000288.												0																		---	---	---	---
ASB7	140460	broad.mit.edu	37	15	101152483	101152483	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:101152483C>T	uc002bwk.2	+	4	831	c.62C>T	c.(61-63)GCG>GTG	p.A21V	ASB7_uc002bwj.2_Missense_Mutation_p.A21V	NM_198243	NP_937886	Q9H672	ASB7_HUMAN	ankyrin repeat and SOCS box-containing protein 7	21	ANK 1.				intracellular signal transduction					skin(1)	1	Lung NSC(78;0.00121)|all_lung(78;0.00152)|Melanoma(26;0.00852)		OV - Ovarian serous cystadenocarcinoma(32;0.00168)|LUSC - Lung squamous cell carcinoma(107;0.0766)|Lung(145;0.103)															---	---	---	---
AXIN1	8312	broad.mit.edu	37	16	339465	339465	+	Silent	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:339465G>A	uc002cgp.1	-	10	2614	c.2437C>T	c.(2437-2439)CTG>TTG	p.L813L	AXIN1_uc002cgq.1_Silent_p.L777L	NM_003502	NP_003493	O15169	AXIN1_HUMAN	axin 1 isoform a	813	DIX.				activation of JUN kinase activity|activation of protein kinase activity|apoptosis|axial mesoderm formation|canonical Wnt receptor signaling pathway involved in neural plate anterior/posterior pattern formation|cellular protein complex assembly|cellular response to organic cyclic compound|cytoplasmic microtubule organization|determination of left/right symmetry|dorsal/ventral axis specification|embryonic eye morphogenesis|embryonic skeletal joint morphogenesis|forebrain anterior/posterior pattern formation|muscle cell development|negative regulation of canonical Wnt receptor signaling pathway|negative regulation of fat cell differentiation|olfactory placode formation|optic placode formation|positive regulation of JNK cascade|positive regulation of peptidyl-serine phosphorylation|positive regulation of peptidyl-threonine phosphorylation|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process|positive regulation of transcription, DNA-dependent|positive regulation of ubiquitin-protein ligase activity|regulation of catenin import into nucleus|tail morphogenesis|Wnt receptor signaling pathway involved in forebrain neuron fate commitment|Wnt receptor signaling pathway involved in somitogenesis	APC-Axin-1-beta-catenin complex|Axin-APC-beta-catenin-GSK3B complex|beta-catenin destruction complex|cell cortex|cytoplasmic membrane-bounded vesicle|cytoplasmic microtubule|cytosol|lateral plasma membrane|nucleus|perinuclear region of cytoplasm|postsynaptic density	armadillo repeat domain binding|beta-catenin binding|GTPase activator activity|I-SMAD binding|p53 binding|protein complex scaffold|protein homodimerization activity|protein kinase binding|signal transducer activity|ubiquitin protein ligase binding			breast(1)|liver(1)	2		all_cancers(16;2.75e-07)|all_epithelial(16;1.6e-06)|Hepatocellular(16;0.000105)|Lung NSC(18;0.00774)|all_lung(18;0.0187)																---	---	---	---
RAB11FIP3	9727	broad.mit.edu	37	16	560666	560666	+	Silent	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:560666C>T	uc002chf.2	+	9	1845	c.1506C>T	c.(1504-1506)AAC>AAT	p.N502N	RAB11FIP3_uc010uuf.1_Silent_p.N206N|RAB11FIP3_uc010uug.1_Silent_p.N237N	NM_014700	NP_055515	O75154	RFIP3_HUMAN	rab11-family interacting protein 3 isoform 1	502	Potential.|ARF-binding domain (ABD).				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)																---	---	---	---
RAB40C	57799	broad.mit.edu	37	16	677527	677527	+	Missense_Mutation	SNP	G	A	A	rs145997805		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:677527G>A	uc002chr.2	+	6	867	c.751G>A	c.(751-753)GGC>AGC	p.G251S	RAB40C_uc002chq.2_Missense_Mutation_p.G232S|WFIKKN1_uc002chs.1_5'Flank	NM_021168	NP_066991	Q96S21	RB40C_HUMAN	RAB40C, member RAS oncogene family	251					protein transport|small GTPase mediated signal transduction	plasma membrane	GTP binding				0		Hepatocellular(780;0.0218)																---	---	---	---
CACNA1H	8912	broad.mit.edu	37	16	1250577	1250577	+	Intron	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:1250577C>T	uc002cks.2	+						CACNA1H_uc002ckt.2_Intron	NM_021098	NP_066921			calcium channel, voltage-dependent, T type,						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)													---	---	---	---
TPSAB1	7177	broad.mit.edu	37	16	1291270	1291270	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:1291270G>A	uc002ckz.2	+	3	230	c.178G>A	c.(178-180)GGG>AGG	p.G60R	TPSAB1_uc010uux.1_Missense_Mutation_p.G5R	NM_003294	NP_003285	Q15661	TRYB1_HUMAN	tryptase alpha/beta 1 precursor	60	Peptidase S1.				defense response|proteolysis	extracellular space	protein binding|serine-type endopeptidase activity				0		Hepatocellular(780;0.00369)																---	---	---	---
BAIAP3	8938	broad.mit.edu	37	16	1392188	1392188	+	Silent	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:1392188C>T	uc002clk.1	+	11	966	c.966C>T	c.(964-966)TTC>TTT	p.F322F	BAIAP3_uc002clj.2_Silent_p.F304F|BAIAP3_uc010uuz.1_Silent_p.F287F|BAIAP3_uc010uva.1_Silent_p.F259F|BAIAP3_uc010uvb.1_Silent_p.F339F|BAIAP3_uc010uvc.1_Silent_p.F287F	NM_003933	NP_003924	O94812	BAIP3_HUMAN	BAI1-associated protein 3	322					G-protein coupled receptor protein signaling pathway|neurotransmitter secretion		protein C-terminus binding			pancreas(1)	1		Hepatocellular(780;0.0893)																---	---	---	---
BAIAP3	8938	broad.mit.edu	37	16	1392189	1392189	+	Missense_Mutation	SNP	A	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:1392189A>C	uc002clk.1	+	11	967	c.967A>C	c.(967-969)AAA>CAA	p.K323Q	BAIAP3_uc002clj.2_Missense_Mutation_p.K305Q|BAIAP3_uc010uuz.1_Missense_Mutation_p.K288Q|BAIAP3_uc010uva.1_Missense_Mutation_p.K260Q|BAIAP3_uc010uvb.1_Missense_Mutation_p.K340Q|BAIAP3_uc010uvc.1_Missense_Mutation_p.K288Q	NM_003933	NP_003924	O94812	BAIP3_HUMAN	BAI1-associated protein 3	323					G-protein coupled receptor protein signaling pathway|neurotransmitter secretion		protein C-terminus binding			pancreas(1)	1		Hepatocellular(780;0.0893)																---	---	---	---
HAGH	3029	broad.mit.edu	37	16	1869197	1869197	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:1869197C>T	uc002cna.2	-	5	867	c.460G>A	c.(460-462)GCG>ACG	p.A154T	HAGH_uc002cmz.2_Missense_Mutation_p.A106T|HAGH_uc010uvp.1_Intron|HAGH_uc002cnb.1_Missense_Mutation_p.A106T|HAGH_uc010bry.1_Missense_Mutation_p.A154T	NM_005326	NP_005317	Q16775	GLO2_HUMAN	hydroxyacylglutathione hydrolase isoform 1	154					glutathione biosynthetic process	cytoplasm|mitochondrial matrix|mitochondrial matrix	hydroxyacylglutathione hydrolase activity|zinc ion binding			ovary(1)	1		Hepatocellular(780;0.00335)			Glutathione(DB00143)													---	---	---	---
HAGH	3029	broad.mit.edu	37	16	1869933	1869933	+	Silent	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:1869933G>A	uc002cna.2	-	4	804	c.397C>T	c.(397-399)CTG>TTG	p.L133L	HAGH_uc002cmz.2_Silent_p.L85L|HAGH_uc010uvp.1_Silent_p.L133L|HAGH_uc002cnb.1_Silent_p.L85L|HAGH_uc010bry.1_Silent_p.L133L	NM_005326	NP_005317	Q16775	GLO2_HUMAN	hydroxyacylglutathione hydrolase isoform 1	133					glutathione biosynthetic process	cytoplasm|mitochondrial matrix|mitochondrial matrix	hydroxyacylglutathione hydrolase activity|zinc ion binding			ovary(1)	1		Hepatocellular(780;0.00335)			Glutathione(DB00143)													---	---	---	---
TBL3	10607	broad.mit.edu	37	16	2025874	2025874	+	Silent	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:2025874C>T	uc002cnu.1	+	11	1155	c.1053C>T	c.(1051-1053)GTC>GTT	p.V351V	TBL3_uc002cnv.1_Silent_p.V237V|TBL3_uc010bsb.1_Silent_p.V140V|TBL3_uc010bsc.1_Silent_p.V237V|TBL3_uc010uvt.1_5'UTR|TBL3_uc002cnw.1_5'Flank	NM_006453	NP_006444	Q12788	TBL3_HUMAN	transducin beta-like 3	351	WD 7.				G-protein signaling, coupled to cGMP nucleotide second messenger|rRNA processing	nucleolus|small-subunit processome	receptor signaling protein activity				0																		---	---	---	---
TBL3	10607	broad.mit.edu	37	16	2027151	2027151	+	Silent	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:2027151C>T	uc002cnu.1	+	15	1639	c.1537C>T	c.(1537-1539)CTG>TTG	p.L513L	TBL3_uc002cnv.1_Silent_p.L399L|TBL3_uc010bsb.1_Silent_p.L302L|TBL3_uc010bsc.1_Silent_p.L380L|TBL3_uc010uvt.1_5'UTR|TBL3_uc002cnw.1_5'Flank	NM_006453	NP_006444	Q12788	TBL3_HUMAN	transducin beta-like 3	513	WD 10.				G-protein signaling, coupled to cGMP nucleotide second messenger|rRNA processing	nucleolus|small-subunit processome	receptor signaling protein activity				0																		---	---	---	---
TBL3	10607	broad.mit.edu	37	16	2028400	2028400	+	Nonsense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:2028400C>T	uc002cnu.1	+	21	2323	c.2221C>T	c.(2221-2223)CGA>TGA	p.R741*	TBL3_uc002cnv.1_Nonsense_Mutation_p.R627*|TBL3_uc010bsb.1_3'UTR|TBL3_uc010bsc.1_Nonsense_Mutation_p.R608*|TBL3_uc010uvt.1_Nonsense_Mutation_p.R210*|TBL3_uc002cnw.1_RNA	NM_006453	NP_006444	Q12788	TBL3_HUMAN	transducin beta-like 3	741					G-protein signaling, coupled to cGMP nucleotide second messenger|rRNA processing	nucleolus|small-subunit processome	receptor signaling protein activity				0																		---	---	---	---
TBL3	10607	broad.mit.edu	37	16	2028555	2028555	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:2028555C>T	uc002cnu.1	+	22	2398	c.2296C>T	c.(2296-2298)CGG>TGG	p.R766W	TBL3_uc002cnv.1_Missense_Mutation_p.R652W|TBL3_uc010bsc.1_Missense_Mutation_p.R633W|TBL3_uc010uvt.1_Missense_Mutation_p.R235W|TBL3_uc002cnw.1_RNA	NM_006453	NP_006444	Q12788	TBL3_HUMAN	transducin beta-like 3	766					G-protein signaling, coupled to cGMP nucleotide second messenger|rRNA processing	nucleolus|small-subunit processome	receptor signaling protein activity				0																		---	---	---	---
CASKIN1	57524	broad.mit.edu	37	16	2237232	2237232	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:2237232G>A	uc010bsg.1	-	8	802	c.770C>T	c.(769-771)GCC>GTC	p.A257V		NM_020764	NP_065815	Q8WXD9	CSKI1_HUMAN	CASK interacting protein 1	257					signal transduction	cytoplasm				skin(2)	2																		---	---	---	---
ABCA3	21	broad.mit.edu	37	16	2376271	2376271	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:2376271C>T	uc002cpy.1	-	5	771	c.59G>A	c.(58-60)CGG>CAG	p.R20Q	ABCA3_uc010bsk.1_Missense_Mutation_p.R20Q|ABCA3_uc010bsl.1_Missense_Mutation_p.R20Q|ABCA3_uc002cpz.1_Missense_Mutation_p.R20Q	NM_001089	NP_001080	Q99758	ABCA3_HUMAN	ATP-binding cassette, sub-family A member 3	20					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)																---	---	---	---
KREMEN2	79412	broad.mit.edu	37	16	3016136	3016136	+	Intron	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:3016136C>T	uc002csg.2	+						KREMEN2_uc010bsw.1_Intron|KREMEN2_uc002csh.2_Intron|KREMEN2_uc010uwl.1_Intron|KREMEN2_uc010bsx.2_Intron|KREMEN2_uc002csi.2_Intron	NM_172229	NP_757384			kringle-containing transmembrane protein 2						Wnt receptor signaling pathway	integral to membrane				central_nervous_system(2)	2																		---	---	---	---
CLUAP1	23059	broad.mit.edu	37	16	3562457	3562457	+	Silent	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:3562457C>T	uc002cvk.1	+	5	579	c.474C>T	c.(472-474)CTC>CTT	p.L158L	CLUAP1_uc002cvj.1_Silent_p.L158L|CLUAP1_uc002cvl.1_Silent_p.L158L|CLUAP1_uc002cvm.1_Intron	NM_015041	NP_055856	Q96AJ1	CLUA1_HUMAN	clusterin associated protein 1 isoform 1	158						nucleus	protein binding			ovary(1)|breast(1)|pancreas(1)	3																		---	---	---	---
BTBD12	84464	broad.mit.edu	37	16	3647519	3647519	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:3647519C>T	uc002cvp.2	-	7	2171	c.1544G>A	c.(1543-1545)AGA>AAA	p.R515K		NM_032444	NP_115820	Q8IY92	SLX4_HUMAN	BTB (POZ) domain containing 12	515	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	3778724	3778724	+	Silent	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:3778724G>A	uc002cvv.2	-	31	6528	c.6324C>T	c.(6322-6324)TAC>TAT	p.Y2108Y	CREBBP_uc002cvw.2_Silent_p.Y2070Y	NM_004380	NP_004371	Q92793	CBP_HUMAN	CREB binding protein isoform a	2108					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				---	---	---	---
CREBBP	1387	broad.mit.edu	37	16	3786785	3786785	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:3786785G>A	uc002cvv.2	-	27	4630	c.4426C>T	c.(4426-4428)CCA>TCA	p.P1476S	CREBBP_uc002cvw.2_Missense_Mutation_p.P1438S	NM_004380	NP_004371	Q92793	CBP_HUMAN	CREB binding protein isoform a	1476	Cys/His-rich.|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	p.P1476R(1)		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				---	---	---	---
ADCY9	115	broad.mit.edu	37	16	4165103	4165103	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:4165103C>T	uc002cvx.2	-	2	880	c.341G>A	c.(340-342)CGC>CAC	p.R114H		NM_001116	NP_001107	O60503	ADCY9_HUMAN	adenylate cyclase 9	114	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	integral to plasma membrane	adenylate cyclase activity|ATP binding|metal ion binding			ovary(4)|large_intestine(1)|central_nervous_system(1)	6																		---	---	---	---
PPL	5493	broad.mit.edu	37	16	4935051	4935051	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:4935051T>C	uc002cyd.1	-	22	3695	c.3605A>G	c.(3604-3606)TAC>TGC	p.Y1202C		NM_002705	NP_002696	O60437	PEPL_HUMAN	periplakin	1202	Potential.				keratinization	cytoskeleton|desmosome|mitochondrion|nucleus	protein binding|structural constituent of cytoskeleton			ovary(4)|central_nervous_system(1)|skin(1)	6																		---	---	---	---
CIITA	4261	broad.mit.edu	37	16	10997619	10997619	+	Silent	SNP	T	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:10997619T>G	uc002dai.3	+	9	937	c.804T>G	c.(802-804)CCT>CCG	p.P268P	CIITA_uc002daj.3_Silent_p.P269P|CIITA_uc002dak.3_Silent_p.P219P|CIITA_uc002dag.2_Silent_p.P268P|CIITA_uc002dah.2_Silent_p.P220P|CIITA_uc010bup.1_Silent_p.P268P	NM_000246	NP_000237	P33076	C2TA_HUMAN	class II transactivator	268					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|								---	---	---	---
TXNDC11	51061	broad.mit.edu	37	16	11785501	11785501	+	Silent	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:11785501A>G	uc010buu.1	-	9	1688	c.1626T>C	c.(1624-1626)GGT>GGC	p.G542G	TXNDC11_uc002dbg.1_Silent_p.G515G	NM_015914	NP_056998	Q6PKC3	TXD11_HUMAN	thioredoxin domain containing 11	542					cell redox homeostasis	endoplasmic reticulum membrane|integral to membrane					0																		---	---	---	---
RSL1D1	26156	broad.mit.edu	37	16	11933582	11933582	+	Silent	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:11933582T>C	uc002dbp.1	-	8	1189	c.1116A>G	c.(1114-1116)GGA>GGG	p.G372G	RSL1D1_uc010buv.1_Silent_p.G371G|RSL1D1_uc010uyw.1_Silent_p.G152G|RSL1D1_uc010buw.2_RNA	NM_015659	NP_056474	O76021	RL1D1_HUMAN	ribosomal L1 domain containing 1	372					regulation of protein localization|translation	large ribosomal subunit|nucleolus	protein binding|RNA binding|structural constituent of ribosome				0																		---	---	---	---
SNX29	92017	broad.mit.edu	37	16	12450080	12450080	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:12450080G>A	uc002dby.3	+	9	744	c.688G>A	c.(688-690)GCC>ACC	p.A230T		NM_001080530	NP_001073999	Q8TEQ0	SNX29_HUMAN	sorting nexin 29	230					cell communication		phosphatidylinositol binding			ovary(1)	1																		---	---	---	---
C16orf45	89927	broad.mit.edu	37	16	15528522	15528522	+	Silent	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:15528522G>A	uc002ddo.2	+	1	198	c.12G>A	c.(10-12)AAG>AAA	p.K4K		NM_033201	NP_149978	Q96MC5	CP045_HUMAN	hypothetical protein LOC89927 isoform 1	4				MELKQSLSTHLEAEKPLRRYGAVEETAWKTERLGRN -> M WGDLTETGCMGRRSAKKD (in Ref. 3; AAH23603).						ovary(1)	1																		---	---	---	---
KIAA0430	9665	broad.mit.edu	37	16	15729564	15729564	+	Silent	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:15729564T>C	uc002ddr.2	-	3	973	c.780A>G	c.(778-780)GTA>GTG	p.V260V	KIAA0430_uc002ddq.2_Silent_p.V259V|KIAA0430_uc010uzv.1_Silent_p.V259V|KIAA0430_uc010uzw.1_Silent_p.V259V|KIAA0430_uc010uzx.1_Silent_p.V259V	NM_014647	NP_055462	Q9Y4F3	LKAP_HUMAN	limkain b1	259						peroxisome	nucleotide binding|RNA binding				0																		---	---	---	---
SMG1	23049	broad.mit.edu	37	16	18881194	18881194	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:18881194C>A	uc002dfm.2	-	19	2978	c.2615G>T	c.(2614-2616)GGG>GTG	p.G872V	SMG1_uc010bwb.2_Missense_Mutation_p.G732V	NM_015092	NP_055907	Q96Q15	SMG1_HUMAN	PI-3-kinase-related kinase SMG-1	872	Interaction with SMG8 and SMG9.				DNA repair|mRNA export from nucleus|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay|peptidyl-serine phosphorylation|phosphatidylinositol phosphorylation|protein autophosphorylation	cytoplasm|nucleus	ATP binding|metal ion binding|protein binding|protein serine/threonine kinase activity			breast(5)|stomach(4)|lung(4)|kidney(2)|ovary(1)	16																		---	---	---	---
GDE1	51573	broad.mit.edu	37	16	19516251	19516251	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:19516251T>C	uc002dgh.2	-	5	964	c.800A>G	c.(799-801)TAC>TGC	p.Y267C	GDE1_uc002dgi.2_Missense_Mutation_p.Y157C	NM_016641	NP_057725	Q9NZC3	GDE1_HUMAN	glycerophosphodiester phosphodiesterase 1	267	Helical; (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	19584464	19584464	+	Silent	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:19584464T>C	uc002dgn.1	+	4	321	c.309T>C	c.(307-309)GAT>GAC	p.D103D	C16orf62_uc002dgo.1_Silent_p.D103D|C16orf62_uc010vas.1_5'UTR|C16orf62_uc002dgm.1_Silent_p.D103D	NM_020314	NP_064710	Q7Z3J2	CP062_HUMAN	hypothetical protein LOC57020	103						integral to membrane				ovary(1)	1																		---	---	---	---
ERI2	112479	broad.mit.edu	37	16	20810683	20810683	+	Intron	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:20810683C>T	uc010vbb.1	-						ERI2_uc002dht.3_Intron|ERI2_uc002dhs.2_Intron|ERI2_uc010bwh.2_Intron|ERI2_uc010vbc.1_5'UTR|ERI2_uc002dhu.1_Intron	NM_001142725	NP_001136197			exoribonuclease 2 isoform 1							intracellular	exonuclease activity|nucleic acid binding|zinc ion binding			large_intestine(1)	1																		---	---	---	---
DCUN1D3	123879	broad.mit.edu	37	16	20873739	20873739	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:20873739A>G	uc002dhz.2	-	2	263	c.122T>C	c.(121-123)GTA>GCA	p.V41A	ERI2_uc002dht.3_Intron	NM_173475	NP_775746	Q8IWE4	DCNL3_HUMAN	DCN1, defective in cullin neddylation 1, domain	41					negative regulation of cell growth|negative regulation of S phase of mitotic cell cycle|positive regulation of apoptosis|response to gamma radiation|response to UV-C	perinuclear region of cytoplasm				ovary(2)	2				GBM - Glioblastoma multiforme(48;0.249)														---	---	---	---
SCNN1G	6340	broad.mit.edu	37	16	23200810	23200810	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:23200810G>A	uc002dlm.1	+	3	575	c.436G>A	c.(436-438)GTC>ATC	p.V146I		NM_001039	NP_001030	P51170	SCNNG_HUMAN	sodium channel, nonvoltage-gated 1, gamma	146	Extracellular (By similarity).				excretion|sensory perception of taste	apical plasma membrane|integral to plasma membrane	ligand-gated sodium channel activity|WW domain binding			ovary(2)|skin(2)|large_intestine(1)|pancreas(1)	6				GBM - Glioblastoma multiforme(48;0.0366)	Amiloride(DB00594)|Triamterene(DB00384)													---	---	---	---
GGA2	23062	broad.mit.edu	37	16	23497419	23497419	+	Nonsense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:23497419G>A	uc002dlq.2	-	8	791	c.715C>T	c.(715-717)CGA>TGA	p.R239*	GGA2_uc010bxo.1_RNA	NM_015044	NP_055859	Q9UJY4	GGA2_HUMAN	ADP-ribosylation factor binding protein 2	239	GAT.				intracellular protein transport|vesicle-mediated transport	clathrin adaptor complex|clathrin-coated vesicle|endosome membrane|trans-Golgi network	ADP-ribosylation factor binding			ovary(1)|central_nervous_system(1)	2				GBM - Glioblastoma multiforme(48;0.0386)														---	---	---	---
RBBP6	5930	broad.mit.edu	37	16	24573472	24573472	+	Nonsense_Mutation	SNP	G	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:24573472G>T	uc002dmh.2	+	10	2319	c.1279G>T	c.(1279-1281)GGA>TGA	p.G427*	RBBP6_uc010vcb.1_Nonsense_Mutation_p.G294*|RBBP6_uc002dmi.2_Nonsense_Mutation_p.G427*|RBBP6_uc010bxr.2_Nonsense_Mutation_p.G427*|RBBP6_uc002dmk.2_Nonsense_Mutation_p.G294*	NM_006910	NP_008841	Q7Z6E9	RBBP6_HUMAN	retinoblastoma-binding protein 6 isoform 1	427					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	24950688	24950688	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:24950688C>T	uc002dnb.2	-	17	1814	c.1721G>A	c.(1720-1722)GGC>GAC	p.G574D	ARHGAP17_uc002dmy.2_5'Flank|ARHGAP17_uc002dmz.2_Missense_Mutation_p.G98D|ARHGAP17_uc002dna.2_Missense_Mutation_p.G301D|ARHGAP17_uc002dnc.2_Intron|ARHGAP17_uc010vcf.1_Intron	NM_001006634	NP_001006635	Q68EM7	RHG17_HUMAN	nadrin isoform 1	574	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	24958858	24958858	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:24958858G>A	uc002dnb.2	-	14	1279	c.1186C>T	c.(1186-1188)CCC>TCC	p.P396S	ARHGAP17_uc002dna.2_Missense_Mutation_p.P123S|ARHGAP17_uc002dnc.2_Missense_Mutation_p.P396S|ARHGAP17_uc010vcf.1_Missense_Mutation_p.P217S	NM_001006634	NP_001006635	Q68EM7	RHG17_HUMAN	nadrin isoform 1	396	Rho-GAP.				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)														---	---	---	---
HS3ST4	9951	broad.mit.edu	37	16	26146938	26146938	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:26146938T>C	uc002dof.2	+	2	1132	c.740T>C	c.(739-741)GTG>GCG	p.V247A		NM_006040	NP_006031	Q9Y661	HS3S4_HUMAN	heparan sulfate D-glucosaminyl	247	Lumenal (Potential).				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)														---	---	---	---
MVP	9961	broad.mit.edu	37	16	29855917	29855917	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:29855917C>T	uc002dui.2	+	11	1822	c.1738C>T	c.(1738-1740)CGG>TGG	p.R580W	uc002dtf.2_Intron|BOLA2_uc010bzb.1_Intron|MVP_uc002duj.2_Missense_Mutation_p.R580W|MVP_uc010vea.1_Missense_Mutation_p.R174W	NM_005115	NP_005106	Q14764	MVP_HUMAN	major vault protein	580					mRNA transport|protein transport|response to drug|transmembrane transport	cytoplasm|nuclear pore|ribonucleoprotein complex	protein binding			skin(2)|ovary(1)|central_nervous_system(1)	4																		---	---	---	---
MVP	9961	broad.mit.edu	37	16	29857269	29857269	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:29857269C>T	uc002dui.2	+	12	2191	c.2107C>T	c.(2107-2109)CGC>TGC	p.R703C	uc002dtf.2_Intron|BOLA2_uc010bzb.1_Intron|MVP_uc002duj.2_Missense_Mutation_p.R703C|MVP_uc010vea.1_Missense_Mutation_p.R297C	NM_005115	NP_005106	Q14764	MVP_HUMAN	major vault protein	703					mRNA transport|protein transport|response to drug|transmembrane transport	cytoplasm|nuclear pore|ribonucleoprotein complex	protein binding			skin(2)|ovary(1)|central_nervous_system(1)	4																		---	---	---	---
SEZ6L2	26470	broad.mit.edu	37	16	29888640	29888640	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:29888640C>T	uc002duq.3	-	11	2101	c.1861G>A	c.(1861-1863)GGG>AGG	p.G621R	uc002dtf.2_Intron|BOLA2_uc010bzb.1_Intron|SEZ6L2_uc002dup.3_Missense_Mutation_p.G551R|SEZ6L2_uc002dur.3_Missense_Mutation_p.G551R|SEZ6L2_uc002dus.3_Missense_Mutation_p.G507R|SEZ6L2_uc010vec.1_Missense_Mutation_p.G621R|SEZ6L2_uc010ved.1_Missense_Mutation_p.G577R	NM_201575	NP_963869	Q6UXD5	SE6L2_HUMAN	seizure related 6 homolog (mouse)-like 2 isoform	621	CUB 3.|Extracellular (Potential).					endoplasmic reticulum membrane|integral to membrane|plasma membrane				ovary(1)|skin(1)	2																		---	---	---	---
ITGAL	3683	broad.mit.edu	37	16	30529139	30529139	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:30529139T>C	uc002dyi.3	+	28	3231	c.3055T>C	c.(3055-3057)TTC>CTC	p.F1019L	ITGAL_uc002dyj.3_Missense_Mutation_p.F935L|ITGAL_uc010vev.1_Missense_Mutation_p.F253L	NM_002209	NP_002200	P20701	ITAL_HUMAN	integrin alpha L isoform a precursor	1019	Extracellular (Potential).				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)													---	---	---	---
PHKG2	5261	broad.mit.edu	37	16	30767523	30767523	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:30767523T>C	uc002dzk.1	+	7	670	c.577T>C	c.(577-579)TAT>CAT	p.Y193H	PHKG2_uc002dzi.1_Missense_Mutation_p.Y193H|PHKG2_uc002dzj.1_Missense_Mutation_p.Y91H	NM_000294	NP_000285	P15735	PHKG2_HUMAN	phosphorylase kinase, gamma 2 (testis)	193	Protein kinase.				glucose metabolic process|glycogen biosynthetic process|glycogen catabolic process	cytosol	ATP binding|calmodulin binding|phosphorylase kinase activity			ovary(1)	1			Colorectal(24;0.198)															---	---	---	---
RNF40	9810	broad.mit.edu	37	16	30780693	30780693	+	Missense_Mutation	SNP	G	A	A	rs11556799		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:30780693G>A	uc002dzq.2	+	16	2557	c.2434G>A	c.(2434-2436)GAG>AAG	p.E812K	RNF40_uc010caa.2_Missense_Mutation_p.E812K|RNF40_uc010cab.2_Missense_Mutation_p.E712K|RNF40_uc010vfa.1_Missense_Mutation_p.E144K|RNF40_uc002dzr.2_Missense_Mutation_p.E812K|RNF40_uc010vfb.1_Missense_Mutation_p.E504K|RNF40_uc010vfc.1_Missense_Mutation_p.E144K	NM_014771	NP_055586	O75150	BRE1B_HUMAN	ring finger protein 40	812	Potential.				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)															---	---	---	---
SETD1A	9739	broad.mit.edu	37	16	30975576	30975576	+	Silent	SNP	C	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:30975576C>A	uc002ead.1	+	6	1487	c.801C>A	c.(799-801)TCC>TCA	p.S267S	SETD1A_uc002eae.1_Silent_p.S267S	NM_014712	NP_055527	O15047	SET1A_HUMAN	SET domain containing 1A	267	Ser-rich.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	chromosome|nuclear speck|Set1C/COMPASS complex	histone-lysine N-methyltransferase activity|nucleotide binding|protein binding|RNA binding			ovary(2)|skin(1)	3																		---	---	---	---
ZNF646	9726	broad.mit.edu	37	16	31090856	31090856	+	Missense_Mutation	SNP	C	A	A	rs143026772		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:31090856C>A	uc002eap.2	+	2	3500	c.3211C>A	c.(3211-3213)CGC>AGC	p.R1071S		NM_014699	NP_055514	O15015	ZN646_HUMAN	zinc finger protein 646	1071	C2H2-type 18.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|protein binding|zinc ion binding			breast(2)	2																		---	---	---	---
FUS	2521	broad.mit.edu	37	16	31196405	31196405	+	Silent	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:31196405C>T	uc002ebf.2	+	6	752	c.669C>T	c.(667-669)GGC>GGT	p.G223G	FUS_uc002ebe.1_Silent_p.G219G|FUS_uc002ebh.2_Silent_p.G222G|FUS_uc002ebg.2_Missense_Mutation_p.A30V|FUS_uc002ebi.2_Silent_p.G223G|FUS_uc002ebj.2_Missense_Mutation_p.A30V|FUS_uc002ebk.1_5'Flank	NM_004960	NP_004951	P35637	FUS_HUMAN	fusion (involved in t(12;16) in malignant	223	Gly-rich.				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								---	---	---	---
ITGAD	3681	broad.mit.edu	37	16	31422182	31422182	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:31422182G>A	uc002ebv.1	+	12	1388	c.1339G>A	c.(1339-1341)GAA>AAA	p.E447K	ITGAD_uc010cap.1_Missense_Mutation_p.E447K	NM_005353	NP_005344	Q13349	ITAD_HUMAN	integrin, alpha D precursor	447	Extracellular (Potential).|FG-GAP 5.				cell-cell adhesion|cell-matrix adhesion|immune response|integrin-mediated signaling pathway	integrin complex	receptor activity			skin(1)	1																		---	---	---	---
ARMC5	79798	broad.mit.edu	37	16	31477615	31477615	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:31477615C>A	uc002ecc.2	+	6	2742	c.2213C>A	c.(2212-2214)CCT>CAT	p.P738H	ARMC5_uc010vfn.1_Missense_Mutation_p.P833H|ARMC5_uc010vfo.1_Missense_Mutation_p.P770H|ARMC5_uc002eca.3_3'UTR|ARMC5_uc010vfp.1_Missense_Mutation_p.P546H|ARMC5_uc002ecb.2_3'UTR	NM_001105247	NP_001098717	Q96C12	ARMC5_HUMAN	armadillo repeat containing 5 isoform a	738							binding			pancreas(1)	1																		---	---	---	---
NETO2	81831	broad.mit.edu	37	16	47156771	47156771	+	Intron	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:47156771T>C	uc002eer.1	-						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)			---	---	---	---
PHKB	5257	broad.mit.edu	37	16	47722995	47722995	+	Missense_Mutation	SNP	G	A	A	rs149983469		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:47722995G>A	uc002eev.3	+	27	2726	c.2674G>A	c.(2674-2676)GGA>AGA	p.G892R	PHKB_uc002eeu.3_Missense_Mutation_p.G885R|PHKB_uc002eew.3_Missense_Mutation_p.G133R	NM_000293	NP_000284	Q93100	KPBB_HUMAN	phosphorylase kinase, beta isoform a	892					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)																---	---	---	---
ZNF423	23090	broad.mit.edu	37	16	49671526	49671526	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:49671526C>T	uc002efs.2	-	5	1835	c.1537G>A	c.(1537-1539)GGT>AGT	p.G513S	ZNF423_uc010vgn.1_Missense_Mutation_p.G396S	NM_015069	NP_055884	Q2M1K9	ZN423_HUMAN	zinc finger protein 423	513					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)																---	---	---	---
NKD1	85407	broad.mit.edu	37	16	50642234	50642234	+	Silent	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:50642234G>A	uc002egg.1	+	4	446	c.222G>A	c.(220-222)ACG>ACA	p.T74T		NM_033119	NP_149110	Q969G9	NKD1_HUMAN	naked cuticle homolog 1	74					Wnt receptor signaling pathway	cytoplasm|plasma membrane	calcium ion binding|protein binding				0		all_cancers(37;0.229)		GBM - Glioblastoma multiforme(240;0.243)														---	---	---	---
SALL1	6299	broad.mit.edu	37	16	51173020	51173020	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:51173020A>G	uc010vgs.1	-	2	3144	c.3113T>C	c.(3112-3114)TTT>TCT	p.F1038S	SALL1_uc010vgr.1_Missense_Mutation_p.F941S|SALL1_uc010cbv.2_Intron	NM_002968	NP_002959	Q9NSC2	SALL1_HUMAN	sal-like 1 isoform a	1038	C2H2-type 7.				adrenal gland development|branching involved in ureteric bud morphogenesis|embryonic digestive tract development|embryonic digit morphogenesis|gonad development|histone deacetylation|inductive cell-cell signaling|mesenchymal to epithelial transition involved in metanephros morphogenesis|negative regulation of transcription from RNA polymerase II promoter|olfactory bulb interneuron differentiation|olfactory bulb mitral cell layer development|olfactory nerve development|outer ear morphogenesis|pituitary gland development|positive regulation of transcription from RNA polymerase II promoter|positive regulation of Wnt receptor signaling pathway|ureteric bud invasion|ventricular septum development	chromocenter|cytoplasm|heterochromatin|nucleus	beta-catenin binding|DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			skin(5)|ovary(3)	8		all_cancers(37;0.0322)	COAD - Colon adenocarcinoma(2;0.24)															---	---	---	---
CHD9	80205	broad.mit.edu	37	16	53265618	53265618	+	Silent	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:53265618A>G	uc002ehb.2	+	9	2597	c.2433A>G	c.(2431-2433)GAA>GAG	p.E811E	CHD9_uc002egy.2_Silent_p.E811E|CHD9_uc002eha.1_Silent_p.E811E|CHD9_uc002ehc.2_Silent_p.E811E|CHD9_uc002ehd.2_Silent_p.E337E	NM_025134	NP_079410	Q3L8U1	CHD9_HUMAN	chromodomain helicase DNA binding protein 9	811	Chromo 2.				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)																---	---	---	---
IRX6	79190	broad.mit.edu	37	16	55361814	55361814	+	Intron	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:55361814A>G	uc002ehy.2	+						IRX6_uc002ehx.2_Intron	NM_024335	NP_077311			iroquois homeobox protein 6							nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			central_nervous_system(5)|ovary(1)	6																		---	---	---	---
LPCAT2	54947	broad.mit.edu	37	16	55571546	55571546	+	Splice_Site	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:55571546T>C	uc002eie.3	+	8	1033	c.852_splice	c.e8+2	p.E284_splice	LPCAT2_uc002eic.2_Splice_Site_p.E14_splice	NM_017839	NP_060309			lysophosphatidylcholine acyltransferase 2						cellular membrane organization|platelet activating factor biosynthetic process	endoplasmic reticulum membrane|Golgi membrane|Golgi stack|integral to membrane	1-acylglycerophosphocholine O-acyltransferase activity|1-alkylglycerophosphocholine O-acetyltransferase activity|calcium ion binding				0																		---	---	---	---
OGFOD1	55239	broad.mit.edu	37	16	56509460	56509460	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:56509460A>G	uc002ejb.2	+	12	1551	c.1450A>G	c.(1450-1452)AAA>GAA	p.K484E	OGFOD1_uc002ejc.2_Missense_Mutation_p.K344E	NM_018233	NP_060703	Q8N543	OGFD1_HUMAN	2-oxoglutarate and iron-dependent oxygenase	484							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)													---	---	---	---
RSPRY1	89970	broad.mit.edu	37	16	57238640	57238640	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:57238640G>A	uc002elb.2	+	2	348	c.70G>A	c.(70-72)GAA>AAA	p.E24K	RSPRY1_uc002elc.2_Missense_Mutation_p.E24K|RSPRY1_uc002eld.2_Missense_Mutation_p.E24K|RSPRY1_uc002ele.1_Missense_Mutation_p.E24K	NM_133368	NP_588609	Q96DX4	RSPRY_HUMAN	ring finger and SPRY domain containing 1	24						extracellular region	zinc ion binding			ovary(1)	1																		---	---	---	---
RSPRY1	89970	broad.mit.edu	37	16	57243008	57243008	+	Missense_Mutation	SNP	T	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:57243008T>A	uc002elb.2	+	4	703	c.425T>A	c.(424-426)GTC>GAC	p.V142D	RSPRY1_uc002elc.2_Missense_Mutation_p.V142D|RSPRY1_uc002eld.2_Missense_Mutation_p.V142D	NM_133368	NP_588609	Q96DX4	RSPRY_HUMAN	ring finger and SPRY domain containing 1	142						extracellular region	zinc ion binding			ovary(1)	1																		---	---	---	---
CX3CL1	6376	broad.mit.edu	37	16	57416914	57416914	+	Silent	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:57416914T>C	uc002eli.2	+	3	1231	c.1164T>C	c.(1162-1164)GGT>GGC	p.G388G		NM_002996	NP_002987	P78423	X3CL1_HUMAN	chemokine (C-X3-C motif) ligand 1 precursor	388	Cytoplasmic (Potential).				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																		---	---	---	---
ZNF319	57567	broad.mit.edu	37	16	58030557	58030557	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:58030557C>T	uc002emx.1	-	2	2236	c.1613G>A	c.(1612-1614)CGC>CAC	p.R538H		NM_020807	NP_065858	Q9P2F9	ZN319_HUMAN	zinc finger protein 319	538					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0																		---	---	---	---
CCDC113	29070	broad.mit.edu	37	16	58312436	58312436	+	Silent	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:58312436C>T	uc002ene.2	+	8	1021	c.942C>T	c.(940-942)GCC>GCT	p.A314A	CCDC113_uc010vid.1_Silent_p.A260A	NM_014157	NP_054876	Q9H0I3	CC113_HUMAN	coiled-coil domain containing 113 isoform 1	314	Potential.					protein complex					0																		---	---	---	---
SETD6	79918	broad.mit.edu	37	16	58552047	58552047	+	Silent	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:58552047T>C	uc002ens.2	+	6	944	c.885T>C	c.(883-885)CAT>CAC	p.H295H	SETD6_uc002enr.2_Silent_p.H271H|SETD6_uc010cdm.2_RNA	NM_001160305	NP_001153777	Q8TBK2	SETD6_HUMAN	SET domain containing 6 isoform a	295					negative regulation of NF-kappaB transcription factor activity|peptidyl-lysine monomethylation|regulation of inflammatory response	nucleus	NF-kappaB binding|protein-lysine N-methyltransferase activity			ovary(1)	1																		---	---	---	---
CNOT1	23019	broad.mit.edu	37	16	58575519	58575519	+	Silent	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:58575519A>G	uc002env.2	-	34	4979	c.4686T>C	c.(4684-4686)GGT>GGC	p.G1562G	CNOT1_uc002enw.2_RNA|CNOT1_uc002enu.3_Silent_p.G1557G|CNOT1_uc010vik.1_Silent_p.G519G	NM_016284	NP_057368	A5YKK6	CNOT1_HUMAN	CCR4-NOT transcription complex, subunit 1	1562					nuclear-transcribed mRNA poly(A) tail shortening|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasmic mRNA processing body|cytosol				ovary(4)|central_nervous_system(2)	6				Kidney(780;0.0722)|OV - Ovarian serous cystadenocarcinoma(108;0.173)|Epithelial(162;0.239)														---	---	---	---
CNOT1	23019	broad.mit.edu	37	16	58577764	58577764	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:58577764C>T	uc002env.2	-	31	4474	c.4181G>A	c.(4180-4182)CGT>CAT	p.R1394H	CNOT1_uc002enw.2_RNA|CNOT1_uc002enu.3_Missense_Mutation_p.R1389H|CNOT1_uc002enx.2_Missense_Mutation_p.R1394H|CNOT1_uc010vik.1_Missense_Mutation_p.R351H	NM_016284	NP_057368	A5YKK6	CNOT1_HUMAN	CCR4-NOT transcription complex, subunit 1	1394					nuclear-transcribed mRNA poly(A) tail shortening|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasmic mRNA processing body|cytosol				ovary(4)|central_nervous_system(2)	6				Kidney(780;0.0722)|OV - Ovarian serous cystadenocarcinoma(108;0.173)|Epithelial(162;0.239)														---	---	---	---
CNOT1	23019	broad.mit.edu	37	16	58619354	58619354	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:58619354G>A	uc002env.2	-	8	987	c.694C>T	c.(694-696)CGG>TGG	p.R232W	CNOT1_uc002enw.2_RNA|CNOT1_uc002enu.3_Missense_Mutation_p.R232W|CNOT1_uc002enx.2_Missense_Mutation_p.R232W|CNOT1_uc002enz.1_Intron	NM_016284	NP_057368	A5YKK6	CNOT1_HUMAN	CCR4-NOT transcription complex, subunit 1	232					nuclear-transcribed mRNA poly(A) tail shortening|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasmic mRNA processing body|cytosol				ovary(4)|central_nervous_system(2)	6				Kidney(780;0.0722)|OV - Ovarian serous cystadenocarcinoma(108;0.173)|Epithelial(162;0.239)														---	---	---	---
CDH11	1009	broad.mit.edu	37	16	64981926	64981926	+	Silent	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:64981926A>G	uc002eoi.2	-	13	2405	c.1971T>C	c.(1969-1971)CGT>CGC	p.R657R	CDH11_uc010cdn.2_RNA|CDH11_uc002eoj.2_3'UTR|CDH11_uc010vin.1_Silent_p.R531R	NM_001797	NP_001788	P55287	CAD11_HUMAN	cadherin 11, type 2 preproprotein	657	Cytoplasmic (Potential).				adherens junction organization|cell junction assembly|homophilic cell adhesion|ossification|skeletal system development	integral to membrane|plasma membrane	calcium ion binding|protein binding			lung(10)|ovary(3)|skin(1)	14		Ovarian(137;0.0973)		OV - Ovarian serous cystadenocarcinoma(108;0.205)				T	USP6	aneurysmal bone cysts					TSP Lung(24;0.17)			---	---	---	---
PDP2	57546	broad.mit.edu	37	16	66919301	66919301	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:66919301G>T	uc002eqk.1	+	2	1276	c.1114G>T	c.(1114-1116)GCC>TCC	p.A372S		NM_020786	NP_065837	Q9P2J9	PDP2_HUMAN	pyruvate dehydrogenase phosphatase isoenzyme 2	372					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)														---	---	---	---
FAM65A	79567	broad.mit.edu	37	16	67574388	67574388	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:67574388T>C	uc010vjp.1	+	9	815	c.719T>C	c.(718-720)GTA>GCA	p.V240A	FAM65A_uc010cei.1_Missense_Mutation_p.V62A|FAM65A_uc002eth.2_Missense_Mutation_p.V220A|FAM65A_uc010cej.2_Missense_Mutation_p.V223A|FAM65A_uc002eti.1_Missense_Mutation_p.V183A|FAM65A_uc010vjq.1_Missense_Mutation_p.V234A|FAM65A_uc002etj.1_Missense_Mutation_p.V219A|FAM65A_uc002etk.2_Missense_Mutation_p.V219A	NM_024519	NP_078795	Q6ZS17	FA65A_HUMAN	hypothetical protein LOC79567	224						cytoplasm	binding			ovary(2)|central_nervous_system(1)	3		Acute lymphoblastic leukemia(13;3.76e-06)|all_hematologic(13;0.000303)|Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.0474)|Epithelial(162;0.117)														---	---	---	---
CTCF	10664	broad.mit.edu	37	16	67644736	67644736	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:67644736A>G	uc002etl.2	+	3	291	c.1A>G	c.(1-3)ATG>GTG	p.M1V	CTCF_uc010cek.2_Intron	NM_006565	NP_006556	P49711	CTCF_HUMAN	CCCTC-binding factor	1					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)														---	---	---	---
TSNAXIP1	55815	broad.mit.edu	37	16	67861399	67861399	+	Silent	SNP	C	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:67861399C>A	uc002euj.2	+	15	2047	c.1653C>A	c.(1651-1653)CCC>CCA	p.P551P	TSNAXIP1_uc010vjz.1_Silent_p.P428P|TSNAXIP1_uc002euf.3_Silent_p.P284P|TSNAXIP1_uc010vka.1_Silent_p.P605P|TSNAXIP1_uc010vkb.1_Silent_p.P536P|TSNAXIP1_uc002eug.3_Silent_p.P259P|TSNAXIP1_uc002euh.3_Silent_p.P259P|TSNAXIP1_uc002eui.3_Silent_p.P259P|TSNAXIP1_uc002euk.2_Silent_p.P284P	NM_018430	NP_060900	Q2TAA8	TXIP1_HUMAN	translin-associated factor X interacting protein	551					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)														---	---	---	---
EDC4	23644	broad.mit.edu	37	16	67914865	67914865	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:67914865C>T	uc002eur.2	+	18	2669	c.2503C>T	c.(2503-2505)CGT>TGT	p.R835C	EDC4_uc010cer.2_Missense_Mutation_p.R454C|EDC4_uc002eus.2_Missense_Mutation_p.R565C|EDC4_uc002eut.1_5'Flank	NM_014329	NP_055144	Q6P2E9	EDC4_HUMAN	autoantigen RCD8	835					exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay	cytoplasmic mRNA processing body|cytosol|nucleus	protein binding			ovary(2)|central_nervous_system(2)	4		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.0042)|Epithelial(162;0.0185)|all cancers(182;0.121)														---	---	---	---
DPEP3	64180	broad.mit.edu	37	16	68013540	68013540	+	Splice_Site	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:68013540A>G	uc002evc.3	-	2	583	c.489_splice	c.e2+1	p.Q163_splice	DPEP3_uc010cex.2_Splice_Site_p.Q163_splice	NM_022357	NP_071752			dipeptidase 3 isoform a						meiosis	anchored to membrane	dipeptidase activity|dipeptidyl-peptidase activity|metal ion binding|metalloexopeptidase activity			breast(3)	3		Ovarian(137;0.192)		OV - Ovarian serous cystadenocarcinoma(108;0.0117)|Epithelial(162;0.0481)|all cancers(182;0.236)														---	---	---	---
PLA2G15	23659	broad.mit.edu	37	16	68288877	68288877	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:68288877C>T	uc002evr.2	+	3	423	c.340C>T	c.(340-342)CGT>TGT	p.R114C	PLA2G15_uc010vld.1_Missense_Mutation_p.R114C|PLA2G15_uc010vle.1_Silent_p.Y61Y|PLA2G15_uc010vlf.1_Intron|PLA2G15_uc002evs.2_Translation_Start_Site	NM_012320	NP_036452	Q8NCC3	PAG15_HUMAN	lysophospholipase 3 (lysosomal phospholipase A2)	114					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	68597936	68597936	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:68597936C>A	uc010cff.2	+	5	1538	c.1246C>A	c.(1246-1248)CAT>AAT	p.H416N	ZFP90_uc002ewb.2_3'UTR|ZFP90_uc002ewc.2_3'UTR|ZFP90_uc002ewd.2_Missense_Mutation_p.H416N|ZFP90_uc002ewe.2_Missense_Mutation_p.H416N	NM_133458	NP_597715	Q8TF47	ZFP90_HUMAN	zinc finger protein 90	416	C2H2-type 7.				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)														---	---	---	---
NIP7	51388	broad.mit.edu	37	16	69375201	69375201	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:69375201A>G	uc002exa.2	+	4	588	c.401A>G	c.(400-402)TAC>TGC	p.Y134C	COG8_uc002ewy.2_5'Flank|COG8_uc002ewz.3_5'Flank|NIP7_uc002exb.2_Intron	NM_016101	NP_057185	Q9Y221	NIP7_HUMAN	nuclear import 7	134	PUA.				ribosome assembly	nucleolus	protein binding|RNA binding			breast(1)	1		Ovarian(137;0.101)																---	---	---	---
NFAT5	10725	broad.mit.edu	37	16	69681002	69681002	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:69681002A>G	uc002exm.1	+	3	1479	c.271A>G	c.(271-273)ACC>GCC	p.T91A	NFAT5_uc002exh.1_Silent_p.L24L|NFAT5_uc002exi.2_Missense_Mutation_p.T15A|NFAT5_uc002exj.1_Missense_Mutation_p.T15A|NFAT5_uc002exk.1_Missense_Mutation_p.T15A|NFAT5_uc002exl.1_Missense_Mutation_p.T109A|NFAT5_uc002exn.1_Missense_Mutation_p.T109A	NM_006599	NP_006590	O94916	NFAT5_HUMAN	nuclear factor of activated T-cells 5 isoform c	91	Ser-rich.				excretion|signal transduction|transcription from RNA polymerase II promoter	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity				0																		---	---	---	---
NQO1	1728	broad.mit.edu	37	16	69746984	69746984	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:69746984A>G	uc002exp.2	-	5	657	c.466T>C	c.(466-468)TAC>CAC	p.Y156H	NQO1_uc010cfm.2_Missense_Mutation_p.Y135H|NQO1_uc002exq.2_Intron|NQO1_uc002exr.2_Missense_Mutation_p.Y118H|NQO1_uc010vll.1_Intron	NM_000903	NP_000894	P15559	NQO1_HUMAN	NAD(P)H menadione oxidoreductase 1,	156		FAD.			nitric oxide biosynthetic process|regulation of cellular amino acid metabolic process|response to toxin|synaptic transmission, cholinergic|xenobiotic metabolic process	cytosol	coenzyme binding|cytochrome-b5 reductase activity|electron carrier activity|NAD(P)H dehydrogenase (quinone) activity				0					Dicumarol(DB00266)|Menadione(DB00170)													---	---	---	---
PDPR	55066	broad.mit.edu	37	16	70190456	70190456	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:70190456C>A	uc002eyf.1	+	19	3271	c.2314C>A	c.(2314-2316)CTG>ATG	p.L772M	CLEC18C_uc002exy.2_Intron|PDPR_uc010vlr.1_Missense_Mutation_p.L672M|PDPR_uc002eyg.1_Missense_Mutation_p.L439M|PDPR_uc002eyh.2_Missense_Mutation_p.L117M|PDPR_uc010vls.1_Missense_Mutation_p.L117M	NM_017990	NP_060460	Q8NCN5	PDPR_HUMAN	pyruvate dehydrogenase phosphatase regulatory	772					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	70384462	70384462	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:70384462G>A	uc002eyv.2	+	2	131	c.60G>A	c.(58-60)ATG>ATA	p.M20I	DDX19B_uc010vly.1_Intron|DDX19A_uc002eys.2_Intron|DDX19A_uc010cfq.1_5'UTR|DDX19A_uc010cfr.2_5'UTR|DDX19A_uc010cfs.2_5'UTR|DDX19A_uc010vlz.1_Missense_Mutation_p.M20I	NM_018332	NP_060802	Q9NUU7	DD19A_HUMAN	DDX19-like protein	20					mRNA transport|protein transport|transmembrane transport	cytoplasm|nuclear membrane|nuclear pore	ATP binding|ATP-dependent helicase activity|RNA binding				0		Ovarian(137;0.221)																---	---	---	---
ST3GAL2	6483	broad.mit.edu	37	16	70416789	70416789	+	Silent	SNP	G	A	A	rs143187183		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:70416789G>A	uc002eyw.2	-	5	2906	c.798C>T	c.(796-798)CAC>CAT	p.H266H	ST3GAL2_uc002eyx.2_Silent_p.H266H	NM_006927	NP_008858	Q16842	SIA4B_HUMAN	ST3 beta-galactoside alpha-2,3-sialyltransferase	266	Lumenal (Potential).				amino sugar metabolic process	extracellular region|Golgi cisterna membrane|integral to Golgi membrane	beta-galactoside alpha-2,3-sialyltransferase activity			ovary(1)	1		Ovarian(137;0.0694)																---	---	---	---
COG4	25839	broad.mit.edu	37	16	70514975	70514975	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:70514975G>A	uc002ezc.2	-	19	2319	c.2308C>T	c.(2308-2310)CGC>TGC	p.R770C	COG4_uc002eza.2_Missense_Mutation_p.R107C|COG4_uc002ezb.2_Missense_Mutation_p.R226C|COG4_uc010cfu.2_RNA|COG4_uc002ezd.2_Missense_Mutation_p.R749C|COG4_uc002eze.2_Missense_Mutation_p.R464C	NM_015386	NP_056201	Q9H9E3	COG4_HUMAN	component of oligomeric golgi complex 4	766	E domain; essential for proper cell surface glycosylation.				Golgi organization|Golgi vesicle prefusion complex stabilization|protein transport|retrograde vesicle-mediated transport, Golgi to ER	Golgi membrane|Golgi transport complex	protein binding				0		Ovarian(137;0.0694)																---	---	---	---
SF3B3	23450	broad.mit.edu	37	16	70575742	70575742	+	Intron	SNP	G	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:70575742G>T	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)																---	---	---	---
FTSJD1	55783	broad.mit.edu	37	16	71319292	71319292	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:71319292G>A	uc010cga.2	-	3	938	c.532C>T	c.(532-534)CAT>TAT	p.H178Y	FTSJD1_uc002ezy.3_Missense_Mutation_p.H178Y|FTSJD1_uc002ezz.3_Missense_Mutation_p.H178Y	NM_001099642	NP_001093112	Q8IYT2	FTSJ1_HUMAN	FtsJ methyltransferase domain containing 1	178						integral to membrane	methyltransferase activity|nucleic acid binding			skin(1)	1																		---	---	---	---
ZFHX3	463	broad.mit.edu	37	16	72822536	72822536	+	Silent	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:72822536C>T	uc002fck.2	-	10	10312	c.9639G>A	c.(9637-9639)CCG>CCA	p.P3213P	ZFHX3_uc002fcl.2_Silent_p.P2299P	NM_006885	NP_008816	Q15911	ZFHX3_HUMAN	zinc finger homeobox 3 isoform A	3213	Poly-Pro.				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	p.P3213Q(1)		ovary(2)|skin(2)	4		Ovarian(137;0.13)																---	---	---	---
ZFHX3	463	broad.mit.edu	37	16	72991359	72991359	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:72991359C>T	uc002fck.2	-	2	3359	c.2686G>A	c.(2686-2688)GCC>ACC	p.A896T	ZFHX3_uc002fcl.2_Intron	NM_006885	NP_008816	Q15911	ZFHX3_HUMAN	zinc finger homeobox 3 isoform A	896					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	72991598	72991598	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:72991598G>T	uc002fck.2	-	2	3120	c.2447C>A	c.(2446-2448)GCC>GAC	p.A816D	ZFHX3_uc002fcl.2_Intron	NM_006885	NP_008816	Q15911	ZFHX3_HUMAN	zinc finger homeobox 3 isoform A	816	C2H2-type 5; atypical.				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)																---	---	---	---
ZFP1	162239	broad.mit.edu	37	16	75203736	75203736	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:75203736C>T	uc002fdo.2	+	4	892	c.728C>T	c.(727-729)CCG>CTG	p.P243L	ZFP1_uc002fdp.2_Missense_Mutation_p.P188L|ZFP1_uc010cgt.2_Missense_Mutation_p.P210L|ZFP1_uc010cgs.2_Missense_Mutation_p.P188L|ZFP1_uc002fdq.2_Missense_Mutation_p.P243L	NM_153688	NP_710155	Q6P2D0	ZFP1_HUMAN	zinc finger protein 1 homolog	243	C2H2-type 3.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			upper_aerodigestive_tract(1)|ovary(1)	2																		---	---	---	---
TMEM231	79583	broad.mit.edu	37	16	75573924	75573924	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:75573924G>A	uc002fem.2	-	7	982	c.919C>T	c.(919-921)CGG>TGG	p.R307W	CHST5_uc002fej.1_Intron|TMEM231_uc002fek.2_Missense_Mutation_p.R336W|TMEM231_uc002fel.2_Missense_Mutation_p.R191W	NM_001077418	NP_001070886	Q9H6L2	TM231_HUMAN	transmembrane protein 231 isoform 2	307						integral to membrane					0																		---	---	---	---
ADAT1	23536	broad.mit.edu	37	16	75654578	75654578	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:75654578T>C	uc002feo.1	-	3	222	c.120A>G	c.(118-120)ATA>ATG	p.I40M	ADAT1_uc002fep.1_Translation_Start_Site	NM_012091	NP_036223	Q9BUB4	ADAT1_HUMAN	adenosine deaminase, tRNA-specific 1	40					tRNA processing		metal ion binding|RNA binding|tRNA-specific adenosine deaminase activity			ovary(1)|skin(1)	2																		---	---	---	---
KARS	3735	broad.mit.edu	37	16	75665480	75665480	+	Silent	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:75665480C>T	uc002feq.2	-	9	1134	c.1086G>A	c.(1084-1086)GTG>GTA	p.V362V	KARS_uc002fer.2_Silent_p.V390V|KARS_uc002fes.2_Silent_p.V206V	NM_005548	NP_005539	Q15046	SYK_HUMAN	lysyl-tRNA synthetase isoform 2	362					interspecies interaction between organisms|lysyl-tRNA aminoacylation|tRNA processing	cytosol|extracellular region|mitochondrial matrix|nucleus|plasma membrane|soluble fraction	ATP binding|lysine-tRNA ligase activity|metal ion binding|tRNA binding			ovary(2)	2					L-Lysine(DB00123)													---	---	---	---
CLEC3A	10143	broad.mit.edu	37	16	78064388	78064388	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:78064388T>C	uc002ffh.3	+	3	325	c.244T>C	c.(244-246)TCA>CCA	p.S82P		NM_005752	NP_005743	O75596	CLC3A_HUMAN	C-type lectin domain family 3 member A	82	C-type lectin.				skeletal system development	extracellular region	sugar binding				0																		---	---	---	---
MAF	4094	broad.mit.edu	37	16	79633506	79633506	+	Silent	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:79633506C>T	uc002ffn.2	-	1	1117	c.294G>A	c.(292-294)CCG>CCA	p.P98P	MAF_uc002ffm.2_Silent_p.P98P	NM_001031804	NP_001026974	O75444	MAF_HUMAN	v-maf musculoaponeurotic fibrosarcoma oncogene	98					transcription from RNA polymerase II promoter	chromatin|nucleus	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			lung(1)	1		all_epithelial(2;0.139)|Lung NSC(2;0.186)|Melanoma(2;0.211)		UCEC - Uterine corpus endometrioid carcinoma (2;0.0178)				T	IGH@	MM								---	---	---	---
CENPN	55839	broad.mit.edu	37	16	81066251	81066251	+	Nonsense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:81066251G>A	uc002ffy.3	+	11	1804	c.1014G>A	c.(1012-1014)TGG>TGA	p.W338*		NM_001100625	NP_001094095	Q96H22	CENPN_HUMAN	centromere protein N isoform 1	Error:Variant_position_missing_in_Q96H22_after_alignment					CenH3-containing nucleosome assembly at centromere|mitotic prometaphase	condensed chromosome kinetochore|cytosol|nucleoplasm					0																		---	---	---	---
ATMIN	23300	broad.mit.edu	37	16	81077340	81077340	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:81077340G>A	uc002ffz.1	+	4	1255	c.1237G>A	c.(1237-1239)GTG>ATG	p.V413M	ATMIN_uc002fga.2_Missense_Mutation_p.V255M|ATMIN_uc010vnn.1_Missense_Mutation_p.V184M|ATMIN_uc002fgb.1_Missense_Mutation_p.V255M	NM_015251	NP_056066	O43313	ATMIN_HUMAN	ATM interactor	413	Required for formation of RAD51 foci.				response to DNA damage stimulus	nucleus	zinc ion binding				0																		---	---	---	---
GAN	8139	broad.mit.edu	37	16	81411097	81411097	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:81411097G>A	uc002fgo.2	+	11	1838	c.1690G>A	c.(1690-1692)GAC>AAC	p.D564N		NM_022041	NP_071324	Q9H2C0	GAN_HUMAN	gigaxonin	564	Kelch 6.				cell death	cytoplasm|neurofilament	protein binding			ovary(2)	2		Colorectal(91;0.153)																---	---	---	---
CMIP	80790	broad.mit.edu	37	16	81641219	81641219	+	Silent	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:81641219C>T	uc002fgp.2	+	2	420	c.348C>T	c.(346-348)GAC>GAT	p.D116D	CMIP_uc002fgq.1_Silent_p.D22D|CMIP_uc010vnq.1_5'Flank	NM_198390	NP_938204	Q8IY22	CMIP_HUMAN	c-Maf-inducing protein isoform C-mip	82	PH.					cytoplasm|nucleus					0																		---	---	---	---
CMIP	80790	broad.mit.edu	37	16	81711882	81711882	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:81711882G>A	uc002fgp.2	+	10	1109	c.1037G>A	c.(1036-1038)CGC>CAC	p.R346H	CMIP_uc002fgq.1_Missense_Mutation_p.R252H|CMIP_uc010vnq.1_Missense_Mutation_p.R159H|CMIP_uc002fgr.1_Missense_Mutation_p.R193H	NM_198390	NP_938204	Q8IY22	CMIP_HUMAN	c-Maf-inducing protein isoform C-mip	312						cytoplasm|nucleus					0																		---	---	---	---
MPHOSPH6	10200	broad.mit.edu	37	16	82197715	82197715	+	Silent	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:82197715A>G	uc002fgw.2	-	2	185	c.136T>C	c.(136-138)TTG>CTG	p.L46L		NM_005792	NP_005783	Q99547	MPH6_HUMAN	M-phase phosphoprotein 6	46					M phase of mitotic cell cycle|maturation of 5.8S rRNA	cytoplasm|nucleolus	protein binding|RNA binding				0																		---	---	---	---
OSGIN1	29948	broad.mit.edu	37	16	83999139	83999139	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:83999139G>A	uc002fha.2	+	7	1593	c.1210G>A	c.(1210-1212)GAC>AAC	p.D404N	OSGIN1_uc002fhb.2_Missense_Mutation_p.D321N|OSGIN1_uc002fhc.2_Missense_Mutation_p.D321N	NM_013370	NP_037502	Q9UJX0	OSGI1_HUMAN	oxidative stress induced growth inhibitor 1	404					cell differentiation|multicellular organismal development|negative regulation of cell growth		growth factor activity				0																		---	---	---	---
NECAB2	54550	broad.mit.edu	37	16	84024174	84024174	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:84024174T>C	uc002fhd.2	+	6	552	c.535T>C	c.(535-537)TCG>CCG	p.S179P	NECAB2_uc002fhe.2_Missense_Mutation_p.S96P	NM_019065	NP_061938	Q7Z6G3	NECA2_HUMAN	neuronal calcium-binding protein 2	179	Potential.				antibiotic biosynthetic process	cytoplasm	calcium ion binding|oxidoreductase activity|protein binding			ovary(2)	2																		---	---	---	---
KLHL36	79786	broad.mit.edu	37	16	84691257	84691257	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:84691257G>A	uc002fig.2	+	3	985	c.844G>A	c.(844-846)GTC>ATC	p.V282I	KLHL36_uc010chl.2_Missense_Mutation_p.V281I	NM_024731	NP_079007	Q8N4N3	KLH36_HUMAN	kelch-like 36	282										skin(2)	2																		---	---	---	---
JPH3	57338	broad.mit.edu	37	16	87723260	87723260	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:87723260T>C	uc002fkd.2	+	4	1548	c.1294T>C	c.(1294-1296)TAC>CAC	p.Y432H	JPH3_uc010vou.1_RNA	NM_020655	NP_065706	Q8WXH2	JPH3_HUMAN	junctophilin 3	432	Cytoplasmic (Potential).				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)														---	---	---	---
BANP	54971	broad.mit.edu	37	16	88061228	88061228	+	Silent	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:88061228G>A	uc002fkr.2	+	8	1232	c.1008G>A	c.(1006-1008)ACG>ACA	p.T336T	BANP_uc002fkp.2_Silent_p.T306T|BANP_uc002fkq.2_Silent_p.T306T|BANP_uc010vow.1_Silent_p.T344T|BANP_uc002fks.3_Silent_p.T305T|BANP_uc002fko.1_Silent_p.T242T|BANP_uc010vov.1_Silent_p.T311T	NM_079837	NP_524576	Q8N9N5	BANP_HUMAN	BTG3 associated nuclear protein isoform b	337	Necessary and sufficient for TP53 activation (By similarity).|Interaction with CUX1 and HDAC1 (By similarity).				cell cycle|chromatin modification|multicellular organismal development|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding				0				BRCA - Breast invasive adenocarcinoma(80;0.00551)														---	---	---	---
GALNS	2588	broad.mit.edu	37	16	88904031	88904031	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:88904031T>C	uc002fly.3	-	5	654	c.565A>G	c.(565-567)AGA>GGA	p.R189G	GALNS_uc010cid.2_Missense_Mutation_p.R195G|GALNS_uc002flz.3_Intron	NM_000512	NP_000503	P34059	GALNS_HUMAN	galactosamine (N-acetyl)-6-sulfate sulfatase	189						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)													---	---	---	---
ANKRD11	29123	broad.mit.edu	37	16	89350573	89350573	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:89350573T>C	uc002fmx.1	-	9	2838	c.2377A>G	c.(2377-2379)AAG>GAG	p.K793E	ANKRD11_uc002fmy.1_Missense_Mutation_p.K793E|ANKRD11_uc002fnc.1_Missense_Mutation_p.K793E|ANKRD11_uc002fnb.1_Missense_Mutation_p.K750E	NM_013275	NP_037407	Q6UB99	ANR11_HUMAN	ankyrin repeat domain 11	793	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)														---	---	---	---
FANCA	2175	broad.mit.edu	37	16	89838164	89838164	+	Silent	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:89838164A>G	uc002fou.1	-	23	2115	c.2073T>C	c.(2071-2073)AAT>AAC	p.N691N	FANCA_uc010vpn.1_Silent_p.N691N	NM_000135	NP_000126	O15360	FANCA_HUMAN	Fanconi anemia, complementation group A isoform	691					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				---	---	---	---
TUBB3	10381	broad.mit.edu	37	16	90001171	90001171	+	Silent	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:90001171T>C	uc002fph.1	+	4	377	c.312T>C	c.(310-312)GGT>GGC	p.G104G	TUBB3_uc002fpf.2_Silent_p.G451G|TUBB3_uc010ciz.1_Silent_p.G32G|TUBB3_uc002fpg.1_5'UTR|TUBB3_uc002fpi.1_Silent_p.G32G|TUBB3_uc002fpj.1_Silent_p.G32G|TUBB3_uc010cjb.1_5'UTR|TUBB3_uc002fpk.1_5'UTR	NM_006086	NP_006077	Q13509	TBB3_HUMAN	tubulin, beta, 4	104					'de novo' posttranslational protein folding|axon guidance|microtubule-based movement|protein polymerization	cytoplasm|microtubule	GTP binding|GTPase activity|structural molecule activity			ovary(2)|pancreas(1)	3		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)														---	---	---	---
PRDM7	11105	broad.mit.edu	37	16	90130185	90130185	+	Intron	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:90130185T>C	uc010cje.2	-						PRDM7_uc002fqo.2_5'Flank|PRDM7_uc010cjf.2_Intron|PRDM7_uc010cjg.1_5'Flank|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)														---	---	---	---
VPS53	55275	broad.mit.edu	37	17	440304	440304	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:440304C>T	uc002frn.2	-	18	2126	c.1979G>A	c.(1978-1980)CGC>CAC	p.R660H	VPS53_uc002frk.2_Missense_Mutation_p.R179H|VPS53_uc010cjo.1_Missense_Mutation_p.R660H|VPS53_uc002frl.2_RNA|VPS53_uc002frm.2_Missense_Mutation_p.R631H|VPS53_uc002fro.2_Missense_Mutation_p.R462H|VPS53_uc010cjp.1_Missense_Mutation_p.R383H	NM_018289	NP_060759	Q5VIR6	VPS53_HUMAN	vacuolar protein sorting 53 isoform 2	660				STRKYFTQ -> NMAKSHLY (in Ref. 6; AAL55842).	protein transport	endosome membrane|Golgi apparatus					0				UCEC - Uterine corpus endometrioid carcinoma (25;0.0265)														---	---	---	---
ABR	29	broad.mit.edu	37	17	986830	986830	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:986830T>C	uc002fsd.2	-	5	679	c.569A>G	c.(568-570)AAC>AGC	p.N190S	ABR_uc002fse.2_Missense_Mutation_p.N144S|ABR_uc002fsg.2_Missense_Mutation_p.N153S|ABR_uc002fsh.1_Missense_Mutation_p.N74S	NM_021962	NP_068781	Q12979	ABR_HUMAN	active breakpoint cluster region-related	190	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	GTPase activator activity|protein binding|Rho guanyl-nucleotide exchange factor activity			upper_aerodigestive_tract(1)	1				UCEC - Uterine corpus endometrioid carcinoma (25;0.0228)														---	---	---	---
MYO1C	4641	broad.mit.edu	37	17	1386944	1386944	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:1386944G>A	uc002fsp.2	-	3	527	c.307C>T	c.(307-309)CGT>TGT	p.R103C	MYO1C_uc002fsn.2_Missense_Mutation_p.R84C|MYO1C_uc002fso.2_Missense_Mutation_p.R68C|MYO1C_uc010vqj.1_Missense_Mutation_p.R68C|MYO1C_uc010vqk.1_Missense_Mutation_p.R79C	NM_001080779	NP_001074248	O00159	MYO1C_HUMAN	myosin IC isoform a	103	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)														---	---	---	---
SCARF1	8578	broad.mit.edu	37	17	1540138	1540138	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:1540138C>T	uc002fsz.1	-	10	1548	c.1498G>A	c.(1498-1500)GAC>AAC	p.D500N	SCARF1_uc002fsy.1_Intron|SCARF1_uc002fta.1_RNA|SCARF1_uc010cjv.1_Missense_Mutation_p.D414N	NM_003693	NP_003684	Q14162	SREC_HUMAN	scavenger receptor class F, member 1 isoform 1	500	Pro/Ser-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)														---	---	---	---
SMYD4	114826	broad.mit.edu	37	17	1686408	1686408	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:1686408C>T	uc002ftm.3	-	10	2350	c.2182G>A	c.(2182-2184)GTG>ATG	p.V728M	SMYD4_uc002ftn.1_Missense_Mutation_p.V583M	NM_052928	NP_443160	Q8IYR2	SMYD4_HUMAN	SET and MYND domain containing 4	728							zinc ion binding			skin(3)|kidney(2)	5																		---	---	---	---
HIC1	3090	broad.mit.edu	37	17	1961619	1961619	+	Silent	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:1961619G>A	uc010cjy.2	+	2	1692	c.1692G>A	c.(1690-1692)GCG>GCA	p.A564A	HIC1_uc002fty.3_Silent_p.A545A|HIC1_uc002ftz.3_Silent_p.A545A	NM_001098202	NP_001091672	Q14526	HIC1_HUMAN	hypermethylated in cancer 1 isoform 2	564					multicellular organismal development	nucleus	DNA binding|protein binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			large_intestine(1)	1				READ - Rectum adenocarcinoma(1115;0.236)														---	---	---	---
TSR1	55720	broad.mit.edu	37	17	2228067	2228067	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:2228067C>T	uc002fuj.2	-	13	3034	c.2077G>A	c.(2077-2079)GTC>ATC	p.V693I	SRR_uc002fue.1_3'UTR|SRR_uc002fui.1_3'UTR	NM_018128	NP_060598	Q2NL82	TSR1_HUMAN	TSR1, 20S rRNA accumulation	693					ribosome assembly	nucleolus	protein binding			ovary(1)	1																		---	---	---	---
SGSM2	9905	broad.mit.edu	37	17	2265057	2265057	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:2265057A>G	uc002fun.3	+	3	435	c.260A>G	c.(259-261)CAC>CGC	p.H87R	SGSM2_uc002fum.3_Missense_Mutation_p.H87R|SGSM2_uc010vqw.1_Missense_Mutation_p.H87R	NM_001098509	NP_001091979	O43147	SGSM2_HUMAN	RUN and TBC1 domain containing 1 isoform 2	87	RUN.					intracellular	Rab GTPase activator activity				0				Colorectal(2;5.15e-05)|READ - Rectum adenocarcinoma(2;0.000115)														---	---	---	---
OR1A1	8383	broad.mit.edu	37	17	3119126	3119126	+	Missense_Mutation	SNP	T	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:3119126T>A	uc010vrc.1	+	1	212	c.212T>A	c.(211-213)ATC>AAC	p.I71N		NM_014565	NP_055380	Q9P1Q5	OR1A1_HUMAN	olfactory receptor, family 1, subfamily A,	71	Helical; Name=2; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)|skin(1)	2																		---	---	---	---
TRPV3	162514	broad.mit.edu	37	17	3446788	3446788	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:3446788C>T	uc002fvt.1	-	5	768	c.446G>A	c.(445-447)CGC>CAC	p.R149H	TRPV3_uc010vrh.1_Missense_Mutation_p.R133H|TRPV3_uc010vri.1_Missense_Mutation_p.R104H|TRPV3_uc010vrj.1_Missense_Mutation_p.R133H|TRPV3_uc010vrk.1_RNA|TRPV3_uc010vrl.1_Missense_Mutation_p.R133H|TRPV3_uc010vrm.1_RNA|TRPV3_uc002fvr.2_Missense_Mutation_p.R149H|TRPV3_uc002fvu.2_Missense_Mutation_p.R149H	NM_145068	NP_659505	Q8NET8	TRPV3_HUMAN	transient receptor potential cation channel,	149	Cytoplasmic (Potential).					integral to membrane	calcium channel activity			ovary(4)	4					Menthol(DB00825)													---	---	---	---
SHPK	23729	broad.mit.edu	37	17	3518704	3518704	+	Silent	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:3518704C>T	uc002fvz.1	-	6	1054	c.951G>A	c.(949-951)GTG>GTA	p.V317V		NM_013276	NP_037408	Q9UHJ6	SHPK_HUMAN	carbohydrate kinase-like	317					carbohydrate metabolic process	cytoplasm	ATP binding|sedoheptulokinase activity			ovary(1)	1				COAD - Colon adenocarcinoma(5;0.0828)														---	---	---	---
SHPK	23729	broad.mit.edu	37	17	3524671	3524671	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:3524671G>A	uc002fvz.1	-	5	786	c.683C>T	c.(682-684)CCA>CTA	p.P228L		NM_013276	NP_037408	Q9UHJ6	SHPK_HUMAN	carbohydrate kinase-like	228					carbohydrate metabolic process	cytoplasm	ATP binding|sedoheptulokinase activity			ovary(1)	1				COAD - Colon adenocarcinoma(5;0.0828)														---	---	---	---
ITGAE	3682	broad.mit.edu	37	17	3662700	3662700	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:3662700C>T	uc002fwo.3	-	8	961	c.862G>A	c.(862-864)GTC>ATC	p.V288I		NM_002208	NP_002199	P38570	ITAE_HUMAN	integrin, alpha E precursor	288	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)														---	---	---	---
P2RX1	5023	broad.mit.edu	37	17	3807690	3807690	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:3807690G>T	uc002fww.2	-	4	802	c.361C>A	c.(361-363)CCA>ACA	p.P121T		NM_002558	NP_002549	P51575	P2RX1_HUMAN	purinergic receptor P2X1	121	Extracellular (Potential).				platelet activation	integral to plasma membrane	calcium channel activity|extracellular ATP-gated cation channel activity|purinergic nucleotide receptor activity			ovary(1)|skin(1)	2				LUAD - Lung adenocarcinoma(2;1.9e-05)|Lung(3;0.0173)														---	---	---	---
ANKFY1	51479	broad.mit.edu	37	17	4077241	4077241	+	Silent	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:4077241G>A	uc002fxq.1	-	20	2924	c.2886C>T	c.(2884-2886)GGC>GGT	p.G962G	ANKFY1_uc002fxn.2_Silent_p.G1004G|ANKFY1_uc002fxo.2_Silent_p.G963G|ANKFY1_uc002fxp.2_Silent_p.G961G|ANKFY1_uc010ckp.2_Silent_p.G904G	NM_016376	NP_057460	Q9P2R3	ANFY1_HUMAN	ankyrin repeat and FYVE domain containing 1	962	ANK 18.			G -> A (in Ref. 1; BAA90300).		endosome membrane	metal ion binding|protein binding			ovary(2)|skin(1)	3																		---	---	---	---
MYBBP1A	10514	broad.mit.edu	37	17	4455529	4455529	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:4455529C>T	uc002fyb.3	-	7	858	c.796G>A	c.(796-798)GCC>ACC	p.A266T	MYBBP1A_uc002fxz.3_Missense_Mutation_p.A266T	NM_014520	NP_055335	Q9BQG0	MBB1A_HUMAN	MYB binding protein 1a isoform 2	266	Nuclear export signal 2 (By similarity).|Interaction with MYB (By similarity).				nucleocytoplasmic transport|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|NLS-dependent protein nuclear import complex|nucleolus	DNA binding|DNA-directed DNA polymerase activity|transcription factor binding			ovary(1)|skin(1)	2																		---	---	---	---
SMTNL2	342527	broad.mit.edu	37	17	4510734	4510734	+	Silent	SNP	C	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:4510734C>A	uc002fyf.1	+	8	1405	c.1338C>A	c.(1336-1338)GTC>GTA	p.V446V	SMTNL2_uc002fye.2_Silent_p.V302V	NM_001114974	NP_001108446	Q2TAL5	SMTL2_HUMAN	smoothelin-like 2 isoform 1	446	CH.										0				READ - Rectum adenocarcinoma(115;0.0325)														---	---	---	---
CAMTA2	23125	broad.mit.edu	37	17	4872815	4872815	+	Silent	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:4872815G>A	uc002gah.1	-	20	3370	c.3262C>T	c.(3262-3264)CTG>TTG	p.L1088L	SPAG7_uc002gad.2_5'Flank|SPAG7_uc002gae.2_5'Flank|SPAG7_uc002gaf.2_5'Flank|CAMTA2_uc010cku.1_Silent_p.L1111L|CAMTA2_uc002gag.1_Silent_p.L1087L|CAMTA2_uc002gai.1_Intron	NM_015099	NP_055914	O94983	CMTA2_HUMAN	calmodulin binding transcription activator 2	1088					cardiac muscle hypertrophy in response to stress|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	nucleus	calmodulin binding|chromatin binding|histone deacetylase binding|transcription factor binding			ovary(1)	1																		---	---	---	---
GPR172B	55065	broad.mit.edu	37	17	4936370	4936370	+	Missense_Mutation	SNP	G	A	A	rs112874988	byFrequency	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:4936370G>A	uc002gap.3	-	5	1942	c.1229C>T	c.(1228-1230)GCA>GTA	p.A410V	GPR172B_uc002gao.3_Missense_Mutation_p.A410V|GPR172B_uc010ckw.2_Missense_Mutation_p.A288V|GPR172B_uc010ckx.2_3'UTR	NM_001104577	NP_001098047	Q9NWF4	RFT_HUMAN	G protein-coupled receptor 172B precursor	410	Helical; (Potential).					integral to plasma membrane	receptor activity|riboflavin transporter activity				0																		---	---	---	---
RABEP1	9135	broad.mit.edu	37	17	5280539	5280539	+	Silent	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:5280539T>C	uc002gbm.3	+	14	2378	c.2154T>C	c.(2152-2154)TGT>TGC	p.C718C	RABEP1_uc010clc.1_Silent_p.C711C|RABEP1_uc010cld.1_Silent_p.C675C|RABEP1_uc010vsw.1_Silent_p.C675C|RABEP1_uc002gbl.3_Silent_p.C718C|NUP88_uc002gbn.2_Intron	NM_004703	NP_004694	Q15276	RABE1_HUMAN	rabaptin, RAB GTPase binding effector protein 1	718	Potential.				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																		---	---	---	---
NLRP1	22861	broad.mit.edu	37	17	5462030	5462030	+	Silent	SNP	T	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:5462030T>A	uc002gci.2	-	4	2541	c.1986A>T	c.(1984-1986)ATA>ATT	p.I662I	NLRP1_uc002gcg.1_Silent_p.I662I|NLRP1_uc002gck.2_Silent_p.I662I|NLRP1_uc002gcj.2_Silent_p.I662I|NLRP1_uc002gcl.2_Silent_p.I662I|NLRP1_uc002gch.3_Silent_p.I662I|NLRP1_uc010clh.2_Silent_p.I662I	NM_033004	NP_127497	Q9C000	NALP1_HUMAN	NLR family, pyrin domain containing 1 isoform 1	662					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)																---	---	---	---
SLC13A5	284111	broad.mit.edu	37	17	6597511	6597511	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:6597511A>G	uc002gdj.2	-	8	1149	c.1061T>C	c.(1060-1062)GTC>GCC	p.V354A	SLC13A5_uc010vtf.1_Missense_Mutation_p.V354A|SLC13A5_uc010clq.2_Missense_Mutation_p.V311A|SLC13A5_uc002gdk.2_Missense_Mutation_p.V337A	NM_177550	NP_808218	Q86YT5	S13A5_HUMAN	solute carrier family 13, member 5 isoform a	354	Helical; (Potential).					integral to membrane	citrate transmembrane transporter activity				0																		---	---	---	---
ASGR2	433	broad.mit.edu	37	17	7011811	7011811	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:7011811G>T	uc002gep.3	-	4	587	c.322C>A	c.(322-324)CTG>ATG	p.L108M	ASGR2_uc010vtk.1_5'Flank|ASGR2_uc002gem.1_Missense_Mutation_p.L48M|ASGR2_uc002gen.1_Missense_Mutation_p.L89M|ASGR2_uc002geo.1_Missense_Mutation_p.L103M|ASGR2_uc002ger.3_Missense_Mutation_p.L108M|ASGR2_uc002geq.3_Missense_Mutation_p.L84M|ASGR2_uc010clw.2_Missense_Mutation_p.L84M|ASGR2_uc010vtl.1_RNA	NM_001181	NP_001172	P07307	ASGR2_HUMAN	asialoglycoprotein receptor 2 isoform a	108	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)													---	---	---	---
DVL2	1856	broad.mit.edu	37	17	7129405	7129405	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:7129405G>A	uc002gez.1	-	15	2272	c.1990C>T	c.(1990-1992)CTC>TTC	p.L664F	uc002gey.1_5'Flank|MIR324_hsa-mir-324|MI0000813_5'Flank|DVL2_uc010vtr.1_Missense_Mutation_p.L658F	NM_004422	NP_004413	O14641	DVL2_HUMAN	dishevelled 2	664					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																		---	---	---	---
CHRNB1	1140	broad.mit.edu	37	17	7358710	7358710	+	Silent	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:7358710T>C	uc002ghb.2	+	9	1193	c.1152T>C	c.(1150-1152)GGT>GGC	p.G384G	CHRNB1_uc010vty.1_Silent_p.G312G|CHRNB1_uc010vtz.1_Silent_p.G218G	NM_000747	NP_000738	P11230	ACHB_HUMAN	nicotinic acetylcholine receptor beta 1 subunit	384	Cytoplasmic (Potential).				behavioral response to nicotine|muscle contraction|muscle fiber development|neuromuscular synaptic transmission|postsynaptic membrane organization|regulation of membrane potential|synaptic transmission, cholinergic	cell junction|nicotinic acetylcholine-gated receptor-channel complex|postsynaptic membrane	acetylcholine binding|receptor activity			ovary(2)	2		Prostate(122;0.157)																---	---	---	---
POLR2A	5430	broad.mit.edu	37	17	7415821	7415821	+	Silent	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:7415821A>G	uc002ghf.3	+	27	4752	c.4518A>G	c.(4516-4518)GCA>GCG	p.A1506A		NM_000937	NP_000928	P24928	RPB1_HUMAN	DNA-directed RNA polymerase II A	1506					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)																---	---	---	---
EIF4A1	1973	broad.mit.edu	37	17	7478438	7478438	+	Silent	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:7478438T>C	uc002gho.1	+	12	1532	c.207T>C	c.(205-207)GGT>GGC	p.G69G	EIF4A1_uc002ghr.1_Silent_p.G69G|EIF4A1_uc002ghq.1_Silent_p.G69G|EIF4A1_uc002ghp.1_Silent_p.G69G|SNORD10_uc002ght.2_5'Flank|SNORA67_uc010cml.1_5'Flank	NM_001416	NP_001407	P60842	IF4A1_HUMAN	eukaryotic translation initiation factor 4A	69	Helicase ATP-binding.				nuclear-transcribed mRNA poly(A) tail shortening	cytosol|eukaryotic translation initiation factor 4F complex	ATP binding|ATP-dependent helicase activity|mRNA binding|protein binding|RNA cap binding|translation initiation factor activity			ovary(1)	1																		---	---	---	---
EIF4A1	1973	broad.mit.edu	37	17	7480954	7480954	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:7480954T>C	uc002gho.1	+	16	2161	c.836T>C	c.(835-837)ATC>ACC	p.I279T	EIF4A1_uc002ghr.1_Missense_Mutation_p.I279T|EIF4A1_uc002ghq.1_Missense_Mutation_p.I279T|EIF4A1_uc002ghp.1_Missense_Mutation_p.I279T|SNORA67_uc010cml.1_5'Flank|CD68_uc002ghv.2_5'Flank|CD68_uc002ghu.2_5'Flank	NM_001416	NP_001407	P60842	IF4A1_HUMAN	eukaryotic translation initiation factor 4A	279	Helicase C-terminal.				nuclear-transcribed mRNA poly(A) tail shortening	cytosol|eukaryotic translation initiation factor 4F complex	ATP binding|ATP-dependent helicase activity|mRNA binding|protein binding|RNA cap binding|translation initiation factor activity			ovary(1)	1																		---	---	---	---
SHBG	6462	broad.mit.edu	37	17	7534540	7534540	+	Missense_Mutation	SNP	A	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:7534540A>T	uc002gie.2	+	4	454	c.416A>T	c.(415-417)GAC>GTC	p.D139V	SHBG_uc010cmo.2_Intron|SHBG_uc010cmp.2_Missense_Mutation_p.D81V|SHBG_uc010cmq.2_Intron|SHBG_uc010cmr.2_Intron|SHBG_uc010cms.2_Intron|SHBG_uc010cmt.2_Missense_Mutation_p.D81V|SHBG_uc010cmu.2_Missense_Mutation_p.D81V|SHBG_uc010cmz.2_Missense_Mutation_p.D81V|SHBG_uc010cmv.2_Intron|SHBG_uc010cmw.2_Intron|SHBG_uc010cmx.2_Intron|SHBG_uc010cmy.2_Missense_Mutation_p.D81V|SHBG_uc002gid.3_Missense_Mutation_p.D81V|SHBG_uc010cnd.2_Intron|SHBG_uc010cna.2_Intron|SHBG_uc010vue.1_Missense_Mutation_p.D139V|SHBG_uc010vuf.1_Missense_Mutation_p.D139V|SHBG_uc010cnb.2_Missense_Mutation_p.D139V|SHBG_uc010cnc.2_Intron	NM_001040	NP_001031	P04278	SHBG_HUMAN	sex hormone-binding globulin isoform 1	139	Laminin G-like 1.				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)													---	---	---	---
TP53	7157	broad.mit.edu	37	17	7578206	7578206	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:7578206T>C	uc002gim.2	-	6	837	c.643A>G	c.(643-645)AGT>GGT	p.S215G	TP53_uc002gig.1_Missense_Mutation_p.S215G|TP53_uc002gih.2_Missense_Mutation_p.S215G|TP53_uc010cne.1_5'Flank|TP53_uc010cnf.1_Missense_Mutation_p.S83G|TP53_uc010cng.1_Missense_Mutation_p.S83G|TP53_uc002gii.1_Missense_Mutation_p.S83G|TP53_uc010cnh.1_Missense_Mutation_p.S215G|TP53_uc010cni.1_Missense_Mutation_p.S215G|TP53_uc002gij.2_Missense_Mutation_p.S215G|TP53_uc010cnj.1_Intron|TP53_uc002gin.2_Missense_Mutation_p.S122G|TP53_uc002gio.2_Missense_Mutation_p.S83G|TP53_uc010vug.1_Missense_Mutation_p.S176G	NM_001126112	NP_001119584	P04637	P53_HUMAN	tumor protein p53 isoform a	215	Required for interaction with FBXO42.||Interaction with HIPK1 (By similarity).|Interaction with AXIN1 (By similarity).		S -> R (in sporadic cancers; somatic mutation).|S -> C (in sporadic cancers; somatic mutation).|S -> K (in sporadic cancers; somatic mutation; requires 2 nucleotide substitutions).|S -> N (in sporadic cancers; somatic mutation).|S -> T (in sporadic cancers; somatic mutation).|S -> G (in sporadic cancers; somatic mutation).|S -> I (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.S215R(16)|p.S215I(15)|p.0?(7)|p.S215G(6)|p.S215N(6)|p.S215C(5)|p.S215fs*32(4)|p.S215T(3)|p.S215S(2)|p.H214fs*5(2)|p.K164_P219del(1)|p.H214fs*7(1)|p.S215fs*27(1)|p.S215del(1)|p.H214_S215insX(1)|p.D208_V216delDRNTFRHSV(1)|p.S215fs*29(1)|p.T211_S215delTFRHS(1)|p.D208fs*1(1)|p.S215fs*31(1)|p.S215_V218>R(1)|p.T211fs*28(1)|p.R213_S215>X(1)|p.D207_V216del10(1)|p.S215_V216insX(1)|p.R213fs*32(1)|p.R209fs*6(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	7681690	7681690	+	Missense_Mutation	SNP	A	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:7681690A>C	uc002giu.1	+	34	5458	c.5444A>C	c.(5443-5445)GAC>GCC	p.D1815A		NM_020877	NP_065928	Q9P225	DYH2_HUMAN	dynein heavy chain domain 3	1815	AAA 1 (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)																---	---	---	---
DNAH2	146754	broad.mit.edu	37	17	7727267	7727267	+	Silent	SNP	C	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:7727267C>A	uc002giu.1	+	74	11459	c.11445C>A	c.(11443-11445)CGC>CGA	p.R3815R	DNAH2_uc010cnm.1_Silent_p.R753R	NM_020877	NP_065928	Q9P225	DYH2_HUMAN	dynein heavy chain domain 3	3815	AAA 6 (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	7750450	7750450	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:7750450T>C	uc002giw.1	+	10	1313	c.937T>C	c.(937-939)TAT>CAT	p.Y313H	KDM6B_uc002gix.2_5'Flank	NM_001080424	NP_001073893	O15054	KDM6B_HUMAN	lysine (K)-specific demethylase 6B	313	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																		---	---	---	---
CHD3	1107	broad.mit.edu	37	17	7793929	7793929	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:7793929G>A	uc002gje.2	+	3	404	c.254G>A	c.(253-255)CGG>CAG	p.R85Q	CHD3_uc002gjd.2_Missense_Mutation_p.R144Q|CHD3_uc002gjf.2_Missense_Mutation_p.R85Q|CHD3_uc002gjg.1_5'Flank	NM_001005273	NP_001005273	Q12873	CHD3_HUMAN	chromodomain helicase DNA binding protein 3	85					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|protein binding|zinc ion binding			breast(1)	1		Prostate(122;0.202)																---	---	---	---
CHD3	1107	broad.mit.edu	37	17	7806333	7806333	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:7806333C>T	uc002gje.2	+	22	3599	c.3449C>T	c.(3448-3450)ACT>ATT	p.T1150I	CHD3_uc002gjd.2_Missense_Mutation_p.T1209I|CHD3_uc002gjf.2_Missense_Mutation_p.T1150I|CHD3_uc002gjh.2_5'Flank	NM_001005273	NP_001005273	Q12873	CHD3_HUMAN	chromodomain helicase DNA binding protein 3	1150	Helicase C-terminal.				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|protein binding|zinc ion binding			breast(1)	1		Prostate(122;0.202)																---	---	---	---
ALOXE3	59344	broad.mit.edu	37	17	8014693	8014693	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:8014693A>G	uc010cnr.2	-	8	1311	c.941T>C	c.(940-942)CTG>CCG	p.L314P	ALOXE3_uc002gka.2_Missense_Mutation_p.L470P|ALOXE3_uc010vuo.1_Missense_Mutation_p.L446P|ALOXE3_uc010vup.1_RNA	NM_021628	NP_067641	Q9BYJ1	LOXE3_HUMAN	arachidonate lipoxygenase 3 isoform 2	314	Lipoxygenase.				leukotriene biosynthetic process		iron ion binding|lipoxygenase activity			skin(3)|lung(1)|central_nervous_system(1)	5																		---	---	---	---
ARHGEF15	22899	broad.mit.edu	37	17	8222486	8222486	+	Intron	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:8222486T>C	uc002glc.2	+						ARHGEF15_uc002gld.2_Intron|ARHGEF15_uc010vuw.1_Intron	NM_173728	NP_776089			Rho guanine exchange factor 15						negative regulation of synapse maturation|regulation of Rho protein signal transduction	dendrite|intracellular	GTPase activator activity|Rho guanyl-nucleotide exchange factor activity			ovary(2)|skin(1)	3																		---	---	---	---
CCDC42	146849	broad.mit.edu	37	17	8647039	8647039	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:8647039G>A	uc002gln.2	-	3	426	c.199C>T	c.(199-201)CGC>TGC	p.R67C	CCDC42_uc002glo.2_Missense_Mutation_p.R67C	NM_144681	NP_653282	Q96M95	CCD42_HUMAN	coiled-coil domain containing 42 isoform 1	67	Potential.									ovary(1)	1																		---	---	---	---
PIK3R5	23533	broad.mit.edu	37	17	8783949	8783949	+	3'UTR	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:8783949G>A	uc002glt.2	-	19					PIK3R5_uc010vuz.1_3'UTR|PIK3R5_uc002glu.3_3'UTR	NM_014308	NP_055123			phosphoinositide-3-kinase, regulatory subunit 5						platelet activation	cytosol|membrane|nucleus				breast(2)|large_intestine(1)|central_nervous_system(1)|skin(1)	5																		---	---	---	---
PIK3R5	23533	broad.mit.edu	37	17	8808147	8808147	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:8808147C>T	uc002glt.2	-	5	426	c.359G>A	c.(358-360)TGC>TAC	p.C120Y	PIK3R5_uc010vuz.1_Missense_Mutation_p.C120Y|PIK3R5_uc002glu.3_5'UTR|PIK3R5_uc010coa.1_Missense_Mutation_p.C120Y|PIK3R5_uc010cob.1_5'UTR	NM_014308	NP_055123	Q8WYR1	PI3R5_HUMAN	phosphoinositide-3-kinase, regulatory subunit 5	120					platelet activation	cytosol|membrane|nucleus				breast(2)|large_intestine(1)|central_nervous_system(1)|skin(1)	5																		---	---	---	---
USP43	124739	broad.mit.edu	37	17	9631637	9631637	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:9631637T>C	uc010cod.2	+	15	2702	c.2702T>C	c.(2701-2703)CTG>CCG	p.L901P	USP43_uc002gma.3_Missense_Mutation_p.L590P|USP43_uc010vva.1_Missense_Mutation_p.L896P|USP43_uc010coe.2_Missense_Mutation_p.L698P|USP43_uc002gmc.3_Missense_Mutation_p.L413P	NM_153210	NP_694942	Q70EL4	UBP43_HUMAN	ubiquitin specific protease 43	901					ubiquitin-dependent protein catabolic process		cysteine-type peptidase activity|ubiquitin thiolesterase activity			ovary(2)|lung(1)|breast(1)|central_nervous_system(1)	5																		---	---	---	---
MYH13	8735	broad.mit.edu	37	17	10233812	10233812	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:10233812A>G	uc002gmk.1	-	21	2417	c.2327T>C	c.(2326-2328)CTT>CCT	p.L776P		NM_003802	NP_003793	Q9UKX3	MYH13_HUMAN	myosin, heavy polypeptide 13, skeletal muscle	776	Myosin head-like.				muscle contraction	muscle myosin complex|myofibril|myosin filament	actin binding|ATP binding|calmodulin binding|microfilament motor activity			ovary(4)|skin(2)	6																		---	---	---	---
MYH13	8735	broad.mit.edu	37	17	10265437	10265437	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:10265437G>T	uc002gmk.1	-	5	593	c.503C>A	c.(502-504)ACT>AAT	p.T168N		NM_003802	NP_003793	Q9UKX3	MYH13_HUMAN	myosin, heavy polypeptide 13, skeletal muscle	168	Myosin head-like.				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	10307897	10307897	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:10307897G>A	uc002gmm.2	-	22	2533	c.2438C>T	c.(2437-2439)GCA>GTA	p.A813V	uc002gml.1_Intron	NM_002472	NP_002463	P13535	MYH8_HUMAN	myosin, heavy chain 8, skeletal muscle,	813	IQ.				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				---	---	---	---
MYH8	4626	broad.mit.edu	37	17	10323483	10323483	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:10323483T>C	uc002gmm.2	-	3	157	c.62A>G	c.(61-63)AAA>AGA	p.K21R	uc002gml.1_Intron	NM_002472	NP_002463	P13535	MYH8_HUMAN	myosin, heavy chain 8, skeletal muscle,	21	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	10359800	10359800	+	Splice_Site	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:10359800A>G	uc002gmn.2	-	17	2079	c.1968_splice	c.e17+1	p.R656_splice	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																		---	---	---	---
MYH2	4620	broad.mit.edu	37	17	10444003	10444003	+	Missense_Mutation	SNP	T	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:10444003T>A	uc010coi.2	-	11	1044	c.916A>T	c.(916-918)ATT>TTT	p.I306F	uc002gml.1_Intron|MYH2_uc002gmp.3_Missense_Mutation_p.I306F|MYH2_uc010coj.2_Missense_Mutation_p.I306F	NM_001100112	NP_001093582	Q9UKX2	MYH2_HUMAN	myosin heavy chain IIa	306	Myosin head-like.				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																		---	---	---	---
MYH2	4620	broad.mit.edu	37	17	10447066	10447066	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:10447066T>C	uc010coi.2	-	8	831	c.703A>G	c.(703-705)AAC>GAC	p.N235D	uc002gml.1_Intron|MYH2_uc002gmp.3_Missense_Mutation_p.N235D|MYH2_uc010coj.2_Missense_Mutation_p.N235D	NM_001100112	NP_001093582	Q9UKX2	MYH2_HUMAN	myosin heavy chain IIa	235	Myosin head-like.				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	10533034	10533034	+	Silent	SNP	A	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:10533034A>T	uc002gmq.1	-	39	5753	c.5676T>A	c.(5674-5676)GCT>GCA	p.A1892A		NM_002470	NP_002461	P11055	MYH3_HUMAN	myosin, heavy chain 3, skeletal muscle,	1892	Potential.				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	10543522	10543522	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:10543522C>T	uc002gmq.1	-	21	2550	c.2473G>A	c.(2473-2475)GTC>ATC	p.V825I		NM_002470	NP_002461	P11055	MYH3_HUMAN	myosin, heavy chain 3, skeletal muscle,	825			V -> D (in DA2A).		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	10543743	10543743	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:10543743C>T	uc002gmq.1	-	20	2410	c.2333G>A	c.(2332-2334)CGG>CAG	p.R778Q		NM_002470	NP_002461	P11055	MYH3_HUMAN	myosin, heavy chain 3, skeletal muscle,	778	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																		---	---	---	---
DNAH9	1770	broad.mit.edu	37	17	11572835	11572835	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:11572835G>A	uc002gne.2	+	17	3145	c.3077G>A	c.(3076-3078)GGT>GAT	p.G1026D	DNAH9_uc010coo.2_Missense_Mutation_p.G320D	NM_001372	NP_001363	Q9NYC9	DYH9_HUMAN	dynein, axonemal, heavy chain 9 isoform 2	1026	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	11593539	11593539	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:11593539A>G	uc002gne.2	+	20	4468	c.4400A>G	c.(4399-4401)GAC>GGC	p.D1467G	DNAH9_uc010coo.2_Missense_Mutation_p.D761G	NM_001372	NP_001363	Q9NYC9	DYH9_HUMAN	dynein, axonemal, heavy chain 9 isoform 2	1467	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	11603193	11603193	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:11603193G>A	uc002gne.2	+	23	5086	c.5018G>A	c.(5017-5019)AGC>AAC	p.S1673N	DNAH9_uc010coo.2_Missense_Mutation_p.S967N	NM_001372	NP_001363	Q9NYC9	DYH9_HUMAN	dynein, axonemal, heavy chain 9 isoform 2	1673	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	11684403	11684403	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:11684403A>G	uc002gne.2	+	39	7698	c.7630A>G	c.(7630-7632)ATT>GTT	p.I2544V	DNAH9_uc010coo.2_Missense_Mutation_p.I1838V	NM_001372	NP_001363	Q9NYC9	DYH9_HUMAN	dynein, axonemal, heavy chain 9 isoform 2	2544	AAA 3 (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)														---	---	---	---
CDRT4	284040	broad.mit.edu	37	17	15341423	15341423	+	Silent	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:15341423T>C	uc002gop.1	-	4	404	c.123A>G	c.(121-123)AGA>AGG	p.R41R	CDRT4_uc010vvw.1_3'UTR	NM_173622	NP_775893	Q8N9R6	CDRT4_HUMAN	CMT1A duplicated region transcript 4	41											0				UCEC - Uterine corpus endometrioid carcinoma (92;0.0874)														---	---	---	---
FAM18B2	201158	broad.mit.edu	37	17	15458649	15458649	+	Silent	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:15458649T>C	uc002goq.2	-	2	225	c.42A>G	c.(40-42)TCA>TCG	p.S14S	CDRT4_uc010vvw.1_5'UTR|FAM18B2_uc010vvx.1_Silent_p.S14S|FAM18B2_uc010cor.2_Silent_p.S14S	NM_145301	NP_660344	Q96ET8	F18B2_HUMAN	hypothetical protein LOC201158 isoform 1	14						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	15938118	15938118	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:15938118T>C	uc002gpo.2	-	45	7336	c.7096A>G	c.(7096-7098)ACG>GCG	p.T2366A	NCOR1_uc002gpn.2_Missense_Mutation_p.T2263A|NCOR1_uc002gpl.2_Missense_Mutation_p.T380A|NCOR1_uc002gpm.2_Missense_Mutation_p.T885A|NCOR1_uc010vwb.1_Missense_Mutation_p.T950A|NCOR1_uc010coy.2_Missense_Mutation_p.T1274A	NM_006311	NP_006302	O75376	NCOR1_HUMAN	nuclear receptor co-repressor 1	2366	Interaction with C1D (By similarity).				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	16456551	16456551	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:16456551T>C	uc002gqi.2	-	6	1358	c.905A>G	c.(904-906)CAA>CGA	p.Q302R		NM_020653	NP_065704	Q9HBT7	ZN287_HUMAN	zinc finger protein 287	295					viral reproduction	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding				0				UCEC - Uterine corpus endometrioid carcinoma (92;0.083)														---	---	---	---
RAI1	10743	broad.mit.edu	37	17	17701243	17701243	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:17701243C>T	uc002grm.2	+	3	5450	c.4981C>T	c.(4981-4983)CGG>TGG	p.R1661W	RAI1_uc002grn.1_Missense_Mutation_p.R1661W	NM_030665	NP_109590	Q7Z5J4	RAI1_HUMAN	retinoic acid induced 1	1661						cytoplasm|nucleus	zinc ion binding			central_nervous_system(1)|skin(1)	2				READ - Rectum adenocarcinoma(1115;0.0276)														---	---	---	---
SREBF1	6720	broad.mit.edu	37	17	17723569	17723569	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:17723569G>A	uc002gru.1	-	2	552	c.358C>T	c.(358-360)CCT>TCT	p.P120S	SREBF1_uc002grp.1_5'Flank|SREBF1_uc002grq.1_5'UTR|SREBF1_uc002grr.1_5'UTR|SREBF1_uc002grs.1_Missense_Mutation_p.P96S|SREBF1_uc002grt.1_Missense_Mutation_p.P150S|SREBF1_uc010cpp.1_Missense_Mutation_p.P96S|SREBF1_uc010cpq.1_Missense_Mutation_p.P120S	NM_004176	NP_004167	P36956	SRBP1_HUMAN	sterol regulatory element binding transcription	120	Pro/Ser-rich.|Cytoplasmic (Potential).				cellular response to starvation|cholesterol metabolic process|positive regulation of transcription from RNA polymerase II promoter|regulation of transcription from RNA polymerase II promoter	endoplasmic reticulum|endoplasmic reticulum membrane|ER to Golgi transport vesicle membrane|Golgi membrane|integral to membrane|nuclear envelope|nucleus	protein binding|protein binding|sequence-specific DNA binding transcription factor activity|sterol response element binding			skin(1)	1																		---	---	---	---
TOM1L2	146691	broad.mit.edu	37	17	17766051	17766051	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:17766051C>T	uc002grz.3	-	11	1353	c.1196G>A	c.(1195-1197)CGC>CAC	p.R399H	TOM1L2_uc002gry.3_Missense_Mutation_p.R349H|TOM1L2_uc010vwy.1_Missense_Mutation_p.R346H|TOM1L2_uc010cpr.2_Missense_Mutation_p.R354H|TOM1L2_uc010vwz.1_Missense_Mutation_p.R251H|TOM1L2_uc010vxa.1_Missense_Mutation_p.R301H|TOM1L2_uc002grv.3_Missense_Mutation_p.R132H	NM_001082968	NP_001076437	Q6ZVM7	TM1L2_HUMAN	target of myb1-like 2 isoform 3	399					intracellular protein transport	intracellular					0	all_neural(463;0.228)																	---	---	---	---
TOM1L2	146691	broad.mit.edu	37	17	17788040	17788040	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:17788040C>T	uc002grz.3	-	5	566	c.409G>A	c.(409-411)GTT>ATT	p.V137I	TOM1L2_uc002gry.3_Missense_Mutation_p.V87I|TOM1L2_uc010vwy.1_Missense_Mutation_p.V137I|TOM1L2_uc010cpr.2_Intron|TOM1L2_uc010vwz.1_Intron|TOM1L2_uc010vxa.1_Intron|TOM1L2_uc010vxb.1_Missense_Mutation_p.V87I	NM_001082968	NP_001076437	Q6ZVM7	TM1L2_HUMAN	target of myb1-like 2 isoform 3	137	VHS.				intracellular protein transport	intracellular					0	all_neural(463;0.228)																	---	---	---	---
C17orf39	79018	broad.mit.edu	37	17	17965231	17965231	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:17965231T>C	uc002gsg.1	+	5	949	c.781T>C	c.(781-783)TGC>CGC	p.C261R		NM_024052	NP_076957	Q8IVV7	CQ039_HUMAN	hypothetical protein LOC79018	261										skin(1)	1	all_neural(463;0.228)																	---	---	---	---
MYO15A	51168	broad.mit.edu	37	17	18053797	18053797	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:18053797G>A	uc010vxh.1	+	35	7605	c.7267G>A	c.(7267-7269)GGT>AGT	p.G2423S		NM_016239	NP_057323	Q9UKN7	MYO15_HUMAN	myosin XV	2423	Tail.				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)																	---	---	---	---
FLII	2314	broad.mit.edu	37	17	18149141	18149141	+	Silent	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:18149141A>G	uc002gsr.1	-	27	3471	c.3420T>C	c.(3418-3420)CCT>CCC	p.P1140P	FLII_uc002gsq.1_Silent_p.P1011P|FLII_uc010cpy.1_Silent_p.P1129P|FLII_uc010vxn.1_Silent_p.P1109P|FLII_uc010vxo.1_Silent_p.P1085P	NM_002018	NP_002009	Q13045	FLII_HUMAN	flightless I homolog	1140					multicellular organismal development|muscle contraction|regulation of transcription, DNA-dependent|transcription, DNA-dependent	centrosome|nucleus	actin binding			central_nervous_system(1)|skin(1)	2	all_neural(463;0.228)																	---	---	---	---
FBXW10	10517	broad.mit.edu	37	17	18653098	18653098	+	Missense_Mutation	SNP	G	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:18653098G>C	uc002guk.2	+	3	966	c.734G>C	c.(733-735)GGA>GCA	p.G245A	FBXW10_uc002guj.2_Missense_Mutation_p.G245A|FBXW10_uc002gul.2_Missense_Mutation_p.G245A|FBXW10_uc010cqh.1_Missense_Mutation_p.G245A	NM_031456	NP_113644	Q5XX13	FBW10_HUMAN	F-box and WD-40 domain protein 10	245										ovary(1)	1																		---	---	---	---
EPN2	22905	broad.mit.edu	37	17	19213292	19213292	+	Silent	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:19213292C>T	uc002gvd.3	+	5	1309	c.861C>T	c.(859-861)AGC>AGT	p.S287S	EPN2_uc010cql.1_Silent_p.S2S|EPN2_uc002gve.3_Silent_p.S230S|EPN2_uc002gvf.3_Silent_p.S2S|EPN2_uc010vyo.1_Silent_p.S2S|EPN2_uc002gvg.1_Silent_p.S230S|EPN2_uc010vyp.1_Silent_p.S230S|EPN2_uc010vyq.1_Silent_p.S230S|EPN2_uc002gvh.1_Silent_p.S287S	NM_014964	NP_055779	O95208	EPN2_HUMAN	epsin 2 isoform b	287	UIM 1.				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)																	---	---	---	---
RNF112	7732	broad.mit.edu	37	17	19319116	19319116	+	Silent	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:19319116T>C	uc010vyw.1	+	14	1723	c.1524T>C	c.(1522-1524)CAT>CAC	p.H508H	RNF112_uc010vyv.1_Silent_p.H509H	NM_007148	NP_009079	Q7Z5V9	Q7Z5V9_HUMAN	ring finger protein 112	508							GTP binding|GTPase activity|zinc ion binding			ovary(2)	2																		---	---	---	---
SLC47A1	55244	broad.mit.edu	37	17	19458936	19458936	+	Silent	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:19458936G>A	uc002gvy.1	+	8	758	c.672G>A	c.(670-672)CAG>CAA	p.Q224Q	SLC47A1_uc010vyy.1_RNA|SLC47A1_uc002gvx.2_Silent_p.Q224Q|SLC47A1_uc010vyz.1_Silent_p.Q201Q|SLC47A1_uc010cqp.1_Intron|SLC47A1_uc010cqq.1_Intron|SLC47A1_uc010vza.1_5'UTR|SLC47A1_uc010vzb.1_5'UTR|SLC47A1_uc010vzc.1_5'Flank|SNORA59B_uc002gvz.1_5'Flank	NM_018242	NP_060712	Q96FL8	S47A1_HUMAN	solute carrier family 47, member 1	224	Helical; (Potential).					integral to membrane|plasma membrane	drug:hydrogen antiporter activity				0	all_cancers(12;2.49e-05)|all_epithelial(12;0.00263)|Hepatocellular(7;0.00345)																	---	---	---	---
ALDH3A2	224	broad.mit.edu	37	17	19555102	19555102	+	Intron	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:19555102A>G	uc002gwb.1	+						ALDH3A2_uc002gwa.1_Intron|ALDH3A2_uc010cqr.1_Intron|ALDH3A2_uc002gwc.1_Intron	NM_000382	NP_000373			aldehyde dehydrogenase 3A2 isoform 2						cellular aldehyde metabolic process|central nervous system development|epidermis development|lipid metabolic process|peripheral nervous system development	endoplasmic reticulum membrane|integral to membrane	3-chloroallyl aldehyde dehydrogenase activity|aldehyde dehydrogenase (NAD) activity|aldehyde dehydrogenase			ovary(2)	2	all_cancers(12;1.39e-05)|all_epithelial(12;0.00158)|Breast(13;0.245)				NADH(DB00157)													---	---	---	---
ULK2	9706	broad.mit.edu	37	17	19728482	19728482	+	Silent	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:19728482T>C	uc002gwm.3	-	12	1358	c.849A>G	c.(847-849)CCA>CCG	p.P283P	ULK2_uc002gwn.2_Silent_p.P283P	NM_001142610	NP_001136082	Q8IYT8	ULK2_HUMAN	unc-51-like kinase 2	283					signal transduction		ATP binding|protein binding|protein serine/threonine kinase activity			skin(2)|large_intestine(1)|stomach(1)	4	all_cancers(12;4.97e-05)|all_epithelial(12;0.00362)|Breast(13;0.186)																	---	---	---	---
KCNJ12	3768	broad.mit.edu	37	17	21319591	21319591	+	Missense_Mutation	SNP	C	T	T	rs142223673	byFrequency	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:21319591C>T	uc002gyv.1	+	3	1642	c.937C>T	c.(937-939)CGC>TGC	p.R313C		NM_021012	NP_066292	Q14500	IRK12_HUMAN	potassium inwardly-rectifying channel, subfamily	313	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)			---	---	---	---
FAM27L	284123	broad.mit.edu	37	17	21826233	21826233	+	RNA	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:21826233G>A	uc002gyz.2	+	2		c.343G>A				NR_028336				Homo sapiens family with sequence similarity 27-like, mRNA (cDNA clone MGC:35151 IMAGE:5169482), complete cds.												0				UCEC - Uterine corpus endometrioid carcinoma (53;0.11)|BRCA - Breast invasive adenocarcinoma(1;0.00463)														---	---	---	---
KSR1	8844	broad.mit.edu	37	17	25910125	25910125	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:25910125C>T	uc010crg.2	+	5	1008	c.563C>T	c.(562-564)TCG>TTG	p.S188L	KSR1_uc002gzj.1_RNA	NM_014238	NP_055053	Q8IVT5	KSR1_HUMAN	kinase suppressor of ras	323					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)														---	---	---	---
NOS2	4843	broad.mit.edu	37	17	26105730	26105730	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:26105730G>T	uc002gzu.2	-	11	1531	c.1267C>A	c.(1267-1269)CTC>ATC	p.L423I	NOS2_uc010crh.1_Missense_Mutation_p.L423I|NOS2_uc010wab.1_Missense_Mutation_p.L423I	NM_000625	NP_000616	P35228	NOS2_HUMAN	nitric oxide synthase 2A	423				L -> I (in Ref. 2; AAA59171).	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)													---	---	---	---
NLK	51701	broad.mit.edu	37	17	26370225	26370225	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:26370225C>T	uc010crj.2	+	1	538	c.326C>T	c.(325-327)GCC>GTC	p.A109V	NLK_uc010cri.1_RNA	NM_016231	NP_057315	Q9UBE8	NLK_HUMAN	nemo like kinase	109	Poly-Ala.				intracellular protein kinase cascade|negative regulation of Wnt receptor signaling pathway|peptidyl-threonine phosphorylation|regulation of transcription, DNA-dependent|serine phosphorylation of STAT3 protein|transcription, DNA-dependent|transforming growth factor beta receptor signaling pathway|Wnt receptor signaling pathway	cytoplasm|nucleus	ATP binding|magnesium ion binding|MAP kinase activity|SH2 domain binding|transcription factor binding|ubiquitin protein ligase binding			ovary(1)|lung(1)|central_nervous_system(1)	3	all_lung(13;0.000343)|Lung NSC(42;0.00184)			UCEC - Uterine corpus endometrioid carcinoma (53;0.168)														---	---	---	---
VTN	7448	broad.mit.edu	37	17	26697187	26697187	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:26697187A>G	uc002hbc.2	-	1	187	c.38T>C	c.(37-39)CTG>CCG	p.L13P	SARM1_uc010wah.1_Intron|SEBOX_uc010crk.1_5'Flank|SARM1_uc010waj.1_Intron|SARM1_uc010crl.1_5'Flank	NM_000638	NP_000629	P04004	VTNC_HUMAN	vitronectin precursor	13					cell adhesion mediated by integrin|immune response|negative regulation of endopeptidase activity|positive regulation of peptidyl-tyrosine phosphorylation|positive regulation of protein binding|positive regulation of receptor-mediated endocytosis|positive regulation of smooth muscle cell migration|positive regulation of vascular endothelial growth factor receptor signaling pathway|smooth muscle cell-matrix adhesion	alphav-beta3 integrin-vitronectin complex|extracellular space	heparin binding|integrin binding|scavenger receptor activity			ovary(1)|kidney(1)	2	all_lung(13;0.000533)|Lung NSC(42;0.00171)			UCEC - Uterine corpus endometrioid carcinoma (53;0.153)	Urokinase(DB00013)													---	---	---	---
FOXN1	8456	broad.mit.edu	37	17	26861379	26861379	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:26861379C>T	uc010crm.2	+	7	1156	c.958C>T	c.(958-960)CGG>TGG	p.R320W	FOXN1_uc002hbj.2_Missense_Mutation_p.R320W	NM_003593	NP_003584	O15353	FOXN1_HUMAN	forkhead box N1	320	Fork-head.				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)																	---	---	---	---
TLCD1	116238	broad.mit.edu	37	17	27051553	27051553	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:27051553T>C	uc002hco.2	-	4	834	c.719A>G	c.(718-720)CAC>CGC	p.H240R	TLCD1_uc010waw.1_Missense_Mutation_p.H193R	NM_138463	NP_612472	Q96CP7	TLCD1_HUMAN	TLC domain containing 1 isoform 1	240						integral to membrane					0	Lung NSC(42;0.00431)																	---	---	---	---
NEK8	284086	broad.mit.edu	37	17	27061164	27061164	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:27061164C>A	uc002hcp.2	+	2	211	c.211C>A	c.(211-213)CTG>ATG	p.L71M		NM_178170	NP_835464	Q86SG6	NEK8_HUMAN	NIMA-related kinase 8	71	Protein kinase.					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)																	---	---	---	---
ABHD15	116236	broad.mit.edu	37	17	27889596	27889596	+	Nonsense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:27889596G>A	uc002hed.1	-	2	1454	c.1390C>T	c.(1390-1392)CGA>TGA	p.R464*		NM_198147	NP_937790	Q6UXT9	ABH15_HUMAN	abhydrolase domain containing 15 precursor	464						extracellular region	carboxylesterase activity				0																		---	---	---	---
ABHD15	116236	broad.mit.edu	37	17	27890051	27890051	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:27890051C>T	uc002hed.1	-	2	999	c.935G>A	c.(934-936)CGT>CAT	p.R312H		NM_198147	NP_937790	Q6UXT9	ABH15_HUMAN	abhydrolase domain containing 15 precursor	312						extracellular region	carboxylesterase activity				0																		---	---	---	---
GIT1	28964	broad.mit.edu	37	17	27905318	27905318	+	Silent	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:27905318T>C	uc002hef.2	-	9	1096	c.882A>G	c.(880-882)GCA>GCG	p.A294A	GIT1_uc002heg.2_Silent_p.A303A|GIT1_uc010wbg.1_Silent_p.A303A|GIT1_uc010csb.1_Silent_p.A294A	NM_014030	NP_054749	Q9Y2X7	GIT1_HUMAN	G protein-coupled receptor kinase interactor 1	294	ARHGEF6-binding (By similarity).|PTK2-binding (By similarity).				regulation of ARF GTPase activity|regulation of G-protein coupled receptor protein signaling pathway	cytoplasm|focal adhesion	ARF GTPase activator activity|protein binding|zinc ion binding				0				READ - Rectum adenocarcinoma(3;0.0419)|Colorectal(3;0.069)														---	---	---	---
EFCAB5	374786	broad.mit.edu	37	17	28405466	28405466	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:28405466A>G	uc002het.2	+	15	3163	c.2971A>G	c.(2971-2973)ACA>GCA	p.T991A	EFCAB5_uc010cse.2_Missense_Mutation_p.T746A|EFCAB5_uc010csf.2_Intron	NM_198529	NP_940931	A4FU69	EFCB5_HUMAN	EF-hand calcium binding domain 5 isoform a	991							calcium ion binding			ovary(1)|skin(1)	2																		---	---	---	---
TMIGD1	388364	broad.mit.edu	37	17	28656274	28656274	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:28656274A>G	uc002hfa.1	-	3	429	c.356T>C	c.(355-357)GTT>GCT	p.V119A	TMIGD1_uc010csh.1_Missense_Mutation_p.V119A	NM_206832	NP_996663	Q6UXZ0	TMIG1_HUMAN	transmembrane and immunoglobulin domain	119	Extracellular (Potential).					integral to membrane					0																		---	---	---	---
ATAD5	79915	broad.mit.edu	37	17	29203465	29203465	+	Silent	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:29203465A>G	uc002hfs.1	+	15	4027	c.3681A>G	c.(3679-3681)GGA>GGG	p.G1227G		NM_024857	NP_079133	Q96QE3	ATAD5_HUMAN	ATPase family, AAA domain containing 5	1227					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)																---	---	---	---
OMG	4974	broad.mit.edu	37	17	29623208	29623208	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:29623208T>C	uc002hgj.2	-	2	355	c.142A>G	c.(142-144)ACA>GCA	p.T48A	NF1_uc002hgg.2_Intron|NF1_uc002hgh.2_Intron|NF1_uc002hgi.1_Intron|NF1_uc010cso.2_Intron	NM_002544	NP_002535	P23515	OMGP_HUMAN	oligodendrocyte myelin glycoprotein precursor	48	LRRNT.				cell adhesion|negative regulation of axonogenesis|nerve growth factor receptor signaling pathway	anchored to membrane|plasma membrane				ovary(1)|central_nervous_system(1)	2		all_cancers(10;6.97e-11)|all_epithelial(10;0.0051)|all_hematologic(16;0.0149)|Breast(31;0.0155)|Myeloproliferative disorder(56;0.0255)|Acute lymphoblastic leukemia(14;0.0257)|all_lung(9;0.0468)|Lung NSC(157;0.094)		UCEC - Uterine corpus endometrioid carcinoma (4;6.64e-05)|all cancers(4;1.81e-13)|Epithelial(4;4.04e-12)|OV - Ovarian serous cystadenocarcinoma(4;9.49e-12)|GBM - Glioblastoma multiforme(4;0.121)														---	---	---	---
C17orf79	55352	broad.mit.edu	37	17	30179860	30179860	+	Missense_Mutation	SNP	T	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:30179860T>A	uc002hgp.2	-	3	464	c.356A>T	c.(355-357)GAG>GTG	p.E119V	C17orf79_uc010css.2_RNA	NM_018405	NP_060875	Q9NQ92	COPR5_HUMAN	chromosome 17 open reading frame 79	119					histone H4-R3 methylation|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	histone binding				0		all_cancers(10;4.54e-07)|all_hematologic(16;0.0216)|Acute lymphoblastic leukemia(14;0.0255)|Myeloproliferative disorder(56;0.0393)|Ovarian(249;0.1)																---	---	---	---
RHOT1	55288	broad.mit.edu	37	17	30526516	30526516	+	Silent	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:30526516T>C	uc002hgz.2	+	13	1286	c.1047T>C	c.(1045-1047)GTT>GTC	p.V349V	RHOT1_uc002hgw.2_Silent_p.V349V|RHOT1_uc002hgy.2_Silent_p.V349V|RHOT1_uc002hha.2_Silent_p.V222V|RHOT1_uc010csv.2_RNA|RHOT1_uc002hgx.2_Silent_p.V222V|RHOT1_uc010wby.1_Silent_p.V349V|RHOT1_uc002hhb.2_Silent_p.V328V|RHOT1_uc002hgv.2_Silent_p.V349V	NM_018307	NP_060777	Q8IXI2	MIRO1_HUMAN	ras homolog gene family, member T1 isoform 3	349	Mitochondrial intermembrane (Potential).				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)																---	---	---	---
C17orf75	64149	broad.mit.edu	37	17	30668242	30668242	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:30668242G>T	uc002hhg.2	-	2	233	c.202C>A	c.(202-204)CCC>ACC	p.P68T		NM_022344	NP_071739	Q9HAS0	NJMU_HUMAN	hypothetical protein LOC64149	68					spermatogenesis					ovary(1)	1		Breast(31;0.116)|Ovarian(249;0.182)	BRCA - Breast invasive adenocarcinoma(9;0.239)															---	---	---	---
PEX12	5193	broad.mit.edu	37	17	33902822	33902822	+	Silent	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:33902822T>C	uc002hjp.2	-	3	1675	c.1059A>G	c.(1057-1059)AAA>AAG	p.K353K		NM_000286	NP_000277	O00623	PEX12_HUMAN	peroxisomal biogenesis factor 12	353	Cytoplasmic (Potential).				protein import into peroxisome matrix	integral to peroxisomal membrane	protein C-terminus binding|zinc ion binding				0				UCEC - Uterine corpus endometrioid carcinoma (308;0.0182)														---	---	---	---
MMP28	79148	broad.mit.edu	37	17	34105964	34105964	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:34105964C>T	uc002hjy.1	-	3	566	c.307G>A	c.(307-309)GCT>ACT	p.A103T	MMP28_uc002hjw.1_RNA|MMP28_uc002hjz.1_RNA|MMP28_uc002hka.2_Missense_Mutation_p.A103T	NM_024302	NP_077278	Q9H239	MMP28_HUMAN	matrix metalloproteinase 28 isoform 1	103					proteolysis	proteinaceous extracellular matrix	calcium ion binding|metalloendopeptidase activity|zinc ion binding			skin(1)	1		Ovarian(249;0.17)		UCEC - Uterine corpus endometrioid carcinoma (308;0.0185)														---	---	---	---
TAF15	8148	broad.mit.edu	37	17	34171919	34171919	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:34171919G>A	uc002hkd.2	+	15	1702	c.1616G>A	c.(1615-1617)AGT>AAT	p.S539N	TAF15_uc002hkc.2_Missense_Mutation_p.S536N	NM_139215	NP_631961	Q92804	RBP56_HUMAN	TBP-associated factor 15 isoform 1	539	Arg/Gly-rich.|17.|21 X approximate tandem repeats of D-R- [S,G](0,3)-G-G-Y-G-G.				positive regulation of transcription, DNA-dependent	cytoplasm|nucleus	DNA binding|nucleotide binding|protein binding|RNA binding|zinc ion binding		TAF15/NR4A3(33)	bone(33)|lung(1)|skin(1)	35		Ovarian(249;0.17)		UCEC - Uterine corpus endometrioid carcinoma (308;0.0193)				T	TEC|CHN1|ZNF384	extraskeletal myxoid chondrosarcomas|ALL								---	---	---	---
SYNRG	11276	broad.mit.edu	37	17	35931996	35931996	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:35931996G>A	uc002hoa.2	-	9	1075	c.992C>T	c.(991-993)CCC>CTC	p.P331L	SYNRG_uc010wde.1_Missense_Mutation_p.P253L|SYNRG_uc010wdf.1_Missense_Mutation_p.P253L|SYNRG_uc002hoc.2_Missense_Mutation_p.P252L|SYNRG_uc002hoe.2_Missense_Mutation_p.P253L|SYNRG_uc002hod.2_Missense_Mutation_p.P253L|SYNRG_uc010wdg.1_Missense_Mutation_p.P253L|SYNRG_uc002hob.2_Missense_Mutation_p.P331L|SYNRG_uc002hof.2_Missense_Mutation_p.P43L|SYNRG_uc010cvd.1_Missense_Mutation_p.P131L|SYNRG_uc002hog.1_Missense_Mutation_p.P465L|SYNRG_uc010wdh.1_3'UTR	NM_007247	NP_009178	Q9UMZ2	SYNRG_HUMAN	synergin, gamma isoform 1	331	EH.				endocytosis|intracellular protein transport	AP-1 adaptor complex	calcium ion binding			ovary(2)	2																		---	---	---	---
GPR179	440435	broad.mit.edu	37	17	36499258	36499258	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:36499258C>T	uc002hpz.2	-	1	436	c.415G>A	c.(415-417)GAG>AAG	p.E139K		NM_001004334	NP_001004334	Q6PRD1	GP179_HUMAN	GPR158-like 1 precursor	139	Extracellular (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)																---	---	---	---
SRCIN1	80725	broad.mit.edu	37	17	36709076	36709076	+	Silent	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:36709076C>T	uc002hqd.2	-	12	2442	c.2217G>A	c.(2215-2217)TCG>TCA	p.S739S	SRCIN1_uc002hqf.1_Silent_p.S611S|SRCIN1_uc002hqe.2_Silent_p.S593S|SRCIN1_uc002hqg.2_Silent_p.S45S	NM_025248	NP_079524	Q9C0H9	SRCN1_HUMAN	SNAP25-interacting protein	611	Potential.				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																		---	---	---	---
PIP4K2B	8396	broad.mit.edu	37	17	36955562	36955562	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:36955562C>T	uc002hqs.2	-	1	597	c.116G>A	c.(115-117)AGC>AAC	p.S39N	PIP4K2B_uc010wdt.1_Missense_Mutation_p.S39N	NM_003559	NP_003550	P78356	PI42B_HUMAN	phosphatidylinositol-5-phosphate 4-kinase, type	39	PIPK.				cell surface receptor linked signaling pathway	endoplasmic reticulum membrane|plasma membrane	1-phosphatidylinositol-4-phosphate 5-kinase activity|1-phosphatidylinositol-5-phosphate 4-kinase activity|ATP binding|receptor signaling protein activity			ovary(1)	1																		---	---	---	---
STAC2	342667	broad.mit.edu	37	17	37370565	37370565	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:37370565G>A	uc002hrs.2	-	8	1081	c.862C>T	c.(862-864)CGG>TGG	p.R288W	STAC2_uc010cvt.2_Missense_Mutation_p.R146W	NM_198993	NP_945344	Q6ZMT1	STAC2_HUMAN	SH3 and cysteine rich domain 2	288					intracellular signal transduction		metal ion binding			pancreas(1)	1																		---	---	---	---
MED1	5469	broad.mit.edu	37	17	37580080	37580080	+	Intron	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:37580080A>G	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)			---	---	---	---
ERBB2	2064	broad.mit.edu	37	17	37880159	37880159	+	Intron	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:37880159G>A	uc002hso.2	+						ERBB2_uc002hsm.2_Intron|ERBB2_uc010cwa.2_Intron|ERBB2_uc002hsp.2_Intron|ERBB2_uc010cwb.2_Intron|ERBB2_uc010wek.1_Intron	NM_004448	NP_004439			erbB-2 isoform a						cell proliferation|heart development|phosphatidylinositol 3-kinase cascade|phosphatidylinositol-mediated signaling|positive regulation of cell adhesion|positive regulation of epithelial cell proliferation|positive regulation of MAP kinase activity|protein autophosphorylation|regulation of angiogenesis|regulation of microtubule-based process|regulation of transcription, DNA-dependent|transcription, DNA-dependent|wound healing	integral to membrane|nucleus|perinuclear region of cytoplasm|receptor complex	ATP binding|DNA binding|epidermal growth factor receptor activity|ErbB-3 class receptor binding|identical protein binding|protein C-terminus binding|protein heterodimerization activity|protein phosphatase binding|receptor signaling protein tyrosine kinase activity			lung(73)|central_nervous_system(16)|ovary(16)|stomach(14)|breast(9)|upper_aerodigestive_tract(5)|large_intestine(3)|liver(3)|endometrium(2)|skin(1)|pancreas(1)	143	all_cancers(6;1.06e-93)|all_epithelial(6;2.33e-113)|Breast(7;9.37e-100)|Lung NSC(9;9.76e-10)|all_lung(9;5.34e-09)|Colorectal(19;0.000442)|Esophageal squamous(10;0.052)	Ovarian(249;0.0547)|Colorectal(1115;0.234)	UCEC - Uterine corpus endometrioid carcinoma (11;0.000126)|Epithelial(3;9.42e-64)|all cancers(3;5.61e-57)|BRCA - Breast invasive adenocarcinoma(8;2.5e-45)|STAD - Stomach adenocarcinoma(3;9.03e-13)|Colorectal(5;6.23e-08)|COAD - Colon adenocarcinoma(5;8.58e-06)|Lung(15;0.00193)|LUAD - Lung adenocarcinoma(14;0.0664)|OV - Ovarian serous cystadenocarcinoma(8;0.0917)|LUSC - Lung squamous cell carcinoma(15;0.171)	UCEC - Uterine corpus endometrioid carcinoma (308;0.0767)	Lapatinib(DB01259)|Letrozole(DB01006)|Trastuzumab(DB00072)		1	A|Mis|O		breast|ovarian|other tumour types|NSCLC|gastric					TCGA GBM(5;<1E-08)			---	---	---	---
ERBB2	2064	broad.mit.edu	37	17	37880220	37880220	+	Missense_Mutation	SNP	T	C	C	rs121913470		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:37880220T>C	uc002hso.2	+	19	2502	c.2264T>C	c.(2263-2265)TTG>TCG	p.L755S	ERBB2_uc002hsm.2_Missense_Mutation_p.L725S|ERBB2_uc010cwa.2_Missense_Mutation_p.L740S|ERBB2_uc002hsp.2_Missense_Mutation_p.L558S|ERBB2_uc010cwb.2_Missense_Mutation_p.L755S|ERBB2_uc010wek.1_Missense_Mutation_p.L479S	NM_004448	NP_004439	P04626	ERBB2_HUMAN	erbB-2 isoform a	755	Cytoplasmic (Potential).|Protein kinase.		L -> P (in a lung adenocarcinoma sample; somatic mutation).		cell proliferation|heart development|phosphatidylinositol 3-kinase cascade|phosphatidylinositol-mediated signaling|positive regulation of cell adhesion|positive regulation of epithelial cell proliferation|positive regulation of MAP kinase activity|protein autophosphorylation|regulation of angiogenesis|regulation of microtubule-based process|regulation of transcription, DNA-dependent|transcription, DNA-dependent|wound healing	integral to membrane|nucleus|perinuclear region of cytoplasm|receptor complex	ATP binding|DNA binding|epidermal growth factor receptor activity|ErbB-3 class receptor binding|identical protein binding|protein C-terminus binding|protein heterodimerization activity|protein phosphatase binding|receptor signaling protein tyrosine kinase activity	p.L755S(4)|p.L755P(2)|p.L755_S760>A(1)		lung(73)|central_nervous_system(16)|ovary(16)|stomach(14)|breast(9)|upper_aerodigestive_tract(5)|large_intestine(3)|liver(3)|endometrium(2)|skin(1)|pancreas(1)	143	all_cancers(6;1.06e-93)|all_epithelial(6;2.33e-113)|Breast(7;9.37e-100)|Lung NSC(9;9.76e-10)|all_lung(9;5.34e-09)|Colorectal(19;0.000442)|Esophageal squamous(10;0.052)	Ovarian(249;0.0547)|Colorectal(1115;0.234)	UCEC - Uterine corpus endometrioid carcinoma (11;0.000126)|Epithelial(3;9.42e-64)|all cancers(3;5.61e-57)|BRCA - Breast invasive adenocarcinoma(8;2.5e-45)|STAD - Stomach adenocarcinoma(3;9.03e-13)|Colorectal(5;6.23e-08)|COAD - Colon adenocarcinoma(5;8.58e-06)|Lung(15;0.00193)|LUAD - Lung adenocarcinoma(14;0.0664)|OV - Ovarian serous cystadenocarcinoma(8;0.0917)|LUSC - Lung squamous cell carcinoma(15;0.171)	UCEC - Uterine corpus endometrioid carcinoma (308;0.0767)	Lapatinib(DB01259)|Letrozole(DB01006)|Trastuzumab(DB00072)	L755S(LN229_CENTRAL_NERVOUS_SYSTEM)	1	A|Mis|O		breast|ovarian|other tumour types|NSCLC|gastric					TCGA GBM(5;<1E-08)			---	---	---	---
RAPGEFL1	51195	broad.mit.edu	37	17	38345617	38345617	+	Silent	SNP	C	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:38345617C>A	uc010cwu.1	+	6	976	c.486C>A	c.(484-486)TCC>TCA	p.S162S	RAPGEFL1_uc010wfd.1_Silent_p.S98S	NM_016339	NP_057423	Q9UHV5	RPGFL_HUMAN	Rap guanine nucleotide exchange factor	368					G-protein coupled receptor protein signaling pathway|nervous system development|small GTPase mediated signal transduction	intracellular|membrane fraction	guanyl-nucleotide exchange factor activity			ovary(1)|central_nervous_system(1)|skin(1)	3																		---	---	---	---
KRT10	3858	broad.mit.edu	37	17	38978353	38978353	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:38978353T>C	uc002hvi.2	-	1	511	c.485A>G	c.(484-486)GAC>GGC	p.D162G	KRT10_uc010cxd.2_5'Flank|TMEM99_uc002hvj.1_Intron	NM_000421	NP_000412	P13645	K1C10_HUMAN	keratin 10	162	Coil 1A.|Rod.|Gly-rich.				epidermis development		protein binding|structural constituent of epidermis				0		Breast(137;0.000301)																---	---	---	---
KRT12	3859	broad.mit.edu	37	17	39019849	39019849	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:39019849C>T	uc002hvk.2	-	5	1007	c.983G>A	c.(982-984)CGT>CAT	p.R328H		NM_000223	NP_000214	Q99456	K1C12_HUMAN	keratin 12	328	Rod.|Coil 2.				visual perception	intermediate filament	structural molecule activity			ovary(1)	1		Breast(137;0.000301)																---	---	---	---
KRT39	390792	broad.mit.edu	37	17	39116750	39116750	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:39116750C>T	uc002hvo.1	-	6	1036	c.1000G>A	c.(1000-1002)GAT>AAT	p.D334N	KRT39_uc010wfm.1_Missense_Mutation_p.D67N	NM_213656	NP_998821	Q6A163	K1C39_HUMAN	type I hair keratin KA35	334	Coil 2.|Rod.					intermediate filament	structural molecule activity				0		Breast(137;0.00043)|Ovarian(249;0.15)																---	---	---	---
KRT39	390792	broad.mit.edu	37	17	39119905	39119905	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:39119905G>T	uc002hvo.1	-	3	718	c.682C>A	c.(682-684)CTT>ATT	p.L228I	KRT39_uc010wfm.1_5'UTR	NM_213656	NP_998821	Q6A163	K1C39_HUMAN	type I hair keratin KA35	228	Rod.|Coil 1B.					intermediate filament	structural molecule activity				0		Breast(137;0.00043)|Ovarian(249;0.15)																---	---	---	---
KRT36	8689	broad.mit.edu	37	17	39643897	39643897	+	Silent	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:39643897A>G	uc002hwt.2	-	4	792	c.792T>C	c.(790-792)GAT>GAC	p.D264D		NM_003771	NP_003762	O76013	KRT36_HUMAN	keratin 36	264	Rod.|Coil 2.					intermediate filament	protein binding|structural constituent of epidermis				0		Breast(137;0.000286)																---	---	---	---
KRT17	3872	broad.mit.edu	37	17	39777031	39777031	+	Missense_Mutation	SNP	G	A	A	rs139939142		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:39777031G>A	uc002hxh.2	-	6	1182	c.1061C>T	c.(1060-1062)GCC>GTC	p.A354V	JUP_uc010wfs.1_Intron	NM_000422	NP_000413	Q04695	K1C17_HUMAN	keratin 17	354	Coil 2.|Rod.				epidermis development	cytoplasm|intermediate filament	protein binding|structural constituent of cytoskeleton			ovary(1)|skin(1)	2		Breast(137;0.000307)												Steatocystoma_Multiplex				---	---	---	---
NT5C3L	115024	broad.mit.edu	37	17	39985098	39985098	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:39985098T>C	uc002hyc.3	-	7	622	c.613A>G	c.(613-615)AAA>GAA	p.K205E	NT5C3L_uc002hxx.3_Missense_Mutation_p.K70E|NT5C3L_uc010wfu.1_Missense_Mutation_p.K70E|NT5C3L_uc002hyb.3_Missense_Mutation_p.K128E|NT5C3L_uc002hyd.3_Missense_Mutation_p.K128E|NT5C3L_uc002hxy.3_Missense_Mutation_p.K163E|NT5C3L_uc002hxz.3_Missense_Mutation_p.K128E|NT5C3L_uc002hya.3_Intron	NM_052935	NP_443167	C9JKC4	C9JKC4_HUMAN	5'-nucleotidase, cytosolic III-like	171						cytoplasm	5'-nucleotidase activity|magnesium ion binding				0		Breast(137;0.000162)		BRCA - Breast invasive adenocarcinoma(366;0.15)														---	---	---	---
KCNH4	23415	broad.mit.edu	37	17	40318476	40318476	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:40318476G>A	uc002hzb.2	-	10	2012	c.1679C>T	c.(1678-1680)GCG>GTG	p.A560V		NM_012285	NP_036417	Q9UQ05	KCNH4_HUMAN	potassium voltage-gated channel, subfamily H,	560	Cytoplasmic (Potential).|cNMP.				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)														---	---	---	---
PTRF	284119	broad.mit.edu	37	17	40556736	40556736	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:40556736G>A	uc002hzo.2	-	2	1301	c.1142C>T	c.(1141-1143)GCC>GTC	p.A381V	PTRF_uc010wgi.1_Missense_Mutation_p.A363V	NM_012232	NP_036364	Q6NZI2	PTRF_HUMAN	polymerase I and transcript release factor	381					regulation of transcription, DNA-dependent|termination of RNA polymerase I transcription|transcription initiation from RNA polymerase I promoter	caveola|cytosol|endoplasmic reticulum|microsome|mitochondrion|nucleoplasm	protein binding|rRNA primary transcript binding			breast(1)	1		all_cancers(22;0.00146)|Breast(137;0.00116)|all_epithelial(22;0.0134)		BRCA - Breast invasive adenocarcinoma(366;0.193)														---	---	---	---
NAGLU	4669	broad.mit.edu	37	17	40695233	40695233	+	Silent	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:40695233C>T	uc002hzv.2	+	6	1549	c.1209C>T	c.(1207-1209)ATC>ATT	p.I403I		NM_000263	NP_000254	P54802	ANAG_HUMAN	alpha-N-acetylglucosaminidase precursor	403						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)													---	---	---	---
CNTNAP1	8506	broad.mit.edu	37	17	40839789	40839789	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:40839789G>A	uc002iay.2	+	8	1312	c.1096G>A	c.(1096-1098)GGA>AGA	p.G366R	CNTNAP1_uc010wgs.1_RNA	NM_003632	NP_003623	P78357	CNTP1_HUMAN	contactin associated protein 1 precursor	366	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)														---	---	---	---
NAGS	162417	broad.mit.edu	37	17	42084701	42084701	+	Silent	SNP	C	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:42084701C>A	uc002ies.2	+	5	1107	c.1107C>A	c.(1105-1107)ACC>ACA	p.T369T	PYY_uc002ieq.2_5'Flank|NAGS_uc010czn.2_Silent_p.T369T|NAGS_uc002iet.2_5'UTR	NM_153006	NP_694551	Q8N159	NAGS_HUMAN	N-acetylglutamate synthase	369					arginine biosynthetic process|urea cycle	mitochondrial matrix	acetyl-CoA:L-glutamate N-acetyltransferase activity				0		Breast(137;0.00536)|Prostate(33;0.0724)		BRCA - Breast invasive adenocarcinoma(366;0.113)	L-Glutamic Acid(DB00142)											OREG0024449	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
C17orf53	78995	broad.mit.edu	37	17	42225684	42225684	+	Silent	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:42225684C>T	uc002ifi.1	+	3	698	c.513C>T	c.(511-513)GGC>GGT	p.G171G	C17orf53_uc010czq.1_Silent_p.G171G|C17orf53_uc002ifj.1_Silent_p.G171G|C17orf53_uc002ifk.1_RNA	NM_024032	NP_076937	Q8N3J3	CQ053_HUMAN	hypothetical protein LOC78995	171											0		Breast(137;0.0364)|Prostate(33;0.0376)		BRCA - Breast invasive adenocarcinoma(366;0.114)														---	---	---	---
RUNDC3A	10900	broad.mit.edu	37	17	42390852	42390852	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:42390852C>T	uc002igl.3	+	4	713	c.439C>T	c.(439-441)CGT>TGT	p.R147C	RUNDC3A_uc002igi.2_Missense_Mutation_p.R147C|RUNDC3A_uc002igj.2_Missense_Mutation_p.R142C|RUNDC3A_uc002igk.2_Missense_Mutation_p.R143C	NM_001144825	NP_001138297	Q59EK9	RUN3A_HUMAN	RUN domain containing 3A isoform 1	147	Interaction with RAP2A (By similarity).|RUN.				small GTPase mediated signal transduction		small GTPase regulator activity				0		Prostate(33;0.0233)		BRCA - Breast invasive adenocarcinoma(366;0.189)														---	---	---	---
DBF4B	80174	broad.mit.edu	37	17	42815766	42815766	+	Silent	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:42815766G>A	uc002ihf.2	+	9	900	c.687G>A	c.(685-687)CCG>CCA	p.P229P	DBF4B_uc010wjb.1_RNA|DBF4B_uc002ihe.2_Silent_p.P43P|DBF4B_uc010wjc.1_Silent_p.P213P	NM_145663	NP_663696	Q8NFT6	DBF4B_HUMAN	DBF4 homolog B isoform 1	229					cell cycle	nucleus	nucleic acid binding|zinc ion binding				0		Prostate(33;0.0322)																---	---	---	---
DBF4B	80174	broad.mit.edu	37	17	42828490	42828490	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:42828490C>T	uc002ihf.2	+	14	1930	c.1717C>T	c.(1717-1719)CCG>TCG	p.P573S	DBF4B_uc010wjc.1_Intron	NM_145663	NP_663696	Q8NFT6	DBF4B_HUMAN	DBF4 homolog B isoform 1	573					cell cycle	nucleus	nucleic acid binding|zinc ion binding				0		Prostate(33;0.0322)																---	---	---	---
ARHGAP27	201176	broad.mit.edu	37	17	43481633	43481633	+	Splice_Site	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:43481633A>G	uc002iix.2	-	6	905	c.456_splice	c.e6+1	p.R152_splice	ARHGAP27_uc010dak.2_Splice_Site_p.R125_splice|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)																	---	---	---	---
IMP5	162540	broad.mit.edu	37	17	43923925	43923925	+	Silent	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:43923925C>T	uc010wka.1	+	1	1653	c.1653C>T	c.(1651-1653)GGC>GGT	p.G551G	LOC100128977_uc010wjz.1_Intron	NM_175882	NP_787078	Q8IUH8	IMP5_HUMAN	intramembrane protease 5 precursor	551	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	44159885	44159885	+	Silent	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:44159885T>C	uc002ikb.2	-	3	1540	c.1455A>G	c.(1453-1455)GTA>GTG	p.V485V	KIAA1267_uc002ikc.2_Silent_p.V485V|KIAA1267_uc002ikd.2_Silent_p.V485V|KIAA1267_uc010dav.2_Silent_p.V485V	NM_015443	NP_056258	Q7Z3B3	K1267_HUMAN	hypothetical protein LOC284058	485						MLL1 complex	protein binding			skin(2)	2		Melanoma(429;0.211)																---	---	---	---
WNT3	7473	broad.mit.edu	37	17	44847150	44847150	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:44847150G>A	uc002ikv.2	-	3	706	c.587C>T	c.(586-588)ACG>ATG	p.T196M		NM_030753	NP_110380	P56703	WNT3_HUMAN	wingless-type MMTV integration site family,	196					canonical Wnt receptor signaling pathway involved in mesenchymal stem cell differentiation|canonical Wnt receptor signaling pathway involved in osteoblast differentiation|cellular response to retinoic acid|dorsal/ventral axis specification|embryonic forelimb morphogenesis|embryonic hindlimb morphogenesis|embryonic pattern specification|head morphogenesis|hemopoietic stem cell proliferation|inner ear morphogenesis|limb bud formation|mammary gland epithelium development|mesoderm formation|midbrain-hindbrain boundary development|negative regulation of fat cell differentiation|positive regulation of cell proliferation|Spemann organizer formation at the anterior end of the primitive streak|Wnt receptor signaling pathway, calcium modulating pathway	early endosome|extracellular space|late endosome|membrane fraction|membrane raft|plasma membrane|proteinaceous extracellular matrix	frizzled binding|frizzled-2 binding|signal transducer activity			lung(2)	2			BRCA - Breast invasive adenocarcinoma(9;0.0257)															---	---	---	---
C17orf57	124989	broad.mit.edu	37	17	45479506	45479506	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:45479506A>G	uc002iln.2	+	18	2365	c.1954A>G	c.(1954-1956)AAA>GAA	p.K652E	C17orf57_uc002ilm.2_Missense_Mutation_p.K556E	NM_152347	NP_689560	Q8IY85	CQ057_HUMAN	hypothetical protein LOC124989	652	EF-hand 3.						calcium ion binding			breast(1)|central_nervous_system(1)|skin(1)	3																		---	---	---	---
ZNF652	22834	broad.mit.edu	37	17	47389292	47389292	+	Silent	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:47389292G>A	uc002iov.3	-	4	1625	c.1161C>T	c.(1159-1161)TGC>TGT	p.C387C	ZNF652_uc002iow.2_Silent_p.C387C|ZNF652_uc002iou.3_RNA	NM_001145365	NP_001138837	Q9Y2D9	ZN652_HUMAN	zinc finger protein 652	387	C2H2-type 6.				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)															---	---	---	---
COL1A1	1277	broad.mit.edu	37	17	48263813	48263813	+	Silent	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:48263813G>A	uc002iqm.2	-	49	3996	c.3870C>T	c.(3868-3870)TTC>TTT	p.F1290F		NM_000088	NP_000079	P02452	CO1A1_HUMAN	alpha 1 type I collagen preproprotein	1290	Fibrillar collagen NC1.				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						---	---	---	---
SPATA20	64847	broad.mit.edu	37	17	48625675	48625675	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:48625675G>A	uc002irf.2	+	2	250	c.109G>A	c.(109-111)GCG>ACG	p.A37T	SPATA20_uc002irc.2_5'UTR|SPATA20_uc002ire.2_5'UTR|SPATA20_uc002ird.2_Missense_Mutation_p.A53T|SPATA20_uc010wmv.1_Missense_Mutation_p.A37T|SPATA20_uc002irg.2_RNA	NM_022827	NP_073738	Q8TB22	SPT20_HUMAN	spermatogenesis associated 20	37					cell differentiation|mannose metabolic process|multicellular organismal development|spermatogenesis	extracellular region	mannose-6-phosphate isomerase activity|protein binding				0	Breast(11;1.23e-18)		BRCA - Breast invasive adenocarcinoma(22;9.38e-09)															---	---	---	---
WFIKKN2	124857	broad.mit.edu	37	17	48917822	48917822	+	Silent	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:48917822G>A	uc002isv.3	+	2	1867	c.1173G>A	c.(1171-1173)CTG>CTA	p.L391L	WFIKKN2_uc010dbu.2_Silent_p.L298L	NM_175575	NP_783165	Q8TEU8	WFKN2_HUMAN	WFIKKN2 protein	391	BPTI/Kunitz inhibitor 2.					extracellular region	metalloendopeptidase inhibitor activity|protein binding|serine-type endopeptidase inhibitor activity			ovary(2)|skin(1)	3			BRCA - Breast invasive adenocarcinoma(22;1.09e-08)															---	---	---	---
STXBP4	252983	broad.mit.edu	37	17	53150304	53150304	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:53150304G>A	uc002iuf.1	+	13	1262	c.1055G>A	c.(1054-1056)CGG>CAG	p.R352Q	STXBP4_uc010dcd.1_Missense_Mutation_p.R330Q	NM_178509	NP_848604	Q6ZWJ1	STXB4_HUMAN	syntaxin binding protein 4	352	Potential.					cytoplasm	calcium ion binding			ovary(1)	1																		---	---	---	---
MSI2	124540	broad.mit.edu	37	17	55334919	55334919	+	Intron	SNP	C	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:55334919C>A	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								---	---	---	---
BZRAP1	9256	broad.mit.edu	37	17	56385903	56385903	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:56385903C>T	uc002ivx.3	-	22	5601	c.4730G>A	c.(4729-4731)CGG>CAG	p.R1577Q	BZRAP1_uc002ivw.2_5'Flank|BZRAP1_uc010dcs.2_Missense_Mutation_p.R1517Q|BZRAP1_uc010wnt.1_Missense_Mutation_p.R1577Q	NM_004758	NP_004749	O95153	RIMB1_HUMAN	peripheral benzodiazepine receptor-associated	1577						mitochondrion	benzodiazepine receptor binding			upper_aerodigestive_tract(2)|skin(1)	3	Medulloblastoma(34;0.127)|all_neural(34;0.237)																	---	---	---	---
SEPT4	5414	broad.mit.edu	37	17	56598179	56598179	+	Silent	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:56598179G>A	uc002iwm.1	-	11	1430	c.1302C>T	c.(1300-1302)ACC>ACT	p.T434T	MTMR4_uc002iwj.2_5'Flank|SEPT4_uc002iwk.1_Silent_p.T287T|SEPT4_uc010wnw.1_Silent_p.T287T|SEPT4_uc002iwl.1_Silent_p.T287T|SEPT4_uc002iwn.1_Silent_p.T335T|SEPT4_uc002iwo.1_Silent_p.T415T|SEPT4_uc002iwp.1_3'UTR|SEPT4_uc010wnx.1_Silent_p.T449T|SEPT4_uc010wny.1_Silent_p.T426T|SEPT4_uc010dcy.1_3'UTR	NM_004574	NP_004565	O43236	SEPT4_HUMAN	septin 4 isoform 1	434					apoptosis|cell cycle|cytokinesis|regulation of apoptosis	cytoskeleton|mitochondrion|nucleus	GTP binding|GTPase activity|protein binding|structural molecule activity				0	Medulloblastoma(34;0.127)|all_neural(34;0.237)															OREG0024614	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
DHX40	79665	broad.mit.edu	37	17	57684469	57684469	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:57684469G>A	uc002ixn.1	+	18	2423	c.2276G>A	c.(2275-2277)CGT>CAT	p.R759H	DHX40_uc010woe.1_Missense_Mutation_p.R682H|DHX40_uc010wof.1_Missense_Mutation_p.R274H	NM_024612	NP_078888	Q8IX18	DHX40_HUMAN	DEAH (Asp-Glu-Ala-His) box polypeptide 40	759							ATP binding|ATP-dependent helicase activity|nucleic acid binding				0	all_neural(34;0.0878)|Medulloblastoma(34;0.0922)																	---	---	---	---
RPS6KB1	6198	broad.mit.edu	37	17	58008996	58008996	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:58008996G>A	uc002ixy.2	+	7	704	c.601G>A	c.(601-603)GAA>AAA	p.E201K	RPS6KB1_uc010ddj.1_Missense_Mutation_p.E201K|RPS6KB1_uc010wom.1_Missense_Mutation_p.E148K|RPS6KB1_uc010won.1_Missense_Mutation_p.E178K|RPS6KB1_uc010woo.1_Missense_Mutation_p.E136K	NM_003161	NP_003152	P23443	KS6B1_HUMAN	ribosomal protein S6 kinase, 70kDa, polypeptide	201	Protein kinase.				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)															---	---	---	---
USP32	84669	broad.mit.edu	37	17	58422974	58422974	+	Intron	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:58422974A>G	uc002iyo.1	-						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)															---	---	---	---
PPM1D	8493	broad.mit.edu	37	17	58740749	58740749	+	Nonsense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:58740749C>T	uc002iyt.1	+	6	1876	c.1654C>T	c.(1654-1656)CGA>TGA	p.R552*	PPM1D_uc010ddm.1_RNA	NM_003620	NP_003611	O15297	PPM1D_HUMAN	protein phosphatase 1D	552					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)													OREG0031485	type=REGULATORY REGION|TFbs=ESR1|Dataset=Estrogen Receptor Alpha Binding Sites|EvidenceSubtype=Chromatin immunoprecipitation with tag sequencing (ChIP-TS)	---	---	---	---
BCAS3	54828	broad.mit.edu	37	17	59147661	59147661	+	Intron	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:59147661T>C	uc002iyv.3	+						BCAS3_uc002iyu.3_Intron|BCAS3_uc002iyw.3_Intron|BCAS3_uc002iyy.3_Intron|BCAS3_uc002iyz.3_Intron|BCAS3_uc002iza.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)															---	---	---	---
TBX2	6909	broad.mit.edu	37	17	59479200	59479200	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:59479200A>G	uc010wox.1	+	2	832	c.551A>G	c.(550-552)AAA>AGA	p.K184R	TBX2_uc002ize.2_Missense_Mutation_p.K174R|TBX2_uc002izg.2_Missense_Mutation_p.K30R	NM_005994	NP_005985	Q13207	TBX2_HUMAN	T-box 2	184	T-box.				cell aging|positive regulation of cell proliferation		sequence-specific DNA binding				0																		---	---	---	---
TBX4	9496	broad.mit.edu	37	17	59556119	59556119	+	Silent	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:59556119G>A	uc002izi.2	+	5	726	c.681G>A	c.(679-681)GTG>GTA	p.V227V	TBX4_uc010ddo.2_Silent_p.V227V|TBX4_uc010woy.1_Silent_p.V227V	NM_018488	NP_060958	P57082	TBX4_HUMAN	T-box 4	227	T-box.				leg morphogenesis|skeletal system morphogenesis	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity			skin(2)	2																		---	---	---	---
INTS2	57508	broad.mit.edu	37	17	59989372	59989372	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:59989372G>A	uc002izn.2	-	6	809	c.733C>T	c.(733-735)CGC>TGC	p.R245C	INTS2_uc002izm.2_Missense_Mutation_p.R237C	NM_020748	NP_065799	Q9H0H0	INT2_HUMAN	integrator complex subunit 2	245					snRNA processing	integral to membrane|integrator complex|nuclear membrane	protein binding			ovary(1)|lung(1)|pancreas(1)	3																		---	---	---	---
TLK2	11011	broad.mit.edu	37	17	60637441	60637441	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:60637441G>A	uc010ddp.2	+	10	1053	c.785G>A	c.(784-786)CGA>CAA	p.R262Q	TLK2_uc002izx.3_Missense_Mutation_p.R110Q|TLK2_uc002izz.3_Missense_Mutation_p.R262Q|TLK2_uc002jaa.3_Missense_Mutation_p.R230Q|TLK2_uc010wpd.1_Missense_Mutation_p.R230Q	NM_006852	NP_006843	Q86UE8	TLK2_HUMAN	tousled-like kinase 2 isoform A	262	Potential.		R -> Q.		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	60741937	60741937	+	Silent	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:60741937T>C	uc002jad.2	+	2	549	c.147T>C	c.(145-147)CAT>CAC	p.H49H	MRC2_uc002jac.2_Silent_p.H49H	NM_006039	NP_006030	Q9UBG0	MRC2_HUMAN	mannose receptor, C type 2	49	Extracellular (Potential).|Ricin B-type lectin.				endocytosis	integral to membrane	receptor activity|sugar binding			ovary(1)|central_nervous_system(1)|skin(1)	3																		---	---	---	---
TANC2	26115	broad.mit.edu	37	17	61432191	61432191	+	Silent	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:61432191A>G	uc002jal.3	+	12	1823	c.1800A>G	c.(1798-1800)CTA>CTG	p.L600L	TANC2_uc010wpe.1_Silent_p.L510L|TANC2_uc002jam.1_5'UTR	NM_025185	NP_079461	Q9HCD6	TANC2_HUMAN	tetratricopeptide repeat, ankyrin repeat and	600							binding			ovary(2)	2																		---	---	---	---
DDX42	11325	broad.mit.edu	37	17	61877844	61877844	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:61877844A>G	uc002jbu.2	+	7	745	c.488A>G	c.(487-489)TAC>TGC	p.Y163C	DDX42_uc002jbv.2_Missense_Mutation_p.Y163C|DDX42_uc002jbw.1_Translation_Start_Site	NM_007372	NP_031398	Q86XP3	DDX42_HUMAN	DEAD box polypeptide 42 protein	163					protein localization|regulation of anti-apoptosis	Cajal body|cytoplasm|nuclear speck	ATP binding|ATP-dependent helicase activity|protein binding|RNA binding			ovary(2)|skin(2)|large_intestine(1)	5																		---	---	---	---
DDX42	11325	broad.mit.edu	37	17	61887869	61887869	+	Intron	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:61887869G>A	uc002jbu.2	+						DDX42_uc002jbv.2_Intron|DDX42_uc002jbw.1_Intron|DDX42_uc002jbx.2_Intron|DDX42_uc002jby.2_5'Flank	NM_007372	NP_031398			DEAD box polypeptide 42 protein						protein localization|regulation of anti-apoptosis	Cajal body|cytoplasm|nuclear speck	ATP binding|ATP-dependent helicase activity|protein binding|RNA binding			ovary(2)|skin(2)|large_intestine(1)	5																		---	---	---	---
GH1	2688	broad.mit.edu	37	17	61995190	61995190	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:61995190T>C	uc002jdj.2	-	4	448	c.386A>G	c.(385-387)TAC>TGC	p.Y129C	GH1_uc002jdi.2_Missense_Mutation_p.Y114C|GH1_uc002jdk.2_Missense_Mutation_p.Y89C|GH1_uc002jdl.2_Intron|GH1_uc002jdm.2_Intron|GH1_uc002jdn.2_Intron	NM_000515	NP_000506	P01241	SOMA_HUMAN	growth hormone 1 isoform 1	129					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																		---	---	---	---
LRRC37A3	374819	broad.mit.edu	37	17	62856813	62856813	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:62856813G>T	uc002jey.2	-	11	3982	c.3451C>A	c.(3451-3453)CTG>ATG	p.L1151M	LRRC37A3_uc010wqg.1_Missense_Mutation_p.L269M|LRRC37A3_uc002jex.1_Missense_Mutation_p.L128M|LRRC37A3_uc010wqf.1_Missense_Mutation_p.L189M|LRRC37A3_uc010dek.1_Missense_Mutation_p.L157M	NM_199340	NP_955372	O60309	L37A3_HUMAN	leucine rich repeat containing 37, member A3	1151	Extracellular (Potential).|LRR 11.					integral to membrane					0																		---	---	---	---
BPTF	2186	broad.mit.edu	37	17	65919004	65919004	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:65919004C>T	uc002jgf.2	+	14	5667	c.5606C>T	c.(5605-5607)CCA>CTA	p.P1869L	BPTF_uc002jge.2_Missense_Mutation_p.P1995L	NM_182641	NP_872579	Q12830	BPTF_HUMAN	bromodomain PHD finger transcription factor	1995					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)															---	---	---	---
PRKAR1A	5573	broad.mit.edu	37	17	66522019	66522019	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:66522019G>A	uc002jhg.2	+	7	854	c.674G>A	c.(673-675)GGC>GAC	p.G225D	PRKAR1A_uc002jhh.2_Missense_Mutation_p.G225D|PRKAR1A_uc002jhi.2_Missense_Mutation_p.G225D|PRKAR1A_uc002jhj.2_Missense_Mutation_p.G225D|PRKAR1A_uc002jhk.2_Missense_Mutation_p.G101D|PRKAR1A_uc002jhl.2_Missense_Mutation_p.G225D|PRKAR1A_uc002jhm.2_Missense_Mutation_p.G225D	NM_212471	NP_997636	P10644	KAP0_HUMAN	cAMP-dependent protein kinase, regulatory	225	cAMP 1.				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				---	---	---	---
ABCA8	10351	broad.mit.edu	37	17	66883541	66883541	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:66883541A>G	uc002jhp.2	-	23	3310	c.3131T>C	c.(3130-3132)ATA>ACA	p.I1044T	ABCA8_uc002jhq.2_Missense_Mutation_p.I1084T|ABCA8_uc010wqq.1_Missense_Mutation_p.I1084T|ABCA8_uc010wqr.1_Missense_Mutation_p.I1023T	NM_007168	NP_009099	O94911	ABCA8_HUMAN	ATP-binding cassette, sub-family A member 8	1044	Helical; (Potential).					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)																	---	---	---	---
ABCA9	10350	broad.mit.edu	37	17	67013867	67013867	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:67013867G>A	uc002jhu.2	-	21	2974	c.2831C>T	c.(2830-2832)GCC>GTC	p.A944V	ABCA9_uc010dez.2_Missense_Mutation_p.A944V	NM_080283	NP_525022	Q8IUA7	ABCA9_HUMAN	ATP-binding cassette, sub-family A, member 9	944					transport	integral to membrane	ATP binding|ATPase activity			ovary(4)|upper_aerodigestive_tract(1)|central_nervous_system(1)	6	Breast(10;1.47e-12)																	---	---	---	---
ABCA5	23461	broad.mit.edu	37	17	67270253	67270253	+	Missense_Mutation	SNP	T	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:67270253T>A	uc002jif.2	-	19	3829	c.2611A>T	c.(2611-2613)ATT>TTT	p.I871F	ABCA5_uc002jic.2_Missense_Mutation_p.I94F|ABCA5_uc002jid.2_5'UTR|ABCA5_uc002jie.2_RNA|ABCA5_uc002jig.2_Missense_Mutation_p.I871F|ABCA5_uc002jih.2_Missense_Mutation_p.I871F|ABCA5_uc010dfe.2_Missense_Mutation_p.I871F	NM_018672	NP_061142	Q8WWZ7	ABCA5_HUMAN	ATP-binding cassette, sub-family A , member 5	871	Helical; (Potential).				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	67522747	67522747	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:67522747T>C	uc002jij.2	+	10	1066	c.778T>C	c.(778-780)TGG>CGG	p.W260R		NM_002758	NP_002749	P52564	MP2K6_HUMAN	mitogen-activated protein kinase kinase 6	260	Protein kinase.				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)																	---	---	---	---
SDK2	54549	broad.mit.edu	37	17	71389889	71389889	+	Splice_Site	SNP	C	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:71389889C>A	uc010dfm.2	-	27	3709	c.3709_splice	c.e27-1	p.V1237_splice	SDK2_uc002jjt.3_Splice_Site_p.V396_splice|SDK2_uc010dfn.2_Splice_Site_p.V916_splice	NM_001144952	NP_001138424			sidekick 2						cell adhesion	integral to membrane				ovary(2)	2																		---	---	---	---
SDK2	54549	broad.mit.edu	37	17	71411968	71411968	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:71411968C>T	uc010dfm.2	-	17	2350	c.2350G>A	c.(2350-2352)GAG>AAG	p.E784K	SDK2_uc010dfn.2_Missense_Mutation_p.E463K	NM_001144952	NP_001138424	Q58EX2	SDK2_HUMAN	sidekick 2	784	Extracellular (Potential).|Fibronectin type-III 2.				cell adhesion	integral to membrane				ovary(2)	2																		---	---	---	---
GPR142	350383	broad.mit.edu	37	17	72366809	72366809	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:72366809G>T	uc010wqy.1	+	3	508	c.508G>T	c.(508-510)GGG>TGG	p.G170W	GPR142_uc010wqx.1_Missense_Mutation_p.G82W	NM_181790	NP_861455	Q7Z601	GP142_HUMAN	G protein-coupled receptor 142	170	Helical; Name=1; (Potential).					cell junction|cytoplasm|integral to membrane	G-protein coupled receptor activity			ovary(2)|central_nervous_system(1)|skin(1)	4																		---	---	---	---
C17orf77	146723	broad.mit.edu	37	17	72584997	72584997	+	Intron	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:72584997C>T	uc002jla.1	+						CD300LD_uc002jkz.2_Intron	NM_152460	NP_689673			hypothetical protein LOC146723							extracellular region					0																		---	---	---	---
GRIN2C	2905	broad.mit.edu	37	17	72850958	72850958	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:72850958C>T	uc002jlt.1	-	2	430	c.274G>A	c.(274-276)GGC>AGC	p.G92S	GRIN2C_uc010wrh.1_RNA|GRIN2C_uc002jlu.1_Missense_Mutation_p.G92S|GRIN2C_uc002jlv.1_Missense_Mutation_p.G92S	NM_000835	NP_000826	Q14957	NMDE3_HUMAN	N-methyl-D-aspartate receptor subunit 2C	92	Extracellular (Potential).				glutamate signaling pathway	cell junction|outer membrane-bounded periplasmic space|postsynaptic membrane	extracellular-glutamate-gated ion channel activity|N-methyl-D-aspartate selective glutamate receptor activity			ovary(2)|breast(2)	4	all_lung(278;0.172)|Lung NSC(278;0.207)				Glycine(DB00145)|L-Glutamic Acid(DB00142)|Loperamide(DB00836)													---	---	---	---
FADS6	283985	broad.mit.edu	37	17	72874593	72874593	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:72874593A>G	uc002jmd.1	-	6	932	c.920T>C	c.(919-921)GTG>GCG	p.V307A	FADS6_uc010wrn.1_Missense_Mutation_p.V161A	NM_178128	NP_835229	Q8N9I5	FADS6_HUMAN	fatty acid desaturase domain family, member 6	313					fatty acid biosynthetic process	integral to membrane	oxidoreductase activity				0	all_lung(278;0.172)|Lung NSC(278;0.207)																	---	---	---	---
ARMC7	79637	broad.mit.edu	37	17	73106691	73106691	+	Silent	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:73106691G>A	uc002jmw.1	+	2	527	c.225G>A	c.(223-225)GAG>GAA	p.E75E	ARMC7_uc002jmv.1_Silent_p.E75E|ARMC7_uc010wru.1_Intron	NM_024585	NP_078861	Q9H6L4	ARMC7_HUMAN	armadillo repeat containing 7	75	ARM 1.						binding			pancreas(1)	1	all_lung(278;0.14)|Lung NSC(278;0.168)		LUSC - Lung squamous cell carcinoma(166;0.162)|Lung(188;0.235)															---	---	---	---
GGA3	23163	broad.mit.edu	37	17	73238544	73238544	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:73238544C>T	uc002jni.1	-	8	629	c.620G>A	c.(619-621)CGG>CAG	p.R207Q	GGA3_uc002jnj.1_Missense_Mutation_p.R174Q|GGA3_uc010wrw.1_Missense_Mutation_p.R85Q|GGA3_uc002jnk.1_Missense_Mutation_p.R135Q|GGA3_uc010wrx.1_Missense_Mutation_p.R85Q|GGA3_uc010wry.1_Missense_Mutation_p.R135Q|GGA3_uc010wrz.1_3'UTR	NM_138619	NP_619525	Q9NZ52	GGA3_HUMAN	ADP-ribosylation factor binding protein 3	207	GAT.|Binds to ARF1 (in long isoform).				intracellular protein transport|vesicle-mediated transport	clathrin adaptor complex|endosome membrane|trans-Golgi network	ADP-ribosylation factor binding			ovary(1)|breast(1)	2			all cancers(21;2.39e-06)|Epithelial(20;2.38e-05)															---	---	---	---
MIF4GD	57409	broad.mit.edu	37	17	73266256	73266256	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:73266256C>A	uc002jnr.2	-	2	150	c.21G>T	c.(19-21)GAG>GAT	p.E7D	MIF4GD_uc002jno.2_Missense_Mutation_p.E7D|MIF4GD_uc002jnp.2_Missense_Mutation_p.E7D|MIF4GD_uc002jnq.2_Missense_Mutation_p.E7D			A9UHW6	MI4GD_HUMAN	RecName: Full=MIF4G domain-containing protein; AltName: Full=SLBP-interacting protein 1;          Short=hSLIP1;	7	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	73274325	73274325	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:73274325G>A	uc002jns.3	-	4	1461	c.551C>T	c.(550-552)GCC>GTC	p.A184V	SLC25A19_uc010dge.2_Missense_Mutation_p.A127V|SLC25A19_uc002jnv.3_Missense_Mutation_p.A184V|SLC25A19_uc002jnu.3_Missense_Mutation_p.A184V|SLC25A19_uc002jnw.3_Missense_Mutation_p.A184V|SLC25A19_uc002jnt.3_Missense_Mutation_p.A184V	NM_021734	NP_068380	Q9HC21	TPC_HUMAN	solute carrier family 25, member 19	184	Solcar 2.|Helical; Name=4; (Potential).					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)															---	---	---	---
UNK	85451	broad.mit.edu	37	17	73811316	73811316	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:73811316G>A	uc002jpm.2	+	8	1171	c.1171G>A	c.(1171-1173)GCC>ACC	p.A391T		NM_001080419	NP_001073888	Q9C0B0	UNK_HUMAN	zinc finger CCCH-type domain containing 5	315	C3H1-type 5.						nucleic acid binding|zinc ion binding				0			all cancers(21;2.61e-06)|Epithelial(20;7.39e-06)|BRCA - Breast invasive adenocarcinoma(9;0.00194)|LUSC - Lung squamous cell carcinoma(166;0.154)															---	---	---	---
EVPL	2125	broad.mit.edu	37	17	74003968	74003968	+	Missense_Mutation	SNP	A	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:74003968A>C	uc002jqi.2	-	22	5546	c.5318T>G	c.(5317-5319)ATC>AGC	p.I1773S	EVPL_uc010wss.1_Missense_Mutation_p.I1795S|EVPL_uc010wst.1_Missense_Mutation_p.I1243S	NM_001988	NP_001979	Q92817	EVPL_HUMAN	envoplakin	1773	Globular 2.				keratinization|peptide cross-linking	cornified envelope|cytoplasm|desmosome	protein binding, bridging|structural molecule activity			pancreas(2)|central_nervous_system(1)|skin(1)	4																		---	---	---	---
EVPL	2125	broad.mit.edu	37	17	74011573	74011573	+	Missense_Mutation	SNP	T	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:74011573T>A	uc002jqi.2	-	15	2075	c.1847A>T	c.(1846-1848)AAG>ATG	p.K616M	EVPL_uc010wss.1_Missense_Mutation_p.K638M|EVPL_uc010wst.1_Missense_Mutation_p.K86M	NM_001988	NP_001979	Q92817	EVPL_HUMAN	envoplakin	616	Globular 1.				keratinization|peptide cross-linking	cornified envelope|cytoplasm|desmosome	protein binding, bridging|structural molecule activity			pancreas(2)|central_nervous_system(1)|skin(1)	4																		---	---	---	---
GALR2	8811	broad.mit.edu	37	17	74071198	74071198	+	Silent	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:74071198C>T	uc002jqm.1	+	1	315	c.234C>T	c.(232-234)TGC>TGT	p.C78C	SRP68_uc010wsu.1_5'Flank|SRP68_uc002jqk.1_5'Flank|SRP68_uc002jql.1_5'Flank	NM_003857	NP_003848	O43603	GALR2_HUMAN	galanin receptor 2	78	Helical; Name=2; (Potential).				digestion|elevation of cytosolic calcium ion concentration|feeding behavior|learning or memory|muscle contraction	integral to membrane|plasma membrane	galanin receptor activity				0																		---	---	---	---
SPHK1	8877	broad.mit.edu	37	17	74382558	74382558	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:74382558G>A	uc002jrf.1	+	7	1152	c.343G>A	c.(343-345)GCG>ACG	p.A115T	SPHK1_uc002jrg.1_Missense_Mutation_p.A64T|SPHK1_uc002jrh.2_Missense_Mutation_p.A129T|SPHK1_uc002jrj.2_Missense_Mutation_p.A201T|SPHK1_uc002jri.2_Missense_Mutation_p.A115T|SPHK1_uc002jrk.3_Missense_Mutation_p.A115T	NM_001142602	NP_001136074	Q9NYA1	SPHK1_HUMAN	sphingosine kinase 1 isoform 3	115	DAGKc.			NA -> KP (in Ref. 4; CAB92131).	'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																OREG0024750	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
SPHK1	8877	broad.mit.edu	37	17	74382601	74382601	+	Intron	SNP	G	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:74382601G>T	uc002jrf.1	+						SPHK1_uc002jrg.1_Intron|SPHK1_uc002jrh.2_Intron|SPHK1_uc002jrj.2_Intron|SPHK1_uc002jri.2_Intron|SPHK1_uc002jrk.3_Intron	NM_001142602	NP_001136074			sphingosine kinase 1 isoform 3						'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																OREG0024750	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
ST6GALNAC1	55808	broad.mit.edu	37	17	74625524	74625524	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:74625524A>G	uc002jsh.2	-	2	575	c.401T>C	c.(400-402)GTG>GCG	p.V134A	ST6GALNAC1_uc002jsi.2_Missense_Mutation_p.V2A|ST6GALNAC1_uc002jsj.2_RNA	NM_018414	NP_060884	Q9NSC7	SIA7A_HUMAN	sialyltransferase 7A	134	Lumenal (Potential).				protein glycosylation	integral to Golgi membrane	alpha-N-acetylgalactosaminide alpha-2,6-sialyltransferase activity				0																		---	---	---	---
SEPT9	10801	broad.mit.edu	37	17	75398173	75398173	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:75398173G>A	uc002jts.3	+	3	235	c.109G>A	c.(109-111)GAG>AAG	p.E37K	SEPT9_uc010wtk.1_Missense_Mutation_p.E18K|SEPT9_uc002jtt.3_5'UTR|SEPT9_uc002jtu.3_Missense_Mutation_p.E19K|SEPT9_uc002jtv.2_Missense_Mutation_p.E30K|SEPT9_uc002jtw.2_5'UTR|SEPT9_uc002jtx.1_5'UTR|SEPT9_uc010wtl.1_5'Flank	NM_001113491	NP_001106963	Q9UHD8	SEPT9_HUMAN	septin 9 isoform a	37					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	76497340	76497340	+	RNA	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:76497340G>A	uc002jvt.1	+	2		c.2799G>A								Homo sapiens cDNA FLJ45552 fis, clone BRTHA2038279.																														---	---	---	---
USP36	57602	broad.mit.edu	37	17	76802332	76802332	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:76802332G>A	uc002jvz.1	-	15	2447	c.2122C>T	c.(2122-2124)CGT>TGT	p.R708C	USP36_uc002jwa.1_Missense_Mutation_p.R708C|USP36_uc002jwb.1_Missense_Mutation_p.R345C|USP36_uc002jwc.1_Missense_Mutation_p.R408C	NM_025090	NP_079366	Q9P275	UBP36_HUMAN	ubiquitin specific peptidase 36	708					ubiquitin-dependent protein catabolic process	nucleolus	cysteine-type peptidase activity|ubiquitin thiolesterase activity			lung(2)|ovary(1)|breast(1)|kidney(1)	5			BRCA - Breast invasive adenocarcinoma(99;0.000842)|OV - Ovarian serous cystadenocarcinoma(97;0.151)															---	---	---	---
C1QTNF1	114897	broad.mit.edu	37	17	77043870	77043870	+	Silent	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:77043870C>T	uc002jwp.2	+	4	886	c.546C>T	c.(544-546)ACC>ACT	p.T182T	C1QTNF1_uc002jwq.2_Silent_p.T100T|C1QTNF1_uc002jwr.3_Silent_p.T192T|C1QTNF1_uc002jws.2_Silent_p.T182T|C1QTNF1_uc002jwt.2_Silent_p.T280T	NM_030968	NP_112230	Q9BXJ1	C1QT1_HUMAN	C1q and tumor necrosis factor related protein 1	182	C1q.					collagen				ovary(1)	1			BRCA - Breast invasive adenocarcinoma(99;0.0294)|OV - Ovarian serous cystadenocarcinoma(97;0.201)															---	---	---	---
SLC26A11	284129	broad.mit.edu	37	17	78223002	78223002	+	Silent	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:78223002C>T	uc002jyb.1	+	16	1841	c.1572C>T	c.(1570-1572)ATC>ATT	p.I524I	SLC26A11_uc002jyc.1_Silent_p.I524I|SLC26A11_uc002jyd.1_Silent_p.I524I|SLC26A11_uc010dhv.1_Silent_p.I524I	NM_173626	NP_775897	Q86WA9	S2611_HUMAN	solute carrier family 26, member 11	524	Extracellular (Potential).|STAS.					endoplasmic reticulum|Golgi apparatus|integral to membrane|lysosomal membrane|plasma membrane	anion:anion antiporter activity|secondary active sulfate transmembrane transporter activity				0	all_neural(118;0.0538)		OV - Ovarian serous cystadenocarcinoma(97;0.0344)|BRCA - Breast invasive adenocarcinoma(99;0.0908)															---	---	---	---
Unknown	0	broad.mit.edu	37	17	78280997	78280997	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:78280997G>A	uc002jyf.2	+	13	2640	c.2497G>A	c.(2497-2499)GAC>AAC	p.D833N	uc002jyg.1_Missense_Mutation_p.D564N	NM_020954	NP_066005			hypothetical protein LOC57714																														---	---	---	---
Unknown	0	broad.mit.edu	37	17	78293144	78293144	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:78293144C>T	uc002jyf.2	+	17	3199	c.3056C>T	c.(3055-3057)TCG>TTG	p.S1019L	uc002jyg.1_Intron	NM_020954	NP_066005			hypothetical protein LOC57714																														---	---	---	---
AZI1	22994	broad.mit.edu	37	17	79167877	79167877	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:79167877G>A	uc002jzp.1	-	18	2379	c.2179C>T	c.(2179-2181)CGG>TGG	p.R727W	AZI1_uc002jzm.1_Missense_Mutation_p.R154W|AZI1_uc002jzn.1_Missense_Mutation_p.R724W|AZI1_uc002jzo.1_Missense_Mutation_p.R724W|AZI1_uc010wum.1_Missense_Mutation_p.R727W|AZI1_uc002jzq.2_5'UTR	NM_014984	NP_055799	Q9UPN4	AZI1_HUMAN	5-azacytidine induced 1 isoform a	727					cell differentiation|G2/M transition of mitotic cell cycle|multicellular organismal development|spermatogenesis	centrosome|cytosol|intracellular membrane-bounded organelle				central_nervous_system(2)|large_intestine(1)|ovary(1)	4	all_neural(118;0.0804)|Melanoma(429;0.242)		BRCA - Breast invasive adenocarcinoma(99;0.0272)|OV - Ovarian serous cystadenocarcinoma(97;0.117)															---	---	---	---
P4HB	5034	broad.mit.edu	37	17	79803049	79803049	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:79803049C>T	uc002kbn.1	-	10	1614	c.1417G>A	c.(1417-1419)GGT>AGT	p.G473S	P4HB_uc002kbl.1_Missense_Mutation_p.G150S|P4HB_uc002kbm.1_Missense_Mutation_p.G150S	NM_000918	NP_000909	P07237	PDIA1_HUMAN	prolyl 4-hydroxylase, beta subunit precursor	473	Thioredoxin 2.				cell redox homeostasis|glycerol ether metabolic process|lipid metabolic process|lipoprotein metabolic process|peptidyl-proline hydroxylation to 4-hydroxy-L-proline	cell surface|endoplasmic reticulum lumen|ER-Golgi intermediate compartment|extracellular region|melanosome|plasma membrane	electron carrier activity|procollagen-proline 4-dioxygenase activity|protein disulfide isomerase activity|protein disulfide oxidoreductase activity				0	all_neural(118;0.0878)|Ovarian(332;0.12)		BRCA - Breast invasive adenocarcinoma(99;0.013)|OV - Ovarian serous cystadenocarcinoma(97;0.0509)															---	---	---	---
FASN	2194	broad.mit.edu	37	17	80044937	80044937	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:80044937T>C	uc002kdu.2	-	21	3533	c.3416A>G	c.(3415-3417)CAA>CGA	p.Q1139R	FASN_uc002kdw.1_Missense_Mutation_p.Q355R	NM_004104	NP_004095	P49327	FAS_HUMAN	fatty acid synthase	1139					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)													---	---	---	---
FOXK2	3607	broad.mit.edu	37	17	80540637	80540637	+	Silent	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:80540637C>T	uc002kfn.2	+	5	1101	c.930C>T	c.(928-930)CTC>CTT	p.L310L	FOXK2_uc002kfm.1_Silent_p.L310L|FOXK2_uc010diu.2_Intron	NM_004514	NP_004505	Q01167	FOXK2_HUMAN	forkhead box K2	310	DNA-binding; major groove.|Fork-head.	Magnesium; via carbonyl oxygen.			embryo development|pattern specification process|regulation of sequence-specific DNA binding transcription factor activity|regulation of transcription from RNA polymerase II promoter|tissue development	transcription factor complex	DNA bending activity|double-stranded DNA binding|magnesium ion 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	Breast(20;0.00106)|all_neural(118;0.0952)		OV - Ovarian serous cystadenocarcinoma(97;0.0371)|BRCA - Breast invasive adenocarcinoma(99;0.0415)															---	---	---	---
USP14	9097	broad.mit.edu	37	18	198068	198068	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:198068G>A	uc002kkf.1	+	9	913	c.697G>A	c.(697-699)GCA>ACA	p.A233T	USP14_uc002kkg.1_Missense_Mutation_p.A198T|USP14_uc010wyr.1_Missense_Mutation_p.A222T	NM_005151	NP_005142	P54578	UBP14_HUMAN	ubiquitin specific protease 14 isoform a	233					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)																---	---	---	---
ADCYAP1	116	broad.mit.edu	37	18	905450	905450	+	Silent	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:905450C>T	uc010dkg.2	+	2	182	c.63C>T	c.(61-63)AGC>AGT	p.S21S	ADCYAP1_uc010dkh.2_Silent_p.S21S	NM_001099733	NP_001093203	P18509	PACA_HUMAN	adenylate cyclase activating polypeptide	21					activation of adenylate cyclase activity|cell-cell signaling|female pregnancy|nerve growth factor receptor signaling pathway|regulation of G-protein coupled receptor protein signaling pathway	extracellular region|soluble fraction	neuropeptide hormone activity|peptide hormone receptor binding				0																		---	---	---	---
SMCHD1	23347	broad.mit.edu	37	18	2694677	2694677	+	Nonsense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:2694677G>A	uc002klm.3	+	8	1215	c.1026G>A	c.(1024-1026)TGG>TGA	p.W342*		NM_015295	NP_056110	A6NHR9	SMHD1_HUMAN	structural maintenance of chromosomes flexible	342					chromosome organization		ATP binding				0																		---	---	---	---
DLGAP1	9229	broad.mit.edu	37	18	3729307	3729307	+	Silent	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:3729307C>T	uc002kmf.2	-	4	1486	c.1419G>A	c.(1417-1419)TCG>TCA	p.S473S	DLGAP1_uc010wyz.1_Silent_p.S473S|DLGAP1_uc002kme.1_Silent_p.S171S|DLGAP1_uc010dkn.2_Silent_p.S171S|DLGAP1_uc010wyw.1_Silent_p.S179S|DLGAP1_uc010wyx.1_Silent_p.S185S|DLGAP1_uc010wyy.1_Silent_p.S185S|DLGAP1_uc002kmg.2_Silent_p.S171S|DLGAP1_uc002kmk.2_Silent_p.S473S	NM_004746	NP_004737	O14490	DLGP1_HUMAN	discs large homolog-associated protein 1 isoform	473					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	3879216	3879216	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:3879216C>T	uc002kmf.2	-	1	920	c.853G>A	c.(853-855)GTG>ATG	p.V285M	DLGAP1_uc010wyz.1_Missense_Mutation_p.V285M|DLGAP1_uc002kmk.2_Missense_Mutation_p.V285M|uc002kml.1_Intron	NM_004746	NP_004737	O14490	DLGP1_HUMAN	discs large homolog-associated protein 1 isoform	285					synaptic transmission	cell junction|postsynaptic density|postsynaptic membrane				ovary(2)|pancreas(1)|skin(1)	4		Colorectal(8;0.0257)																---	---	---	---
ZFP161	7541	broad.mit.edu	37	18	5291912	5291912	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:5291912A>G	uc002kmq.2	-	4	456	c.295T>C	c.(295-297)TCC>CCC	p.S99P	ZFP161_uc002kmr.2_Missense_Mutation_p.S99P|ZFP161_uc010dkp.2_Missense_Mutation_p.S99P	NM_003409	NP_003400	O43829	ZF161_HUMAN	zinc finger protein 161 homolog	99	BTB.				negative regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1																		---	---	---	---
LAMA1	284217	broad.mit.edu	37	18	6995426	6995426	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:6995426T>C	uc002knm.2	-	34	4920	c.4826A>G	c.(4825-4827)AAT>AGT	p.N1609S	LAMA1_uc010wzj.1_Missense_Mutation_p.N1085S	NM_005559	NP_005550	P25391	LAMA1_HUMAN	laminin, alpha 1 precursor	1609	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	7002329	7002329	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:7002329T>C	uc002knm.2	-	30	4410	c.4316A>G	c.(4315-4317)TAC>TGC	p.Y1439C	LAMA1_uc010wzj.1_Missense_Mutation_p.Y915C	NM_005559	NP_005550	P25391	LAMA1_HUMAN	laminin, alpha 1 precursor	1439	Laminin EGF-like 15.				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)													---	---	---	---
PTPRM	5797	broad.mit.edu	37	18	8376531	8376531	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:8376531T>C	uc002knn.3	+	24	3862	c.3359T>C	c.(3358-3360)GTC>GCC	p.V1120A	PTPRM_uc010dkv.2_Missense_Mutation_p.V1133A|PTPRM_uc010wzl.1_Missense_Mutation_p.V907A	NM_002845	NP_002836	P28827	PTPRM_HUMAN	protein tyrosine phosphatase, receptor type, M	1120	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)																---	---	---	---
KIAA0802	23255	broad.mit.edu	37	18	8784510	8784510	+	Missense_Mutation	SNP	C	T	T	rs147236744	byFrequency	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:8784510C>T	uc002knr.2	+	6	1542	c.1400C>T	c.(1399-1401)ACG>ATG	p.T467M	KIAA0802_uc002knq.2_Missense_Mutation_p.T467M|KIAA0802_uc010dkw.1_Missense_Mutation_p.T305M	NM_015210	NP_056025	Q9Y4B5	CC165_HUMAN	hypothetical protein LOC23255	818	Potential.										0																		---	---	---	---
VAPA	9218	broad.mit.edu	37	18	9914310	9914310	+	Silent	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:9914310G>A	uc002kok.2	+	1	356	c.57G>A	c.(55-57)CCG>CCA	p.P19P	VAPA_uc002koj.2_Silent_p.P19P	NM_194434	NP_919415	Q9P0L0	VAPA_HUMAN	vesicle-associated membrane protein-associated	19	Cytoplasmic (Potential).|MSP.				cell death|cellular membrane fusion|neuron projection development|positive regulation of I-kappaB kinase/NF-kappaB cascade|protein localization in endoplasmic reticulum|sphingolipid metabolic process	endoplasmic reticulum membrane|integral to membrane|plasma membrane|vesicle	protein heterodimerization activity|signal transducer activity|structural molecule activity				0																		---	---	---	---
CIDEA	1149	broad.mit.edu	37	18	12277149	12277149	+	Silent	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:12277149C>T	uc002kqt.3	+	5	605	c.540C>T	c.(538-540)TCC>TCT	p.S180S	CIDEA_uc002kqu.3_Silent_p.S214S|CIDEA_uc010dlc.2_RNA	NM_001279	NP_001270	O60543	CIDEA_HUMAN	cell death-inducing DFFA-like effector a isoform	180					DNA damage response, signal transduction resulting in induction of apoptosis|DNA fragmentation involved in apoptotic nuclear change|lipid metabolic process|lipid storage|negative regulation of apoptosis|negative regulation of cytokine secretion|negative regulation of lipid catabolic process|negative regulation of transforming growth factor beta receptor signaling pathway|negative regulation of tumor necrosis factor production|positive regulation of sequestering of triglyceride|temperature homeostasis	mitochondrial envelope|nucleus	protein homodimerization activity			ovary(1)|central_nervous_system(1)	2																		---	---	---	---
TUBB6	84617	broad.mit.edu	37	18	12325235	12325235	+	Silent	SNP	G	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:12325235G>T	uc002kqw.2	+	4	492	c.447G>T	c.(445-447)ACG>ACT	p.T149T	TUBB6_uc002kqv.2_Silent_p.T77T|TUBB6_uc010dld.2_RNA|TUBB6_uc002kqx.2_Silent_p.T112T|TUBB6_uc002kqy.2_Intron	NM_032525	NP_115914	Q9BUF5	TBB6_HUMAN	tubulin, beta 6	149					'de novo' posttranslational protein folding|microtubule-based movement|protein polymerization	cytoplasm|microtubule	GTP binding|GTPase activity|structural molecule activity				0				READ - Rectum adenocarcinoma(1;0.0649)														---	---	---	---
NPC1	4864	broad.mit.edu	37	18	21140242	21140242	+	Silent	SNP	C	T	T	rs146105340		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:21140242C>T	uc002kum.3	-	6	1108	c.834G>A	c.(832-834)GCG>GCA	p.A278A	NPC1_uc010xaz.1_Silent_p.A62A|NPC1_uc010xba.1_Silent_p.A123A	NM_000271	NP_000262	O15118	NPC1_HUMAN	Niemann-Pick disease, type C1 precursor	278	Helical; (Potential).				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)																	---	---	---	---
LAMA3	3909	broad.mit.edu	37	18	21402312	21402312	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:21402312G>A	uc002kuq.2	+	20	2487	c.2401G>A	c.(2401-2403)GGC>AGC	p.G801S	LAMA3_uc002kur.2_Missense_Mutation_p.G801S	NM_198129	NP_937762	Q16787	LAMA3_HUMAN	laminin alpha 3 subunit isoform 1	801	Domain IV 1 (domain IV B).				cell adhesion|epidermis development|hemidesmosome assembly|regulation of cell adhesion|regulation of cell migration|regulation of embryonic development	laminin-1 complex	receptor binding|structural molecule activity			ovary(8)|skin(2)|central_nervous_system(1)	11	all_cancers(21;7.81e-05)|all_epithelial(16;4.45e-07)|Lung NSC(20;0.00156)|all_lung(20;0.00508)|Colorectal(14;0.0202)|Ovarian(20;0.17)				Alteplase(DB00009)|Anistreplase(DB00029)|Reteplase(DB00015)|Tenecteplase(DB00031)													---	---	---	---
LAMA3	3909	broad.mit.edu	37	18	21526163	21526163	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:21526163C>T	uc002kuq.2	+	70	9352	c.9266C>T	c.(9265-9267)GCC>GTC	p.A3089V	LAMA3_uc002kur.2_Missense_Mutation_p.A3033V|LAMA3_uc002kus.3_Missense_Mutation_p.A1480V|LAMA3_uc002kut.3_Missense_Mutation_p.A1424V	NM_198129	NP_937762	Q16787	LAMA3_HUMAN	laminin alpha 3 subunit isoform 1	3089	Laminin G-like 4.				cell adhesion|epidermis development|hemidesmosome assembly|regulation of cell adhesion|regulation of cell migration|regulation of embryonic development	laminin-1 complex	receptor binding|structural molecule activity			ovary(8)|skin(2)|central_nervous_system(1)	11	all_cancers(21;7.81e-05)|all_epithelial(16;4.45e-07)|Lung NSC(20;0.00156)|all_lung(20;0.00508)|Colorectal(14;0.0202)|Ovarian(20;0.17)				Alteplase(DB00009)|Anistreplase(DB00029)|Reteplase(DB00015)|Tenecteplase(DB00031)													---	---	---	---
CABYR	26256	broad.mit.edu	37	18	21739839	21739839	+	3'UTR	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:21739839T>C	uc002kux.2	+	5					CABYR_uc010xbb.1_3'UTR|CABYR_uc002kuy.2_Silent_p.A315A|CABYR_uc002kuz.2_Intron|CABYR_uc002kva.2_3'UTR|CABYR_uc002kvb.2_Silent_p.A217A|CABYR_uc002kvc.2_Silent_p.A315A|CABYR_uc010dlw.2_Intron	NM_012189	NP_036321			calcium-binding tyrosine						ciliary or flagellar motility|signal transduction|sperm capacitation	cytoplasm|cytoskeleton|flagellum|motile cilium|nucleus	calcium ion binding|cAMP-dependent protein kinase regulator activity|enzyme binding|protein heterodimerization activity|SH3 domain binding				0	all_cancers(21;9.13e-05)|all_epithelial(16;5.49e-07)|Lung NSC(20;0.00171)|all_lung(20;0.0055)|Colorectal(14;0.0305)|Ovarian(20;0.17)																	---	---	---	---
CDH2	1000	broad.mit.edu	37	18	25572760	25572760	+	Silent	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:25572760A>G	uc002kwg.2	-	9	1662	c.1203T>C	c.(1201-1203)GCT>GCC	p.A401A	CDH2_uc010xbn.1_Silent_p.A370A	NM_001792	NP_001783	P19022	CADH2_HUMAN	cadherin 2, type 1 preproprotein	401	Extracellular (Potential).|Cadherin 3.				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																		---	---	---	---
DSC2	1824	broad.mit.edu	37	18	28648306	28648306	+	Intron	SNP	G	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:28648306G>C	uc002kwl.3	-						DSC2_uc002kwk.3_Missense_Mutation_p.S838C	NM_024422	NP_077740			desmocollin 2 isoform Dsc2a preproprotein						homophilic cell adhesion	desmosome|integral to membrane	calcium ion binding			ovary(2)|skin(1)	3			OV - Ovarian serous cystadenocarcinoma(10;0.0241)															---	---	---	---
DSG2	1829	broad.mit.edu	37	18	29126099	29126099	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:29126099C>T	uc002kwu.3	+	15	2938	c.2750C>T	c.(2749-2751)GCG>GTG	p.A917V	uc002kwv.3_Intron	NM_001943	NP_001934	Q14126	DSG2_HUMAN	desmoglein 2 preproprotein	917	Desmoglein repeat 2.|Cytoplasmic (Potential).				cellular component disassembly involved in apoptosis|homophilic cell adhesion	desmosome|integral to membrane	calcium ion binding			central_nervous_system(5)|ovary(2)|breast(1)|skin(1)	9			OV - Ovarian serous cystadenocarcinoma(10;0.0068)															---	---	---	---
C18orf34	374864	broad.mit.edu	37	18	30846988	30846988	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:30846988T>G	uc002kxn.2	-	13	1443	c.1301A>C	c.(1300-1302)GAT>GCT	p.D434A	C18orf34_uc010dme.1_5'UTR|C18orf34_uc010xbr.1_Missense_Mutation_p.D434A|C18orf34_uc010dmf.1_Intron|C18orf34_uc002kxo.2_Missense_Mutation_p.D434A|C18orf34_uc002kxp.2_Missense_Mutation_p.D434A	NM_001105528	NP_001098998	Q5BJE1	CR034_HUMAN	hypothetical protein LOC374864 isoform 1	434										ovary(1)	1																		---	---	---	---
ASXL3	80816	broad.mit.edu	37	18	31323668	31323668	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:31323668C>A	uc010dmg.1	+	12	3911	c.3856C>A	c.(3856-3858)CAG>AAG	p.Q1286K	ASXL3_uc002kxq.2_Missense_Mutation_p.Q993K	NM_030632	NP_085135	Q9C0F0	ASXL3_HUMAN	additional sex combs like 3	1286	Ser-rich.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	metal ion binding			ovary(2)|pancreas(1)	3																		---	---	---	---
NOL4	8715	broad.mit.edu	37	18	31709979	31709979	+	Silent	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:31709979G>A	uc010dmi.2	-	2	499	c.270C>T	c.(268-270)GGC>GGT	p.G90G	NOL4_uc002kxr.3_5'UTR|NOL4_uc010xbt.1_Silent_p.G16G|NOL4_uc010dmh.2_Silent_p.G16G|NOL4_uc010xbu.1_Silent_p.G90G|NOL4_uc002kxt.3_Silent_p.G90G|NOL4_uc010xbw.1_5'UTR	NM_003787	NP_003778	O94818	NOL4_HUMAN	nucleolar protein 4	90						nucleolus	RNA binding			ovary(3)	3																		---	---	---	---
DTNA	1837	broad.mit.edu	37	18	32418091	32418091	+	Silent	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:32418091C>T	uc010dmn.1	+	11	1129	c.1128C>T	c.(1126-1128)AAC>AAT	p.N376N	DTNA_uc010xbx.1_Intron|DTNA_uc002kxv.3_Intron|DTNA_uc002kxw.2_Intron|DTNA_uc010dmj.2_Intron|DTNA_uc002kxz.2_Intron|DTNA_uc002kxy.2_Intron|DTNA_uc010dml.2_Intron|DTNA_uc002kyb.3_Silent_p.N373N|DTNA_uc010dmm.2_Silent_p.N376N|DTNA_uc010xby.1_Intron|DTNA_uc010dmo.2_Intron|DTNA_uc002kyd.3_Intron|DTNA_uc010xbz.1_Silent_p.N85N|DTNA_uc010xca.1_Intron|DTNA_uc002kye.2_Silent_p.N55N	NM_001390	NP_001381	Q9Y4J8	DTNA_HUMAN	dystrobrevin alpha isoform 1	376					neuromuscular synaptic transmission|signal transduction|striated muscle contraction	cell junction|cytoplasm|synapse	calcium ion binding|protein binding|zinc ion binding				0																		---	---	---	---
ZNF271	10778	broad.mit.edu	37	18	32887409	32887409	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:32887409G>T	uc002kyq.3	+	3	1813	c.821G>T	c.(820-822)GGG>GTG	p.G274V	ZNF271_uc002kyp.3_Missense_Mutation_p.G274V|ZNF271_uc002kyr.3_Missense_Mutation_p.G274V	NR_024565				SubName: Full=cDNA FLJ13394 fis, clone PLACE1001304, highly similar to Homo sapiens zinc finger protein 271 (ZNF271), mRNA;												0																		---	---	---	---
ELP2	55250	broad.mit.edu	37	18	33725927	33725927	+	Silent	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:33725927G>A	uc002kzk.1	+	10	919	c.909G>A	c.(907-909)CAG>CAA	p.Q303Q	ELP2_uc010xcg.1_Silent_p.Q368Q|ELP2_uc002kzl.1_RNA|ELP2_uc002kzm.1_Silent_p.Q277Q|ELP2_uc010xch.1_Silent_p.Q342Q|ELP2_uc002kzn.1_Silent_p.Q277Q|ELP2_uc002kzo.1_Silent_p.Q233Q	NM_018255	NP_060725	Q6IA86	ELP2_HUMAN	elongator protein 2	303	WD 6.				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	33783079	33783079	+	Silent	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:33783079T>C	uc002kzq.3	+	5	968	c.945T>C	c.(943-945)TTT>TTC	p.F315F		NM_017947	NP_060417	Q96EN8	MOCOS_HUMAN	molybdenum cofactor sulfurase	315					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)													---	---	---	---
PIK3C3	5289	broad.mit.edu	37	18	39542552	39542552	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:39542552C>T	uc002lap.2	+	3	414	c.356C>T	c.(355-357)GCA>GTA	p.A119V	PIK3C3_uc010xcl.1_Missense_Mutation_p.A56V|PIK3C3_uc002lao.2_Missense_Mutation_p.A119V	NM_002647	NP_002638	Q8NEB9	PK3C3_HUMAN	catalytic phosphatidylinositol 3-kinase 3	119					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)			---	---	---	---
PIK3C3	5289	broad.mit.edu	37	18	39584340	39584340	+	Missense_Mutation	SNP	A	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:39584340A>C	uc002lap.2	+	10	1063	c.1005A>C	c.(1003-1005)AAA>AAC	p.K335N	PIK3C3_uc010xcl.1_Missense_Mutation_p.K272N	NM_002647	NP_002638	Q8NEB9	PK3C3_HUMAN	catalytic phosphatidylinositol 3-kinase 3	335				FLKCVN -> ILTSVI (in Ref. 1; CAA87094).	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)			---	---	---	---
SYT4	6860	broad.mit.edu	37	18	40853540	40853540	+	Intron	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:40853540A>G	uc002law.2	-						SYT4_uc010dng.2_Intron|SYT4_uc010xcm.1_Intron|SYT4_uc010dnh.2_Intron	NM_020783	NP_065834			synaptotagmin IV							cell junction|integral to membrane|synaptic vesicle membrane	transporter activity			skin(5)	5																		---	---	---	---
SETBP1	26040	broad.mit.edu	37	18	42643209	42643209	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:42643209G>A	uc010dni.2	+	6	4633	c.4337G>A	c.(4336-4338)GGC>GAC	p.G1446D		NM_015559	NP_056374	Q9Y6X0	SETBP_HUMAN	SET binding protein 1 isoform a	1446						nucleus	DNA binding			upper_aerodigestive_tract(2)|large_intestine(1)	3				Colorectal(1;0.0622)|COAD - Colon adenocarcinoma(74;0.201)										Schinzel-Giedion_syndrome				---	---	---	---
KIAA1632	57724	broad.mit.edu	37	18	43446869	43446869	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:43446869T>C	uc002lbm.2	-	38	6615	c.6515A>G	c.(6514-6516)TAC>TGC	p.Y2172C	KIAA1632_uc010xcq.1_Missense_Mutation_p.Y726C|KIAA1632_uc010xcr.1_RNA|KIAA1632_uc010xcs.1_RNA|KIAA1632_uc002lbn.2_Missense_Mutation_p.Y1047C	NM_020964	NP_066015	Q9HCE0	EPG5_HUMAN	hypothetical protein LOC57724	2172					autophagy						0																		---	---	---	---
KIAA1632	57724	broad.mit.edu	37	18	43534980	43534980	+	Missense_Mutation	SNP	T	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:43534980T>A	uc002lbm.2	-	2	488	c.388A>T	c.(388-390)ACT>TCT	p.T130S	KIAA1632_uc002lbo.1_Missense_Mutation_p.T130S	NM_020964	NP_066015	Q9HCE0	EPG5_HUMAN	hypothetical protein LOC57724	130					autophagy						0																		---	---	---	---
RNF165	494470	broad.mit.edu	37	18	44013298	44013298	+	Silent	SNP	C	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:44013298C>A	uc002lcb.1	+	2	258	c.207C>A	c.(205-207)GCC>GCA	p.A69A	RNF165_uc002lby.1_Silent_p.A2A|RNF165_uc010dnn.1_Intron	NM_152470	NP_689683	Q6ZSG1	RN165_HUMAN	ring finger protein 165	69							zinc ion binding				0				READ - Rectum adenocarcinoma(1;0.0873)														---	---	---	---
TCEB3B	51224	broad.mit.edu	37	18	44560728	44560728	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:44560728C>T	uc002lcr.1	-	1	1261	c.908G>A	c.(907-909)AGT>AAT	p.S303N	KATNAL2_uc010dnq.1_Intron|KATNAL2_uc002lco.2_Intron|KATNAL2_uc002lcp.3_Intron	NM_016427	NP_057511	Q8IYF1	ELOA2_HUMAN	elongin A2	303					regulation of transcription elongation, DNA-dependent|transcription from RNA polymerase II promoter	integral to membrane|nucleus	DNA binding			ovary(2)|large_intestine(1)|pancreas(1)	4																		---	---	---	---
KATNAL2	83473	broad.mit.edu	37	18	44625640	44625640	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:44625640G>A	uc002lco.2	+	13	1216	c.1022G>A	c.(1021-1023)CGC>CAC	p.R341H	KATNAL2_uc002lcp.3_Missense_Mutation_p.R268H	NM_031303	NP_112593	Q8IYT4	KATL2_HUMAN	katanin p60 subunit A-like 2	413						cytoplasm|microtubule	ATP binding|microtubule-severing ATPase activity			ovary(1)|skin(1)|central_nervous_system(1)|pancreas(1)	4																		---	---	---	---
MYO5B	4645	broad.mit.edu	37	18	47527696	47527696	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:47527696C>T	uc002leb.2	-	5	829	c.541G>A	c.(541-543)GCC>ACC	p.A181T	MYO5B_uc002lec.1_Missense_Mutation_p.A180T	NM_001080467	NP_001073936	Q9ULV0	MYO5B_HUMAN	myosin VB	181	Myosin head-like.				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)														---	---	---	---
MAPK4	5596	broad.mit.edu	37	18	48252501	48252501	+	Silent	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:48252501C>T	uc002lev.2	+	5	2023	c.1023C>T	c.(1021-1023)GCC>GCT	p.A341A	MAPK4_uc010xdm.1_Silent_p.A130A|MAPK4_uc010doz.2_Intron	NM_002747	NP_002738	P31152	MK04_HUMAN	mitogen-activated protein kinase 4	341					cell cycle		ATP binding|MAP kinase activity			lung(4)|skin(2)	6		Colorectal(6;0.0297)		Colorectal(21;0.156)														---	---	---	---
DCC	1630	broad.mit.edu	37	18	50432690	50432690	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:50432690T>C	uc002lfe.1	+	3	1276	c.689T>C	c.(688-690)ATT>ACT	p.I230T	DCC_uc010xdr.1_Missense_Mutation_p.I78T	NM_005215	NP_005206	P43146	DCC_HUMAN	netrin receptor DCC precursor	230	Extracellular (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)														---	---	---	---
DCC	1630	broad.mit.edu	37	18	50589756	50589756	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:50589756G>T	uc002lfe.1	+	6	1654	c.1067G>T	c.(1066-1068)GGA>GTA	p.G356V	DCC_uc010xdr.1_Missense_Mutation_p.G204V|DCC_uc010dpf.1_Missense_Mutation_p.G11V	NM_005215	NP_005206	P43146	DCC_HUMAN	netrin receptor DCC precursor	356	Extracellular (Potential).|Ig-like C2-type 4.				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	50734156	50734156	+	Silent	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:50734156T>C	uc002lfe.1	+	11	2417	c.1830T>C	c.(1828-1830)ACT>ACC	p.T610T	DCC_uc010xdr.1_Silent_p.T458T|DCC_uc010dpf.1_Silent_p.T265T	NM_005215	NP_005206	P43146	DCC_HUMAN	netrin receptor DCC precursor	610	Extracellular (Potential).|Fibronectin type-III 2.				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)														---	---	---	---
STARD6	147323	broad.mit.edu	37	18	51851080	51851080	+	Silent	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:51851080A>G	uc010xdt.1	-	6	645	c.645T>C	c.(643-645)CAT>CAC	p.H215H		NM_139171	NP_631910	P59095	STAR6_HUMAN	START domain containing protein 6	215					lipid transport		lipid binding			ovary(1)	1				Colorectal(16;0.021)|READ - Rectum adenocarcinoma(59;0.188)														---	---	---	---
CDH20	28316	broad.mit.edu	37	18	59217329	59217329	+	Silent	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:59217329A>G	uc010dps.1	+	10	1779	c.1767A>G	c.(1765-1767)ACA>ACG	p.T589T	CDH20_uc002lif.2_Silent_p.T583T	NM_031891	NP_114097	Q9HBT6	CAD20_HUMAN	cadherin 20, type 2 preproprotein	589	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)																---	---	---	---
TNFRSF11A	8792	broad.mit.edu	37	18	60027284	60027284	+	Splice_Site	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:60027284T>C	uc002lin.2	+	6	654	c.616_splice	c.e6+2	p.E206_splice	TNFRSF11A_uc010dpv.2_Splice_Site_p.G206_splice	NM_003839	NP_003830			tumor necrosis factor receptor superfamily,						adaptive immune response|cell-cell signaling|circadian temperature homeostasis|monocyte chemotaxis|osteoclast differentiation|positive regulation of cell proliferation|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 JUN kinase activity|positive regulation of NF-kappaB transcription factor activity|response to interleukin-1|response to lipopolysaccharide	external side of plasma membrane|integral to membrane	metal ion binding|tumor necrosis factor receptor activity			breast(2)|lung(1)	3		Colorectal(73;0.188)												Paget_Disease_of_Bone				---	---	---	---
SERPINB5	5268	broad.mit.edu	37	18	61166461	61166461	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:61166461C>A	uc002liz.3	+	6	818	c.676C>A	c.(676-678)CTC>ATC	p.L226I		NM_002639	NP_002630	P36952	SPB5_HUMAN	serine (or cysteine) proteinase inhibitor, clade	226					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	61262391	61262391	+	Silent	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:61262391G>A	uc002ljc.2	+	7	912	c.744G>A	c.(742-744)CTG>CTA	p.L248L	SERPINB13_uc002ljd.2_Silent_p.L112L|SERPINB13_uc010xep.1_Silent_p.L257L|SERPINB13_uc010xeq.1_Silent_p.L69L|SERPINB13_uc010xer.1_Silent_p.L69L	NM_012397	NP_036529	Q9UIV8	SPB13_HUMAN	serine (or cysteine) proteinase inhibitor, clade	248					regulation of proteolysis|response to UV	cytoplasm|extracellular region	serine-type endopeptidase inhibitor activity			ovary(1)	1																		---	---	---	---
SERPINB2	5055	broad.mit.edu	37	18	61569106	61569106	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:61569106G>A	uc010xeu.1	+	7	1001	c.668G>A	c.(667-669)CGT>CAT	p.R223H	SERPINB2_uc002ljo.2_Missense_Mutation_p.R223H|SERPINB2_uc010dqh.2_Missense_Mutation_p.R153H|SERPINB2_uc002ljp.1_Missense_Mutation_p.R28H|SERPINB2_uc002ljq.1_Missense_Mutation_p.R28H	NM_001143818	NP_001137290	P05120	PAI2_HUMAN	serine (or cysteine) proteinase inhibitor, clade	223					anti-apoptosis|blood coagulation|fibrinolysis|regulation of proteolysis	extracellular space|Golgi apparatus|plasma membrane	serine-type endopeptidase inhibitor activity			lung(1)|skin(1)	2		Esophageal squamous(42;0.131)			Alteplase(DB00009)|Anistreplase(DB00029)|Reteplase(DB00015)|Tenecteplase(DB00031)|Urokinase(DB00013)													---	---	---	---
SERPINB8	5271	broad.mit.edu	37	18	61654178	61654178	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:61654178T>C	uc002ljv.2	+	7	960	c.791T>C	c.(790-792)GTT>GCT	p.V264A	SERPINB8_uc002lju.2_Missense_Mutation_p.V264A|SERPINB8_uc010xex.1_Missense_Mutation_p.V82A	NM_198833	NP_942130	P50452	SPB8_HUMAN	serine (or cysteine) proteinase inhibitor, clade	264					regulation of proteolysis	cytosol	protein binding|serine-type endopeptidase inhibitor activity			skin(1)	1		Esophageal squamous(42;0.129)																---	---	---	---
CCDC102B	79839	broad.mit.edu	37	18	66504559	66504559	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:66504559T>C	uc002lkk.2	+	4	782	c.559T>C	c.(559-561)TAT>CAT	p.Y187H	CCDC102B_uc002lki.2_Missense_Mutation_p.Y187H|CCDC102B_uc002lkj.1_Missense_Mutation_p.Y187H	NM_001093729	NP_001087198	Q68D86	C102B_HUMAN	coiled-coil domain containing 102B	187										ovary(1)|lung(1)|skin(1)	3		Esophageal squamous(42;0.0559)|Colorectal(73;0.0604)																---	---	---	---
CYB5A	1528	broad.mit.edu	37	18	71922998	71922998	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:71922998T>C	uc002lli.2	-	4	412	c.301A>G	c.(301-303)ACT>GCT	p.T101A	CYB5A_uc002llh.2_3'UTR	NM_148923	NP_683725	P00167	CYB5_HUMAN	cytochrome b-5 isoform 1	101					electron transport chain|water-soluble vitamin metabolic process	endoplasmic reticulum membrane|integral to membrane|microsome|mitochondrial outer membrane	aldo-keto reductase (NADP) activity|cytochrome-c oxidase activity|enzyme binding|heme binding				0		Esophageal squamous(42;0.0749)|Prostate(75;0.157)|Melanoma(33;0.211)			Methoxyflurane(DB01028)													---	---	---	---
CNDP2	55748	broad.mit.edu	37	18	72173245	72173245	+	Silent	SNP	C	T	T	rs145623404		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:72173245C>T	uc002llm.1	+	4	528	c.366C>T	c.(364-366)GAC>GAT	p.D122D	CNDP2_uc002lln.1_Intron|CNDP2_uc002llo.2_Silent_p.D122D|CNDP2_uc002llp.1_5'Flank	NM_018235	NP_060705	Q96KP4	CNDP2_HUMAN	CNDP dipeptidase 2	122						cytoplasm	carboxypeptidase activity|metal ion binding|metallopeptidase activity|protein binding|tripeptidase activity			ovary(2)|skin(1)	3		Esophageal squamous(42;0.131)|Prostate(75;0.173)		BRCA - Breast invasive adenocarcinoma(31;0.22)														---	---	---	---
ZNF407	55628	broad.mit.edu	37	18	72344963	72344963	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:72344963T>C	uc002llw.2	+	1	2045	c.1988T>C	c.(1987-1989)TTG>TCG	p.L663S	ZNF407_uc010xfc.1_Missense_Mutation_p.L663S|ZNF407_uc010dqu.1_Missense_Mutation_p.L663S|ZNF407_uc002llu.2_Missense_Mutation_p.L662S	NM_017757	NP_060227	Q9C0G0	ZN407_HUMAN	zinc finger protein 407 isoform 1	663					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(2)	2		Esophageal squamous(42;0.131)|Prostate(75;0.173)		BRCA - Breast invasive adenocarcinoma(31;0.184)														---	---	---	---
ATP9B	374868	broad.mit.edu	37	18	77090050	77090050	+	Silent	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:77090050C>T	uc002lmx.2	+	17	1988	c.1974C>T	c.(1972-1974)GGC>GGT	p.G658G	ATP9B_uc002lmw.1_Silent_p.G658G|ATP9B_uc002lmz.1_Silent_p.G352G	NM_198531	NP_940933	O43861	ATP9B_HUMAN	ATPase, class II, type 9B	658	Cytoplasmic (Potential).				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	77287542	77287542	+	Nonsense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:77287542C>T	uc010xfg.1	+	10	3250	c.2797C>T	c.(2797-2799)CGA>TGA	p.R933*	NFATC1_uc002lnd.2_3'UTR|NFATC1_uc002lne.2_3'UTR|NFATC1_uc010xfh.1_Nonsense_Mutation_p.R703*|NFATC1_uc010xfj.1_Nonsense_Mutation_p.R461*|NFATC1_uc002lnf.2_Nonsense_Mutation_p.R920*|NFATC1_uc002lng.2_3'UTR|NFATC1_uc010xfk.1_Nonsense_Mutation_p.R690*|NFATC1_uc010drc.2_RNA	NM_006162	NP_006153	O95644	NFAC1_HUMAN	nuclear factor of activated T-cells, cytosolic	933	Nuclear export signal.|Trans-activation domain B (TAD-B).				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)														---	---	---	---
CTDP1	9150	broad.mit.edu	37	18	77477994	77477994	+	Missense_Mutation	SNP	C	T	T	rs148053048		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:77477994C>T	uc002lnh.1	+	10	2542	c.2395C>T	c.(2395-2397)CGC>TGC	p.R799C	CTDP1_uc002lni.1_Missense_Mutation_p.R799C|CTDP1_uc010drd.1_Missense_Mutation_p.R799C	NM_004715	NP_004706	Q9Y5B0	CTDP1_HUMAN	CTD (carboxy-terminal domain, RNA polymerase II,	799					positive regulation of viral transcription|protein dephosphorylation|transcription elongation from RNA polymerase II promoter|viral reproduction	nucleoplasm	CTD phosphatase activity|DNA-directed RNA polymerase activity				0		Esophageal squamous(42;0.0157)|Melanoma(33;0.144)		OV - Ovarian serous cystadenocarcinoma(15;5.2e-06)|BRCA - Breast invasive adenocarcinoma(31;0.0277)														---	---	---	---
ADNP2	22850	broad.mit.edu	37	18	77894507	77894507	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:77894507C>T	uc002lnw.2	+	4	1666	c.1211C>T	c.(1210-1212)ACC>ATC	p.T404I		NM_014913	NP_055728	Q6IQ32	ADNP2_HUMAN	ADNP homeobox 2	404	Pro-rich.				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)														---	---	---	---
ODF3L2	284451	broad.mit.edu	37	19	463927	463927	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:463927G>A	uc002lor.2	-	4	1023	c.787C>T	c.(787-789)CGC>TGC	p.R263C	SHC2_uc002loq.3_5'Flank|ODF3L2_uc010drp.2_Missense_Mutation_p.R227C	NM_182577	NP_872383	Q3SX64	OD3L2_HUMAN	outer dense fiber of sperm tails 3-like 2	263	DUF1309 3.										0																		---	---	---	---
EFNA2	1943	broad.mit.edu	37	19	1298588	1298588	+	Nonsense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:1298588C>T	uc002lry.1	+	3	493	c.493C>T	c.(493-495)CGA>TGA	p.R165*		NM_001405	NP_001396	O43921	EFNA2_HUMAN	ephrin-A2 precursor	165					cell-cell signaling	anchored to membrane|plasma membrane	ephrin receptor binding				0		Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;7.93e-06)|all_lung(49;1.25e-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)														---	---	---	---
PCSK4	54760	broad.mit.edu	37	19	1481823	1481823	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:1481823C>T	uc002ltb.1	-	15	2265	c.2203G>A	c.(2203-2205)GCC>ACC	p.A735T	C19orf25_uc010xgn.1_5'Flank|C19orf25_uc002lsy.3_5'Flank|C19orf25_uc010dsk.2_5'Flank|C19orf25_uc010xgo.1_5'Flank|C19orf25_uc002lsx.1_5'Flank|PCSK4_uc002lsz.2_Missense_Mutation_p.A222T|PCSK4_uc002lta.2_3'UTR	NM_017573	NP_060043	Q6UW60	PCSK4_HUMAN	proprotein convertase subtilisin/kexin type 4	735					proteolysis	integral to membrane	serine-type endopeptidase activity				0		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)														---	---	---	---
MEX3D	399664	broad.mit.edu	37	19	1556528	1556528	+	Silent	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:1556528C>T	uc010dsn.2	-	2	990	c.990G>A	c.(988-990)GCG>GCA	p.A330A		NM_203304	NP_976049	Q86XN8	MEX3D_HUMAN	ring finger and KH domain containing 1	330	KH 2.				mRNA destabilization|posttranscriptional regulation of gene expression by mRNA localization|regulation of anti-apoptosis	nucleus|perinuclear region of cytoplasm	AU-rich element binding|zinc ion binding			lung(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)														---	---	---	---
C19orf36	113177	broad.mit.edu	37	19	2097640	2097640	+	Intron	SNP	C	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:2097640C>A	uc002luw.1	+						C19orf36_uc002lux.1_Intron|C19orf36_uc010xgw.1_Intron	NM_001039846	NP_001034935			hypothetical protein LOC113177 isoform 3							extracellular region					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)														---	---	---	---
AP3D1	8943	broad.mit.edu	37	19	2132531	2132531	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:2132531C>T	uc002luz.2	-	5	624	c.401G>A	c.(400-402)GGT>GAT	p.G134D	AP3D1_uc002luy.2_Missense_Mutation_p.G134D|AP3D1_uc002lva.2_Missense_Mutation_p.G134D	NM_003938	NP_003929	O14617	AP3D1_HUMAN	adaptor-related protein complex 3, delta 1	134					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)														---	---	---	---
AP3D1	8943	broad.mit.edu	37	19	2138702	2138702	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:2138702T>C	uc002luz.2	-	2	331	c.108A>G	c.(106-108)ATA>ATG	p.I36M	AP3D1_uc002luy.2_Missense_Mutation_p.I36M|AP3D1_uc002lva.2_Missense_Mutation_p.I36M	NM_003938	NP_003929	O14617	AP3D1_HUMAN	adaptor-related protein complex 3, delta 1	36	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)														---	---	---	---
SPPL2B	56928	broad.mit.edu	37	19	2291464	2291464	+	Intron	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:2291464C>T	uc010dsw.1	+						LINGO3_uc010dsx.1_Silent_p.L104L|uc002lvo.1_Nonsense_Mutation_p.Q93*					SubName: Full=Putative uncharacterized protein ENSP00000371624;							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)														---	---	---	---
SPPL2B	56928	broad.mit.edu	37	19	2353015	2353015	+	Silent	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:2353015G>A	uc002lvs.2	+	16	1667	c.1587G>A	c.(1585-1587)ACG>ACA	p.T529T	SPPL2B_uc002lvr.2_3'UTR	NM_152988	NP_694533	Q8TCT7	PSL1_HUMAN	signal peptide peptidase-like 2B isoform 2	529	Pro-rich.					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)														---	---	---	---
LMNB2	84823	broad.mit.edu	37	19	2438407	2438407	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:2438407C>T	uc002lvy.2	-	3	551	c.464G>A	c.(463-465)AGT>AAT	p.S155N	LMNB2_uc002lwa.1_Missense_Mutation_p.S175N	NM_032737	NP_116126	Q03252	LMNB2_HUMAN	lamin B2	155	Rod.|Coil 1B.					nuclear inner membrane	structural molecule activity			large_intestine(1)|ovary(1)	2		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)														---	---	---	---
GADD45B	4616	broad.mit.edu	37	19	2476521	2476521	+	Intron	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:2476521T>C	uc002lwb.1	+						GADD45B_uc010dtd.1_Intron|GADD45B_uc002lwc.1_5'UTR	NM_015675	NP_056490			growth arrest and DNA-damage-inducible, beta						activation of MAPKKK activity|apoptosis|cell differentiation|multicellular organismal development|response to stress						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)														---	---	---	---
CELF5	60680	broad.mit.edu	37	19	3282474	3282474	+	Silent	SNP	C	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:3282474C>A	uc002lxm.2	+	8	1054	c.1017C>A	c.(1015-1017)GCC>GCA	p.A339A	CELF5_uc002lxl.1_Silent_p.A339A|CELF5_uc010dtj.1_Silent_p.A314A|CELF5_uc010xhg.1_Silent_p.A225A|CELF5_uc002lxn.2_RNA	NM_021938	NP_068757	Q8N6W0	CELF5_HUMAN	bruno-like 5, RNA binding protein	339					mRNA processing	cytoplasm|nucleus	nucleotide binding|RNA binding			ovary(2)	2																		---	---	---	---
C19orf29	58509	broad.mit.edu	37	19	3623848	3623848	+	Silent	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:3623848G>A	uc002lyh.2	-	2	533	c.480C>T	c.(478-480)TTC>TTT	p.F160F	C19orf29_uc010dtn.2_5'Flank|C19orf29_uc002lyi.3_Silent_p.F160F|C19orf29_uc010dto.2_RNA	NM_001080543	NP_001074012	Q8WUQ7	CS029_HUMAN	chromosome 19 open reading frame 29	160	Potential.					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	3735632	3735632	+	Missense_Mutation	SNP	G	T	T	rs146458179		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:3735632G>T	uc010xhv.1	+	8	1154	c.1154G>T	c.(1153-1155)CGG>CTG	p.R385L	TJP3_uc010xhs.1_Missense_Mutation_p.R352L|TJP3_uc010xht.1_Missense_Mutation_p.R316L|TJP3_uc010xhu.1_Missense_Mutation_p.R361L|TJP3_uc010xhw.1_Missense_Mutation_p.R371L	NM_014428	NP_055243	O95049	ZO3_HUMAN	tight junction protein 3	366						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)														---	---	---	---
APBA3	9546	broad.mit.edu	37	19	3760205	3760205	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:3760205C>A	uc002lyp.1	-	2	235	c.58G>T	c.(58-60)GGG>TGG	p.G20W	MRPL54_uc002lyq.3_5'Flank	NM_004886	NP_004877	O96018	APBA3_HUMAN	amyloid beta (A4) precursor protein-binding,	20					intracellular signal transduction|protein transport	intracellular|membrane	protein binding				0		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.00467)|STAD - Stomach adenocarcinoma(1328;0.18)														---	---	---	---
MATK	4145	broad.mit.edu	37	19	3778984	3778984	+	Intron	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:3778984G>A	uc002lyt.2	-						MATK_uc002lyv.2_Intron|MATK_uc002lyu.2_Intron|MATK_uc010dtq.2_Intron	NM_139355	NP_647612			megakaryocyte-associated tyrosine kinase isoform						cell proliferation|mesoderm development|positive regulation of cell proliferation	cytoplasm|nucleus	ATP binding|non-membrane spanning protein tyrosine kinase activity			stomach(2)|ovary(1)|lung(1)|large_intestine(1)	5		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.00461)|STAD - Stomach adenocarcinoma(1328;0.18)														---	---	---	---
FSD1	79187	broad.mit.edu	37	19	4306033	4306033	+	Missense_Mutation	SNP	G	A	A	rs117912557	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:4306033G>A	uc002lzy.2	+	2	259	c.106G>A	c.(106-108)GTG>ATG	p.V36M	FSD1_uc010xie.1_Missense_Mutation_p.V23M|FSD1_uc010xif.1_Missense_Mutation_p.V10M|FSD1_uc002lzz.2_Missense_Mutation_p.V36M	NM_024333	NP_077309	Q9BTV5	FSD1_HUMAN	fibronectin type III and SPRY domain containing	36	Potential.				cell division|mitosis	cleavage furrow|microtubule|microtubule organizing center|nucleus				skin(1)	1				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.034)|STAD - Stomach adenocarcinoma(1328;0.18)														---	---	---	---
FEM1A	55527	broad.mit.edu	37	19	4793005	4793005	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:4793005G>A	uc002mbf.2	+	1	1278	c.1139G>A	c.(1138-1140)CGC>CAC	p.R380H	uc002mbg.1_RNA	NM_018708	NP_061178	Q9BSK4	FEM1A_HUMAN	fem-1 homolog a	380					regulation of ubiquitin-protein ligase activity	cytoplasm	binding|ubiquitin-protein ligase activity				0		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0139)														---	---	---	---
PTPRS	5802	broad.mit.edu	37	19	5214660	5214660	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:5214660G>T	uc002mbv.2	-	29	4640	c.4406C>A	c.(4405-4407)CCT>CAT	p.P1469H	PTPRS_uc002mbu.1_Missense_Mutation_p.P1038H|PTPRS_uc010xin.1_Missense_Mutation_p.P1011H|PTPRS_uc002mbw.2_Missense_Mutation_p.P1431H|PTPRS_uc002mbx.2_Missense_Mutation_p.P1026H|PTPRS_uc002mby.2_Missense_Mutation_p.P1022H	NM_002850	NP_002841	Q13332	PTPRS_HUMAN	protein tyrosine phosphatase, receptor type,	1469	Cytoplasmic (Potential).|Tyrosine-protein phosphatase 1.				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)														---	---	---	---
SAFB2	9667	broad.mit.edu	37	19	5616158	5616158	+	Silent	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:5616158C>T	uc002mcd.2	-	4	740	c.528G>A	c.(526-528)CAG>CAA	p.Q176Q	SAFB2_uc010xio.1_Silent_p.Q176Q|SAFB2_uc010xip.1_RNA	NM_014649	NP_055464	Q14151	SAFB2_HUMAN	scaffold attachment factor B2	176					regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	DNA binding|nucleotide binding|protein binding|RNA binding				0				UCEC - Uterine corpus endometrioid carcinoma (162;0.000228)														---	---	---	---
SAFB	6294	broad.mit.edu	37	19	5667881	5667881	+	Nonsense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:5667881C>T	uc002mcf.2	+	20	2655	c.2602C>T	c.(2602-2604)CGA>TGA	p.R868*	SAFB_uc002mcg.2_Nonsense_Mutation_p.R870*|SAFB_uc002mce.3_Nonsense_Mutation_p.R869*|SAFB_uc010xir.1_Nonsense_Mutation_p.R867*|SAFB_uc010xis.1_Nonsense_Mutation_p.R801*|SAFB_uc010xit.1_Nonsense_Mutation_p.R712*|SAFB_uc010xiu.1_Nonsense_Mutation_p.R669*	NM_002967	NP_002958	Q15424	SAFB1_HUMAN	scaffold attachment factor B	868	Interaction with SAFB2.|Gly-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)														---	---	---	---
ACER1	125981	broad.mit.edu	37	19	6312455	6312455	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:6312455G>A	uc002mel.2	-	2	227	c.149C>T	c.(148-150)CCG>CTG	p.P50L		NM_133492	NP_597999	Q8TDN7	ACER1_HUMAN	alkaline ceramidase 1	50	Cytoplasmic (Potential).					endoplasmic reticulum membrane|integral to membrane	ceramidase activity				0																		---	---	---	---
GPR108	56927	broad.mit.edu	37	19	6732118	6732118	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:6732118C>T	uc002mfp.2	-	13	1220	c.1174G>A	c.(1174-1176)GCC>ACC	p.A392T	GPR108_uc010duv.2_5'UTR|GPR108_uc002mfn.2_Missense_Mutation_p.A63T|GPR108_uc002mfo.3_Missense_Mutation_p.A150T|GPR108_uc010duw.2_RNA	NM_001080452	NP_001073921	Q9NPR9	GP108_HUMAN	G protein-coupled receptor 108 isoform 1	392						integral to membrane					0																		---	---	---	---
ZNF557	79230	broad.mit.edu	37	19	7083119	7083119	+	Silent	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:7083119C>T	uc002mgb.2	+	8	1121	c.636C>T	c.(634-636)AGC>AGT	p.S212S	ZNF557_uc002mga.2_Silent_p.S219S|ZNF557_uc002mgc.2_Silent_p.S219S	NM_001044388	NP_001037853	Q8N988	ZN557_HUMAN	zinc finger protein 557 isoform b	212	C2H2-type 3.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)|pancreas(1)	2				Lung(535;0.179)														---	---	---	---
INSR	3643	broad.mit.edu	37	19	7122771	7122771	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:7122771C>T	uc002mgd.1	-	19	3492	c.3383G>A	c.(3382-3384)CGC>CAC	p.R1128H	INSR_uc002mge.1_Missense_Mutation_p.R1116H	NM_000208	NP_000199	P06213	INSR_HUMAN	insulin receptor isoform Long precursor	1128	Protein kinase.|Cytoplasmic (Potential).				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)													---	---	---	---
STXBP2	6813	broad.mit.edu	37	19	7707085	7707085	+	Intron	SNP	C	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:7707085C>A	uc002mha.3	+						STXBP2_uc002mhb.3_Intron|STXBP2_uc010dvj.2_Intron|STXBP2_uc010xjr.1_Intron|STXBP2_uc010dvk.2_Intron|STXBP2_uc002mhc.3_Intron|STXBP2_uc002mhe.1_5'Flank	NM_006949	NP_008880			syntaxin binding protein 2 isoform a						leukocyte mediated cytotoxicity|neutrophil degranulation|protein transport|regulation of mast cell degranulation|vesicle docking involved in exocytosis	azurophil granule|cytolytic granule|cytosol|specific granule|tertiary granule	syntaxin-3 binding			central_nervous_system(1)	1																		---	---	---	---
MAP2K7	5609	broad.mit.edu	37	19	7975418	7975418	+	Nonsense_Mutation	SNP	C	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:7975418C>A	uc002mit.2	+	5	593	c.528C>A	c.(526-528)TGC>TGA	p.C176*	MAP2K7_uc002miv.2_Nonsense_Mutation_p.C176*|MAP2K7_uc010xka.1_RNA|MAP2K7_uc010xkb.1_Nonsense_Mutation_p.C176*|MAP2K7_uc010dvv.2_Nonsense_Mutation_p.C51*	NM_145185	NP_660186	O14733	MP2K7_HUMAN	mitogen-activated protein kinase kinase 7	176	Protein kinase.				activation of JUN kinase activity|innate immune response|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor 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	cytosol|nucleus	ATP binding|JUN kinase kinase activity|magnesium ion binding|protein binding|protein kinase binding|protein phosphatase binding|protein serine/threonine kinase activity|protein tyrosine kinase activity			large_intestine(7)|central_nervous_system(2)|ovary(1)|lung(1)	11					Etoposide(DB00773)													---	---	---	---
FBN3	84467	broad.mit.edu	37	19	8153030	8153030	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:8153030C>A	uc002mjf.2	-	51	6431	c.6410G>T	c.(6409-6411)GGG>GTG	p.G2137V	FBN3_uc002mje.2_5'UTR	NM_032447	NP_115823	Q75N90	FBN3_HUMAN	fibrillin 3 precursor	2137	EGF-like 34; calcium-binding.					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	8173063	8173063	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:8173063T>C	uc002mjf.2	-	36	4699	c.4678A>G	c.(4678-4680)ATT>GTT	p.I1560V		NM_032447	NP_115823	Q75N90	FBN3_HUMAN	fibrillin 3 precursor	1560						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	8188879	8188879	+	Silent	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:8188879T>C	uc002mjf.2	-	22	2766	c.2745A>G	c.(2743-2745)GAA>GAG	p.E915E		NM_032447	NP_115823	Q75N90	FBN3_HUMAN	fibrillin 3 precursor	915	TB 5.					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	8398023	8398023	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:8398023A>G	uc010dwa.2	-	7	1877	c.1811T>C	c.(1810-1812)GTG>GCG	p.V604A	KANK3_uc002mjp.1_Silent_p.G149G	NM_198471	NP_940873	Q6NY19	KANK3_HUMAN	ankyrin repeat domain 47	604											0																		---	---	---	---
RAB11B	9230	broad.mit.edu	37	19	8468449	8468449	+	3'UTR	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:8468449C>T	uc002mju.3	+	5						NM_004218	NP_004209			RAB11B, member RAS oncogene family						cell cycle|protein transport|small GTPase mediated signal transduction	plasma membrane	GDP binding|GTP binding|GTPase activity				0																		---	---	---	---
PRAM1	84106	broad.mit.edu	37	19	8564477	8564477	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:8564477G>A	uc002mkd.2	-	2	235	c.215C>T	c.(214-216)CCG>CTG	p.P72L	PRAM1_uc002mkc.2_Missense_Mutation_p.P72L	NM_032152	NP_115528	Q96QH2	PRAM_HUMAN	PML-RARA regulated adaptor molecule 1	120	5.|Pro-rich.|8 X 12 AA repeats of K-P-P-[PQ]-P-[EQ]- [VAF]-T-D-L-P-K.						lipid binding|protein binding				0																		---	---	---	---
MUC16	94025	broad.mit.edu	37	19	9011353	9011353	+	Silent	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:9011353G>A	uc002mkp.2	-	36	39084	c.38880C>T	c.(38878-38880)TAC>TAT	p.Y12960Y	MUC16_uc010xki.1_Intron	NM_024690	NP_078966	Q8WXI7	MUC16_HUMAN	mucin 16	12962	SEA 6.|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																		---	---	---	---
MUC16	94025	broad.mit.edu	37	19	9075993	9075993	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:9075993G>A	uc002mkp.2	-	3	11657	c.11453C>T	c.(11452-11454)CCC>CTC	p.P3818L		NM_024690	NP_078966	Q8WXI7	MUC16_HUMAN	mucin 16	3819	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																		---	---	---	---
OR1M1	125963	broad.mit.edu	37	19	9204849	9204849	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:9204849C>T	uc010xkj.1	+	1	929	c.929C>T	c.(928-930)ACC>ATC	p.T310I		NM_001004456	NP_001004456	Q8NGA1	OR1M1_HUMAN	olfactory receptor, family 1, subfamily M,	310	Cytoplasmic (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			skin(3)	3																		---	---	---	---
ZNF699	374879	broad.mit.edu	37	19	9406261	9406261	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:9406261T>C	uc002mlc.1	-	5	1819	c.1819A>G	c.(1819-1821)AGA>GGA	p.R607G		NM_198535	NP_940937	Q32M78	ZN699_HUMAN	zinc finger protein 699	607	C2H2-type 15.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0																		---	---	---	---
ZNF699	374879	broad.mit.edu	37	19	9406684	9406684	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:9406684C>T	uc002mlc.1	-	5	1396	c.1396G>A	c.(1396-1398)GTG>ATG	p.V466M		NM_198535	NP_940937	Q32M78	ZN699_HUMAN	zinc finger protein 699	466	C2H2-type 10.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0																		---	---	---	---
ZNF560	147741	broad.mit.edu	37	19	9578765	9578765	+	Silent	SNP	A	G	G	rs139159517		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:9578765A>G	uc002mlp.1	-	10	1068	c.858T>C	c.(856-858)TGT>TGC	p.C286C	ZNF560_uc010dwr.1_Silent_p.C180C	NM_152476	NP_689689	Q96MR9	ZN560_HUMAN	zinc finger protein 560	286	C2H2-type 1; degenerate.				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																		---	---	---	---
ZNF561	93134	broad.mit.edu	37	19	9721320	9721320	+	Silent	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:9721320A>G	uc002mlu.2	-	6	1222	c.1017T>C	c.(1015-1017)TGT>TGC	p.C339C	ZNF561_uc010dwu.2_Silent_p.C270C|ZNF561_uc010xkr.1_Silent_p.C203C	NM_152289	NP_689502	Q8N587	ZN561_HUMAN	zinc finger protein 561	339	C2H2-type 8.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1																		---	---	---	---
EIF3G	8666	broad.mit.edu	37	19	10227644	10227644	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:10227644C>T	uc002mnd.2	-	7	491	c.427G>A	c.(427-429)GAG>AAG	p.E143K		NM_003755	NP_003746	O75821	EIF3G_HUMAN	eukaryotic translation initiation factor 3,	143						cytosol|eukaryotic translation initiation factor 3 complex|nucleus|perinuclear region of cytoplasm	nucleotide binding|protein binding|translation initiation factor activity				0			OV - Ovarian serous cystadenocarcinoma(20;3.53e-09)|Epithelial(33;4.91e-06)|all cancers(31;1.1e-05)															---	---	---	---
S1PR2	9294	broad.mit.edu	37	19	10335189	10335189	+	Silent	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:10335189G>A	uc002mnl.2	-	2	504	c.393C>T	c.(391-393)CAC>CAT	p.H131H		NM_004230	NP_004221	O95136	S1PR2_HUMAN	endothelial differentiation, sphingolipid	131	Cytoplasmic (By similarity).				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																		---	---	---	---
TYK2	7297	broad.mit.edu	37	19	10465191	10465191	+	Silent	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:10465191G>A	uc002moc.3	-	19	3090	c.2712C>T	c.(2710-2712)GGC>GGT	p.G904G	TYK2_uc010dxe.2_Silent_p.G719G	NM_003331	NP_003322	P29597	TYK2_HUMAN	tyrosine kinase 2	904	ATP (By similarity).|Protein 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	10578017	10578017	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:10578017A>G	uc002moj.2	+	15	2489	c.2381A>G	c.(2380-2382)GAT>GGT	p.D794G	PDE4A_uc002mok.2_Missense_Mutation_p.D768G|PDE4A_uc002mol.2_Missense_Mutation_p.D733G|PDE4A_uc002mom.2_Missense_Mutation_p.D555G|PDE4A_uc002mon.2_Missense_Mutation_p.D249G|PDE4A_uc002moo.2_3'UTR	NM_001111307	NP_001104777	P27815	PDE4A_HUMAN	phosphodiesterase 4A isoform 1	794					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)													---	---	---	---
KEAP1	9817	broad.mit.edu	37	19	10600407	10600407	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:10600407C>T	uc002moq.1	-	4	1604	c.1448G>A	c.(1447-1449)CGC>CAC	p.R483H	KEAP1_uc002mop.1_Missense_Mutation_p.R201H|KEAP1_uc002mor.1_Missense_Mutation_p.R483H	NM_012289	NP_036421	Q14145	KEAP1_HUMAN	kelch-like ECH-associated protein 1	483	Kelch 4.			R->A: Loss of interaction with NFE2L2. Abolishes repression of NFE2L2-dependent gene expression. Loss of interaction with PGAM5.	regulation of transcription, DNA-dependent|transcription, DNA-dependent	centrosome|midbody|nucleus	protein binding			lung(12)|breast(3)|ovary(1)|pancreas(1)	17			OV - Ovarian serous cystadenocarcinoma(20;2.71e-09)|Epithelial(33;2.32e-06)|all cancers(31;1.42e-05)															---	---	---	---
ILF3	3609	broad.mit.edu	37	19	10798066	10798066	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:10798066G>T	uc002mpn.2	+	18	2421	c.2104G>T	c.(2104-2106)GGT>TGT	p.G702C	ILF3_uc002mpo.2_Missense_Mutation_p.G706C|ILF3_uc002mpq.2_Silent_p.A4A	NM_012218	NP_036350	Q12906	ILF3_HUMAN	interleukin enhancer binding factor 3 isoform a	702	Poly-Gly.|Interaction with PRMT1.				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)															---	---	---	---
ILF3	3609	broad.mit.edu	37	19	10798318	10798318	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:10798318T>C	uc002mpn.2	+	18	2673	c.2356T>C	c.(2356-2358)TAC>CAC	p.Y786H	ILF3_uc002mpo.2_Missense_Mutation_p.Y790H|ILF3_uc002mpq.2_Silent_p.P88P	NM_012218	NP_036350	Q12906	ILF3_HUMAN	interleukin enhancer binding factor 3 isoform a	786	Interaction with PRMT1.				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)															---	---	---	---
EPOR	2057	broad.mit.edu	37	19	11488744	11488744	+	Silent	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:11488744G>A	uc002mrj.1	-	8	1579	c.1443C>T	c.(1441-1443)TCC>TCT	p.S481S	EPOR_uc002mrh.2_Silent_p.S140S|EPOR_uc002mri.2_Silent_p.S308S|EPOR_uc002mrk.1_Silent_p.S308S|EPOR_uc002mrl.1_RNA|EPOR_uc010xlx.1_RNA|EPOR_uc010xly.1_Silent_p.S308S	NM_000121	NP_000112	P19235	EPOR_HUMAN	erythropoietin receptor precursor	481	Cytoplasmic (Potential).					extracellular region|integral to plasma membrane	erythropoietin receptor activity|identical protein binding			ovary(1)	1					Darbepoetin alfa(DB00012)|Epoetin alfa(DB00016)											OREG0025254	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
RGL3	57139	broad.mit.edu	37	19	11526704	11526704	+	Silent	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:11526704A>G	uc002mrp.2	-	5	610	c.546T>C	c.(544-546)AGT>AGC	p.S182S	RGL3_uc002mrn.2_5'UTR|RGL3_uc002mrm.2_5'UTR|RGL3_uc002mro.2_Silent_p.S182S	NM_001035223	NP_001030300	Q3MIN7	RGL3_HUMAN	ral guanine nucleotide dissociation	182	N-terminal Ras-GEF.				regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	intracellular				ovary(1)	1																		---	---	---	---
PRKCSH	5589	broad.mit.edu	37	19	11552174	11552174	+	Splice_Site	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:11552174T>C	uc002mrt.2	+	6	804	c.468_splice	c.e6+2	p.Q156_splice	PRKCSH_uc002mru.2_Splice_Site_p.Q156_splice|PRKCSH_uc010xlz.1_Splice_Site_p.Q156_splice|PRKCSH_uc010dya.2_Intron|PRKCSH_uc002mrv.1_Splice_Site_p.Q156_splice|PRKCSH_uc010dyb.2_Splice_Site_p.Q156_splice	NM_002743	NP_002734			protein kinase C substrate 80K-H isoform 1						innate immune response|intracellular protein kinase cascade|post-translational protein modification|protein folding|protein N-linked glycosylation via asparagine	endoplasmic reticulum lumen	calcium ion binding|protein kinase C binding				0																		---	---	---	---
ZNF491	126069	broad.mit.edu	37	19	11917140	11917140	+	Silent	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:11917140G>A	uc002mso.1	+	3	657	c.372G>A	c.(370-372)ACG>ACA	p.T124T		NM_152356	NP_689569	Q8N8L2	ZN491_HUMAN	zinc finger protein 491	124	C2H2-type 2; degenerate.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(2)	2																		---	---	---	---
ZNF440	126070	broad.mit.edu	37	19	11942998	11942998	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:11942998G>A	uc002msp.1	+	4	1163	c.1007G>A	c.(1006-1008)GGA>GAA	p.G336E		NM_152357	NP_689570	Q8IYI8	ZN440_HUMAN	zinc finger protein 440	336					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0																		---	---	---	---
ZNF439	90594	broad.mit.edu	37	19	11979349	11979349	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:11979349A>G	uc002mss.2	+	3	1593	c.1465A>G	c.(1465-1467)ACA>GCA	p.T489A	ZNF439_uc002msr.2_Missense_Mutation_p.T353A	NM_152262	NP_689475	Q8NDP4	ZN439_HUMAN	zinc finger protein 439	489	C2H2-type 11.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			skin(1)	1																		---	---	---	---
ZNF563	147837	broad.mit.edu	37	19	12429703	12429703	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:12429703C>T	uc002mtp.2	-	4	1374	c.1136G>A	c.(1135-1137)AGC>AAC	p.S379N		NM_145276	NP_660319	Q8TA94	ZN563_HUMAN	zinc finger protein 563	379	C2H2-type 9.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0																		---	---	---	---
DHPS	1725	broad.mit.edu	37	19	12787910	12787910	+	Intron	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:12787910A>G	uc002muh.1	-						DHPS_uc002muf.1_Intron|DHPS_uc002mug.1_Intron|DHPS_uc002mui.1_Intron|DHPS_uc002muj.1_Intron|DHPS_uc002muk.1_Intron	NM_001930	NP_001921			deoxyhypusine synthase isoform a						peptidyl-lysine modification to hypusine|positive regulation of cell proliferation|post-translational protein modification|spermidine catabolic process to deoxyhypusine, using deoxyhypusine synthase|translation	cytosol	deoxyhypusine synthase activity|protein binding			central_nervous_system(1)	1					Sulfadoxine(DB01299)													---	---	---	---
ASNA1	439	broad.mit.edu	37	19	12856268	12856268	+	Silent	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:12856268G>A	uc002muv.2	+	3	401	c.387G>A	c.(385-387)AAG>AAA	p.K129K	ASNA1_uc002muw.2_Silent_p.K128K	NM_004317	NP_004308	O43681	ASNA_HUMAN	arsA arsenite transporter, ATP-binding, homolog	129					response to arsenic-containing substance	endoplasmic reticulum|nucleolus|soluble fraction	arsenite-transporting ATPase activity|ATP binding|metal ion binding			ovary(2)	2					Adenosine triphosphate(DB00171)													---	---	---	---
CCDC130	81576	broad.mit.edu	37	19	13869974	13869974	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:13869974C>T	uc002mxb.1	+	9	964	c.461C>T	c.(460-462)GCC>GTC	p.A154V	CCDC130_uc010xnf.1_3'UTR|CCDC130_uc002mxc.1_Missense_Mutation_p.A154V|CCDC130_uc002mxd.1_Missense_Mutation_p.A9V|CCDC130_uc010dzf.1_Missense_Mutation_p.A48V	NM_030818	NP_110445	P13994	CC130_HUMAN	coiled-coil domain containing 130	154					response to virus		protein binding				0			OV - Ovarian serous cystadenocarcinoma(19;6.02e-23)|Epithelial(5;2.58e-18)															---	---	---	---
MRI1	84245	broad.mit.edu	37	19	13882975	13882975	+	Silent	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:13882975C>T	uc002mxe.2	+	6	1056	c.990C>T	c.(988-990)CAC>CAT	p.H330H	MRI1_uc002mxf.2_Silent_p.H283H|C19orf53_uc002mxg.2_5'Flank	NM_001031727	NP_001026897	Q9BV20	MTNA_HUMAN	translation initiation factor eIF-2B subunit	330					L-methionine salvage from methylthioadenosine	cell projection|cytoplasm|nucleus	identical protein binding|S-methyl-5-thioribose-1-phosphate isomerase activity			ovary(1)	1																		---	---	---	---
OR7C2	26658	broad.mit.edu	37	19	15052652	15052652	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:15052652A>G	uc010xoc.1	+	1	352	c.352A>G	c.(352-354)ACG>GCG	p.T118A		NM_012377	NP_036509	O60412	OR7C2_HUMAN	olfactory receptor, family 7, subfamily C,	118	Helical; Name=3; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(2)|skin(1)	3	Ovarian(108;0.203)																	---	---	---	---
CCDC105	126402	broad.mit.edu	37	19	15132704	15132704	+	Silent	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:15132704A>G	uc002nae.2	+	6	1323	c.1224A>G	c.(1222-1224)CAA>CAG	p.Q408Q		NM_173482	NP_775753	Q8IYK2	CC105_HUMAN	coiled-coil domain containing 105	408					microtubule cytoskeleton organization	microtubule				ovary(1)	1																		---	---	---	---
ILVBL	10994	broad.mit.edu	37	19	15234360	15234360	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:15234360C>T	uc002nam.2	-	3	284	c.163G>A	c.(163-165)GGA>AGA	p.G55R	ILVBL_uc010dzw.2_5'UTR|ILVBL_uc010dzx.1_Missense_Mutation_p.G55R	NM_006844	NP_006835	A1L0T0	ILVBL_HUMAN	ilvB (bacterial acetolactate synthase)-like	55						integral to membrane	magnesium ion binding|thiamine pyrophosphate binding|transferase activity			ovary(2)	2																		---	---	---	---
NOTCH3	4854	broad.mit.edu	37	19	15273303	15273303	+	Silent	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:15273303T>C	uc002nan.2	-	32	5962	c.5886A>G	c.(5884-5886)GGA>GGG	p.G1962G		NM_000435	NP_000426	Q9UM47	NOTC3_HUMAN	Notch homolog 3 precursor	1962	Cytoplasmic (Potential).|ANK 4.				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	15290312	15290312	+	Intron	SNP	A	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:15290312A>C	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)															---	---	---	---
PGLYRP2	114770	broad.mit.edu	37	19	15586783	15586783	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:15586783C>T	uc002nbf.3	-	2	831	c.698G>A	c.(697-699)CGA>CAA	p.R233Q	PGLYRP2_uc002nbg.3_Missense_Mutation_p.R233Q	NM_052890	NP_443122	Q96PD5	PGRP2_HUMAN	peptidoglycan recognition protein 2 precursor	233					defense response to Gram-positive bacterium|detection of bacterium|innate immune response|peptide amidation|peptidoglycan catabolic process	extracellular region|intracellular|membrane	N-acetylmuramoyl-L-alanine amidase activity|peptidoglycan receptor activity|zinc ion binding			ovary(3)	3																		---	---	---	---
CYP4F12	66002	broad.mit.edu	37	19	15795920	15795920	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:15795920A>G	uc002nbl.2	+	9	1089	c.1028A>G	c.(1027-1029)AAC>AGC	p.N343S		NM_023944	NP_076433			cytochrome P450, family 4, subfamily F,											skin(3)|ovary(2)|central_nervous_system(2)	7	Acute lymphoblastic leukemia(2;0.0367)																	---	---	---	---
OR10H5	284433	broad.mit.edu	37	19	15905157	15905157	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:15905157A>G	uc010xos.1	+	1	299	c.299A>G	c.(298-300)CAG>CGG	p.Q100R		NM_001004466	NP_001004466	Q8NGA6	O10H5_HUMAN	olfactory receptor, family 10, subfamily H,	100	Helical; Name=3; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)	1																		---	---	---	---
CHERP	10523	broad.mit.edu	37	19	16643424	16643424	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:16643424T>C	uc002nei.1	-	5	733	c.659A>G	c.(658-660)GAC>GGC	p.D220G	MED26_uc002nee.2_Intron|CHERP_uc002nej.2_Missense_Mutation_p.D188G	NM_006387	NP_006378	Q8IWX8	CHERP_HUMAN	calcium homeostasis endoplasmic reticulum	220	CID.				cellular calcium ion homeostasis|negative regulation of cell proliferation|nervous system development|RNA processing	endoplasmic reticulum|perinuclear region of cytoplasm	RNA binding			ovary(2)	2																		---	---	---	---
NWD1	284434	broad.mit.edu	37	19	16910805	16910805	+	Nonsense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:16910805C>T	uc002neu.3	+	17	3990	c.3568C>T	c.(3568-3570)CAG>TAG	p.Q1190*	NWD1_uc002net.3_Nonsense_Mutation_p.Q1055*|NWD1_uc002nev.3_Nonsense_Mutation_p.Q984*			Q149M9	NWD1_HUMAN	RecName: Full=NACHT and WD repeat domain-containing protein 1;	1190	WD 9.						ATP binding			skin(3)|ovary(2)|pancreas(2)	7																		---	---	---	---
CPAMD8	27151	broad.mit.edu	37	19	17104391	17104391	+	Silent	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:17104391C>T	uc002nfb.2	-	12	1274	c.1242G>A	c.(1240-1242)GAG>GAA	p.E414E		NM_015692	NP_056507	Q8IZJ3	CPMD8_HUMAN	C3 and PZP-like, alpha-2-macroglobulin domain	367						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	17108029	17108029	+	Silent	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:17108029C>T	uc002nfb.2	-	11	1160	c.1128G>A	c.(1126-1128)CAG>CAA	p.Q376Q		NM_015692	NP_056507	Q8IZJ3	CPMD8_HUMAN	C3 and PZP-like, alpha-2-macroglobulin domain	329						extracellular space|plasma membrane	serine-type endopeptidase inhibitor activity			ovary(4)|breast(4)|large_intestine(3)|pancreas(1)|skin(1)	13																		---	---	---	---
DDA1	79016	broad.mit.edu	37	19	17424920	17424920	+	Intron	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:17424920C>T	uc002ngd.2	+						DDA1_uc002nge.2_Intron	NM_024050	NP_076955			DET1 and DDB1 associated 1											ovary(1)	1																		---	---	---	---
FCHO1	23149	broad.mit.edu	37	19	17895030	17895030	+	Silent	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:17895030C>T	uc010ebb.2	+	24	2401	c.2212C>T	c.(2212-2214)CTG>TTG	p.L738L	FCHO1_uc002nhg.3_Silent_p.L738L|FCHO1_uc002nhh.2_Silent_p.L738L|FCHO1_uc010xpw.1_Silent_p.L688L|FCHO1_uc002nhi.2_Silent_p.L194L|FCHO1_uc002nhj.2_Silent_p.L82L	NM_001161358	NP_001154830	O14526	FCHO1_HUMAN	FCH domain only 1 isoform b	738										breast(1)	1																OREG0025350	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
B3GNT3	10331	broad.mit.edu	37	19	17922845	17922845	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:17922845C>T	uc002nhk.1	+	3	1118	c.1033C>T	c.(1033-1035)CGC>TGC	p.R345C	B3GNT3_uc002nhl.1_Missense_Mutation_p.R345C|B3GNT3_uc010ebd.1_Missense_Mutation_p.R345C|B3GNT3_uc010ebe.1_Missense_Mutation_p.R345C	NM_014256	NP_055071	Q9Y2A9	B3GN3_HUMAN	UDP-GlcNAc:betaGal	345	Lumenal (Potential).				protein glycosylation	Golgi membrane|integral to plasma membrane	galactosyltransferase activity			upper_aerodigestive_tract(1)	1																		---	---	---	---
MAST3	23031	broad.mit.edu	37	19	18255913	18255913	+	Silent	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:18255913C>T	uc002nhz.3	+	23	2826	c.2826C>T	c.(2824-2826)CCC>CCT	p.P942P		NM_015016	NP_055831	O60307	MAST3_HUMAN	microtubule associated serine/threonine kinase	942							ATP binding|magnesium ion binding|protein binding|protein serine/threonine kinase activity			large_intestine(2)|ovary(2)|stomach(1)	5																		---	---	---	---
SF4	57794	broad.mit.edu	37	19	19413137	19413137	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:19413137G>A	uc002nmh.2	-	7	826	c.824C>T	c.(823-825)GCG>GTG	p.A275V	SF4_uc002nmf.2_5'UTR|SF4_uc002nmg.2_5'UTR|SF4_uc002nmi.2_Missense_Mutation_p.A65V|SF4_uc002nmj.2_Missense_Mutation_p.A65V|SF4_uc010xqr.1_RNA|SF4_uc010xqs.1_RNA	NM_172231	NP_757386	Q8IWZ8	SUGP1_HUMAN	splicing factor 4	275	SURP motif 2.				nuclear mRNA splicing, via spliceosome	nucleoplasm|spliceosomal complex	RNA binding				0																		---	---	---	---
SF4	57794	broad.mit.edu	37	19	19416751	19416751	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:19416751C>T	uc002nmh.2	-	4	447	c.445G>A	c.(445-447)GCC>ACC	p.A149T	SF4_uc002nmg.2_5'Flank|SF4_uc002nmi.2_5'UTR|SF4_uc002nmj.2_5'UTR|SF4_uc010xqr.1_RNA|SF4_uc010xqs.1_RNA	NM_172231	NP_757386	Q8IWZ8	SUGP1_HUMAN	splicing factor 4	149					nuclear mRNA splicing, via spliceosome	nucleoplasm|spliceosomal complex	RNA binding				0																		---	---	---	---
TSSK6	83983	broad.mit.edu	37	19	19625867	19625867	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:19625867G>A	uc002nmr.2	-	1	603	c.370C>T	c.(370-372)CGC>TGC	p.R124C	TSSK6_uc002nmq.2_RNA|NDUFA13_uc002nms.2_5'Flank|NDUFA13_uc010xqx.1_5'Flank|NDUFA13_uc010xqy.1_5'Flank	NM_032037	NP_114426	Q9BXA6	TSSK6_HUMAN	testis-specific serine kinase 6	124	Protein kinase.				multicellular organismal development|sperm chromatin condensation		ATP binding|magnesium ion binding|protein serine/threonine kinase activity			stomach(1)	1																		---	---	---	---
LPAR2	9170	broad.mit.edu	37	19	19735210	19735210	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:19735210C>T	uc002nnb.3	-	3	1050	c.911G>A	c.(910-912)CGC>CAC	p.R304H	LPAR2_uc002nna.3_Missense_Mutation_p.R304H|LPAR2_uc002nnc.3_Missense_Mutation_p.R304H	NM_004720	NP_004711	Q9HBW0	LPAR2_HUMAN	lysophosphatidic acid receptor 2	304	Cytoplasmic (Potential).				activation of phospholipase C activity|elevation of cytosolic calcium ion concentration	cell surface|integral to plasma membrane	LIM domain binding|lipid binding			ovary(1)|breast(1)	2																		---	---	---	---
GMIP	51291	broad.mit.edu	37	19	19750997	19750997	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:19750997T>C	uc002nnd.2	-	7	551	c.434A>G	c.(433-435)CAC>CGC	p.H145R	GMIP_uc010xrb.1_Missense_Mutation_p.H145R|GMIP_uc010xrc.1_Missense_Mutation_p.H145R	NM_016573	NP_057657	Q9P107	GMIP_HUMAN	GEM interacting protein	145					negative regulation of Rho GTPase activity|small GTPase mediated signal transduction	cytosol	metal ion binding|protein binding|Rho GTPase activator activity			ovary(1)	1																		---	---	---	---
ZNF85	7639	broad.mit.edu	37	19	21117757	21117757	+	Missense_Mutation	SNP	A	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:21117757A>T	uc002npg.3	+	3	260	c.133A>T	c.(133-135)ATT>TTT	p.I45F	ZNF85_uc002npf.2_RNA|ZNF85_uc002nph.1_RNA|ZNF85_uc010ecn.2_Intron|ZNF85_uc010eco.2_5'Flank|ZNF85_uc002npi.2_5'Flank	NM_003429	NP_003420	Q03923	ZNF85_HUMAN	zinc finger protein 85	45	KRAB.					nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|transcription corepressor activity|zinc ion binding			central_nervous_system(1)	1																		---	---	---	---
ZNF714	148206	broad.mit.edu	37	19	21300842	21300842	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:21300842G>A	uc002npo.3	+	6	1735	c.1375G>A	c.(1375-1377)GGC>AGC	p.G459S	ZNF714_uc002npl.2_Missense_Mutation_p.G304S|ZNF714_uc010ecp.1_Missense_Mutation_p.G410S|ZNF714_uc002npn.2_RNA	NM_182515	NP_872321	Q96N38	ZN714_HUMAN	zinc finger protein 714	459	C2H2-type 13.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0																		---	---	---	---
ZNF100	163227	broad.mit.edu	37	19	21909939	21909939	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:21909939T>G	uc002nqi.2	-	5	1374	c.1175A>C	c.(1174-1176)AAG>ACG	p.K392T	ZNF100_uc002nqh.2_Missense_Mutation_p.K328T	NM_173531	NP_775802	Q8IYN0	ZN100_HUMAN	zinc finger protein 100	392	C2H2-type 8.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0																		---	---	---	---
ZNF100	163227	broad.mit.edu	37	19	21910635	21910635	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:21910635T>C	uc002nqi.2	-	5	678	c.479A>G	c.(478-480)GAA>GGA	p.E160G	ZNF100_uc002nqh.2_Missense_Mutation_p.E96G	NM_173531	NP_775802	Q8IYN0	ZN100_HUMAN	zinc finger protein 100	160					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0																		---	---	---	---
ZNF492	57615	broad.mit.edu	37	19	22847817	22847817	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:22847817A>G	uc002nqw.3	+	4	1590	c.1346A>G	c.(1345-1347)TAC>TGC	p.Y449C		NM_020855	NP_065906	Q9P255	ZN492_HUMAN	zinc finger protein 492	449	C2H2-type 12; degenerate.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0		all_cancers(12;0.0266)|all_lung(12;0.00187)|Lung NSC(12;0.0019)|all_epithelial(12;0.00203)|Hepatocellular(1079;0.244)																---	---	---	---
ZNF536	9745	broad.mit.edu	37	19	30935350	30935350	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:30935350G>A	uc002nsu.1	+	2	1019	c.881G>A	c.(880-882)CGC>CAC	p.R294H	ZNF536_uc010edd.1_Missense_Mutation_p.R294H	NM_014717	NP_055532	O15090	ZN536_HUMAN	zinc finger protein 536	294	C2H2-type 3.				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)																	---	---	---	---
ZNF536	9745	broad.mit.edu	37	19	31025777	31025777	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:31025777T>C	uc002nsu.1	+	3	2332	c.2194T>C	c.(2194-2196)TCT>CCT	p.S732P	ZNF536_uc010edd.1_Missense_Mutation_p.S732P	NM_014717	NP_055532	O15090	ZN536_HUMAN	zinc finger protein 536	732					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	31768795	31768795	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:31768795A>G	uc002nsy.3	-	2	1969	c.1904T>C	c.(1903-1905)CTT>CCT	p.L635P		NM_020856	NP_065907	Q63HK5	TSH3_HUMAN	zinc finger protein 537	635					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	31768856	31768856	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:31768856T>C	uc002nsy.3	-	2	1908	c.1843A>G	c.(1843-1845)AAA>GAA	p.K615E		NM_020856	NP_065907	Q63HK5	TSH3_HUMAN	zinc finger protein 537	615	Potential.				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)																	---	---	---	---
ZNF507	22847	broad.mit.edu	37	19	32844364	32844364	+	Missense_Mutation	SNP	A	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:32844364A>T	uc002nte.2	+	3	900	c.628A>T	c.(628-630)ACC>TCC	p.T210S	ZNF507_uc002ntc.2_Missense_Mutation_p.T210S|ZNF507_uc010xrn.1_Missense_Mutation_p.T210S|ZNF507_uc002ntd.2_Missense_Mutation_p.T210S	NM_001136156	NP_001129628	Q8TCN5	ZN507_HUMAN	zinc finger protein 507	210					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)|pancreas(1)|kidney(1)|central_nervous_system(1)|skin(1)	5	Esophageal squamous(110;0.162)																	---	---	---	---
SLC7A9	11136	broad.mit.edu	37	19	33353425	33353425	+	Silent	SNP	C	T	T	rs75036167		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:33353425C>T	uc002ntv.3	-	5	663	c.546G>A	c.(544-546)GCG>GCA	p.A182A	SLC7A9_uc002ntt.3_Intron|SLC7A9_uc002ntu.3_Silent_p.A182A|SLC7A9_uc002ntw.3_Intron	NM_001126335	NP_001119807	P82251	BAT1_HUMAN	solute carrier family 7, member 9	182	Helical; (Potential).		A -> T (in CSNU; type III; frequent mutation; mild loss of amino acid transport activity).		blood coagulation|cellular amino acid metabolic process|ion transport|leukocyte migration|protein complex assembly	integral to plasma membrane	L-cystine transmembrane transporter activity|neutral amino acid transmembrane transporter activity|peptide antigen binding			skin(1)	1	Esophageal squamous(110;0.137)				L-Cystine(DB00138)													---	---	---	---
CHST8	64377	broad.mit.edu	37	19	34263223	34263223	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:34263223C>T	uc002nus.3	+	5	1035	c.530C>T	c.(529-531)ACG>ATG	p.T177M	CHST8_uc002nut.3_Missense_Mutation_p.T177M|CHST8_uc002nuu.2_Missense_Mutation_p.T177M	NM_001127895	NP_001121367	Q9H2A9	CHST8_HUMAN	carbohydrate (N-acetylgalactosamine 4-0)	177	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)																	---	---	---	---
KIAA0355	9710	broad.mit.edu	37	19	34791738	34791738	+	Silent	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:34791738G>A	uc002nvd.3	+	2	1219	c.360G>A	c.(358-360)GTG>GTA	p.V120V	KIAA0355_uc010edk.1_Silent_p.V110V	NM_014686	NP_055501	O15063	K0355_HUMAN	hypothetical protein LOC9710	120										ovary(1)	1	Esophageal squamous(110;0.162)																	---	---	---	---
FXYD5	53827	broad.mit.edu	37	19	35657211	35657211	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:35657211G>A	uc002nyg.1	+	8	556	c.470G>A	c.(469-471)GGC>GAC	p.G157D	FXYD5_uc010xsq.1_Missense_Mutation_p.G157D|FXYD5_uc002nyh.1_Missense_Mutation_p.G157D|FXYD5_uc002nyi.1_Missense_Mutation_p.G94D|FXYD5_uc002nyj.1_5'Flank	NM_014164	NP_054883	Q96DB9	FXYD5_HUMAN	FXYD domain-containing ion transport regulator 5	157	Helical; (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)															---	---	---	---
MLL4	9757	broad.mit.edu	37	19	36210830	36210830	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:36210830C>T	uc010eei.2	+	3	581	c.581C>T	c.(580-582)ACT>ATT	p.T194I		NM_014727	NP_055542	Q9UMN6	MLL4_HUMAN	myeloid/lymphoid or mixed-lineage leukemia 4	194					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)															---	---	---	---
MLL4	9757	broad.mit.edu	37	19	36218345	36218345	+	Missense_Mutation	SNP	A	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:36218345A>T	uc010eei.2	+	17	4124	c.4124A>T	c.(4123-4125)GAC>GTC	p.D1375V		NM_014727	NP_055542	Q9UMN6	MLL4_HUMAN	myeloid/lymphoid or mixed-lineage leukemia 4	1375	PHD-type 3.				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)															---	---	---	---
CLIP3	25999	broad.mit.edu	37	19	36508623	36508623	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:36508623A>G	uc010eeq.1	-	10	1667	c.1385T>C	c.(1384-1386)TTC>TCC	p.F462S	uc002ocy.2_Intron|CLIP3_uc002ocz.1_Missense_Mutation_p.F462S	NM_015526	NP_056341	Q96DZ5	CLIP3_HUMAN	CAP-GLY domain containing linker protein 3	462	CAP-Gly 2.				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)															---	---	---	---
THAP8	199745	broad.mit.edu	37	19	36526358	36526358	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:36526358C>T	uc002oda.1	-	4	1354	c.809G>A	c.(808-810)CGG>CAG	p.R270Q	uc002ocy.2_Intron|CLIP3_uc010eeq.1_5'Flank|CLIP3_uc002ocz.1_5'Flank|THAP8_uc010xtb.1_Missense_Mutation_p.R227Q|THAP8_uc010xtc.1_RNA	NM_152658	NP_689871	Q8NA92	THAP8_HUMAN	THAP domain containing 8	270							DNA binding|metal ion binding				0	Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.06)															---	---	---	---
WDR62	284403	broad.mit.edu	37	19	36558302	36558302	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:36558302G>A	uc002odc.2	+	6	747	c.656G>A	c.(655-657)CGC>CAC	p.R219H	WDR62_uc002odd.2_Missense_Mutation_p.R219H|WDR62_uc002odb.2_Missense_Mutation_p.R219H	NM_173636	NP_775907	O43379	WDR62_HUMAN	WD repeat domain 62 isoform 2	219	WD 3.				cerebral cortex development	nucleus					0	Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.06)															---	---	---	---
ZNF382	84911	broad.mit.edu	37	19	37117909	37117909	+	Silent	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:37117909T>C	uc002oek.2	+	5	1223	c.1110T>C	c.(1108-1110)CAT>CAC	p.H370H	ZNF382_uc010efa.2_Silent_p.H321H|ZNF382_uc010efb.2_Silent_p.H369H|ZNF382_uc002oel.2_Silent_p.H369H	NM_032825	NP_116214	Q96SR6	ZN382_HUMAN	zinc finger protein 382	370	Required for transcriptional repression activity; probably mediates sequence- specific DNA-binding (By similarity).|C2H2-type 4.				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)															---	---	---	---
ZNF567	163081	broad.mit.edu	37	19	37210278	37210278	+	Missense_Mutation	SNP	T	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:37210278T>A	uc010xtl.1	+	6	874	c.652T>A	c.(652-654)TCA>ACA	p.S218T	ZNF567_uc002oeo.1_Missense_Mutation_p.S218T|ZNF567_uc010xtk.1_Missense_Mutation_p.S218T|ZNF567_uc002oep.3_Missense_Mutation_p.S187T|ZNF567_uc002oeq.1_Missense_Mutation_p.S187T	NM_152603	NP_689816	Q8N184	ZN567_HUMAN	zinc finger protein 567	218	C2H2-type 1; degenerate.				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)															---	---	---	---
SIPA1L3	23094	broad.mit.edu	37	19	38600972	38600972	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:38600972G>A	uc002ohk.2	+	8	2748	c.2239G>A	c.(2239-2241)GTC>ATC	p.V747I		NM_015073	NP_055888	O60292	SI1L3_HUMAN	signal-induced proliferation-associated 1 like	747	Rap-GAP.				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)															---	---	---	---
CATSPERG	57828	broad.mit.edu	37	19	38858317	38858317	+	Intron	SNP	G	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:38858317G>T	uc002oih.3	+						CATSPERG_uc002oig.3_Intron|CATSPERG_uc002oif.3_Intron|CATSPERG_uc010efw.2_Intron	NM_021185	NP_067008			cation channel, sperm-associated, gamma						cell differentiation|multicellular organismal development|spermatogenesis	integral to membrane				ovary(1)|skin(1)	2																		---	---	---	---
RYR1	6261	broad.mit.edu	37	19	38937416	38937416	+	Intron	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:38937416G>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)													---	---	---	---
RYR1	6261	broad.mit.edu	37	19	38969097	38969097	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:38969097A>G	uc002oit.2	+	31	4607	c.4477A>G	c.(4477-4479)ATG>GTG	p.M1493V	RYR1_uc002oiu.2_Missense_Mutation_p.M1493V	NM_000540	NP_000531	P21817	RYR1_HUMAN	skeletal muscle ryanodine receptor isoform 1	1493	Cytoplasmic.|B30.2/SPRY 3.|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	39051968	39051968	+	Silent	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:39051968C>T	uc002oit.2	+	90	12628	c.12498C>T	c.(12496-12498)GCC>GCT	p.A4166A	RYR1_uc002oiu.2_Silent_p.A4161A|RYR1_uc002oiv.1_Silent_p.A1075A	NM_000540	NP_000531	P21817	RYR1_HUMAN	skeletal muscle ryanodine receptor isoform 1	4166					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)													---	---	---	---
ACTN4	81	broad.mit.edu	37	19	39212308	39212308	+	Silent	SNP	C	T	T	rs149647148		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:39212308C>T	uc002oja.1	+	12	1481	c.1422C>T	c.(1420-1422)GCC>GCT	p.A474A	ACTN4_uc010egc.1_Silent_p.A474A	NM_004924	NP_004915	O43707	ACTN4_HUMAN	actinin, alpha 4	474	Spectrin 2.				platelet activation|platelet degranulation|positive regulation of cellular component movement|positive regulation of sodium:hydrogen antiporter activity|protein transport|regulation of apoptosis	extracellular region|nucleolus|perinuclear region of cytoplasm|platelet alpha granule lumen|protein complex|pseudopodium|ribonucleoprotein complex	actin filament binding|calcium ion binding|integrin binding|nucleoside binding|protein homodimerization activity				0	all_cancers(60;1.57e-05)|Ovarian(47;0.103)		Lung(45;0.00172)|LUSC - Lung squamous cell carcinoma(53;0.00272)															---	---	---	---
ZFP36	7538	broad.mit.edu	37	19	39898923	39898923	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:39898923G>T	uc002olh.1	+	2	623	c.565G>T	c.(565-567)GGC>TGC	p.G189C	ZFP36_uc010egn.1_Silent_p.P61P	NM_003407	NP_003398	P26651	TTP_HUMAN	zinc finger protein 36, C3H type, homolog	189					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)															---	---	---	---
SUPT5H	6829	broad.mit.edu	37	19	39967026	39967026	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:39967026T>C	uc002olo.3	+	30	3430	c.3251T>C	c.(3250-3252)CTC>CCC	p.L1084P	SUPT5H_uc002olp.3_Missense_Mutation_p.L1084P|SUPT5H_uc002olq.3_Missense_Mutation_p.L1080P|SUPT5H_uc002oln.3_Missense_Mutation_p.L1084P|SUPT5H_uc002olr.3_Missense_Mutation_p.L1084P	NM_001111020	NP_001104490	O00267	SPT5H_HUMAN	suppressor of Ty 5 homolog isoform a	1084					cell cycle|chromatin remodeling|mRNA capping|negative regulation of transcription elongation, DNA-dependent|negative regulation of transcription from RNA polymerase II promoter|positive regulation of transcription elongation from RNA polymerase II promoter|positive regulation of transcription from RNA polymerase II promoter|positive regulation of viral transcription|response to organic substance|retroviral genome replication|transcription elongation from RNA polymerase II promoter	nucleoplasm	enzyme binding|protein heterodimerization activity			ovary(3)|pancreas(1)	4	all_cancers(60;6.69e-07)|all_lung(34;2.66e-08)|Lung NSC(34;3e-08)|all_epithelial(25;1.57e-06)|Ovarian(47;0.159)		Epithelial(26;3.9e-26)|all cancers(26;1.35e-23)|LUSC - Lung squamous cell carcinoma(53;0.000657)															---	---	---	---
TIMM50	92609	broad.mit.edu	37	19	39977128	39977128	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:39977128A>G	uc002olu.1	+	8	1131	c.998A>G	c.(997-999)CAT>CGT	p.H333R	TIMM50_uc002olt.1_RNA|TIMM50_uc002olv.1_Missense_Mutation_p.H32R	NM_001001563	NP_001001563	Q3ZCQ8	TIM50_HUMAN	translocase of inner mitochondrial membrane 50	230	Mitochondrial intermembrane (Potential).|FCP1 homology.				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)															---	---	---	---
DYRK1B	9149	broad.mit.edu	37	19	40319090	40319090	+	Silent	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:40319090C>T	uc002omj.2	-	6	934	c.654G>A	c.(652-654)GCG>GCA	p.A218A	DYRK1B_uc002omi.2_Silent_p.A218A|DYRK1B_uc002omk.2_Silent_p.A218A	NM_004714	NP_004705	Q9Y463	DYR1B_HUMAN	dual-specificity tyrosine-(Y)-phosphorylation	218	Protein kinase.				positive regulation of transcription, DNA-dependent	nucleus	ATP binding|protein binding|protein serine/threonine kinase activity|protein tyrosine kinase activity|transcription coactivator activity			ovary(4)|stomach(1)|central_nervous_system(1)|skin(1)	7	all_cancers(60;5.79e-06)|all_lung(34;5.2e-08)|Lung NSC(34;6.14e-08)|Ovarian(47;0.06)		Epithelial(26;5.74e-25)|OV - Ovarian serous cystadenocarcinoma(5;3.13e-24)|all cancers(26;8.59e-23)															---	---	---	---
FCGBP	8857	broad.mit.edu	37	19	40368363	40368363	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:40368363C>T	uc002omp.3	-	28	12993	c.12985G>A	c.(12985-12987)GTG>ATG	p.V4329M		NM_003890	NP_003881	Q9Y6R7	FCGBP_HUMAN	Fc fragment of IgG binding protein precursor	4329						extracellular region	protein binding			ovary(4)|skin(4)|central_nervous_system(1)	9	all_cancers(60;6.03e-06)|all_lung(34;5.58e-08)|Lung NSC(34;6.62e-08)|Ovarian(47;0.06)		Epithelial(26;6.25e-23)|all cancers(26;1.13e-20)															---	---	---	---
HIPK4	147746	broad.mit.edu	37	19	40886898	40886898	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:40886898C>T	uc002onp.2	-	3	1285	c.1000G>A	c.(1000-1002)GAA>AAA	p.E334K		NM_144685	NP_653286	Q8NE63	HIPK4_HUMAN	homeodomain interacting protein kinase 4	334	Protein kinase.					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	40901334	40901334	+	Silent	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:40901334A>G	uc002onr.2	-	7	3194	c.2925T>C	c.(2923-2925)GCT>GCC	p.A975A	PRX_uc002onq.2_Silent_p.A836A|PRX_uc002ons.2_3'UTR	NM_181882	NP_870998	Q9BXM0	PRAX_HUMAN	periaxin isoform 2	975					axon ensheathment	cytoplasm|nucleus|plasma membrane	protein binding			ovary(2)	2			Lung(22;6.24e-05)|LUSC - Lung squamous cell carcinoma(20;0.000384)															---	---	---	---
SPTBN4	57731	broad.mit.edu	37	19	41025339	41025339	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:41025339C>T	uc002ony.2	+	16	3021	c.2935C>T	c.(2935-2937)CGC>TGC	p.R979C	SPTBN4_uc002onx.2_Missense_Mutation_p.R979C|SPTBN4_uc002onz.2_Missense_Mutation_p.R979C|SPTBN4_uc010egx.2_5'UTR	NM_020971	NP_066022	Q9H254	SPTN4_HUMAN	spectrin, beta, non-erythrocytic 4 isoform	979	Spectrin 7.				actin filament capping|axon guidance|cytoskeletal anchoring at plasma membrane|vesicle-mediated transport	cytosol|nuclear matrix|PML body|spectrin	actin binding|ankyrin binding|structural constituent of cytoskeleton			ovary(3)|central_nervous_system(1)|skin(1)	5			Lung(22;0.000114)|LUSC - Lung squamous cell carcinoma(20;0.000384)															---	---	---	---
SNRPA	6626	broad.mit.edu	37	19	41268834	41268834	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:41268834G>A	uc002ooz.2	+	4	990	c.455G>A	c.(454-456)CGC>CAC	p.R152H	SNRPA_uc002opa.2_Missense_Mutation_p.R102H	NM_004596	NP_004587	P09012	SNRPA_HUMAN	small nuclear ribonucleoprotein polypeptide A	152	Pro-rich.					nucleoplasm|spliceosomal complex	nucleotide binding|protein binding|RNA binding			skin(2)|ovary(1)|central_nervous_system(1)	4			LUSC - Lung squamous cell carcinoma(20;0.000219)|Lung(22;0.000959)															---	---	---	---
CEACAM7	1087	broad.mit.edu	37	19	42187806	42187806	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:42187806C>T	uc002ori.1	-	3	618	c.616G>A	c.(616-618)GCC>ACC	p.A206T	CEACAM7_uc010ehx.2_Missense_Mutation_p.A206T|CEACAM7_uc010ehy.1_Intron	NM_006890	NP_008821	Q14002	CEAM7_HUMAN	carcinoembryonic antigen-related cell adhesion	206	Ig-like C2-type.					anchored to membrane|integral to membrane|plasma membrane				ovary(2)	2				OV - Ovarian serous cystadenocarcinoma(3;0.0027)|all cancers(3;0.00979)|Epithelial(262;0.0366)														---	---	---	---
ATP1A3	478	broad.mit.edu	37	19	42490009	42490009	+	Intron	SNP	G	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:42490009G>T	uc002osg.2	-						ATP1A3_uc010xwf.1_Intron|ATP1A3_uc010xwg.1_Intron|ATP1A3_uc010xwh.1_Intron|ATP1A3_uc002osh.2_Intron	NM_152296	NP_689509			Na+/K+ -ATPase alpha 3 subunit						ATP biosynthetic process	endoplasmic reticulum|Golgi apparatus	ATP binding|metal ion binding|sodium:potassium-exchanging ATPase activity			ovary(1)|pancreas(1)	2																		---	---	---	---
CIC	23152	broad.mit.edu	37	19	42794635	42794635	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:42794635G>A	uc002otf.1	+	10	1755	c.1715G>A	c.(1714-1716)CGG>CAG	p.R572Q		NM_015125	NP_055940	Q96RK0	CIC_HUMAN	capicua homolog	572	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								---	---	---	---
PAFAH1B3	5050	broad.mit.edu	37	19	42804382	42804382	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:42804382C>A	uc002otg.2	-	3	561	c.226G>T	c.(226-228)GGC>TGC	p.G76C	PAFAH1B3_uc010xwi.1_Missense_Mutation_p.G76C|PAFAH1B3_uc010xwj.1_Missense_Mutation_p.G76C|PRR19_uc002oth.1_5'Flank|PRR19_uc002oti.2_5'Flank	NM_002573	NP_002564	Q15102	PA1B3_HUMAN	platelet-activating factor acetylhydrolase,	76					lipid catabolic process|nervous system development	cytoplasm	1-alkyl-2-acetylglycerophosphocholine esterase activity|protein binding				0		Prostate(69;0.0704)																---	---	---	---
PSG7	5676	broad.mit.edu	37	19	43433646	43433646	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:43433646T>C	uc002ovl.3	-	4	759	c.657A>G	c.(655-657)ATA>ATG	p.I219M	PSG3_uc002ouf.2_Intron|PSG11_uc002ouw.2_Intron|PSG7_uc002ous.1_5'Flank|PSG7_uc002out.1_Missense_Mutation_p.I38M|PSG10_uc002ouv.1_Intron|PSG6_uc002ovh.1_Intron|PSG6_uc002ovi.2_Intron|PSG6_uc010xwk.1_Intron|PSG11_uc002ovk.1_Intron|PSG7_uc010xwl.1_Missense_Mutation_p.I97M	NM_002783	NP_002774	Q13046	PSG7_HUMAN	pregnancy specific beta-1-glycoprotein 7	219	Ig-like C2-type 1.				female pregnancy	extracellular region					0		Prostate(69;0.00682)																---	---	---	---
PSG6	5675	broad.mit.edu	37	19	43528843	43528843	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:43528843G>A	uc002ovh.1	-	2	537	c.448C>T	c.(448-450)CCG>TCG	p.P150S	PSG11_uc002ouw.2_Silent_p.L150L|PSG10_uc002ouv.1_Intron|PSG6_uc002ovi.2_Intron|PSG6_uc010xwk.1_Intron|PSG11_uc002ovk.1_Silent_p.L150L|PSG11_uc002ovm.1_Silent_p.L144L|PSG11_uc002ovn.1_Silent_p.L150L|PSG11_uc002ovo.1_Intron|PSG11_uc002ovp.1_Intron			Q00889	PSG6_HUMAN	SubName: Full=Putative uncharacterized protein PSG6;	Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment					female pregnancy	extracellular region				ovary(1)|skin(1)	2		Prostate(69;0.00899)																---	---	---	---
PSG6	5675	broad.mit.edu	37	19	43585033	43585033	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:43585033G>A	uc002ovi.2	-	2	523	c.430C>T	c.(430-432)CCG>TCG	p.P144S	PSG6_uc010xwk.1_Intron|PSG2_uc002ovr.2_Silent_p.L144L|PSG2_uc002ovq.3_Silent_p.L144L|PSG2_uc010eiq.1_Silent_p.L144L|PSG2_uc002ovs.3_Silent_p.L144L|PSG2_uc002ovt.3_Silent_p.L144L			Q00889	PSG6_HUMAN	SubName: Full=Putative uncharacterized protein PSG6;	Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment					female pregnancy	extracellular region				ovary(1)|skin(1)	2		Prostate(69;0.00899)																---	---	---	---
PSG5	5673	broad.mit.edu	37	19	43690516	43690516	+	Silent	SNP	G	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:43690516G>T	uc002ovu.2	-	1	173	c.42C>A	c.(40-42)ACC>ACA	p.T14T	PSG6_uc010xwk.1_Intron|PSG5_uc010eir.2_5'Flank|PSG5_uc002ovx.2_Silent_p.T14T|PSG5_uc002ovv.2_Silent_p.T14T|PSG5_uc002ovw.2_Silent_p.T14T	NM_002781	NP_002772	Q15238	PSG5_HUMAN	pregnancy specific beta-1-glycoprotein 5	14					female pregnancy	extracellular region				skin(3)	3		Prostate(69;0.00899)																---	---	---	---
PSG5	5673	broad.mit.edu	37	19	43690517	43690517	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:43690517G>T	uc002ovu.2	-	1	172	c.41C>A	c.(40-42)ACC>AAC	p.T14N	PSG6_uc010xwk.1_Intron|PSG5_uc010eir.2_5'Flank|PSG5_uc002ovx.2_Missense_Mutation_p.T14N|PSG5_uc002ovv.2_Missense_Mutation_p.T14N|PSG5_uc002ovw.2_Missense_Mutation_p.T14N	NM_002781	NP_002772	Q15238	PSG5_HUMAN	pregnancy specific beta-1-glycoprotein 5	14					female pregnancy	extracellular region				skin(3)	3		Prostate(69;0.00899)																---	---	---	---
PSG5	5673	broad.mit.edu	37	19	43690527	43690527	+	Missense_Mutation	SNP	G	C	C	rs142338466		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:43690527G>C	uc002ovu.2	-	1	162	c.31C>G	c.(31-33)CAG>GAG	p.Q11E	PSG6_uc010xwk.1_Intron|PSG5_uc010eir.2_5'Flank|PSG5_uc002ovx.2_Missense_Mutation_p.Q11E|PSG5_uc002ovv.2_Missense_Mutation_p.Q11E|PSG5_uc002ovw.2_Missense_Mutation_p.Q11E	NM_002781	NP_002772	Q15238	PSG5_HUMAN	pregnancy specific beta-1-glycoprotein 5	11					female pregnancy	extracellular region				skin(3)	3		Prostate(69;0.00899)																---	---	---	---
PSG4	5672	broad.mit.edu	37	19	43702142	43702142	+	Intron	SNP	T	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:43702142T>A	uc002ovy.2	-						PSG6_uc010xwk.1_Intron|PSG4_uc002owa.2_Intron|PSG4_uc002owb.2_Intron|PSG4_uc002ovz.2_Intron	NM_002780	NP_002771			pregnancy specific beta-1-glycoprotein 4 isoform						defense response|female pregnancy	extracellular region				ovary(1)	1		Prostate(69;0.00682)																---	---	---	---
C19orf61	56006	broad.mit.edu	37	19	44254780	44254780	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:44254780C>A	uc002oxj.2	-	2	457	c.114G>T	c.(112-114)GAG>GAT	p.E38D	C19orf61_uc002oxk.2_Missense_Mutation_p.E38D|C19orf61_uc010eiy.1_Missense_Mutation_p.E38D	NM_019108	NP_061981	Q9H0W8	SMG9_HUMAN	SMG9 protein	38					nuclear-transcribed mRNA catabolic process, nonsense-mediated decay	intracellular	protein binding				0		Prostate(69;0.0352)																---	---	---	---
ZNF222	7673	broad.mit.edu	37	19	44536932	44536932	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:44536932T>C	uc002oyc.2	+	4	1288	c.1105T>C	c.(1105-1107)TAT>CAT	p.Y369H	ZNF284_uc010ejd.2_Intron|ZNF222_uc002oye.2_Missense_Mutation_p.Y409H|ZNF222_uc002oyd.2_Missense_Mutation_p.Y315H	NM_013360	NP_037492	Q9UK12	ZN222_HUMAN	zinc finger protein 222 isoform 2	369	C2H2-type 9.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(3)	3		Prostate(69;0.0435)																---	---	---	---
ZNF223	7766	broad.mit.edu	37	19	44564726	44564726	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:44564726T>C	uc002oyf.1	+	3	387	c.134T>C	c.(133-135)CTG>CCG	p.L45P	ZNF284_uc010ejd.2_RNA	NM_013361	NP_037493	Q9UK11	ZN223_HUMAN	zinc finger protein 223	45	KRAB.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1		Prostate(69;0.0352)																---	---	---	---
ZNF234	10780	broad.mit.edu	37	19	44661555	44661555	+	Silent	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:44661555G>A	uc002oym.2	+	6	1693	c.1386G>A	c.(1384-1386)GGG>GGA	p.G462G	ZNF234_uc002oyl.3_Silent_p.G462G	NM_006630	NP_006621	Q14588	ZN234_HUMAN	zinc finger protein 234	462	C2H2-type 12.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0		Prostate(69;0.0435)																---	---	---	---
ZNF227	7770	broad.mit.edu	37	19	44738881	44738881	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:44738881A>G	uc002oyu.2	+	6	503	c.298A>G	c.(298-300)ACA>GCA	p.T100A	ZNF227_uc010xwu.1_Missense_Mutation_p.T49A|ZNF227_uc002oyv.2_Missense_Mutation_p.T100A|ZNF227_uc010xwv.1_Missense_Mutation_p.T49A|ZNF227_uc010xww.1_Missense_Mutation_p.T21A|ZNF227_uc002oyw.2_Missense_Mutation_p.T72A|ZNF227_uc010ejh.2_Missense_Mutation_p.T93A|ZNF235_uc002oyx.1_Intron	NM_182490	NP_872296	Q86WZ6	ZN227_HUMAN	zinc finger protein 227	100					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1		Prostate(69;0.0435)																---	---	---	---
ZNF235	9310	broad.mit.edu	37	19	44791462	44791462	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:44791462C>A	uc002oza.3	-	5	2229	c.2126G>T	c.(2125-2127)AGG>ATG	p.R709M	ZNF235_uc002oyx.1_Intron|ZNF235_uc010eji.2_Intron|ZNF235_uc002ozb.3_Missense_Mutation_p.R705M|ZNF235_uc010xwx.1_Missense_Mutation_p.R623M	NM_004234	NP_004225	Q14590	ZN235_HUMAN	zinc finger protein 93 homolog	709					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(2)|large_intestine(1)	3		Prostate(69;0.0352)|all_neural(266;0.116)																---	---	---	---
ZNF235	9310	broad.mit.edu	37	19	44793191	44793191	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:44793191A>G	uc002oza.3	-	5	500	c.397T>C	c.(397-399)TTC>CTC	p.F133L	ZNF235_uc002oyx.1_Intron|ZNF235_uc010eji.2_Intron|ZNF235_uc002ozb.3_Missense_Mutation_p.F129L|ZNF235_uc010xwx.1_Missense_Mutation_p.F47L	NM_004234	NP_004225	Q14590	ZN235_HUMAN	zinc finger protein 93 homolog	133					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(2)|large_intestine(1)	3		Prostate(69;0.0352)|all_neural(266;0.116)																---	---	---	---
PVR	5817	broad.mit.edu	37	19	45164574	45164574	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:45164574G>A	uc002ozm.2	+	7	1465	c.1166G>A	c.(1165-1167)AGC>AAC	p.S389N	PVR_uc010xxb.1_Missense_Mutation_p.S336N|PVR_uc010xxc.1_Missense_Mutation_p.S344N|PVR_uc002ozn.2_Missense_Mutation_p.S334N	NM_006505	NP_006496	P15151	PVR_HUMAN	poliovirus receptor isoform alpha	389	Cytoplasmic (Potential).				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)														---	---	---	---
NKPD1	284353	broad.mit.edu	37	19	45655236	45655236	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:45655236G>A	uc010xxi.1	-	4	2459	c.2459C>T	c.(2458-2460)GCG>GTG	p.A820V		NM_198478	NP_940880			NTPase, KAP family P-loop domain containing 1												0		Ovarian(192;0.0728)|all_neural(266;0.112)		OV - Ovarian serous cystadenocarcinoma(262;0.00863)|GBM - Glioblastoma multiforme(486;0.231)														---	---	---	---
VASP	7408	broad.mit.edu	37	19	46020979	46020979	+	Nonsense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:46020979C>T	uc002pcg.2	+	2	406	c.64C>T	c.(64-66)CGA>TGA	p.R22*	VASP_uc010eki.2_Silent_p.S5S|VASP_uc002pci.2_Nonsense_Mutation_p.R9*	NM_003370	NP_003361	P50552	VASP_HUMAN	vasodilator-stimulated phosphoprotein	22	WH1.				axon guidance|cell junction assembly|T cell receptor signaling pathway	actin cytoskeleton|cytosol|filopodium membrane|focal adhesion|lamellipodium membrane	actin binding|profilin binding|SH3 domain binding				0		Ovarian(192;0.051)|all_neural(266;0.112)		OV - Ovarian serous cystadenocarcinoma(262;0.0145)|GBM - Glioblastoma multiforme(486;0.154)														---	---	---	---
FBXO46	23403	broad.mit.edu	37	19	46216578	46216578	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:46216578G>T	uc002pcy.2	-	2	301	c.176C>A	c.(175-177)GCC>GAC	p.A59D	FBXO46_uc002pcz.2_Missense_Mutation_p.A59D	NM_001080469	NP_001073938	Q6PJ61	FBX46_HUMAN	F-box protein 46	59							protein binding			ovary(1)|lung(1)|breast(1)	3		Ovarian(192;0.179)|all_neural(266;0.224)		OV - Ovarian serous cystadenocarcinoma(262;0.00568)|GBM - Glioblastoma multiforme(486;0.0844)|Epithelial(262;0.201)														---	---	---	---
ZC3H4	23211	broad.mit.edu	37	19	47589663	47589663	+	Missense_Mutation	SNP	T	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:47589663T>A	uc002pga.3	-	6	886	c.848A>T	c.(847-849)GAT>GTT	p.D283V	ZC3H4_uc002pgb.1_Intron	NM_015168	NP_055983	Q9UPT8	ZC3H4_HUMAN	zinc finger CCCH-type containing 4	283	Gly-rich.						nucleic acid binding|zinc ion binding			skin(4)|ovary(2)	6		all_cancers(25;3.3e-08)|all_epithelial(76;2.28e-06)|all_lung(116;7.86e-06)|Lung NSC(112;2.31e-05)|all_neural(266;0.026)|Ovarian(192;0.0392)|Breast(70;0.0889)		OV - Ovarian serous cystadenocarcinoma(262;5.76e-05)|all cancers(93;7.69e-05)|Epithelial(262;0.00354)|GBM - Glioblastoma multiforme(486;0.0372)														---	---	---	---
CCDC9	26093	broad.mit.edu	37	19	47774411	47774411	+	Silent	SNP	C	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:47774411C>A	uc010xym.1	+	11	1365	c.1158C>A	c.(1156-1158)TCC>TCA	p.S386S		NM_015603	NP_056418	Q9Y3X0	CCDC9_HUMAN	coiled-coil domain containing 9	386	Pro-rich.										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)														---	---	---	---
NAPA	8775	broad.mit.edu	37	19	47991592	47991592	+	Silent	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:47991592G>A	uc002pha.1	-	11	1141	c.841C>T	c.(841-843)CTG>TTG	p.L281L	uc002pgz.1_Intron|NAPA_uc002phb.1_Silent_p.L242L|NAPA_uc002phc.1_Silent_p.L168L|NAPA_uc002phd.1_Silent_p.L281L	NM_003827	NP_003818	P54920	SNAA_HUMAN	N-ethylmaleimide-sensitive factor attachment	281					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)														---	---	---	---
CABP5	56344	broad.mit.edu	37	19	48533824	48533824	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:48533824A>G	uc002phu.1	-	6	637	c.512T>C	c.(511-513)ATG>ACG	p.M171T		NM_019855	NP_062829	Q9NP86	CABP5_HUMAN	calcium binding protein 5	171	EF-hand 4.				signal transduction	cytoplasm	calcium ion binding			skin(1)	1		all_cancers(25;1.86e-08)|all_lung(116;1.14e-06)|all_epithelial(76;1.16e-06)|Lung NSC(112;2.54e-06)|all_neural(266;0.0138)|Ovarian(192;0.0261)|Breast(70;0.203)		OV - Ovarian serous cystadenocarcinoma(262;4.09e-05)|all cancers(93;0.000322)|Epithelial(262;0.01)|GBM - Glioblastoma multiforme(486;0.058)														---	---	---	---
PLA2G4C	8605	broad.mit.edu	37	19	48607874	48607874	+	Silent	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:48607874C>T	uc002phx.2	-	4	626	c.228G>A	c.(226-228)ACG>ACA	p.T76T	PLA2G4C_uc002phw.2_Silent_p.T11T|PLA2G4C_uc010elr.2_Silent_p.T76T|PLA2G4C_uc010xzd.1_Silent_p.T86T|PLA2G4C_uc002phy.3_Silent_p.T76T	NM_003706	NP_003697	Q9UP65	PA24C_HUMAN	phospholipase A2, group IVC isoform 1 precursor	76	PLA2c.				arachidonic acid metabolic process|glycerophospholipid catabolic process|inflammatory response|intracellular signal transduction|parturition	cytosol|membrane	calcium-independent phospholipase A2 activity|phospholipid binding			ovary(1)|skin(1)	2		all_cancers(25;2.84e-05)|all_lung(116;4.62e-05)|Lung NSC(112;7.61e-05)|all_epithelial(76;0.000192)|all_neural(266;0.0506)|Ovarian(192;0.113)		OV - Ovarian serous cystadenocarcinoma(262;8.09e-05)|all cancers(93;0.000517)|Epithelial(262;0.0135)|GBM - Glioblastoma multiforme(486;0.0717)														---	---	---	---
LIG1	3978	broad.mit.edu	37	19	48626206	48626206	+	Silent	SNP	C	T	T	rs150917896		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:48626206C>T	uc002pia.1	-	23	2337	c.2217G>A	c.(2215-2217)TCG>TCA	p.S739S	LIG1_uc010xze.1_Silent_p.S432S|LIG1_uc002phz.1_RNA|LIG1_uc002pib.1_RNA|LIG1_uc010xzf.1_Silent_p.S671S|LIG1_uc010xzg.1_Silent_p.S708S	NM_000234	NP_000225	P18858	DNLI1_HUMAN	DNA ligase I	739					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					---	---	---	---
LIG1	3978	broad.mit.edu	37	19	48653011	48653011	+	Intron	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:48653011C>T	uc002pia.1	-						LIG1_uc010xze.1_Intron|LIG1_uc002phz.1_Intron|LIG1_uc002pib.1_Intron|LIG1_uc010xzf.1_Intron|LIG1_uc010xzg.1_Intron|LIG1_uc010xzh.1_Intron	NM_000234	NP_000225			DNA ligase I						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					---	---	---	---
GRIN2D	2906	broad.mit.edu	37	19	48918140	48918140	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:48918140C>T	uc002pjc.3	+	6	1520	c.1432C>T	c.(1432-1434)CGC>TGC	p.R478C		NM_000836	NP_000827	O15399	NMDE4_HUMAN	N-methyl-D-aspartate receptor subunit 2D	478	Extracellular (Potential).					cell junction|outer membrane-bounded periplasmic space|postsynaptic membrane	extracellular-glutamate-gated ion channel activity|protein binding			ovary(3)|breast(3)	6		all_epithelial(76;1.11e-06)|all_lung(116;5.79e-06)|Lung NSC(112;1.18e-05)|all_neural(266;0.0189)|Ovarian(192;0.0261)|Breast(70;0.203)		all cancers(93;0.00014)|OV - Ovarian serous cystadenocarcinoma(262;0.000233)|Epithelial(262;0.0112)|GBM - Glioblastoma multiforme(486;0.0161)	L-Glutamic Acid(DB00142)|Loperamide(DB00836)|Orphenadrine(DB01173)													---	---	---	---
GRIN2D	2906	broad.mit.edu	37	19	48945504	48945504	+	Silent	SNP	G	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:48945504G>C	uc002pjc.3	+	12	2626	c.2538G>C	c.(2536-2538)GCG>GCC	p.A846A	GRIN2D_uc010elx.2_Silent_p.A81A	NM_000836	NP_000827	O15399	NMDE4_HUMAN	N-methyl-D-aspartate receptor subunit 2D	846	Helical; (Potential).					cell junction|outer membrane-bounded periplasmic space|postsynaptic membrane	extracellular-glutamate-gated ion channel activity|protein binding			ovary(3)|breast(3)	6		all_epithelial(76;1.11e-06)|all_lung(116;5.79e-06)|Lung NSC(112;1.18e-05)|all_neural(266;0.0189)|Ovarian(192;0.0261)|Breast(70;0.203)		all cancers(93;0.00014)|OV - Ovarian serous cystadenocarcinoma(262;0.000233)|Epithelial(262;0.0112)|GBM - Glioblastoma multiforme(486;0.0161)	L-Glutamic Acid(DB00142)|Loperamide(DB00836)|Orphenadrine(DB01173)													---	---	---	---
HSD17B14	51171	broad.mit.edu	37	19	49339647	49339647	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:49339647C>T	uc002pkv.1	-	1	288	c.22G>A	c.(22-24)GCC>ACC	p.A8T	HSD17B14_uc010emk.1_Missense_Mutation_p.A8T	NM_016246	NP_057330	Q9BPX1	DHB14_HUMAN	dehydrogenase/reductase (SDR family) member 10	8					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)												OREG0025610	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
PLEKHA4	57664	broad.mit.edu	37	19	49344555	49344555	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:49344555G>A	uc002pkx.2	-	17	2307	c.1756C>T	c.(1756-1758)CGG>TGG	p.R586W	PLEKHA4_uc002pkw.1_Missense_Mutation_p.R101W|PLEKHA4_uc010eml.2_Intron	NM_020904	NP_065955	Q9H4M7	PKHA4_HUMAN	pleckstrin homology domain containing family A	586						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)														---	---	---	---
PLEKHA4	57664	broad.mit.edu	37	19	49364949	49364949	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:49364949C>A	uc002pkx.2	-	4	744	c.193G>T	c.(193-195)GAC>TAC	p.D65Y	PLEKHA4_uc002pkw.1_5'Flank|PLEKHA4_uc010eml.2_Missense_Mutation_p.D65Y	NM_020904	NP_065955	Q9H4M7	PKHA4_HUMAN	pleckstrin homology domain containing family A	65	PH.					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)														---	---	---	---
LHB	3972	broad.mit.edu	37	19	49519503	49519503	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:49519503C>T	uc002plt.2	-	3	257	c.248G>A	c.(247-249)CGC>CAC	p.R83H		NM_000894	NP_000885	P01229	LSHB_HUMAN	luteinizing hormone beta subunit precursor	83					cell-cell signaling|cellular nitrogen compound metabolic process|male gonad development|peptide hormone processing|progesterone biosynthetic process|signal transduction	extracellular region|soluble fraction	hormone activity				0		all_epithelial(76;9.62e-07)|all_lung(116;1.7e-06)|Lung NSC(112;3.55e-06)|all_neural(266;0.0189)|Ovarian(192;0.0261)		all cancers(93;0.000371)|OV - Ovarian serous cystadenocarcinoma(262;0.000503)|GBM - Glioblastoma multiforme(486;0.00518)|Epithelial(262;0.0427)	Lutropin alfa(DB00044)|Menotropins(DB00032)													---	---	---	---
PPFIA3	8541	broad.mit.edu	37	19	49636520	49636520	+	Silent	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:49636520C>T	uc002pmr.2	+	9	1385	c.1053C>T	c.(1051-1053)GCC>GCT	p.A351A	PPFIA3_uc010yai.1_RNA|PPFIA3_uc010emt.2_Silent_p.A275A|PPFIA3_uc010yaj.1_RNA|PPFIA3_uc002pms.2_Silent_p.A219A	NM_003660	NP_003651	O75145	LIPA3_HUMAN	PTPRF interacting protein alpha 3	351	Potential.					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)														---	---	---	---
SLC17A7	57030	broad.mit.edu	37	19	49935893	49935893	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:49935893C>T	uc002pnp.2	-	9	1205	c.1033G>A	c.(1033-1035)GCG>ACG	p.A345T	SLC17A7_uc002pno.2_Missense_Mutation_p.A44T	NM_020309	NP_064705	Q9P2U7	VGLU1_HUMAN	solute carrier family 17, member 7	345	Helical; (Potential).				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)														---	---	---	---
RRAS	6237	broad.mit.edu	37	19	50140100	50140100	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:50140100C>T	uc002pop.1	-	3	370	c.325G>A	c.(325-327)GCC>ACC	p.A109T		NM_006270	NP_006261	P10301	RRAS_HUMAN	related RAS viral (r-ras) oncogene homolog	109					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)														---	---	---	---
SCAF1	58506	broad.mit.edu	37	19	50156426	50156426	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:50156426T>C	uc002poq.2	+	7	2904	c.2780T>C	c.(2779-2781)GTC>GCC	p.V927A		NM_021228	NP_067051	Q9H7N4	SFR19_HUMAN	SR-related CTD-associated factor 1	927					mRNA processing|RNA splicing	nucleus	RNA binding				0		all_lung(116;1.05e-05)|Lung NSC(112;3.77e-05)|all_neural(266;0.196)|Ovarian(192;0.231)		OV - Ovarian serous cystadenocarcinoma(262;0.00113)|GBM - Glioblastoma multiforme(134;0.0204)														---	---	---	---
PTOV1	53635	broad.mit.edu	37	19	50360379	50360379	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:50360379C>T	uc002pqf.1	+	6	876	c.706C>T	c.(706-708)CGC>TGC	p.R236C	PTOV1_uc002ppz.3_RNA|PTOV1_uc002pqb.3_Missense_Mutation_p.R204C|PTOV1_uc002pqa.2_RNA|PTOV1_uc002pqc.1_RNA|PTOV1_uc002pqd.2_RNA|PTOV1_uc002pqe.1_RNA	NM_017432	NP_059128	Q86YD1	PTOV1_HUMAN	prostate tumor overexpressed 1	236	Interaction with FLOT1.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus|perinuclear region of cytoplasm|plasma membrane					0		all_lung(116;1.05e-05)|Lung NSC(112;3.77e-05)|all_neural(266;0.107)|Ovarian(192;0.231)		GBM - Glioblastoma multiforme(134;0.0116)|OV - Ovarian serous cystadenocarcinoma(262;0.0132)														---	---	---	---
MYH14	79784	broad.mit.edu	37	19	50720995	50720995	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:50720995G>A	uc002prr.1	+	3	576	c.529G>A	c.(529-531)GTG>ATG	p.V177M	MYH14_uc010enu.1_Missense_Mutation_p.V177M|MYH14_uc002prq.1_Missense_Mutation_p.V177M	NM_024729	NP_079005	Q7Z406	MYH14_HUMAN	myosin, heavy chain 14 isoform 2	177	Myosin head-like.				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)														---	---	---	---
NR1H2	7376	broad.mit.edu	37	19	50881403	50881403	+	Intron	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:50881403C>T	uc010enw.2	+						NR1H2_uc002prv.3_Intron|NR1H2_uc002prz.3_Intron|NR1H2_uc002psa.3_Intron	NM_007121	NP_009052			nuclear receptor subfamily 1, group H, member 2						negative regulation of cholesterol storage|negative regulation of interferon-gamma-mediated signaling pathway|negative regulation of lipid transport|negative regulation of pinocytosis|negative regulation of transcription, DNA-dependent|positive regulation of cellular protein metabolic process|positive regulation of cholesterol efflux|positive regulation of fatty acid biosynthetic process|positive regulation of lipoprotein lipase activity|positive regulation of transcription from RNA polymerase II promoter|positive regulation of triglyceride biosynthetic process|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor	cytoplasm|nucleoplasm	sequence-specific DNA binding|steroid hormone receptor activity|zinc ion binding				0		all_neural(266;0.057)		OV - Ovarian serous cystadenocarcinoma(262;0.00757)|GBM - Glioblastoma multiforme(134;0.0186)														---	---	---	---
LRRC4B	94030	broad.mit.edu	37	19	51022655	51022655	+	Silent	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:51022655C>T	uc002pss.2	-	3	452	c.315G>A	c.(313-315)ACG>ACA	p.T105T		NM_001080457	NP_001073926	Q9NT99	LRC4B_HUMAN	leucine rich repeat containing 4B precursor	105	LRR 1.|Extracellular (Potential).					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	51133348	51133348	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:51133348G>A	uc002pst.2	-	3	1389	c.755C>T	c.(754-756)GCC>GTC	p.A252V	SYT3_uc002psv.2_Missense_Mutation_p.A252V|SYT3_uc010ycd.1_Missense_Mutation_p.A252V	NM_032298	NP_115674	Q9BQG1	SYT3_HUMAN	synaptotagmin III	252	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)														---	---	---	---
KLK4	9622	broad.mit.edu	37	19	51411999	51411999	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:51411999C>T	uc002pua.1	-	3	311	c.311G>A	c.(310-312)CGG>CAG	p.R104Q	KLK4_uc002pty.1_Missense_Mutation_p.R55Q|KLK4_uc002ptz.1_RNA|KLK4_uc002pub.1_Missense_Mutation_p.R9Q|KLK4_uc002puc.1_RNA|KLK4_uc010eoi.1_Missense_Mutation_p.R9Q|KLK4_uc002pud.1_Missense_Mutation_p.R9Q	NM_004917	NP_004908	Q9Y5K2	KLK4_HUMAN	kallikrein-related peptidase 4 preproprotein	104	Peptidase S1.				proteolysis	extracellular region	metal ion binding|serine-type endopeptidase activity				0		all_neural(266;0.026)		OV - Ovarian serous cystadenocarcinoma(262;0.00624)|GBM - Glioblastoma multiforme(134;0.00878)														---	---	---	---
SIGLEC7	27036	broad.mit.edu	37	19	51650011	51650011	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:51650011G>A	uc002pvv.1	+	5	1097	c.1028G>A	c.(1027-1029)GGC>GAC	p.G343D	SIGLEC7_uc002pvw.1_Missense_Mutation_p.G250D|SIGLEC7_uc010eoq.1_Intron|SIGLEC7_uc010eor.1_Intron	NM_014385	NP_055200	Q9Y286	SIGL7_HUMAN	sialic acid binding Ig-like lectin 7 isoform 1	343	Extracellular (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)														---	---	---	---
SIGLEC12	89858	broad.mit.edu	37	19	52004817	52004817	+	Silent	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:52004817A>G	uc002pwx.1	-	1	227	c.171T>C	c.(169-171)GAT>GAC	p.D57D	SIGLEC12_uc002pww.1_5'Flank|SIGLEC12_uc010eoy.1_5'UTR	NM_053003	NP_443729	Q96PQ1	SIG12_HUMAN	sialic acid binding immunoglobulin-like	57	Ig-like V-type 1.|Extracellular (Potential).				cell adhesion	integral to membrane	sugar binding			ovary(3)|skin(2)	5		all_neural(266;0.0199)		GBM - Glioblastoma multiforme(134;0.00161)|OV - Ovarian serous cystadenocarcinoma(262;0.0102)														---	---	---	---
ZNF175	7728	broad.mit.edu	37	19	52090685	52090685	+	Silent	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:52090685C>T	uc002pxb.2	+	5	1479	c.1101C>T	c.(1099-1101)GAC>GAT	p.D367D		NM_007147	NP_009078	Q9Y473	ZN175_HUMAN	zinc finger protein 175	367	C2H2-type 4.				response to virus	cytoplasm|intermediate filament cytoskeleton|nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding				0		all_neural(266;0.0299)		GBM - Glioblastoma multiforme(134;0.000426)|OV - Ovarian serous cystadenocarcinoma(262;0.0257)														---	---	---	---
ZNF350	59348	broad.mit.edu	37	19	52469312	52469312	+	Missense_Mutation	SNP	G	A	A	rs28997584	byFrequency	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:52469312G>A	uc002pyd.2	-	5	622	c.394C>T	c.(394-396)CGT>TGT	p.R132C	uc002pyb.2_Intron|uc002pyc.2_Intron	NM_021632	NP_067645	Q9GZX5	ZN350_HUMAN	zinc finger protein 350	132					negative regulation of transcription, DNA-dependent|transcription, DNA-dependent	nuclear matrix|transcriptional repressor complex	DNA binding|protein binding|zinc ion binding			breast(1)	1		all_neural(266;0.0505)		GBM - Glioblastoma multiforme(134;0.00124)|OV - Ovarian serous cystadenocarcinoma(262;0.0179)														---	---	---	---
ZNF480	147657	broad.mit.edu	37	19	52825123	52825123	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:52825123A>G	uc010ydl.1	+	5	690	c.620A>G	c.(619-621)GAG>GGG	p.E207G	ZNF480_uc002pyv.2_Missense_Mutation_p.E130G|ZNF480_uc010ydm.1_Missense_Mutation_p.E164G|ZNF480_uc010epn.2_Missense_Mutation_p.E38G|uc002pyw.1_Intron	NM_144684	NP_653285	Q8WV37	ZN480_HUMAN	zinc finger protein 480	207	C2H2-type 1; atypical.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	nucleic acid binding|zinc ion binding			large_intestine(1)	1				GBM - Glioblastoma multiforme(134;0.00212)|OV - Ovarian serous cystadenocarcinoma(262;0.00369)														---	---	---	---
ZNF578	147660	broad.mit.edu	37	19	53005118	53005118	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:53005118C>T	uc002pzp.3	+	4	264	c.20C>T	c.(19-21)GCT>GTT	p.A7V		NM_001099694	NP_001093164	Q96N58	ZN578_HUMAN	zinc finger protein 578	Error:Variant_position_missing_in_Q96N58_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)														---	---	---	---
ZNF137	7696	broad.mit.edu	37	19	53100098	53100098	+	RNA	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:53100098T>C	uc002pzt.2	+	1		c.162T>C				NR_023311				Homo sapiens zinc finger protein 137, mRNA (cDNA clone IMAGE:40016639).												0				GBM - Glioblastoma multiforme(134;0.0212)|OV - Ovarian serous cystadenocarcinoma(262;0.0221)														---	---	---	---
ZNF611	81856	broad.mit.edu	37	19	53209615	53209615	+	Silent	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:53209615G>A	uc002pzz.2	-	7	1010	c.693C>T	c.(691-693)TTC>TTT	p.F231F	ZNF611_uc010eqc.2_Silent_p.F161F|ZNF611_uc010ydo.1_Silent_p.F161F|ZNF611_uc010ydr.1_Silent_p.F162F|ZNF611_uc010ydp.1_Silent_p.F231F|ZNF611_uc010ydq.1_Silent_p.F231F|ZNF611_uc002qaa.3_Silent_p.F161F	NM_030972	NP_112234	Q8N823	ZN611_HUMAN	zinc finger protein 611 isoform a	231	C2H2-type 1; degenerate.				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)														---	---	---	---
ZNF600	162966	broad.mit.edu	37	19	53270137	53270137	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:53270137C>T	uc002qab.3	-	3	1158	c.872G>A	c.(871-873)CGT>CAT	p.R291H		NM_198457	NP_940859	Q6ZNG1	ZN600_HUMAN	zinc finger protein 600	291	C2H2-type 5.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0				OV - Ovarian serous cystadenocarcinoma(262;0.0241)|GBM - Glioblastoma multiforme(134;0.0404)														---	---	---	---
ZNF28	7576	broad.mit.edu	37	19	53303186	53303186	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:53303186T>C	uc002qad.2	-	4	2032	c.1912A>G	c.(1912-1914)AAT>GAT	p.N638D	ZNF28_uc002qac.2_Missense_Mutation_p.N585D|ZNF28_uc010eqe.2_Missense_Mutation_p.N584D	NM_006969	NP_008900	P17035	ZNF28_HUMAN	zinc finger protein 28	638	C2H2-type 16.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			skin(1)	1				GBM - Glioblastoma multiforme(134;0.0386)|Lung(386;0.145)														---	---	---	---
ZNF28	7576	broad.mit.edu	37	19	53304887	53304887	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:53304887T>C	uc002qad.2	-	4	331	c.211A>G	c.(211-213)ACA>GCA	p.T71A	ZNF28_uc002qac.2_Missense_Mutation_p.T18A|ZNF28_uc010eqe.2_Missense_Mutation_p.T17A	NM_006969	NP_008900	P17035	ZNF28_HUMAN	zinc finger protein 28	71	KRAB.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			skin(1)	1				GBM - Glioblastoma multiforme(134;0.0386)|Lung(386;0.145)														---	---	---	---
ZNF468	90333	broad.mit.edu	37	19	53352443	53352443	+	Silent	SNP	C	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:53352443C>A	uc002qaf.2	-	3	190	c.39G>T	c.(37-39)GTG>GTT	p.V13V	ZNF468_uc002qae.2_5'UTR	NM_001008801	NP_001008801	Q5VIY5	ZN468_HUMAN	zinc finger protein ZNF468 isoform 2	13	KRAB.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(2)	2				GBM - Glioblastoma multiforme(134;0.0358)														---	---	---	---
ZNF320	162967	broad.mit.edu	37	19	53383867	53383867	+	Silent	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:53383867T>C	uc002qag.2	-	4	1703	c.1512A>G	c.(1510-1512)AAA>AAG	p.K504K	ZNF320_uc010eqh.1_5'Flank|ZNF320_uc010eqi.1_Intron|ZNF320_uc002qah.2_Silent_p.K450K|ZNF320_uc002qai.2_Silent_p.K504K	NM_207333	NP_997216	A2RRD8	ZN320_HUMAN	zinc finger protein 320	504					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0				GBM - Glioblastoma multiforme(134;0.0534)														---	---	---	---
ZNF347	84671	broad.mit.edu	37	19	53645202	53645202	+	Silent	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:53645202C>T	uc002qbb.1	-	5	948	c.879G>A	c.(877-879)GAG>GAA	p.E293E	ZNF347_uc010eql.1_Silent_p.E294E|ZNF347_uc002qbc.1_Silent_p.E294E	NM_032584	NP_115973	Q96SE7	ZN347_HUMAN	zinc finger protein 347	293	C2H2-type 2.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0				GBM - Glioblastoma multiforme(134;0.0179)														---	---	---	---
ZNF813	126017	broad.mit.edu	37	19	53989909	53989909	+	Silent	SNP	G	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:53989909G>T	uc002qbu.2	+	3	167	c.39G>T	c.(37-39)GTG>GTT	p.V13V	ZNF813_uc010eqq.1_RNA	NM_001004301	NP_001004301	Q6ZN06	ZN813_HUMAN	zinc finger protein 813	13	KRAB.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			large_intestine(1)	1				GBM - Glioblastoma multiforme(134;0.00619)														---	---	---	---
ZNF331	55422	broad.mit.edu	37	19	54074970	54074970	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:54074970A>G	uc002qbx.1	+	6	1556	c.122A>G	c.(121-123)AAC>AGC	p.N41S	ZNF331_uc002qby.1_Missense_Mutation_p.N41S|ZNF331_uc002qbz.1_Missense_Mutation_p.N41S|ZNF331_uc002qca.1_Missense_Mutation_p.N41S|ZNF331_uc010eqr.1_Missense_Mutation_p.N41S|ZNF331_uc002qcb.1_Missense_Mutation_p.N41S|ZNF331_uc002qcc.1_Missense_Mutation_p.N41S|ZNF331_uc002qcd.1_Missense_Mutation_p.N41S	NM_018555	NP_061025	Q9NQX6	ZN331_HUMAN	zinc finger protein 331	41	KRAB.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			skin(3)|upper_aerodigestive_tract(1)|ovary(1)|lung(1)	6				GBM - Glioblastoma multiforme(134;0.00555)				T	?	follicular thyroid adenoma								---	---	---	---
ZNF331	55422	broad.mit.edu	37	19	54081041	54081041	+	Silent	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:54081041A>G	uc002qbx.1	+	7	2661	c.1227A>G	c.(1225-1227)AAA>AAG	p.K409K	ZNF331_uc002qby.1_Silent_p.K409K|ZNF331_uc002qbz.1_Silent_p.K409K|ZNF331_uc002qca.1_Silent_p.K409K|ZNF331_uc010eqr.1_Silent_p.K409K|ZNF331_uc002qcb.1_Silent_p.K409K|ZNF331_uc002qcc.1_Silent_p.K409K|ZNF331_uc002qcd.1_Silent_p.K409K	NM_018555	NP_061025	Q9NQX6	ZN331_HUMAN	zinc finger protein 331	409					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			skin(3)|upper_aerodigestive_tract(1)|ovary(1)|lung(1)	6				GBM - Glioblastoma multiforme(134;0.00555)				T	?	follicular thyroid adenoma								---	---	---	---
NLRP12	91662	broad.mit.edu	37	19	54313161	54313161	+	Silent	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:54313161C>T	uc002qch.3	-	3	1972	c.1752G>A	c.(1750-1752)TCG>TCA	p.S584S	NLRP12_uc010eqw.2_5'Flank|NLRP12_uc002qci.3_Silent_p.S584S|NLRP12_uc002qcj.3_Silent_p.S584S|NLRP12_uc002qck.3_RNA|NLRP12_uc010eqx.2_Silent_p.S584S	NM_144687	NP_653288	P59046	NAL12_HUMAN	NLR family, pyrin domain containing 12 isoform	584					negative regulation of I-kappaB kinase/NF-kappaB cascade|negative regulation of interleukin-1 secretion|negative regulation of interleukin-6 biosynthetic process|negative regulation of protein autophosphorylation|negative regulation of Toll signaling pathway|positive regulation of inflammatory response|positive regulation of interleukin-1 beta secretion|regulation of interleukin-18 biosynthetic process|release of cytoplasmic sequestered NF-kappaB	cytoplasm	ATP binding|caspase activator activity|protein binding			ovary(4)|upper_aerodigestive_tract(2)|lung(1)	7	Ovarian(34;0.19)			GBM - Glioblastoma multiforme(134;0.026)														---	---	---	---
NLRP12	91662	broad.mit.edu	37	19	54314364	54314364	+	Silent	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:54314364G>A	uc002qch.3	-	3	769	c.549C>T	c.(547-549)CAC>CAT	p.H183H	NLRP12_uc010eqw.2_5'Flank|NLRP12_uc002qci.3_Silent_p.H183H|NLRP12_uc002qcj.3_Silent_p.H183H|NLRP12_uc002qck.3_RNA|NLRP12_uc010eqx.2_Silent_p.H183H	NM_144687	NP_653288	P59046	NAL12_HUMAN	NLR family, pyrin domain containing 12 isoform	183					negative regulation of I-kappaB kinase/NF-kappaB cascade|negative regulation of interleukin-1 secretion|negative regulation of interleukin-6 biosynthetic process|negative regulation of protein autophosphorylation|negative regulation of Toll signaling pathway|positive regulation of inflammatory response|positive regulation of interleukin-1 beta secretion|regulation of interleukin-18 biosynthetic process|release of cytoplasmic sequestered NF-kappaB	cytoplasm	ATP binding|caspase activator activity|protein binding			ovary(4)|upper_aerodigestive_tract(2)|lung(1)	7	Ovarian(34;0.19)			GBM - Glioblastoma multiforme(134;0.026)														---	---	---	---
MYADM	91663	broad.mit.edu	37	19	54377624	54377624	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:54377624C>T	uc002qcl.2	+	3	989	c.841C>T	c.(841-843)CGC>TGC	p.R281C	MYADM_uc002qcm.2_Missense_Mutation_p.R281C|MYADM_uc002qcn.2_Missense_Mutation_p.R281C|MYADM_uc002qco.2_Missense_Mutation_p.R281C|MYADM_uc002qcp.2_Missense_Mutation_p.R281C	NM_001020820	NP_001018656	Q96S97	MYADM_HUMAN	myeloid-associated differentiation marker	281	MARVEL 2.					integral to membrane				ovary(1)	1	Ovarian(34;0.19)			GBM - Glioblastoma multiforme(134;0.0488)														---	---	---	---
LILRA5	353514	broad.mit.edu	37	19	54823212	54823212	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:54823212C>T	uc002qfe.2	-	4	451	c.331G>A	c.(331-333)GCA>ACA	p.A111T	LILRA5_uc002qff.2_Missense_Mutation_p.A99T|LILRA5_uc010yev.1_Missense_Mutation_p.A111T|LILRA5_uc010yew.1_Missense_Mutation_p.A99T|LILRA5_uc002qfh.1_Missense_Mutation_p.A99T|LILRA5_uc002qfg.1_Missense_Mutation_p.A111T	NM_021250	NP_067073	A6NI73	LIRA5_HUMAN	leukocyte immunoglobulin-like receptor subfamily	111	Extracellular (Potential).|Ig-like C2-type 1.				innate immune response	extracellular region|integral to membrane	receptor activity			upper_aerodigestive_tract(1)	1	Ovarian(34;0.19)			GBM - Glioblastoma multiforme(193;0.105)														---	---	---	---
LENG8	114823	broad.mit.edu	37	19	54967403	54967403	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:54967403C>T	uc002qfv.1	+	8	1316	c.1172C>T	c.(1171-1173)CCG>CTG	p.P391L	LENG8_uc002qfw.2_Missense_Mutation_p.P428L			Q96PV6	LENG8_HUMAN	RecName: Full=Leukocyte receptor cluster member 8;	391	Ser-rich.						protein binding			central_nervous_system(1)|pancreas(1)	2	Ovarian(34;0.19)			GBM - Glioblastoma multiforme(193;0.139)														---	---	---	---
KIR2DS4	3809	broad.mit.edu	37	19	55350916	55350916	+	Missense_Mutation	SNP	C	T	T	rs150357973		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:55350916C>T	uc002qhm.1	+	4	450	c.404C>T	c.(403-405)CCG>CTG	p.P135L	KIR2DS4_uc010yfj.1_Missense_Mutation_p.P128L|KIR2DS4_uc010yfk.1_RNA|KIR3DL1_uc002qhl.3_Intron|KIR2DS4_uc010esg.1_Missense_Mutation_p.P135L|KIR2DS4_uc002qhn.1_Intron	NM_012314	NP_036446	P43632	KI2S4_HUMAN	killer cell immunoglobulin-like receptor, two	135	Extracellular (Potential).					integral to plasma membrane	receptor activity				0				GBM - Glioblastoma multiforme(193;0.0192)														---	---	---	---
SAPS1	22870	broad.mit.edu	37	19	55751278	55751278	+	Silent	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:55751278C>T	uc002qjw.3	-	13	1721	c.1479G>A	c.(1477-1479)GAG>GAA	p.E493E	SAPS1_uc002qjv.2_Silent_p.E555E	NM_014931	NP_055746	Q9UPN7	PP6R1_HUMAN	SAPS domain family, member 1	493					regulation of phosphoprotein phosphatase activity	cytoplasm	protein phosphatase binding				0		Renal(1328;0.245)	BRCA - Breast invasive adenocarcinoma(297;0.209)	GBM - Glioblastoma multiforme(193;0.0449)														---	---	---	---
BRSK1	84446	broad.mit.edu	37	19	55815485	55815485	+	Intron	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:55815485C>T	uc002qkg.2	+						BRSK1_uc002qkf.2_Intron|BRSK1_uc002qkh.2_Intron	NM_032430	NP_115806			BR serine/threonine kinase 1						establishment of cell polarity|G2/M transition DNA damage checkpoint|neuron differentiation|response to UV	cell junction|cytoplasm|nucleus	magnesium ion binding|protein serine/threonine kinase activity			ovary(2)|stomach(1)|lung(1)|breast(1)|skin(1)	6		Renal(1328;0.245)	BRCA - Breast invasive adenocarcinoma(297;0.209)	GBM - Glioblastoma multiforme(193;0.0474)														---	---	---	---
NLRP9	338321	broad.mit.edu	37	19	56244672	56244672	+	Nonsense_Mutation	SNP	C	T	T	rs140796774		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:56244672C>T	uc002qly.2	-	2	553	c.525G>A	c.(523-525)TGG>TGA	p.W175*		NM_176820	NP_789790	Q7RTR0	NALP9_HUMAN	NLR family, pyrin domain containing 9	175	NACHT.					cytoplasm	ATP binding			skin(4)|ovary(2)|breast(1)	7		Colorectal(82;0.000133)|Ovarian(87;0.133)		GBM - Glioblastoma multiforme(193;0.123)														---	---	---	---
NLRP5	126206	broad.mit.edu	37	19	56538642	56538642	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:56538642C>T	uc002qmj.2	+	7	1043	c.1043C>T	c.(1042-1044)ACG>ATG	p.T348M	NLRP5_uc002qmi.2_Missense_Mutation_p.T329M	NM_153447	NP_703148	P59047	NALP5_HUMAN	NACHT, LRR and PYD containing protein 5	348	NACHT.					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	56733691	56733691	+	Missense_Mutation	SNP	A	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:56733691A>T	uc002qmq.2	-	5	910	c.744T>A	c.(742-744)GAT>GAA	p.D248E	ZSCAN5A_uc010ygi.1_Missense_Mutation_p.D131E|ZSCAN5A_uc002qmr.2_Missense_Mutation_p.D248E|ZSCAN5A_uc002qms.1_Missense_Mutation_p.N247K	NM_024303	NP_077279	Q9BUG6	ZSA5A_HUMAN	zinc finger and SCAN domain containing 5A	248				TD -> N (in Ref. 1; BAC05386).	viral reproduction	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			large_intestine(1)|ovary(1)|skin(1)	3																		---	---	---	---
ZNF471	57573	broad.mit.edu	37	19	57035815	57035815	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:57035815T>C	uc002qnh.2	+	5	512	c.379T>C	c.(379-381)TGG>CGG	p.W127R		NM_020813	NP_065864	Q9BX82	ZN471_HUMAN	zinc finger protein 471	127					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)														---	---	---	---
ZNF470	388566	broad.mit.edu	37	19	57085840	57085840	+	Silent	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:57085840T>C	uc002qnl.3	+	4	814	c.138T>C	c.(136-138)AGT>AGC	p.S46S	ZNF470_uc010etn.2_RNA	NM_001001668	NP_001001668	Q6ECI4	ZN470_HUMAN	zinc finger protein 470	46	KRAB.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)|pancreas(1)	2		Colorectal(82;5.46e-05)|Ovarian(87;0.0822)|Renal(1328;0.157)		GBM - Glioblastoma multiforme(193;0.0294)														---	---	---	---
ZNF835	90485	broad.mit.edu	37	19	57176466	57176466	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:57176466C>T	uc010ygo.1	-	2	167	c.167G>A	c.(166-168)TGT>TAT	p.C56Y	ZNF835_uc010ygn.1_Missense_Mutation_p.C34Y	NM_001005850	NP_001005850			zinc finger protein 835											pancreas(3)|skin(1)	4																		---	---	---	---
PEG3	5178	broad.mit.edu	37	19	57327685	57327685	+	Nonsense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:57327685G>A	uc002qnu.2	-	7	2476	c.2125C>T	c.(2125-2127)CGA>TGA	p.R709*	ZIM2_uc010ygq.1_Intron|ZIM2_uc010ygr.1_Intron|ZIM2_uc002qnr.2_Intron|ZIM2_uc002qnq.2_Intron|ZIM2_uc010etp.2_Intron|ZIM2_uc010ygs.1_Intron|PEG3_uc002qnt.2_Nonsense_Mutation_p.R680*|PEG3_uc002qnv.2_Nonsense_Mutation_p.R709*|PEG3_uc002qnw.2_Nonsense_Mutation_p.R585*|PEG3_uc002qnx.2_Nonsense_Mutation_p.R583*|PEG3_uc010etr.2_Nonsense_Mutation_p.R709*	NM_001146186	NP_001139658	Q9GZU2	PEG3_HUMAN	paternally expressed 3 isoform 1	709					apoptosis|viral reproduction	cytoplasm|nucleus	nucleic acid binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(7)|skin(2)|upper_aerodigestive_tract(1)|large_intestine(1)|pancreas(1)	12		Colorectal(82;0.000256)|all_neural(62;0.103)|Ovarian(87;0.243)		GBM - Glioblastoma multiforme(193;0.0269)														---	---	---	---
ZNF264	9422	broad.mit.edu	37	19	57722991	57722991	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:57722991G>A	uc002qob.2	+	4	939	c.526G>A	c.(526-528)GTC>ATC	p.V176I		NM_003417	NP_003408	O43296	ZN264_HUMAN	zinc finger protein 264	176					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(2)	2		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;0.0135)														---	---	---	---
ZNF548	147694	broad.mit.edu	37	19	57910502	57910502	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:57910502T>C	uc002qom.2	+	3	1097	c.847T>C	c.(847-849)TGC>CGC	p.C283R	ZNF547_uc002qpm.3_Intron|ZNF548_uc002qon.2_Missense_Mutation_p.C286R	NM_152909	NP_690873	Q8NEK5	ZN548_HUMAN	zinc finger protein 548	283	C2H2-type 4.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			breast(1)	1		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;0.026)														---	---	---	---
VN1R1	57191	broad.mit.edu	37	19	57967276	57967276	+	Silent	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:57967276T>C	uc002qos.1	-	1	579	c.579A>G	c.(577-579)CCA>CCG	p.P193P	ZNF547_uc002qpm.3_Intron	NM_020633	NP_065684	Q9GZP7	VN1R1_HUMAN	vomeronasal 1 receptor 1	193	Extracellular (Potential).				response to pheromone	integral to membrane|plasma membrane	pheromone receptor activity			ovary(1)	1		Colorectal(82;5.46e-05)|all_neural(62;0.0218)|Ovarian(87;0.0694)|Renal(1328;0.157)|Breast(46;0.222)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0254)|Lung(386;0.171)														---	---	---	---
ZNF211	10520	broad.mit.edu	37	19	58152349	58152349	+	Silent	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:58152349T>C	uc002qpq.2	+	3	675	c.495T>C	c.(493-495)AGT>AGC	p.S165S	ZNF211_uc010yhb.1_Silent_p.S169S|ZNF211_uc002qpp.2_Silent_p.S178S|ZNF211_uc002qpr.2_Silent_p.S229S|ZNF211_uc002qps.2_Silent_p.S230S|ZNF211_uc002qpt.2_Silent_p.S177S|ZNF211_uc010yhc.1_Silent_p.S177S|ZNF211_uc010yhd.1_Silent_p.S104S|ZNF211_uc010yhe.1_Silent_p.S156S	NM_198855	NP_942152	Q13398	ZN211_HUMAN	zinc finger protein 211 isoform 2	165						nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(2)	2		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;0.026)														---	---	---	---
ZNF418	147686	broad.mit.edu	37	19	58437791	58437791	+	Silent	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:58437791A>G	uc002qqs.1	-	4	2050	c.1758T>C	c.(1756-1758)ACT>ACC	p.T586T	ZNF418_uc010yhn.1_RNA|ZNF418_uc010yho.1_Silent_p.T501T	NM_133460	NP_597717	Q8TF45	ZN418_HUMAN	zinc finger protein 418	586					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0		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;0.0158)														---	---	---	---
ZNF274	10782	broad.mit.edu	37	19	58722922	58722922	+	Intron	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:58722922A>G	uc002qrq.1	+						ZNF274_uc002qrr.1_Intron|ZNF274_uc002qrs.1_Intron|ZNF274_uc010eum.1_Intron	NM_133502	NP_598009			zinc finger protein 274 isoform c						viral reproduction	centrosome|nucleolus	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription corepressor activity|zinc ion binding			ovary(1)	1		Colorectal(82;5.46e-05)|all_neural(62;0.0182)|Ovarian(87;0.0443)|Breast(46;0.0889)|Renal(1328;0.157)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0168)|Lung(386;0.215)														---	---	---	---
ZNF324	25799	broad.mit.edu	37	19	58983290	58983290	+	Silent	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:58983290C>T	uc002qsw.1	+	4	1525	c.1431C>T	c.(1429-1431)GGC>GGT	p.G477G	ZNF324_uc002qsx.1_Silent_p.G254G	NM_014347	NP_055162	O75467	Z324A_HUMAN	zinc finger protein 324	477					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)														---	---	---	---
ZBTB45	84878	broad.mit.edu	37	19	59028728	59028728	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:59028728C>T	uc002qtd.2	-	2	605	c.313G>A	c.(313-315)GCC>ACC	p.A105T	ZBTB45_uc002qte.2_Missense_Mutation_p.A105T|ZBTB45_uc002qtf.2_Missense_Mutation_p.A105T	NM_032792	NP_116181	Q96K62	ZBT45_HUMAN	zinc finger and BTB domain containing 45	105					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)	---	---	---	---
ZCCHC3	85364	broad.mit.edu	37	20	279342	279342	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:279342T>G	uc002wdf.2	+	2	1136	c.1112T>G	c.(1111-1113)GTG>GGG	p.V371G	ZCCHC3_uc002wdg.2_RNA	NM_033089	NP_149080	Q9NUD5	ZCHC3_HUMAN	zinc finger, CCHC domain containing 3	372	CCHC-type 3.						nucleic acid binding|zinc ion binding				0		all_cancers(10;0.000209)|Lung NSC(37;0.0417)|all_lung(30;0.0713)|all_epithelial(17;0.0748)|Breast(17;0.231)	OV - Ovarian serous cystadenocarcinoma(29;0.149)															---	---	---	---
TRIB3	57761	broad.mit.edu	37	20	377091	377091	+	Silent	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:377091C>T	uc002wdm.2	+	4	1340	c.834C>T	c.(832-834)TAC>TAT	p.Y278Y	TRIB3_uc002wdn.2_Silent_p.Y305Y	NM_021158	NP_066981	Q96RU7	TRIB3_HUMAN	tribbles 3	278	Protein kinase.				apoptosis|cellular lipid metabolic process|insulin receptor signaling pathway|negative regulation of fat cell differentiation|negative regulation of fatty acid biosynthetic process|negative regulation of protein kinase activity|nerve growth factor receptor signaling pathway|phosphatidylinositol-mediated signaling|positive regulation of protein binding|positive regulation of ubiquitin-protein ligase activity|regulation of glucose transport|regulation of MAP kinase activity|regulation of transcription, DNA-dependent|response to stress|transcription, DNA-dependent	cytosol|nucleus|plasma membrane	ATP binding|protein kinase activity|protein kinase binding|protein kinase inhibitor activity|transcription corepressor activity|ubiquitin protein ligase binding|ubiquitin-protein ligase regulator activity			central_nervous_system(2)	2		all_epithelial(17;0.165)|Lung NSC(37;0.191)|Breast(17;0.231)		Colorectal(46;0.101)|COAD - Colon adenocarcinoma(99;0.112)														---	---	---	---
RBCK1	10616	broad.mit.edu	37	20	390581	390581	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:390581G>A	uc002wdp.3	+	2	772	c.79G>A	c.(79-81)GCA>ACA	p.A27T	RBCK1_uc010zpl.1_Missense_Mutation_p.A27T|RBCK1_uc010zpm.1_RNA|RBCK1_uc002wdq.3_Intron|RBCK1_uc010fzy.2_RNA|RBCK1_uc002wdr.3_Intron|RBCK1_uc002wdo.2_RNA	NM_031229	NP_112506	Q9BYM8	HOIL1_HUMAN	RanBP-type and C3HC4-type zinc finger containing	27	Interaction with IRF3.|Interaction with TAB2.				interspecies interaction between organisms|negative regulation of NF-kappaB transcription factor activity|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of NF-kappaB transcription factor activity|proteasomal ubiquitin-dependent protein catabolic process|protein linear polyubiquitination|T cell receptor signaling pathway	LUBAC complex	protein binding|ubiquitin binding|ubiquitin-protein ligase activity|zinc ion binding				0		all_epithelial(17;0.172)|Lung NSC(37;0.191)|Breast(17;0.231)																---	---	---	---
SIRPB1	10326	broad.mit.edu	37	20	1551563	1551563	+	Silent	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:1551563G>A	uc010gai.2	-	4	1071	c.972C>T	c.(970-972)GAC>GAT	p.D324D	SIRPB1_uc002wfk.3_Intron	NM_006065	NP_006056	O00241	SIRB1_HUMAN	signal-regulatory protein beta 1 isoform 1	324	Ig-like C1-type 2.|Extracellular (Potential).				cell junction assembly|cell surface receptor linked signaling pathway	integral to plasma membrane	protein binding			ovary(1)	1																		---	---	---	---
ZNF343	79175	broad.mit.edu	37	20	2464853	2464853	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:2464853G>T	uc002wge.1	-	6	1242	c.754C>A	c.(754-756)CTG>ATG	p.L252M	ZNF343_uc010gao.1_Missense_Mutation_p.L252M|ZNF343_uc002wgd.1_Missense_Mutation_p.L162M	NM_024325	NP_077301	Q6P1L6	ZN343_HUMAN	zinc finger protein 343	252					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																		---	---	---	---
ProSAPiP1	9762	broad.mit.edu	37	20	3146872	3146872	+	Silent	SNP	G	A	A	rs150229668	byFrequency	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:3146872G>A	uc002wia.1	-	2	1992	c.594C>T	c.(592-594)GGC>GGT	p.G198G	ProSAPiP1_uc002wib.1_Silent_p.G198G	NM_014731	NP_055546	O60299	PRIP1_HUMAN	ProSAPiP1 protein	198						cell junction|cytoplasm|postsynaptic density|postsynaptic membrane				pancreas(1)	1																		---	---	---	---
ProSAPiP1	9762	broad.mit.edu	37	20	3146987	3146987	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:3146987C>T	uc002wia.1	-	2	1877	c.479G>A	c.(478-480)CGG>CAG	p.R160Q	ProSAPiP1_uc002wib.1_Missense_Mutation_p.R160Q	NM_014731	NP_055546	O60299	PRIP1_HUMAN	ProSAPiP1 protein	160						cell junction|cytoplasm|postsynaptic density|postsynaptic membrane				pancreas(1)	1																		---	---	---	---
ATRN	8455	broad.mit.edu	37	20	3526412	3526412	+	Silent	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:3526412C>T	uc002wim.2	+	4	702	c.612C>T	c.(610-612)GGC>GGT	p.G204G	ATRN_uc002wil.2_Silent_p.G204G	NM_139321	NP_647537	O75882	ATRN_HUMAN	attractin isoform 1	204	Extracellular (Potential).|CUB.				inflammatory response	extracellular space|integral to plasma membrane	receptor activity|sugar binding			ovary(1)|breast(1)	2																		---	---	---	---
ATRN	8455	broad.mit.edu	37	20	3565429	3565429	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:3565429C>T	uc002wim.2	+	18	3176	c.3086C>T	c.(3085-3087)TCG>TTG	p.S1029L	ATRN_uc002wil.2_Missense_Mutation_p.S1029L	NM_139321	NP_647537	O75882	ATRN_HUMAN	attractin isoform 1	1029	Extracellular (Potential).|PSI 4.				inflammatory response	extracellular space|integral to plasma membrane	receptor activity|sugar binding			ovary(1)|breast(1)	2																		---	---	---	---
SIGLEC1	6614	broad.mit.edu	37	20	3682028	3682028	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:3682028G>T	uc002wja.2	-	6	1489	c.1489C>A	c.(1489-1491)CTT>ATT	p.L497I	SIGLEC1_uc002wiz.3_Missense_Mutation_p.L497I	NM_023068	NP_075556	Q9BZZ2	SN_HUMAN	sialoadhesin precursor	497	Ig-like C2-type 4.|Extracellular (Potential).				cell-cell adhesion|cell-matrix adhesion|endocytosis|inflammatory response	extracellular region|integral to membrane|plasma membrane	sugar binding			pancreas(4)|ovary(2)|skin(2)|breast(1)|central_nervous_system(1)	10																		---	---	---	---
SIGLEC1	6614	broad.mit.edu	37	20	3686638	3686638	+	Silent	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:3686638G>A	uc002wja.2	-	3	459	c.459C>T	c.(457-459)GGC>GGT	p.G153G	SIGLEC1_uc002wiz.3_Silent_p.G153G|SIGLEC1_uc002wjc.2_Silent_p.G64G	NM_023068	NP_075556	Q9BZZ2	SN_HUMAN	sialoadhesin precursor	153	Ig-like C2-type 1.|Extracellular (Potential).				cell-cell adhesion|cell-matrix adhesion|endocytosis|inflammatory response	extracellular region|integral to membrane|plasma membrane	sugar binding			pancreas(4)|ovary(2)|skin(2)|breast(1)|central_nervous_system(1)	10																		---	---	---	---
CDC25B	994	broad.mit.edu	37	20	3783630	3783630	+	Intron	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:3783630T>C	uc002wjn.2	+						CDC25B_uc010zqk.1_Intron|CDC25B_uc010zql.1_Intron|CDC25B_uc010zqm.1_Intron|CDC25B_uc002wjl.2_Intron|CDC25B_uc002wjm.2_Intron|CDC25B_uc002wjo.2_Intron|CDC25B_uc002wjp.2_Intron|CDC25B_uc002wjq.2_Intron|CDC25B_uc010gbc.2_5'Flank	NM_021873	NP_068659			cell division cycle 25B isoform 1						cell division|G2/M transition of mitotic cell cycle|mitosis|positive regulation of cell proliferation	cytosol|microtubule organizing center|nucleoplasm	protein binding|protein tyrosine phosphatase activity			lung(3)|ovary(2)	5																		---	---	---	---
RNF24	11237	broad.mit.edu	37	20	3944548	3944548	+	Silent	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:3944548A>G	uc002wkh.2	-	2	387	c.117T>C	c.(115-117)AGT>AGC	p.S39S	RNF24_uc002wki.2_Silent_p.S60S|RNF24_uc002wkj.2_Silent_p.S39S	NM_007219	NP_009150	Q9Y225	RNF24_HUMAN	ring finger protein 24 isoform 1	39	Helical; (Potential).					Golgi membrane|integral to membrane	zinc ion binding				0																		---	---	---	---
RASSF2	9770	broad.mit.edu	37	20	4766870	4766870	+	Intron	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:4766870C>T	uc002wld.2	-						RASSF2_uc002wlc.2_Intron|RASSF2_uc002wle.2_Intron|RASSF2_uc002wlf.2_Intron|RASSF2_uc010gbh.2_Intron	NM_170774	NP_739580			Ras association domain family 2						cell cycle|signal transduction	nucleus	protein binding			ovary(3)|lung(2)|large_intestine(1)	6																		---	---	---	---
SLC23A2	9962	broad.mit.edu	37	20	4848447	4848447	+	Missense_Mutation	SNP	C	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:4848447C>G	uc002wlg.1	-	13	1700	c.1325G>C	c.(1324-1326)AGT>ACT	p.S442T	SLC23A2_uc010zqr.1_Missense_Mutation_p.S327T|SLC23A2_uc002wlh.1_Missense_Mutation_p.S442T	NM_005116	NP_005107	Q9UGH3	S23A2_HUMAN	solute carrier family 23 (nucleobase	442					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																		---	---	---	---
GPCPD1	56261	broad.mit.edu	37	20	5550787	5550787	+	Intron	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:5550787A>G	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																		---	---	---	---
GPCPD1	56261	broad.mit.edu	37	20	5559034	5559034	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:5559034A>G	uc002wme.3	-	8	910	c.697T>C	c.(697-699)TTT>CTT	p.F233L	GPCPD1_uc002wmd.3_Missense_Mutation_p.F52L	NM_019593	NP_062539	Q9NPB8	GPCP1_HUMAN	hypothetical protein LOC56261	233					glycerol metabolic process|lipid metabolic process		carbohydrate binding|glycerophosphodiester phosphodiesterase activity				0																		---	---	---	---
CHGB	1114	broad.mit.edu	37	20	5903023	5903023	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:5903023A>G	uc002wmg.2	+	4	539	c.233A>G	c.(232-234)AAC>AGC	p.N78S	CHGB_uc010zqz.1_Intron	NM_001819	NP_001810	P05060	SCG1_HUMAN	chromogranin B precursor	78						extracellular region	hormone activity			breast(3)|skin(2)|ovary(1)	6																		---	---	---	---
BTBD3	22903	broad.mit.edu	37	20	11898952	11898952	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:11898952A>G	uc002wnz.2	+	1	388	c.29A>G	c.(28-30)AAA>AGA	p.K10R	BTBD3_uc002wny.2_Intron|BTBD3_uc002woa.2_Intron|BTBD3_uc010zrf.1_Intron|BTBD3_uc010zrg.1_5'Flank|BTBD3_uc010zrh.1_5'Flank	NM_014962	NP_055777	Q9Y2F9	BTBD3_HUMAN	BTB/POZ domain containing protein 3 isoform a	10										ovary(2)|central_nervous_system(1)	3																		---	---	---	---
FLRT3	23767	broad.mit.edu	37	20	14307881	14307881	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:14307881T>C	uc002wov.1	-	3	739	c.272A>G	c.(271-273)TAC>TGC	p.Y91C	MACROD2_uc002wot.2_Intron|MACROD2_uc002wou.2_Intron|FLRT3_uc002wow.1_Missense_Mutation_p.Y91C	NM_198391	NP_938205	Q9NZU0	FLRT3_HUMAN	fibronectin leucine rich transmembrane protein 3	91	Extracellular (Potential).|LRR 2.				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)														---	---	---	---
MACROD2	140733	broad.mit.edu	37	20	15918179	15918179	+	Silent	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:15918179T>C	uc002wou.2	+	12	1161	c.897T>C	c.(895-897)TGT>TGC	p.C299C	MACROD2_uc002wot.2_Silent_p.C299C|MACROD2_uc002woz.2_Silent_p.C64C|MACROD2_uc002wpb.2_Silent_p.C64C	NM_080676	NP_542407	A1Z1Q3	MACD2_HUMAN	MACRO domain containing 2 isoform 1	299	Glu-rich.										0		all_neural(2;0.0381)|Acute lymphoblastic leukemia(2;0.175)																---	---	---	---
KIF16B	55614	broad.mit.edu	37	20	16360709	16360709	+	Silent	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:16360709G>A	uc002wpg.1	-	19	2096	c.1938C>T	c.(1936-1938)ATC>ATT	p.I646I	KIF16B_uc002wpe.1_Silent_p.I28I|KIF16B_uc002wpf.1_Silent_p.I28I|KIF16B_uc010gch.1_Silent_p.I646I|KIF16B_uc010gci.1_Silent_p.I646I|KIF16B_uc010gcj.1_Silent_p.I657I	NM_024704	NP_078980	Q96L93	KI16B_HUMAN	kinesin-like motor protein C20orf23	646	Glu-rich.|Potential.				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																		---	---	---	---
PCSK2	5126	broad.mit.edu	37	20	17446087	17446087	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:17446087A>G	uc002wpm.2	+	11	1639	c.1319A>G	c.(1318-1320)CAC>CGC	p.H440R	PCSK2_uc002wpl.2_Missense_Mutation_p.H421R|PCSK2_uc010zrm.1_Missense_Mutation_p.H405R|PCSK2_uc002wpn.2_Missense_Mutation_p.H94R	NM_002594	NP_002585	P16519	NEC2_HUMAN	proprotein convertase subtilisin/kexin type 2	440					enkephalin processing|insulin processing|islet amyloid polypeptide processing	extracellular space|membrane|soluble fraction|transport vesicle	serine-type endopeptidase activity			ovary(3)|central_nervous_system(2)|large_intestine(1)|pancreas(1)	7					Insulin Glargine recombinant(DB00047)|Insulin Lyspro recombinant(DB00046)|Insulin recombinant(DB00030)|Insulin, porcine(DB00071)													---	---	---	---
BFSP1	631	broad.mit.edu	37	20	17479644	17479644	+	Silent	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:17479644A>G	uc002wpo.2	-	6	816	c.777T>C	c.(775-777)TGT>TGC	p.C259C	BFSP1_uc002wpp.2_Silent_p.C134C|BFSP1_uc010zrn.1_Silent_p.C120C|BFSP1_uc010zro.1_Silent_p.C120C	NM_001195	NP_001186	Q12934	BFSP1_HUMAN	filensin isoform 1	259	Rod.|Coil 2.					cytoplasm|intermediate filament|membrane	structural constituent of cytoskeleton|structural constituent of eye lens			central_nervous_system(1)	1																		---	---	---	---
SNX5	27131	broad.mit.edu	37	20	17933262	17933262	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:17933262T>C	uc002wqc.2	-	5	568	c.482A>G	c.(481-483)AAC>AGC	p.N161S	SNX5_uc002wqb.2_RNA|SNX5_uc002wqd.2_Missense_Mutation_p.N161S|SNX5_uc002wqe.2_Missense_Mutation_p.N56S|SNX5_uc010zrt.1_Missense_Mutation_p.N161S	NM_014426	NP_055241	Q9Y5X3	SNX5_HUMAN	sorting nexin 5	161	PX.				cell communication|pinocytosis|protein transport	cytoplasmic vesicle membrane|early endosome membrane|extrinsic to endosome membrane|extrinsic to internal side of plasma membrane|macropinocytic cup|phagocytic cup|ruffle	phosphatidylinositol binding			large_intestine(1)	1																		---	---	---	---
SEC23B	10483	broad.mit.edu	37	20	18523027	18523027	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:18523027G>A	uc002wqz.1	+	13	1935	c.1492G>A	c.(1492-1494)GTG>ATG	p.V498M	SEC23B_uc002wra.1_Missense_Mutation_p.V498M|SEC23B_uc002wrb.1_Missense_Mutation_p.V498M|SEC23B_uc010zsb.1_Missense_Mutation_p.V480M|SEC23B_uc002wrc.1_Missense_Mutation_p.V498M	NM_006363	NP_006354	Q15437	SC23B_HUMAN	Sec23 homolog B	498					ER to Golgi vesicle-mediated transport|intracellular protein transport	COPII vesicle coat|endoplasmic reticulum membrane|ER-Golgi intermediate compartment membrane|Golgi membrane	zinc ion binding			ovary(1)	1																		---	---	---	---
SSTR4	6754	broad.mit.edu	37	20	23016544	23016544	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:23016544G>A	uc002wsr.2	+	1	488	c.424G>A	c.(424-426)GTG>ATG	p.V142M		NM_001052	NP_001043	P31391	SSR4_HUMAN	somatostatin receptor 4	142	Helical; Name=3; (Potential).				G-protein signaling, coupled to cyclic nucleotide second messenger|negative regulation of cell proliferation	integral to plasma membrane	somatostatin receptor activity			ovary(1)	1	Colorectal(13;0.0518)|Lung NSC(19;0.0542)|all_lung(19;0.118)																	---	---	---	---
CST4	1472	broad.mit.edu	37	20	23666571	23666571	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:23666571T>C	uc002wto.1	-	3	442	c.386A>G	c.(385-387)GAC>GGC	p.D129G		NM_001899	NP_001890	P01036	CYTS_HUMAN	cystatin S precursor	129						extracellular region	cysteine-type endopeptidase inhibitor activity			breast(1)	1	Lung NSC(19;0.0789)|Colorectal(13;0.0993)|all_lung(19;0.169)																	---	---	---	---
TMEM90B	79953	broad.mit.edu	37	20	24646035	24646035	+	Silent	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:24646035G>A	uc002wtw.1	+	4	1305	c.672G>A	c.(670-672)CGG>CGA	p.R224R		NM_024893	NP_079169	Q9H7V2	SYNG1_HUMAN	transmembrane protein 90B	224	Extracellular (Potential).				response to biotic stimulus	early endosome membrane|integral to membrane|plasma membrane					0																		---	---	---	---
PYGB	5834	broad.mit.edu	37	20	25276230	25276230	+	Intron	SNP	C	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:25276230C>G	uc002wup.2	+						ABHD12_uc002wuq.2_Intron|ABHD12_uc002wur.2_Intron	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)													---	---	---	---
ZNF337	26152	broad.mit.edu	37	20	25657188	25657188	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:25657188T>C	uc002wva.2	-	4	1258	c.736A>G	c.(736-738)AGC>GGC	p.S246G	uc002wuz.2_RNA|ZNF337_uc010ztg.1_Missense_Mutation_p.S214G|ZNF337_uc002wvb.2_Missense_Mutation_p.S246G|ZNF337_uc002wvc.2_Missense_Mutation_p.S246G	NM_015655	NP_056470	Q9Y3M9	ZN337_HUMAN	zinc finger protein 337	246	C2H2-type 3.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0																		---	---	---	---
MYLK2	85366	broad.mit.edu	37	20	30414668	30414668	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:30414668T>C	uc002wwq.2	+	8	1253	c.1151T>C	c.(1150-1152)ATG>ACG	p.M384T	MYLK2_uc002wws.2_Missense_Mutation_p.M1T	NM_033118	NP_149109	Q9H1R3	MYLK2_HUMAN	skeletal myosin light chain kinase	384	Protein kinase.				cardiac muscle tissue morphogenesis|regulation of muscle filament sliding		ATP binding|calmodulin binding|calmodulin-dependent protein kinase activity|myosin light chain kinase activity			lung(2)|skin(2)|ovary(1)|central_nervous_system(1)	6			Colorectal(19;0.00306)|COAD - Colon adenocarcinoma(19;0.0347)															---	---	---	---
C20orf160	140706	broad.mit.edu	37	20	30605787	30605787	+	Silent	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:30605787G>A	uc002wxf.2	+	4	301	c.288G>A	c.(286-288)CTG>CTA	p.L96L		NM_080625	NP_542192	Q9NUG4	CT160_HUMAN	hypothetical protein LOC140706	96										central_nervous_system(3)|ovary(1)	4																		---	---	---	---
ASXL1	171023	broad.mit.edu	37	20	31022913	31022913	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:31022913G>T	uc002wxs.2	+	12	2824	c.2398G>T	c.(2398-2400)GAT>TAT	p.D800Y	ASXL1_uc010geb.2_Missense_Mutation_p.D691Y	NM_015338	NP_056153	Q8IXJ9	ASXL1_HUMAN	additional sex combs like 1 isoform 1	800					chromatin modification|regulation of transcription, DNA-dependent|transcription, DNA-dependent	PR-DUB complex	metal ion binding|protein binding	p.D800E(1)		haematopoietic_and_lymphoid_tissue(239)|large_intestine(6)|central_nervous_system(2)|ovary(1)	248								F|N|Mis		MDS|CMML								---	---	---	---
ASXL1	171023	broad.mit.edu	37	20	31024206	31024206	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:31024206T>C	uc002wxs.2	+	12	4117	c.3691T>C	c.(3691-3693)TCC>CCC	p.S1231P	ASXL1_uc010geb.2_Missense_Mutation_p.S1122P	NM_015338	NP_056153	Q8IXJ9	ASXL1_HUMAN	additional sex combs like 1 isoform 1	1231					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								---	---	---	---
C20orf112	140688	broad.mit.edu	37	20	31043959	31043959	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:31043959G>A	uc002wxu.3	-	3	506	c.349C>T	c.(349-351)CGG>TGG	p.R117W	C20orf112_uc010gec.2_5'UTR	NM_080616	NP_542183	Q96MY1	CT112_HUMAN	hypothetical protein LOC140688	117											0																		---	---	---	---
BPIL1	80341	broad.mit.edu	37	20	31603255	31603255	+	Missense_Mutation	SNP	C	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:31603255C>G	uc002wyj.2	+	6	663	c.469C>G	c.(469-471)CTG>GTG	p.L157V		NM_025227	NP_079503	Q8N4F0	BPIL1_HUMAN	bactericidal/permeability-increasing	157						extracellular region	lipid binding			skin(2)|large_intestine(1)|ovary(1)	4																		---	---	---	---
C20orf186	149954	broad.mit.edu	37	20	31673894	31673894	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:31673894C>T	uc010zue.1	+	5	865	c.850C>T	c.(850-852)CGC>TGC	p.R284C		NM_182519	NP_872325	P59827	LPLC4_HUMAN	antimicrobial peptide RY2G5 precursor	284						cytoplasm|extracellular region	lipid binding				0																		---	---	---	---
ZNF341	84905	broad.mit.edu	37	20	32332932	32332932	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:32332932G>A	uc002wzy.2	+	3	186	c.166G>A	c.(166-168)GGG>AGG	p.G56R	ZNF341_uc002wzx.2_Missense_Mutation_p.G56R|ZNF341_uc010geq.2_Intron|ZNF341_uc010ger.2_RNA	NM_032819	NP_116208	Q9BYN7	ZN341_HUMAN	zinc finger protein 341	56	C2H2-type 1; atypical.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(2)	2																		---	---	---	---
AHCY	191	broad.mit.edu	37	20	32873446	32873446	+	Intron	SNP	C	T	T	rs35077167		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:32873446C>T	uc002xai.2	-						AHCY_uc002xaj.2_Intron	NM_000687	NP_000678			adenosylhomocysteinase isoform 1						methylation|xenobiotic metabolic process	cytosol|melanosome	adenosylhomocysteinase activity|protein binding				0																		---	---	---	---
NCOA6	23054	broad.mit.edu	37	20	33345217	33345217	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:33345217G>A	uc002xav.2	-	8	3905	c.1334C>T	c.(1333-1335)ACG>ATG	p.T445M	NCOA6_uc002xaw.2_Missense_Mutation_p.T445M|NCOA6_uc010gew.1_Missense_Mutation_p.T402M	NM_014071	NP_054790	Q14686	NCOA6_HUMAN	nuclear receptor coactivator 6	445	TBP/GTF2A-binding region.|NCOA1-binding region.|Gln-rich.|CREBBP-binding region.				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																		---	---	---	---
MYH7B	57644	broad.mit.edu	37	20	33581954	33581954	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:33581954C>T	uc002xbi.1	+	25	2668	c.2576C>T	c.(2575-2577)GCG>GTG	p.A859V		NM_020884	NP_065935	A7E2Y1	MYH7B_HUMAN	myosin, heavy polypeptide 7B, cardiac muscle,	817	IQ.					membrane|myosin filament	actin binding|ATP binding|motor activity			ovary(1)|breast(1)	2			BRCA - Breast invasive adenocarcinoma(18;0.00691)															---	---	---	---
MYH7B	57644	broad.mit.edu	37	20	33583364	33583364	+	Nonsense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:33583364C>T	uc002xbi.1	+	26	3144	c.3052C>T	c.(3052-3054)CAA>TAA	p.Q1018*		NM_020884	NP_065935	A7E2Y1	MYH7B_HUMAN	myosin, heavy polypeptide 7B, cardiac muscle,	976	Potential.					membrane|myosin filament	actin binding|ATP binding|motor activity			ovary(1)|breast(1)	2			BRCA - Breast invasive adenocarcinoma(18;0.00691)															---	---	---	---
MYH7B	57644	broad.mit.edu	37	20	33584260	33584260	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:33584260G>A	uc002xbi.1	+	27	3273	c.3181G>A	c.(3181-3183)GCC>ACC	p.A1061T		NM_020884	NP_065935	A7E2Y1	MYH7B_HUMAN	myosin, heavy polypeptide 7B, cardiac muscle,	1019	Potential.					membrane|myosin filament	actin binding|ATP binding|motor activity			ovary(1)|breast(1)	2			BRCA - Breast invasive adenocarcinoma(18;0.00691)															---	---	---	---
PHF20	51230	broad.mit.edu	37	20	34459689	34459689	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:34459689A>G	uc002xek.1	+	9	1331	c.1220A>G	c.(1219-1221)AAC>AGC	p.N407S	PHF20_uc002xei.1_Missense_Mutation_p.N407S|PHF20_uc010gfo.1_Missense_Mutation_p.N407S|PHF20_uc002xej.1_Missense_Mutation_p.N291S	NM_016436	NP_057520	Q9BVI0	PHF20_HUMAN	PHD finger protein 20	407					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)																	---	---	---	---
C20orf117	140710	broad.mit.edu	37	20	35422878	35422878	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:35422878C>T	uc002xgd.1	-	14	3220	c.2893G>A	c.(2893-2895)GAG>AAG	p.E965K	C20orf117_uc002xge.1_RNA	NM_199181	NP_954650	O94964	K0889_HUMAN	hypothetical protein LOC140710 isoform 2	965											0		Myeloproliferative disorder(115;0.00874)																---	---	---	---
BPI	671	broad.mit.edu	37	20	36932744	36932744	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:36932744G>A	uc002xib.2	+	1	193	c.131G>A	c.(130-132)GGC>GAC	p.G44D		NM_001725	NP_001716	P17213	BPI_HUMAN	bactericidal/permeability-increasing protein	44					defense response to bacterium|negative regulation of interleukin-6 production|negative regulation of interleukin-8 production|negative regulation of macrophage activation|negative regulation of tumor necrosis factor production	extracellular region|integral to plasma membrane	lipid binding|lipopolysaccharide binding			ovary(4)	4		Myeloproliferative disorder(115;0.00878)																---	---	---	---
RALGAPB	57148	broad.mit.edu	37	20	37154687	37154687	+	Splice_Site	SNP	T	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:37154687T>G	uc002xiw.2	+	13	2307	c.2050_splice	c.e13+2	p.G684_splice	RALGAPB_uc002xix.2_Splice_Site_p.G684_splice|RALGAPB_uc002xiy.1_Splice_Site_p.G684_splice|RALGAPB_uc002xiz.2_Splice_Site_p.G462_splice|RALGAPB_uc002xja.1_Splice_Site_p.G411_splice	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																		---	---	---	---
SLC32A1	140679	broad.mit.edu	37	20	37356452	37356452	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:37356452G>A	uc002xjc.2	+	2	1011	c.748G>A	c.(748-750)GTG>ATG	p.V250M		NM_080552	NP_542119	Q9H598	VIAAT_HUMAN	solute carrier family 32, member 1	250	Helical; (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)													---	---	---	---
PLCG1	5335	broad.mit.edu	37	20	39801451	39801451	+	Silent	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:39801451T>C	uc002xjp.1	+	27	3334	c.3213T>C	c.(3211-3213)GAT>GAC	p.D1071D	PLCG1_uc002xjo.1_Silent_p.D1071D|PLCG1_uc010zwe.1_Silent_p.D697D	NM_182811	NP_877963	P19174	PLCG1_HUMAN	phospholipase C, gamma 1 isoform b	1071					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	40045255	40045255	+	Silent	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:40045255G>A	uc002xka.1	-	33	6637	c.6459C>T	c.(6457-6459)GGC>GGT	p.G2153G	CHD6_uc002xjz.1_5'Flank	NM_032221	NP_115597	Q8TD26	CHD6_HUMAN	chromodomain helicase DNA binding protein 6	2153					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	40052223	40052223	+	Silent	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:40052223G>A	uc002xka.1	-	30	4642	c.4464C>T	c.(4462-4464)GAC>GAT	p.D1488D		NM_032221	NP_115597	Q8TD26	CHD6_HUMAN	chromodomain helicase DNA binding protein 6	1488					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)																---	---	---	---
PTPRT	11122	broad.mit.edu	37	20	41306583	41306583	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:41306583C>T	uc002xkg.2	-	7	1260	c.1076G>A	c.(1075-1077)CGA>CAA	p.R359Q	PTPRT_uc010ggj.2_Missense_Mutation_p.R359Q	NM_007050	NP_008981	O14522	PTPRT_HUMAN	protein tyrosine phosphatase, receptor type, T	359	Extracellular (Potential).|Fibronectin type-III 1.				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)																---	---	---	---
L3MBTL	26013	broad.mit.edu	37	20	42168960	42168960	+	Intron	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:42168960G>A	uc010zwh.1	+						L3MBTL_uc002xkl.2_Intron|L3MBTL_uc002xkm.2_Intron|L3MBTL_uc010ggl.2_Intron|L3MBTL_uc002xkn.1_Intron|L3MBTL_uc002xko.2_Intron|L3MBTL_uc002xkp.2_Intron|SGK2_uc002xkq.1_Intron	NM_015478	NP_056293			l(3)mbt-like isoform I						chromatin modification|hemopoiesis|negative regulation of transcription, DNA-dependent|regulation of megakaryocyte differentiation|regulation of mitosis	chromatin|condensed chromosome|nucleoplasm	identical protein binding|methylated histone residue binding|nucleosomal histone binding|SAM domain binding|sequence-specific DNA binding transcription factor activity|zinc ion binding				0		Myeloproliferative disorder(115;0.00452)	COAD - Colon adenocarcinoma(18;0.0031)															---	---	---	---
MYBL2	4605	broad.mit.edu	37	20	42331308	42331308	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:42331308C>T	uc002xlb.1	+	8	1345	c.1130C>T	c.(1129-1131)ACC>ATC	p.T377I	MYBL2_uc010zwj.1_Missense_Mutation_p.T353I|MYBL2_uc002xla.1_Missense_Mutation_p.T377I	NM_002466	NP_002457	P10244	MYBB_HUMAN	MYB-related protein B	377						nucleus	DNA binding|sequence-specific DNA binding transcription factor activity			lung(3)|kidney(2)	5		Myeloproliferative disorder(115;0.00452)	COAD - Colon adenocarcinoma(18;0.0031)															---	---	---	---
GTSF1L	149699	broad.mit.edu	37	20	42355289	42355289	+	Nonsense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:42355289G>A	uc002xld.2	-	1	354	c.46C>T	c.(46-48)CGA>TGA	p.R16*	GTSF1L_uc002xlc.2_Nonsense_Mutation_p.R16*	NM_176791	NP_789761	Q9H1H1	GTSFL_HUMAN	gametocyte specific factor 1-like isoform 1	16	CHHC-type.						metal ion binding				0		Myeloproliferative disorder(115;0.00452)	COAD - Colon adenocarcinoma(18;0.0031)															---	---	---	---
TTPAL	79183	broad.mit.edu	37	20	43109054	43109054	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:43109054A>G	uc002xmc.1	+	3	539	c.415A>G	c.(415-417)AGG>GGG	p.R139G	TTPAL_uc002xmd.1_Missense_Mutation_p.R139G|TTPAL_uc010ggr.1_Silent_p.P16P	NM_024331	NP_077307	Q9BTX7	TTPAL_HUMAN	tocopherol (alpha) transfer protein-like	139	CRAL-TRIO.					intracellular	transporter activity			breast(1)	1																		---	---	---	---
SERINC3	10955	broad.mit.edu	37	20	43139944	43139944	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:43139944C>T	uc002xme.2	-	4	595	c.461G>A	c.(460-462)GGC>GAC	p.G154D	SERINC3_uc002xmf.1_Missense_Mutation_p.G154D|SERINC3_uc010ggs.1_Missense_Mutation_p.G147D|SERINC3_uc010zwp.1_Missense_Mutation_p.G99D	NM_198941	NP_945179	Q13530	SERC3_HUMAN	tumor differentially expressed protein 1	154	Extracellular (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)															---	---	---	---
SPINLW1	57119	broad.mit.edu	37	20	44171335	44171335	+	Intron	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:44171335T>C	uc002xou.2	-						SPINLW1_uc010zxc.1_Intron|SPINLW1_uc002xot.2_Intron|SPINLW1_uc002xov.1_3'UTR	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)																---	---	---	---
TNNC2	7125	broad.mit.edu	37	20	44453445	44453445	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:44453445T>C	uc002xpr.2	-	2	98	c.32A>G	c.(31-33)TAC>TGC	p.Y11C		NM_003279	NP_003270	P02585	TNNC2_HUMAN	fast skeletal muscle troponin C	11					muscle filament sliding|regulation of muscle contraction|skeletal muscle contraction	cytosol|troponin complex	calcium ion binding			upper_aerodigestive_tract(1)	1		Myeloproliferative disorder(115;0.0122)																---	---	---	---
ZSWIM3	140831	broad.mit.edu	37	20	44505588	44505588	+	Nonsense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:44505588C>T	uc002xqd.2	+	2	594	c.391C>T	c.(391-393)CAG>TAG	p.Q131*	ZSWIM3_uc010zxg.1_Nonsense_Mutation_p.Q125*	NM_080752	NP_542790	Q96MP5	ZSWM3_HUMAN	zinc finger, SWIM domain containing 3	131							zinc ion binding			ovary(2)	2		Myeloproliferative disorder(115;0.0122)																---	---	---	---
ZSWIM1	90204	broad.mit.edu	37	20	44512627	44512627	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:44512627T>C	uc010ghi.2	+	2	1509	c.1396T>C	c.(1396-1398)TAT>CAT	p.Y466H	ZSWIM1_uc010zxh.1_Missense_Mutation_p.Y339H	NM_080603	NP_542170	Q9BR11	ZSWM1_HUMAN	zinc finger, SWIM-type containing 1	466							zinc ion binding			skin(1)	1		Myeloproliferative disorder(115;0.028)																---	---	---	---
ZNF335	63925	broad.mit.edu	37	20	44577698	44577698	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:44577698G>A	uc002xqw.2	-	28	4046	c.3923C>T	c.(3922-3924)GCC>GTC	p.A1308V	ZNF335_uc002xqv.2_Missense_Mutation_p.A420V|ZNF335_uc010zxk.1_Missense_Mutation_p.A1153V	NM_022095	NP_071378	Q9H4Z2	ZN335_HUMAN	zinc finger protein 335	1308	Gln-rich.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			skin(3)|ovary(1)	4		Myeloproliferative disorder(115;0.0122)																---	---	---	---
ZNF335	63925	broad.mit.edu	37	20	44590709	44590709	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:44590709C>T	uc002xqw.2	-	10	1769	c.1646G>A	c.(1645-1647)CGG>CAG	p.R549Q	ZNF335_uc010zxk.1_Missense_Mutation_p.R394Q	NM_022095	NP_071378	Q9H4Z2	ZN335_HUMAN	zinc finger protein 335	549					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			skin(3)|ovary(1)	4		Myeloproliferative disorder(115;0.0122)																---	---	---	---
MMP9	4318	broad.mit.edu	37	20	44639185	44639185	+	Silent	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:44639185C>T	uc002xqz.2	+	3	454	c.435C>T	c.(433-435)TTC>TTT	p.F145F		NM_004994	NP_004985	P14780	MMP9_HUMAN	matrix metalloproteinase 9 preproprotein	145					collagen catabolic process|macrophage differentiation|positive regulation of keratinocyte migration|proteolysis	extracellular space|proteinaceous extracellular matrix	collagen binding|metalloendopeptidase activity|zinc ion binding			ovary(1)|pancreas(1)	2		Myeloproliferative disorder(115;0.0122)			Glucosamine(DB01296)|Marimastat(DB00786)|Minocycline(DB01017)|Simvastatin(DB00641)													---	---	---	---
SLC12A5	57468	broad.mit.edu	37	20	44681611	44681611	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:44681611C>T	uc010zxl.1	+	19	2538	c.2462C>T	c.(2461-2463)ACC>ATC	p.T821I	SLC12A5_uc002xrb.2_Missense_Mutation_p.T798I	NM_001134771	NP_001128243	Q9H2X9	S12A5_HUMAN	solute carrier family 12 (potassium-chloride	821					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)													---	---	---	---
ELMO2	63916	broad.mit.edu	37	20	44997545	44997545	+	Silent	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:44997545T>C	uc002xrt.1	-	21	2157	c.1947A>G	c.(1945-1947)GCA>GCG	p.A649A	ELMO2_uc010zxq.1_Silent_p.A381A|ELMO2_uc002xrs.1_Silent_p.A396A|ELMO2_uc002xru.1_Silent_p.A649A|ELMO2_uc010zxr.1_Silent_p.A661A|ELMO2_uc010zxs.1_Silent_p.A466A	NM_133171	NP_573403	Q96JJ3	ELMO2_HUMAN	engulfment and cell motility 2	649	PH.				apoptosis|cell chemotaxis|phagocytosis	cytoskeleton|cytosol|membrane	lyase activity|receptor tyrosine kinase binding|SH3 domain binding			ovary(1)	1		Myeloproliferative disorder(115;0.0122)																---	---	---	---
ZMYND8	23613	broad.mit.edu	37	20	45867661	45867661	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:45867661G>A	uc002xta.1	-	15	2700	c.2446C>T	c.(2446-2448)CGG>TGG	p.R816W	ZMYND8_uc010ghq.1_Missense_Mutation_p.R493W|ZMYND8_uc010ghr.1_Missense_Mutation_p.R791W|ZMYND8_uc002xst.1_Missense_Mutation_p.R744W|ZMYND8_uc002xsu.1_Intron|ZMYND8_uc002xsv.1_Missense_Mutation_p.R744W|ZMYND8_uc002xsw.1_Missense_Mutation_p.R568W|ZMYND8_uc002xsx.1_Missense_Mutation_p.R568W|ZMYND8_uc002xsy.1_Missense_Mutation_p.R791W|ZMYND8_uc002xsz.1_Missense_Mutation_p.R753W|ZMYND8_uc010zxy.1_Missense_Mutation_p.R843W|ZMYND8_uc002xtb.1_Missense_Mutation_p.R836W|ZMYND8_uc002xss.2_Missense_Mutation_p.R816W|ZMYND8_uc010zxz.1_Intron|ZMYND8_uc002xtc.1_Missense_Mutation_p.R836W|ZMYND8_uc002xtd.1_Missense_Mutation_p.R811W|ZMYND8_uc002xte.1_Missense_Mutation_p.R816W|ZMYND8_uc010zya.1_Missense_Mutation_p.R816W|ZMYND8_uc002xtf.1_Missense_Mutation_p.R836W|ZMYND8_uc002xtg.2_Missense_Mutation_p.R810W|ZMYND8_uc010ghs.1_Missense_Mutation_p.R810W|ZMYND8_uc002xsr.1_5'UTR	NM_012408	NP_036540	Q9ULU4	PKCB1_HUMAN	zinc finger, MYND-type containing 8 isoform b	816							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)															---	---	---	---
NCOA3	8202	broad.mit.edu	37	20	46262865	46262865	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:46262865G>T	uc002xtk.2	+	10	1243	c.1038G>T	c.(1036-1038)CAG>CAT	p.Q346H	NCOA3_uc010ght.1_Missense_Mutation_p.Q356H|NCOA3_uc002xtl.2_Missense_Mutation_p.Q346H|NCOA3_uc002xtm.2_Missense_Mutation_p.Q346H|NCOA3_uc002xtn.2_Missense_Mutation_p.Q346H|NCOA3_uc010zyc.1_Missense_Mutation_p.Q141H	NM_181659	NP_858045	Q9Y6Q9	NCOA3_HUMAN	nuclear receptor coactivator 3 isoform a	346					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																		---	---	---	---
ARFGEF2	10564	broad.mit.edu	37	20	47635449	47635449	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:47635449G>A	uc002xtx.3	+	34	4690	c.4538G>A	c.(4537-4539)AGC>AAC	p.S1513N	ARFGEF2_uc010zyf.1_Missense_Mutation_p.S806N	NM_006420	NP_006411	Q9Y6D5	BIG2_HUMAN	ADP-ribosylation factor guanine	1513					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	47710678	47710678	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:47710678A>G	uc002xty.2	+	23	2583	c.2449A>G	c.(2449-2451)ATG>GTG	p.M817V	CSE1L_uc010zyg.1_Missense_Mutation_p.M600V|CSE1L_uc010ghx.2_Missense_Mutation_p.M761V|CSE1L_uc010ghy.2_Missense_Mutation_p.M438V|CSE1L_uc010zyh.1_Missense_Mutation_p.M466V	NM_001316	NP_001307	P55060	XPO2_HUMAN	CSE1 chromosome segregation 1-like protein	817					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)															---	---	---	---
SLC9A8	23315	broad.mit.edu	37	20	48466178	48466178	+	Silent	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:48466178C>T	uc002xuv.1	+	6	705	c.495C>T	c.(493-495)TCC>TCT	p.S165S	SLC9A8_uc010zym.1_5'UTR|SLC9A8_uc010zyj.1_Silent_p.S165S|SLC9A8_uc010zyk.1_Silent_p.S165S|SLC9A8_uc010zyl.1_Silent_p.S137S|SLC9A8_uc010gib.1_Intron	NM_015266	NP_056081	Q9Y2E8	SL9A8_HUMAN	sodium/hydrogen exchanger 8	165	Helical; (Potential).					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	48500546	48500546	+	Silent	SNP	C	T	T	rs148997057		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:48500546C>T	uc002xuv.1	+	14	1644	c.1434C>T	c.(1432-1434)GAC>GAT	p.D478D	SLC9A8_uc010zym.1_Silent_p.D178D|SLC9A8_uc010gic.2_Silent_p.D178D|SLC9A8_uc010gid.2_Silent_p.D102D	NM_015266	NP_056081	Q9Y2E8	SL9A8_HUMAN	sodium/hydrogen exchanger 8	478						Golgi membrane|integral to membrane	sodium:hydrogen antiporter activity			ovary(1)	1			BRCA - Breast invasive adenocarcinoma(9;3.91e-07)															---	---	---	---
ADNP	23394	broad.mit.edu	37	20	49508775	49508775	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:49508775A>G	uc002xvt.1	-	5	2821	c.2476T>C	c.(2476-2478)TTT>CTT	p.F826L	ADNP_uc002xvu.1_Missense_Mutation_p.F826L	NM_015339	NP_056154	Q9H2P0	ADNP_HUMAN	activity-dependent neuroprotector	826						nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(2)	2																		---	---	---	---
MOCS3	27304	broad.mit.edu	37	20	49575531	49575531	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:49575531C>A	uc002xvy.1	+	1	169	c.152C>A	c.(151-153)CCG>CAG	p.P51Q	DPM1_uc002xvw.1_5'Flank|DPM1_uc002xvx.1_5'Flank	NM_014484	NP_055299	O95396	MOCS3_HUMAN	molybdenum cofactor synthesis 3	51					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	49576467	49576467	+	Missense_Mutation	SNP	A	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:49576467A>T	uc002xvy.1	+	1	1105	c.1088A>T	c.(1087-1089)GAC>GTC	p.D363V	DPM1_uc002xvw.1_5'Flank|DPM1_uc002xvx.1_5'Flank	NM_014484	NP_055299	O95396	MOCS3_HUMAN	molybdenum cofactor synthesis 3	363	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																		---	---	---	---
NFATC2	4773	broad.mit.edu	37	20	50090607	50090607	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:50090607T>C	uc002xwd.2	-	5	1838	c.1618A>G	c.(1618-1620)ACG>GCG	p.T540A	NFATC2_uc002xwc.2_Missense_Mutation_p.T540A|NFATC2_uc010zyv.1_Missense_Mutation_p.T321A|NFATC2_uc010zyw.1_Missense_Mutation_p.T321A|NFATC2_uc010zyx.1_Missense_Mutation_p.T520A|NFATC2_uc010zyy.1_Missense_Mutation_p.T321A|NFATC2_uc010zyz.1_Missense_Mutation_p.T321A|NFATC2_uc002xwe.2_Missense_Mutation_p.T520A	NM_173091	NP_775114	Q13469	NFAC2_HUMAN	nuclear factor of activated T-cells,	540	RHD.				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)																	---	---	---	---
TSHZ2	128553	broad.mit.edu	37	20	51870612	51870612	+	Silent	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:51870612C>T	uc002xwo.2	+	2	1571	c.615C>T	c.(613-615)TGC>TGT	p.C205C		NM_173485	NP_775756	Q9NRE2	TSH2_HUMAN	teashirt zinc finger homeobox 2	205					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	56063871	56063871	+	Silent	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:56063871A>G	uc010zzl.1	-	1	213	c.213T>C	c.(211-213)TAT>TAC	p.Y71Y		NM_001008735	NP_001008735			high-mobility group box 1-like 1																														---	---	---	---
TUBB1	81027	broad.mit.edu	37	20	57599135	57599135	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:57599135C>T	uc002yak.2	+	4	922	c.653C>T	c.(652-654)ACG>ATG	p.T218M		NM_030773	NP_110400	Q9H4B7	TBB1_HUMAN	beta tubulin 1, class VI	218					'de novo' posttranslational protein folding|microtubule-based movement|protein polymerization	cytoplasm|microtubule	GTP binding|GTPase activity			ovary(1)	1	all_lung(29;0.00711)		Colorectal(105;0.109)		Colchicine(DB01394)|Docetaxel(DB01248)|Paclitaxel(DB01229)|Vindesine(DB00309)													---	---	---	---
ZNF831	128611	broad.mit.edu	37	20	57769284	57769284	+	Silent	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:57769284T>C	uc002yan.2	+	1	3210	c.3210T>C	c.(3208-3210)GGT>GGC	p.G1070G		NM_178457	NP_848552	Q5JPB2	ZN831_HUMAN	zinc finger protein 831	1070						intracellular	nucleic acid binding|zinc ion binding			skin(13)|ovary(1)	14	all_lung(29;0.0085)																	---	---	---	---
EDN3	1908	broad.mit.edu	37	20	57876652	57876652	+	Silent	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:57876652G>A	uc002yap.2	+	2	609	c.240G>A	c.(238-240)GGG>GGA	p.G80G	EDN3_uc002yao.1_Silent_p.G80G|EDN3_uc002yaq.2_Silent_p.G80G|EDN3_uc002yar.2_Silent_p.G80G|EDN3_uc002yas.2_Silent_p.G80G	NM_000114	NP_000105	P14138	EDN3_HUMAN	endothelin 3 isoform 1 preproprotein	80					cell surface receptor linked signaling pathway|inositol phosphate-mediated signaling|neutrophil chemotaxis|peptide hormone secretion|positive regulation of heart rate|positive regulation of hormone secretion|positive regulation of leukocyte chemotaxis|positive regulation of MAP kinase activity|positive regulation of mitosis|regulation of systemic arterial blood pressure by endothelin|regulation of vasoconstriction|vein smooth muscle contraction	extracellular space|soluble fraction	endothelin B receptor binding|hormone activity			skin(1)	1	all_lung(29;0.0115)																	---	---	---	---
DIDO1	11083	broad.mit.edu	37	20	61512046	61512046	+	Silent	SNP	C	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:61512046C>A	uc002ydr.1	-	16	5526	c.5262G>T	c.(5260-5262)CGG>CGT	p.R1754R	DIDO1_uc002yds.1_Silent_p.R1754R	NM_033081	NP_149072	Q9BTC0	DIDO1_HUMAN	death inducer-obliterator 1 isoform c	1754	Pro-rich.				apoptosis|transcription, DNA-dependent	cytoplasm|nucleus	zinc ion binding			ovary(3)|skin(3)	6	Breast(26;5.68e-08)																	---	---	---	---
DIDO1	11083	broad.mit.edu	37	20	61512109	61512109	+	Silent	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:61512109G>A	uc002ydr.1	-	16	5463	c.5199C>T	c.(5197-5199)ACC>ACT	p.T1733T	DIDO1_uc002yds.1_Silent_p.T1733T	NM_033081	NP_149072	Q9BTC0	DIDO1_HUMAN	death inducer-obliterator 1 isoform c	1733	Pro-rich.				apoptosis|transcription, DNA-dependent	cytoplasm|nucleus	zinc ion binding			ovary(3)|skin(3)	6	Breast(26;5.68e-08)																	---	---	---	---
DIDO1	11083	broad.mit.edu	37	20	61512721	61512721	+	Silent	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:61512721C>T	uc002ydr.1	-	16	4851	c.4587G>A	c.(4585-4587)TTG>TTA	p.L1529L	DIDO1_uc002yds.1_Silent_p.L1529L	NM_033081	NP_149072	Q9BTC0	DIDO1_HUMAN	death inducer-obliterator 1 isoform c	1529					apoptosis|transcription, DNA-dependent	cytoplasm|nucleus	zinc ion binding			ovary(3)|skin(3)	6	Breast(26;5.68e-08)																	---	---	---	---
DIDO1	11083	broad.mit.edu	37	20	61542521	61542521	+	Silent	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:61542521G>A	uc002ydr.1	-	3	708	c.444C>T	c.(442-444)CAC>CAT	p.H148H	DIDO1_uc002yds.1_Silent_p.H148H|DIDO1_uc002ydt.1_Silent_p.H148H|DIDO1_uc002ydu.1_Silent_p.H148H|DIDO1_uc002ydv.1_Silent_p.H148H|DIDO1_uc002ydw.1_Silent_p.H148H|DIDO1_uc002ydx.1_Silent_p.H148H|DIDO1_uc011aao.1_Silent_p.H148H	NM_033081	NP_149072	Q9BTC0	DIDO1_HUMAN	death inducer-obliterator 1 isoform c	148					apoptosis|transcription, DNA-dependent	cytoplasm|nucleus	zinc ion binding			ovary(3)|skin(3)	6	Breast(26;5.68e-08)																	---	---	---	---
C20orf195	79025	broad.mit.edu	37	20	62187774	62187774	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:62187774A>G	uc002yfj.2	+	2	850	c.758A>G	c.(757-759)CAG>CGG	p.Q253R	C20orf195_uc002yfk.2_Missense_Mutation_p.Q253R	NM_024059	NP_076964	Q9BVV2	CT195_HUMAN	hypothetical protein LOC79025	253											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)															---	---	---	---
MYT1	4661	broad.mit.edu	37	20	62871155	62871155	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:62871155A>G	uc002yii.2	+	22	3500	c.3136A>G	c.(3136-3138)AAC>GAC	p.N1046D	MYT1_uc002yij.2_Missense_Mutation_p.N705D|MYT1_uc002yik.2_Missense_Mutation_p.N12D	NM_004535	NP_004526	Q01538	MYT1_HUMAN	myelin transcription factor 1	1046					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)																	---	---	---	---
POTED	317754	broad.mit.edu	37	21	15013667	15013667	+	Missense_Mutation	SNP	T	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:15013667T>A	uc002yjb.1	+	11	1587	c.1535T>A	c.(1534-1536)CTT>CAT	p.L512H		NM_174981	NP_778146	Q86YR6	POTED_HUMAN	pote protein	512	Potential.					plasma membrane				ovary(3)|skin(3)	6																		---	---	---	---
USP25	29761	broad.mit.edu	37	21	17135257	17135257	+	Silent	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:17135257T>C	uc002yjy.1	+	2	310	c.93T>C	c.(91-93)AAT>AAC	p.N31N	USP25_uc011aby.1_Silent_p.N31N|USP25_uc002yjz.1_Silent_p.N31N|USP25_uc010gla.1_Silent_p.N31N	NM_013396	NP_037528	Q9UHP3	UBP25_HUMAN	ubiquitin specific peptidase 25	31	UBA-like.				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)														---	---	---	---
USP16	10600	broad.mit.edu	37	21	30409684	30409684	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:30409684A>G	uc002ymy.2	+	6	738	c.536A>G	c.(535-537)AAC>AGC	p.N179S	USP16_uc002ymx.2_Missense_Mutation_p.N178S|USP16_uc002ymw.2_Missense_Mutation_p.N179S|USP16_uc011acm.1_Missense_Mutation_p.N164S|USP16_uc011acn.1_Intron|USP16_uc011aco.1_5'Flank	NM_006447	NP_006438	Q9Y5T5	UBP16_HUMAN	ubiquitin specific protease 16 isoform a	179					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																		---	---	---	---
USP16	10600	broad.mit.edu	37	21	30419020	30419020	+	Silent	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:30419020A>G	uc002ymy.2	+	14	1591	c.1389A>G	c.(1387-1389)AAA>AAG	p.K463K	USP16_uc002ymx.2_Silent_p.K462K|USP16_uc002ymw.2_Silent_p.K463K|USP16_uc011acm.1_Silent_p.K448K|USP16_uc011acn.1_Silent_p.K129K|USP16_uc011aco.1_Silent_p.K153K	NM_006447	NP_006438	Q9Y5T5	UBP16_HUMAN	ubiquitin specific protease 16 isoform a	463					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																		---	---	---	---
KRTAP19-1	337882	broad.mit.edu	37	21	31852582	31852582	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:31852582C>T	uc011acx.1	-	1	55	c.55G>A	c.(55-57)GGT>AGT	p.G19S		NM_181607	NP_853638	Q8IUB9	KR191_HUMAN	keratin associated protein 19-1	19	26 X 2 AA repeats of G-[YCGS].					intermediate filament					0																		---	---	---	---
KRTAP19-8	728299	broad.mit.edu	37	21	32410747	32410747	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:32410747T>C	uc010glt.2	-	1	49	c.16A>G	c.(16-18)AGC>GGC	p.S6G		NM_001099219	NP_001092689	Q3LI54	KR198_HUMAN	keratin associated protein 19-8	6						intermediate filament				upper_aerodigestive_tract(1)	1																		---	---	---	---
TIAM1	7074	broad.mit.edu	37	21	32513773	32513773	+	Silent	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:32513773C>T	uc002yow.1	-	22	3997	c.3525G>A	c.(3523-3525)AAG>AAA	p.K1175K	TIAM1_uc011adk.1_Silent_p.K1175K|TIAM1_uc011adl.1_Silent_p.K1115K	NM_003253	NP_003244	Q13009	TIAM1_HUMAN	T-cell lymphoma invasion and metastasis 1	1175	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	cell-cell junction|cytosol	receptor signaling protein activity|Rho guanyl-nucleotide exchange factor activity			lung(3)|breast(3)|ovary(2)|large_intestine(2)	10																		---	---	---	---
SFRS15	57466	broad.mit.edu	37	21	33043710	33043710	+	3'UTR	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:33043710C>T	uc002ypd.2	-	20					SFRS15_uc002ype.2_3'UTR|SFRS15_uc010glu.2_3'UTR	NM_020706	NP_065757			splicing factor, arginine/serine-rich 15 isoform							nucleus	nucleotide binding|RNA binding				0																		---	---	---	---
SYNJ1	8867	broad.mit.edu	37	21	34045776	34045776	+	Nonsense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:34045776G>A	uc002yqh.2	-	14	1717	c.1717C>T	c.(1717-1719)CGA>TGA	p.R573*	SYNJ1_uc011ads.1_Nonsense_Mutation_p.R529*|SYNJ1_uc002yqf.2_Nonsense_Mutation_p.R534*|SYNJ1_uc002yqg.2_Nonsense_Mutation_p.R529*|SYNJ1_uc002yqi.2_Nonsense_Mutation_p.R573*	NM_003895	NP_003886	O43426	SYNJ1_HUMAN	synaptojanin 1 isoform a	534	Catalytic (Potential).						inositol-polyphosphate 5-phosphatase activity|nucleotide binding|phosphatidylinositol-4,5-bisphosphate 5-phosphatase activity|RNA binding			ovary(4)|skin(1)	5																		---	---	---	---
ITSN1	6453	broad.mit.edu	37	21	35258765	35258765	+	Splice_Site	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:35258765G>A	uc002yta.1	+	39	5285	c.5017_splice	c.e39+1	p.D1673_splice	DONSON_uc002ysn.1_Intron|ITSN1_uc002ytb.1_Splice_Site_p.D1668_splice|ITSN1_uc002ytj.2_Splice_Site_p.D1612_splice|ITSN1_uc010gmm.1_Splice_Site	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																		---	---	---	---
KCNJ6	3763	broad.mit.edu	37	21	39212954	39212954	+	Intron	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:39212954A>G	uc011aej.1	-						KCNJ6_uc002ywo.2_Intron	NM_002240	NP_002231			potassium inwardly-rectifying channel J6						synaptic transmission	Golgi apparatus|voltage-gated potassium channel complex	G-protein activated inward rectifier potassium channel activity|protein binding			skin(1)	1					Halothane(DB01159)													---	---	---	---
DSCAM	1826	broad.mit.edu	37	21	41414389	41414389	+	Missense_Mutation	SNP	T	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:41414389T>A	uc002yyq.1	-	32	6047	c.5595A>T	c.(5593-5595)GAA>GAT	p.E1865D	DSCAM_uc002yyr.1_RNA	NM_001389	NP_001380	O60469	DSCAM_HUMAN	Down syndrome cell adhesion molecule isoform	1865	Cytoplasmic (Potential).				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)																---	---	---	---
RIPK4	54101	broad.mit.edu	37	21	43162025	43162025	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:43162025T>C	uc002yzn.1	-	8	1376	c.1328A>G	c.(1327-1329)CAC>CGC	p.H443R		NM_020639	NP_065690	P57078	RIPK4_HUMAN	ankyrin repeat domain 3	443						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	43411879	43411879	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:43411879T>C	uc002zab.3	-	3	2540	c.2326A>G	c.(2326-2328)ACC>GCC	p.T776A	ZNF295_uc002yzz.3_Missense_Mutation_p.T575A|ZNF295_uc002yzy.3_Missense_Mutation_p.T776A|ZNF295_uc002zaa.3_Missense_Mutation_p.T776A	NM_001098402	NP_001091872	Q9ULJ3	ZN295_HUMAN	zinc finger protein 295 isoform L	776	C2H2-type 5.				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																		---	---	---	---
PDXK	8566	broad.mit.edu	37	21	45168871	45168871	+	Intron	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:45168871G>A	uc002zdm.3	+						PDXK_uc010gpj.2_Intron|PDXK_uc002zdn.3_Intron|PDXK_uc002zdq.3_Intron	NM_003681	NP_003672			pyridoxal kinase						cell proliferation|pyridoxal 5'-phosphate salvage	cytosol	ATP binding|lithium ion binding|magnesium ion binding|potassium ion binding|protein homodimerization activity|pyridoxal kinase activity|pyridoxal phosphate binding|sodium ion binding|zinc ion binding				0				Colorectal(79;0.109)|READ - Rectum adenocarcinoma(84;0.161)|STAD - Stomach adenocarcinoma(101;0.18)	Pyridoxal(DB00147)|Pyridoxine(DB00165)													---	---	---	---
PDXK	8566	broad.mit.edu	37	21	45175647	45175647	+	Splice_Site	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:45175647T>C	uc002zdm.3	+	10	1024	c.826_splice	c.e10+2	p.A276_splice	PDXK_uc010gpj.2_Intron|PDXK_uc002zdn.3_Splice_Site_p.A248_splice|PDXK_uc002zdq.3_Splice_Site_p.A203_splice	NM_003681	NP_003672			pyridoxal kinase						cell proliferation|pyridoxal 5'-phosphate salvage	cytosol	ATP binding|lithium ion binding|magnesium ion binding|potassium ion binding|protein homodimerization activity|pyridoxal kinase activity|pyridoxal phosphate binding|sodium ion binding|zinc ion binding				0				Colorectal(79;0.109)|READ - Rectum adenocarcinoma(84;0.161)|STAD - Stomach adenocarcinoma(101;0.18)	Pyridoxal(DB00147)|Pyridoxine(DB00165)													---	---	---	---
RRP1	8568	broad.mit.edu	37	21	45217814	45217814	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:45217814G>A	uc002zds.2	+	8	737	c.644G>A	c.(643-645)CGA>CAA	p.R215Q	RRP1_uc011aez.1_Missense_Mutation_p.R215Q|RRP1_uc010gpk.1_Missense_Mutation_p.R65Q|RRP1_uc010gpl.1_Missense_Mutation_p.R113Q|RRP1_uc010gpm.1_Missense_Mutation_p.R82Q	NM_003683	NP_003674	P56182	RRP1_HUMAN	ribosomal RNA processing 1 homolog	215					rRNA processing	nucleolus|preribosome, small subunit precursor					0				COAD - Colon adenocarcinoma(84;0.00753)|Colorectal(79;0.0157)|STAD - Stomach adenocarcinoma(101;0.171)														---	---	---	---
AIRE	326	broad.mit.edu	37	21	45710892	45710892	+	Intron	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:45710892G>A	uc002zei.2	+						AIRE_uc010gpq.2_RNA|AIRE_uc002zej.2_Nonsense_Mutation_p.W68*|AIRE_uc010gpr.2_Nonsense_Mutation_p.W68*	NM_000383	NP_000374			autoimmune regulator isoform 1						positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	chromatin binding|histone binding|transcription regulatory region DNA binding|translation regulator activity|zinc ion binding			skin(1)	1				Colorectal(79;0.0806)										Autoimmune_PolyEndocrinopathy_Candidiasis_Ectodermal_Dystrophy				---	---	---	---
C21orf29	54084	broad.mit.edu	37	21	45941975	45941975	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:45941975T>C	uc002zfe.1	-	9	1423	c.1357A>G	c.(1357-1359)AGT>GGT	p.S453G	C21orf29_uc010gpv.1_Missense_Mutation_p.S385G	NM_144991	NP_659428	Q8WU66	TSEAR_HUMAN	chromosome 21 open reading frame 29 precursor	453	EAR 3.				cell adhesion	extracellular region	structural molecule activity				0																		---	---	---	---
KRTAP10-9	386676	broad.mit.edu	37	21	46047116	46047116	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:46047116T>G	uc002zfp.3	+	1	77	c.28T>G	c.(28-30)TCC>GCC	p.S10A	C21orf29_uc002zfe.1_Intron|C21orf29_uc010gpv.1_Intron	NM_198690	NP_941963	P60411	KR109_HUMAN	keratin associated protein 10-9	10						keratin filament					0																		---	---	---	---
KRTAP10-10	353333	broad.mit.edu	37	21	46057660	46057660	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:46057660G>A	uc002zfq.2	+	1	388	c.326G>A	c.(325-327)TGT>TAT	p.C109Y	C21orf29_uc002zfe.1_Intron|C21orf29_uc010gpv.1_Intron	NM_181688	NP_859016	P60014	KR10A_HUMAN	keratin associated protein 10-10	109	7.|15 X 5 AA repeats of C-C-X(3).					keratin filament					0																		---	---	---	---
PTTG1IP	754	broad.mit.edu	37	21	46276106	46276106	+	Splice_Site	SNP	A	G	G	rs111996189		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:46276106A>G	uc002zgb.1	-	4	659	c.449_splice	c.e4+1	p.R150_splice	PTTG1IP_uc011afj.1_Splice_Site|PTTG1IP_uc011afk.1_Intron	NM_004339	NP_004330			pituitary tumor-transforming gene 1						protein import into nucleus	cytoplasm|integral to membrane|nucleus				ovary(1)	1				Colorectal(79;0.0659)														---	---	---	---
ADARB1	104	broad.mit.edu	37	21	46640923	46640923	+	Silent	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:46640923C>T	uc002zgy.2	+	11	2475	c.2040C>T	c.(2038-2040)CAC>CAT	p.H680H	ADARB1_uc002zgr.2_Silent_p.H680H|ADARB1_uc002zgs.2_RNA|ADARB1_uc002zgw.2_Silent_p.H640H|ADARB1_uc002zgv.2_RNA|ADARB1_uc002zgt.2_Silent_p.H640H|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	680	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)														---	---	---	---
SLC19A1	6573	broad.mit.edu	37	21	46951655	46951655	+	Silent	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:46951655G>A	uc002zhl.1	-	3	716	c.597C>T	c.(595-597)CTC>CTT	p.L199L	SLC19A1_uc010gpy.1_Silent_p.L199L|SLC19A1_uc011aft.1_Silent_p.L159L|SLC19A1_uc002zhm.1_Silent_p.L199L|SLC19A1_uc010gpz.1_Silent_p.L78L	NM_194255	NP_919231	P41440	S19A1_HUMAN	solute carrier family 19 member 1	199	Helical; (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)														---	---	---	---
COL6A1	1291	broad.mit.edu	37	21	47423479	47423479	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:47423479G>A	uc002zhu.1	+	35	2741	c.2639G>A	c.(2638-2640)GGC>GAC	p.G880D	COL6A1_uc010gqd.1_Missense_Mutation_p.G211D|COL6A1_uc002zhv.1_Missense_Mutation_p.G211D|COL6A1_uc002zhw.1_5'UTR	NM_001848	NP_001839	P12109	CO6A1_HUMAN	collagen, type VI, alpha 1 precursor	880	C-terminal globular domain.|VWFA 3.				axon guidance|cell adhesion|protein heterotrimerization	collagen type VI|protein complex	platelet-derived growth factor binding			ovary(1)	1	all_hematologic(128;0.24)			Colorectal(79;0.0265)|READ - Rectum adenocarcinoma(84;0.0649)	Palifermin(DB00039)													---	---	---	---
MCM3AP	8888	broad.mit.edu	37	21	47693312	47693312	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:47693312C>T	uc002zir.1	-	7	2222	c.2186G>A	c.(2185-2187)GGC>GAC	p.G729D		NM_003906	NP_003897	O60318	MCM3A_HUMAN	minichromosome maintenance complex component 3	729					DNA replication|protein import into nucleus	cytosol|nucleus	DNA binding|nucleotide binding			large_intestine(2)|lung(1)|ovary(1)|skin(1)	5	Breast(49;0.112)																	---	---	---	---
PCNT	5116	broad.mit.edu	37	21	47769739	47769739	+	Intron	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:47769739G>A	uc002zji.3	+						PCNT_uc002zjj.2_Intron	NM_006031	NP_006022			pericentrin						cilium assembly|G2/M transition of mitotic cell cycle	cytosol|microtubule	calmodulin binding			ovary(4)|breast(2)|pancreas(2)	8	Breast(49;0.112)																	---	---	---	---
DIP2A	23181	broad.mit.edu	37	21	47931389	47931389	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:47931389G>T	uc002zjo.2	+	8	1147	c.964G>T	c.(964-966)GGG>TGG	p.G322W	DIP2A_uc011afy.1_Missense_Mutation_p.G258W|DIP2A_uc011afz.1_Missense_Mutation_p.G318W|DIP2A_uc002zjl.2_Missense_Mutation_p.G322W|DIP2A_uc002zjm.2_Missense_Mutation_p.G322W|DIP2A_uc010gql.2_Missense_Mutation_p.G279W|DIP2A_uc002zjn.2_Missense_Mutation_p.G322W|DIP2A_uc002zjp.1_Missense_Mutation_p.G67W	NM_015151	NP_055966	Q14689	DIP2A_HUMAN	disco-interacting protein 2A isoform a	322					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)														---	---	---	---
DIP2A	23181	broad.mit.edu	37	21	47965802	47965802	+	Silent	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:47965802G>A	uc002zjo.2	+	20	2505	c.2322G>A	c.(2320-2322)CCG>CCA	p.P774P	DIP2A_uc011afy.1_Silent_p.P710P|DIP2A_uc011afz.1_Silent_p.P770P|DIP2A_uc002zjl.2_Silent_p.P774P|DIP2A_uc002zjm.2_Silent_p.P774P|DIP2A_uc010gql.2_Silent_p.P731P|DIP2A_uc002zjn.2_Silent_p.P774P|DIP2A_uc002zjq.2_Silent_p.P166P	NM_015151	NP_055966	Q14689	DIP2A_HUMAN	disco-interacting protein 2A isoform a	774					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)														---	---	---	---
DIP2A	23181	broad.mit.edu	37	21	47969675	47969675	+	Intron	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:47969675A>G	uc002zjo.2	+						DIP2A_uc011afy.1_Intron|DIP2A_uc011afz.1_Intron|DIP2A_uc002zjn.2_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)														---	---	---	---
IL17RA	23765	broad.mit.edu	37	22	17589454	17589454	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:17589454C>T	uc002zly.2	+	13	1478	c.1345C>T	c.(1345-1347)CGC>TGC	p.R449C	IL17RA_uc010gqt.2_Missense_Mutation_p.R397C	NM_014339	NP_055154	Q96F46	I17RA_HUMAN	interleukin 17A receptor precursor	449	Cytoplasmic (Potential).|SEFIR.				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)														---	---	---	---
CECR1	51816	broad.mit.edu	37	22	17662782	17662782	+	Missense_Mutation	SNP	T	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:17662782T>A	uc002zmk.1	-	8	1582	c.1370A>T	c.(1369-1371)GAG>GTG	p.E457V	CECR1_uc010gqu.1_Missense_Mutation_p.E457V|CECR1_uc011agi.1_Missense_Mutation_p.E415V|CECR1_uc002zmj.1_Missense_Mutation_p.E216V	NM_017424	NP_059120	Q9NZK5	CECR1_HUMAN	cat eye syndrome critical region protein 1	457					adenosine catabolic process|hypoxanthine salvage|inosine biosynthetic process|multicellular organismal development|purine ribonucleoside monophosphate biosynthetic process	extracellular space|Golgi apparatus	adenosine deaminase activity|adenosine receptor binding|growth factor activity|heparin binding|protein homodimerization activity|proteoglycan binding|zinc ion binding			ovary(1)	1		all_epithelial(15;0.0152)|Lung NSC(13;0.0875)|all_lung(157;0.106)																---	---	---	---
USP18	11274	broad.mit.edu	37	22	18650678	18650678	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:18650678T>C	uc002zny.2	+	6	840	c.502T>C	c.(502-504)TAT>CAT	p.Y168H		NM_017414	NP_059110	Q9UMW8	UBP18_HUMAN	ubiquitin specific protease 18	168					regulation of type I interferon-mediated signaling pathway|type I interferon-mediated signaling pathway|ubiquitin-dependent protein catabolic process	cytosol|nucleus	ubiquitin thiolesterase activity|ubiquitin-specific protease activity			breast(1)	1																		---	---	---	---
DGCR2	9993	broad.mit.edu	37	22	19076904	19076904	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:19076904T>C	uc002zoq.1	-	2	427	c.179A>G	c.(178-180)GAG>GGG	p.E60G	DGCR2_uc002zor.1_5'UTR|DGCR2_uc011agr.1_Intron	NM_005137	NP_005128	P98153	IDD_HUMAN	integral membrane protein DGCR2 precursor	60	Extracellular (Potential).|LDL-receptor class A.				cell adhesion|organ morphogenesis	integral to membrane	receptor activity|sugar binding			large_intestine(1)	1	Colorectal(54;0.0993)																	---	---	---	---
CLTCL1	8218	broad.mit.edu	37	22	19183901	19183901	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:19183901T>C	uc002zpb.2	-	27	4142	c.4067A>G	c.(4066-4068)CAC>CGC	p.H1356R	CLTCL1_uc011agv.1_Missense_Mutation_p.H1356R|CLTCL1_uc011agw.1_Missense_Mutation_p.H1335R|CLTCL1_uc011agt.1_Missense_Mutation_p.H147R|CLTCL1_uc011agu.1_Missense_Mutation_p.H147R|CLTCL1_uc010grm.1_Missense_Mutation_p.H116R|CLTCL1_uc002zpe.2_3'UTR|CLTCL1_uc002zpd.1_Missense_Mutation_p.H263R	NM_007098	NP_009029	P53675	CLH2_HUMAN	clathrin, heavy polypeptide-like 1 isoform 1	1356	Involved in binding clathrin light chain (By similarity).|Proximal segment.|Heavy chain arm.				anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis	clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network	protein binding|signal transducer activity|structural molecule activity			ovary(4)|central_nervous_system(1)	5	Colorectal(54;0.0993)							T	?	ALCL								---	---	---	---
DGCR8	54487	broad.mit.edu	37	22	20073776	20073776	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:20073776G>A	uc002zri.2	+	2	640	c.290G>A	c.(289-291)CGC>CAC	p.R97H	DGCR8_uc010grz.2_Missense_Mutation_p.R97H|DGCR8_uc002zrj.2_5'Flank	NM_022720	NP_073557	Q8WYQ5	DGCR8_HUMAN	DiGeorge syndrome critical region gene 8	97	Necessary for nuclear localization and retention.|Necessary for interaction with NCL.				primary miRNA processing	cytoplasm|cytoplasm|microtubule cytoskeleton|nucleolus|nucleoplasm	double-stranded RNA binding|metal ion binding|protein binding				0	Colorectal(54;0.0993)																	---	---	---	---
DGCR8	54487	broad.mit.edu	37	22	20094146	20094146	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:20094146T>C	uc002zri.2	+	11	2271	c.1921T>C	c.(1921-1923)TTT>CTT	p.F641L	DGCR8_uc010grz.2_Missense_Mutation_p.F608L|DGCR8_uc002zrj.2_Missense_Mutation_p.F284L	NM_022720	NP_073557	Q8WYQ5	DGCR8_HUMAN	DiGeorge syndrome critical region gene 8	641	DRBM 2.|Necessary for heme-binding and pri-miRNA processing.|Necessary for interaction with DROSHA.				primary miRNA processing	cytoplasm|cytoplasm|microtubule cytoskeleton|nucleolus|nucleoplasm	double-stranded RNA binding|metal ion binding|protein binding				0	Colorectal(54;0.0993)																	---	---	---	---
ZNF74	7625	broad.mit.edu	37	22	20760453	20760453	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:20760453G>A	uc010gsm.2	+	6	1342	c.1130G>A	c.(1129-1131)CGC>CAC	p.R377H	ZNF74_uc002zsg.2_Missense_Mutation_p.R306H|ZNF74_uc002zsh.2_Missense_Mutation_p.R377H|ZNF74_uc002zsi.2_Missense_Mutation_p.R306H|ZNF74_uc010gsn.2_Missense_Mutation_p.R306H	NM_003426	NP_003417	Q16587	ZNF74_HUMAN	zinc finger protein 74	377	C2H2-type 5.				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)															---	---	---	---
ZNF74	7625	broad.mit.edu	37	22	20760471	20760471	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:20760471C>T	uc010gsm.2	+	6	1360	c.1148C>T	c.(1147-1149)ACG>ATG	p.T383M	ZNF74_uc002zsg.2_Missense_Mutation_p.T312M|ZNF74_uc002zsh.2_Missense_Mutation_p.T383M|ZNF74_uc002zsi.2_Missense_Mutation_p.T312M|ZNF74_uc010gsn.2_Missense_Mutation_p.T312M	NM_003426	NP_003417	Q16587	ZNF74_HUMAN	zinc finger protein 74	383					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)															---	---	---	---
SNAP29	9342	broad.mit.edu	37	22	21224655	21224655	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:21224655C>T	uc011ahw.1	+	2	375	c.268C>T	c.(268-270)CGC>TGC	p.R90C		NM_004782	NP_004773	O95721	SNP29_HUMAN	synaptosomal-associated protein 29	90	Potential.				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)															---	---	---	---
LZTR1	8216	broad.mit.edu	37	22	21346557	21346557	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:21346557C>A	uc002zto.2	+	10	1151	c.1048C>A	c.(1048-1050)CTG>ATG	p.L350M	LZTR1_uc002ztn.2_Missense_Mutation_p.L309M|LZTR1_uc011ahy.1_Missense_Mutation_p.L331M|LZTR1_uc010gsr.1_Missense_Mutation_p.L221M	NM_006767	NP_006758	Q8N653	LZTR1_HUMAN	leucine-zipper-like transcription regulator 1	350					anatomical structure morphogenesis		sequence-specific DNA binding transcription factor activity			ovary(2)|lung(2)	4	all_cancers(11;1.83e-25)|all_epithelial(7;9.19e-23)|Lung NSC(8;3.06e-15)|all_lung(8;5.05e-14)|Melanoma(16;0.000465)|Ovarian(15;0.0028)|Colorectal(54;0.0332)|all_neural(72;0.142)	Lung SC(17;0.0262)	LUSC - Lung squamous cell carcinoma(15;0.000204)|Lung(15;0.00494)|Epithelial(17;0.195)															---	---	---	---
LOC96610	96610	broad.mit.edu	37	22	22724400	22724400	+	RNA	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:22724400C>T	uc011aim.1	+	43		c.4673C>T								Parts of antibodies, mostly variable regions.												0																		---	---	---	---
LOC96610	96610	broad.mit.edu	37	22	22937230	22937230	+	Intron	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:22937230C>T	uc011aim.1	+											Parts of antibodies, mostly variable regions.												0																OREG0026367	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
LOC96610	96610	broad.mit.edu	37	22	23029731	23029731	+	RNA	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:23029731C>T	uc011aim.1	+	128		c.8370C>T								Parts of antibodies, mostly variable regions.												0																		---	---	---	---
LOC96610	96610	broad.mit.edu	37	22	23090394	23090394	+	RNA	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:23090394C>T	uc011aim.1	+	203		c.10688C>T								Parts of antibodies, mostly variable regions.												0																		---	---	---	---
BCR	613	broad.mit.edu	37	22	23523767	23523767	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:23523767C>T	uc002zww.2	+	1	1216	c.620C>T	c.(619-621)GCC>GTC	p.A207V	BCR_uc002zwx.2_Missense_Mutation_p.A207V	NM_004327	NP_004318	P11274	BCR_HUMAN	breakpoint cluster region isoform 1	207	Kinase.|Binding to ABL SH2-domain.				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								---	---	---	---
CABIN1	23523	broad.mit.edu	37	22	24456430	24456430	+	Silent	SNP	C	T	T	rs139493223	byFrequency	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:24456430C>T	uc002zzi.1	+	12	1570	c.1443C>T	c.(1441-1443)AAC>AAT	p.N481N	CABIN1_uc002zzj.1_Silent_p.N431N|CABIN1_uc002zzl.1_Silent_p.N481N	NM_012295	NP_036427	Q9Y6J0	CABIN_HUMAN	calcineurin binding protein 1	481					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																		---	---	---	---
ADRBK2	157	broad.mit.edu	37	22	26070436	26070436	+	Silent	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:26070436T>C	uc003abx.3	+	8	735	c.588T>C	c.(586-588)ATT>ATC	p.I196I	ADRBK2_uc010gux.2_Silent_p.I196I|ADRBK2_uc003abw.2_Silent_p.I83I|ADRBK2_uc003aby.3_RNA	NM_005160	NP_005151	P35626	ARBK2_HUMAN	beta-adrenergic receptor kinase 2	196	Protein kinase.						ATP binding|beta-adrenergic receptor kinase activity|signal transducer activity			lung(3)|ovary(2)|stomach(1)|central_nervous_system(1)	7					Adenosine triphosphate(DB00171)													---	---	---	---
TFIP11	24144	broad.mit.edu	37	22	26895381	26895381	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:26895381G>A	uc003acr.2	-	8	1392	c.1018C>T	c.(1018-1020)CGG>TGG	p.R340W	TFIP11_uc003acs.2_Missense_Mutation_p.R340W|TFIP11_uc003act.2_Missense_Mutation_p.R340W	NM_012143	NP_036275	Q9UBB9	TFP11_HUMAN	tuftelin interacting protein 11	340					biomineral tissue development	catalytic step 2 spliceosome|cytoplasm|nuclear speck	DNA binding|sequence-specific DNA binding transcription factor activity				0																		---	---	---	---
PITPNB	23760	broad.mit.edu	37	22	28269779	28269779	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:28269779C>T	uc003adk.2	-	8	557	c.481G>A	c.(481-483)GCA>ACA	p.A161T	PITPNB_uc011akh.1_Missense_Mutation_p.A163T|PITPNB_uc003adl.2_Missense_Mutation_p.A161T	NM_012399	NP_036531	P48739	PIPNB_HUMAN	phosphatidylinositol transfer protein, beta	161					lipid metabolic process|transport	Golgi apparatus	lipid binding			skin(1)	1																		---	---	---	---
ZNRF3	84133	broad.mit.edu	37	22	29445575	29445575	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:29445575A>G	uc003aeg.2	+	8	1271	c.1106A>G	c.(1105-1107)TAC>TGC	p.Y369C	ZNRF3_uc003aeh.1_Missense_Mutation_p.Y369C	NM_032173	NP_115549	Q9ULT6	ZNRF3_HUMAN	zinc and ring finger 3	469	Cytoplasmic (Potential).					integral to membrane	zinc ion binding			ovary(1)	1																		---	---	---	---
AP1B1	162	broad.mit.edu	37	22	29752431	29752431	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:29752431C>T	uc003afj.2	-	6	884	c.700G>A	c.(700-702)GAC>AAC	p.D234N	AP1B1_uc003afi.2_Missense_Mutation_p.D234N|AP1B1_uc003afk.2_Missense_Mutation_p.D234N|AP1B1_uc003afl.2_Missense_Mutation_p.D234N	NM_001127	NP_001118	Q10567	AP1B1_HUMAN	adaptor-related protein complex 1 beta 1 subunit	234					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	protein binding|protein transporter activity			ovary(1)|skin(1)	2																		---	---	---	---
ASCC2	84164	broad.mit.edu	37	22	30202464	30202464	+	Intron	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:30202464C>T	uc003agr.2	-						ASCC2_uc003ags.2_Intron|ASCC2_uc003agt.2_Intron|ASCC2_uc011akr.1_Intron	NM_032204	NP_115580			activating signal cointegrator 1 complex subunit						regulation of transcription, DNA-dependent|transcription, DNA-dependent						0			OV - Ovarian serous cystadenocarcinoma(5;0.000103)|Epithelial(10;0.0169)|all cancers(5;0.0259)															---	---	---	---
RNF215	200312	broad.mit.edu	37	22	30776082	30776082	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:30776082G>A	uc003ahp.2	-	7	977	c.977C>T	c.(976-978)GCG>GTG	p.A326V	RNF215_uc011akw.1_Missense_Mutation_p.A231V	NM_001017981	NP_001017981	Q9Y6U7	RN215_HUMAN	ring finger protein 215	326	Cytoplasmic (Potential).|RING-type; atypical.					integral to membrane	zinc ion binding			central_nervous_system(1)	1																		---	---	---	---
PES1	23481	broad.mit.edu	37	22	30980384	30980384	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:30980384C>T	uc003aij.1	-	6	672	c.598G>A	c.(598-600)GTG>ATG	p.V200M	PES1_uc003aik.1_Missense_Mutation_p.V200M|PES1_uc003ail.1_Intron|PES1_uc003aim.1_Missense_Mutation_p.V200M|PES1_uc003ain.1_Missense_Mutation_p.V61M|PES1_uc003aio.1_Missense_Mutation_p.V61M	NM_014303	NP_055118	O00541	PESC_HUMAN	pescadillo homolog 1, containing BRCT domain	200	Sufficient for nucleolar localization.				cell proliferation|maturation of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)|maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)|regulation of cell cycle	chromosome|nucleoplasm|PeBoW complex|preribosome, large subunit precursor	protein binding				0																		---	---	---	---
LIMK2	3985	broad.mit.edu	37	22	31674308	31674308	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:31674308T>C	uc003akh.2	+	16	1943	c.1798T>C	c.(1798-1800)TCC>CCC	p.S600P	LIMK2_uc003aki.2_Missense_Mutation_p.S354P|LIMK2_uc003akk.2_Missense_Mutation_p.S579P|LIMK2_uc011aln.1_Missense_Mutation_p.S517P	NM_005569	NP_005560	P53671	LIMK2_HUMAN	LIM domain kinase 2 isoform 2a	600	Protein kinase.					mitochondrion|nucleus	ATP binding|protein serine/threonine kinase activity|zinc ion binding			ovary(2)	2																		---	---	---	---
SFI1	9814	broad.mit.edu	37	22	31952982	31952982	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:31952982T>C	uc003ale.2	+	7	992	c.599T>C	c.(598-600)GTT>GCT	p.V200A	SFI1_uc003ald.1_Missense_Mutation_p.V176A|SFI1_uc003alf.2_Missense_Mutation_p.V200A|SFI1_uc003alg.2_Missense_Mutation_p.V118A|SFI1_uc011alp.1_Missense_Mutation_p.V118A|SFI1_uc011alq.1_Missense_Mutation_p.V176A|SFI1_uc003alh.2_Intron	NM_001007467	NP_001007468	A8K8P3	SFI1_HUMAN	spindle assembly associated Sfi1 homolog isoform	200	HAT 2.				G2/M transition of mitotic cell cycle	centriole|cytosol				central_nervous_system(1)	1																		---	---	---	---
SFI1	9814	broad.mit.edu	37	22	31957358	31957358	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:31957358G>A	uc003ale.2	+	8	1138	c.745G>A	c.(745-747)GCC>ACC	p.A249T	SFI1_uc003ald.1_Missense_Mutation_p.A225T|SFI1_uc003alf.2_Missense_Mutation_p.A249T|SFI1_uc003alg.2_Missense_Mutation_p.A167T|SFI1_uc011alp.1_Missense_Mutation_p.A167T|SFI1_uc011alq.1_Missense_Mutation_p.A225T|SFI1_uc003alh.2_RNA	NM_001007467	NP_001007468	A8K8P3	SFI1_HUMAN	spindle assembly associated Sfi1 homolog isoform	249					G2/M transition of mitotic cell cycle	centriole|cytosol				central_nervous_system(1)	1																OREG0026480	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
RFPL3	10738	broad.mit.edu	37	22	32756401	32756401	+	Missense_Mutation	SNP	G	A	A	rs112751320		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:32756401G>A	uc003amj.2	+	2	741	c.536G>A	c.(535-537)CGC>CAC	p.R179H	RFPL3_uc010gwn.2_Missense_Mutation_p.R150H|RFPL3S_uc003amk.2_RNA|RFPL3S_uc003aml.2_RNA	NM_001098535	NP_001092005	O75679	RFPL3_HUMAN	ret finger protein-like 3 isoform 1	179	B30.2/SPRY.						zinc ion binding			ovary(1)	1																		---	---	---	---
RFPL3	10738	broad.mit.edu	37	22	32756799	32756799	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:32756799C>T	uc003amj.2	+	2	1139	c.934C>T	c.(934-936)CGT>TGT	p.R312C	RFPL3_uc010gwn.2_Missense_Mutation_p.R283C|RFPL3S_uc003amk.2_RNA|RFPL3S_uc003aml.2_RNA	NM_001098535	NP_001092005	O75679	RFPL3_HUMAN	ret finger protein-like 3 isoform 1	312							zinc ion binding			ovary(1)	1																		---	---	---	---
BPIL2	254240	broad.mit.edu	37	22	32815345	32815345	+	Intron	SNP	C	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:32815345C>A	uc003amn.2	-						BPIL2_uc010gwo.2_Intron|BPIL2_uc011amb.1_Intron	NM_174932	NP_777592			bactericidal/permeability-increasing							extracellular region	lipopolysaccharide binding|phospholipid binding			ovary(1)|skin(1)	2																		---	---	---	---
SYN3	8224	broad.mit.edu	37	22	32937651	32937651	+	Missense_Mutation	SNP	C	T	T	rs141167959		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:32937651C>T	uc003amx.2	-	7	982	c.823G>A	c.(823-825)GCC>ACC	p.A275T	SYN3_uc003amy.2_Missense_Mutation_p.A275T|SYN3_uc003amz.2_Missense_Mutation_p.A274T	NM_003490	NP_003481	O14994	SYN3_HUMAN	synapsin III isoform IIIa	275	C; actin-binding and synaptic-vesicle binding.				neurotransmitter secretion	cell junction|synaptic vesicle membrane	ATP binding|ligase activity			skin(1)	1																		---	---	---	---
ISX	91464	broad.mit.edu	37	22	35478654	35478654	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:35478654C>T	uc003anj.2	+	2	1324	c.373C>T	c.(373-375)CGG>TGG	p.R125W	ISX_uc011amg.1_Missense_Mutation_p.R113W	NM_001008494	NP_001008494	Q2M1V0	ISX_HUMAN	intestine-specific homeobox	125	Homeobox.					nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			ovary(3)|skin(2)	5																		---	---	---	---
MCM5	4174	broad.mit.edu	37	22	35804519	35804519	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:35804519G>A	uc003anu.3	+	6	809	c.715G>A	c.(715-717)GGG>AGG	p.G239R	MCM5_uc010gwr.2_Missense_Mutation_p.G48R|MCM5_uc003anv.3_Missense_Mutation_p.G196R|MCM5_uc010gws.1_RNA|MCM5_uc003anw.1_5'Flank	NM_006739	NP_006730	P33992	MCM5_HUMAN	minichromosome maintenance complex component 5	239					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																		---	---	---	---
RBM9	23543	broad.mit.edu	37	22	36164385	36164385	+	Silent	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:36164385G>A	uc003aon.3	-	6	787	c.675C>T	c.(673-675)TTC>TTT	p.F225F	RBM9_uc003aog.3_Silent_p.F135F|RBM9_uc003aol.3_Silent_p.F154F|RBM9_uc003aoj.3_Silent_p.F154F|RBM9_uc003aok.3_Silent_p.F155F|RBM9_uc003aoh.3_Silent_p.F154F|RBM9_uc003aom.3_Silent_p.F136F|RBM9_uc010gwu.2_Silent_p.F134F|RBM9_uc003aoo.3_Silent_p.F224F	NM_001082578	NP_001076047	O43251	RFOX2_HUMAN	RNA binding motif protein 9 isoform 5	164	RRM.	Interaction with RNA (By similarity).			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																		---	---	---	---
FOXRED2	80020	broad.mit.edu	37	22	36892178	36892178	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:36892178T>C	uc003apn.3	-	6	1568	c.1460A>G	c.(1459-1461)AAG>AGG	p.K487R	FOXRED2_uc003apm.3_Missense_Mutation_p.K39R|FOXRED2_uc003apo.3_Missense_Mutation_p.K487R|FOXRED2_uc003app.3_Missense_Mutation_p.K487R	NM_024955	NP_079231	Q8IWF2	FXRD2_HUMAN	FAD-dependent oxidoreductase domain containing 2	487					ER-associated protein catabolic process	endoplasmic reticulum lumen	flavin adenine dinucleotide binding|oxidoreductase activity|protein binding			lung(1)|kidney(1)	2																		---	---	---	---
NCF4	4689	broad.mit.edu	37	22	37273732	37273732	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:37273732G>A	uc003apy.3	+	10	1071	c.887G>A	c.(886-888)CGG>CAG	p.R296Q	NCF4_uc003apz.3_3'UTR	NM_000631	NP_000622	Q15080	NCF4_HUMAN	neutrophil cytosolic factor 4 isoform 1	296					cell communication|immune response|oxidation-reduction process	cytosol|NADPH oxidase complex	phosphatidylinositol binding|protein dimerization activity			ovary(1)	1																		---	---	---	---
TRIOBP	11078	broad.mit.edu	37	22	38151164	38151164	+	Silent	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:38151164C>T	uc003atr.2	+	14	5815	c.5544C>T	c.(5542-5544)TAC>TAT	p.Y1848Y	TRIOBP_uc003atu.2_Silent_p.Y1676Y|TRIOBP_uc003atv.2_Silent_p.Y135Y|TRIOBP_uc003atw.2_Silent_p.Y135Y|TRIOBP_uc003atx.1_5'Flank|TRIOBP_uc010gxh.2_5'Flank	NM_001039141	NP_001034230	Q9H2D6	TARA_HUMAN	TRIO and F-actin binding protein isoform 6	1848	PH.				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)																	---	---	---	---
H1F0	3005	broad.mit.edu	37	22	38201908	38201908	+	Silent	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:38201908G>A	uc003aty.2	+	1	795	c.357G>A	c.(355-357)ACG>ACA	p.T119T	GCAT_uc003atz.2_5'Flank|GCAT_uc003aua.1_5'Flank	NM_005318	NP_005309	P07305	H10_HUMAN	H1 histone family, member 0	119					DNA fragmentation involved in apoptotic nuclear change|nucleosome assembly	actin cytoskeleton|Golgi apparatus|nucleoplasm|nucleosome	DNA binding				0	Melanoma(58;0.045)																	---	---	---	---
GCAT	23464	broad.mit.edu	37	22	38212257	38212257	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:38212257A>G	uc003atz.2	+	8	1057	c.1037A>G	c.(1036-1038)CAC>CGC	p.H346R	GCAT_uc003aua.1_Missense_Mutation_p.H372R	NM_014291	NP_055106	O75600	KBL_HUMAN	glycine C-acetyltransferase precursor	346					biosynthetic process|cellular amino acid metabolic process		glycine C-acetyltransferase activity|pyridoxal phosphate binding|transferase activity, transferring nitrogenous groups				0	Melanoma(58;0.045)				Glycine(DB00145)|Pyridoxal Phosphate(DB00114)													---	---	---	---
DDX17	10521	broad.mit.edu	37	22	38895511	38895511	+	Intron	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:38895511A>G	uc003avy.3	-						DDX17_uc003avx.3_Intron|DDX17_uc011anu.1_Intron	NM_001098504	NP_001091974			DEAD box polypeptide 17 isoform 3						RNA processing	nucleus	ATP binding|ATP-dependent helicase activity|RNA binding|RNA helicase activity|RNA-dependent ATPase activity			skin(3)|upper_aerodigestive_tract(1)	4	Melanoma(58;0.0286)																	---	---	---	---
RPL3	6122	broad.mit.edu	37	22	39709743	39709743	+	Intron	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:39709743C>T	uc003axi.2	-						RPL3_uc003axh.2_Intron|RPL3_uc003axj.2_Intron|RPL3_uc010gxx.2_Intron|RPL3_uc003axg.2_Intron|RPL3_uc003axk.1_Intron	NM_000967	NP_000958			ribosomal protein L3 isoform a						endocrine pancreas development|translational elongation|translational termination|viral transcription	cytosolic large ribosomal subunit|nucleolus	protein binding|RNA binding|structural constituent of ribosome			breast(1)|kidney(1)	2	Melanoma(58;0.04)																	---	---	---	---
TAB1	10454	broad.mit.edu	37	22	39824044	39824044	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:39824044A>G	uc003axt.2	+	10	1212	c.1163A>G	c.(1162-1164)TAC>TGC	p.Y388C	TAB1_uc003axr.2_Missense_Mutation_p.Y464C|TAB1_uc011aok.1_Missense_Mutation_p.Y222C|TAB1_uc003axu.1_Missense_Mutation_p.Y388C	NM_006116	NP_006107	Q15750	TAB1_HUMAN	mitogen-activated protein kinase kinase kinase 7	388					activation of MAPK activity|activation of MAPKKK activity|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 NF-kappaB 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|endosome membrane	catalytic activity|protein binding			breast(1)	1																		---	---	---	---
SMCR7L	54471	broad.mit.edu	37	22	39907986	39907986	+	Silent	SNP	C	A	A	rs144526373		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:39907986C>A	uc003axx.2	+	4	775	c.277C>A	c.(277-279)CGG>AGG	p.R93R	SMCR7L_uc003axw.2_Silent_p.R93R|SMCR7L_uc010gxz.1_5'UTR|SMCR7L_uc003axy.2_5'UTR	NM_019008	NP_061881	Q9NQG6	SMC7L_HUMAN	hypothetical protein LOC54471	93						integral to membrane|mitochondrion				central_nervous_system(1)	1	Melanoma(58;0.04)																	---	---	---	---
SMCR7L	54471	broad.mit.edu	37	22	39908411	39908411	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:39908411C>T	uc003axx.2	+	5	995	c.497C>T	c.(496-498)GCC>GTC	p.A166V	SMCR7L_uc003axw.2_Missense_Mutation_p.A166V|SMCR7L_uc010gxz.1_5'UTR|SMCR7L_uc003axy.2_5'UTR	NM_019008	NP_061881	Q9NQG6	SMC7L_HUMAN	hypothetical protein LOC54471	166						integral to membrane|mitochondrion				central_nervous_system(1)	1	Melanoma(58;0.04)																	---	---	---	---
CACNA1I	8911	broad.mit.edu	37	22	40037070	40037070	+	Silent	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:40037070C>T	uc003ayc.2	+	6	939	c.939C>T	c.(937-939)AGC>AGT	p.S313S	CACNA1I_uc003ayd.2_Silent_p.S313S|CACNA1I_uc003aye.2_Silent_p.S228S|CACNA1I_uc003ayf.2_Silent_p.S228S	NM_021096	NP_066919	Q9P0X4	CAC1I_HUMAN	calcium channel, voltage-dependent, T type,	313	I.|Extracellular (Potential).				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	40066194	40066194	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:40066194G>A	uc003ayc.2	+	25	4346	c.4346G>A	c.(4345-4347)CGT>CAT	p.R1449H	CACNA1I_uc003ayd.2_Missense_Mutation_p.R1414H|CACNA1I_uc003aye.2_Missense_Mutation_p.R1364H|CACNA1I_uc003ayf.2_Missense_Mutation_p.R1329H	NM_021096	NP_066919	Q9P0X4	CAC1I_HUMAN	calcium channel, voltage-dependent, T type,	1449	Cytoplasmic (Potential).				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	40666163	40666163	+	Silent	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:40666163T>C	uc011aor.1	+	6	3055	c.2844T>C	c.(2842-2844)GGT>GGC	p.G948G	TNRC6B_uc003aym.2_Silent_p.G201G|TNRC6B_uc003ayn.3_Intron|TNRC6B_uc003ayo.2_Silent_p.G752G	NM_001162501	NP_001155973	Q9UPQ9	TNR6B_HUMAN	trinucleotide repeat containing 6B isoform 1	948					gene silencing by RNA|regulation of translation	cytoplasmic mRNA processing body	nucleotide binding|RNA binding				0																		---	---	---	---
TNRC6B	23112	broad.mit.edu	37	22	40681682	40681682	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:40681682G>A	uc011aor.1	+	12	3827	c.3616G>A	c.(3616-3618)GCA>ACA	p.A1206T	TNRC6B_uc003aym.2_Missense_Mutation_p.A402T|TNRC6B_uc003ayn.3_Missense_Mutation_p.A1096T|TNRC6B_uc003ayo.2_Missense_Mutation_p.A953T	NM_001162501	NP_001155973	Q9UPQ9	TNR6B_HUMAN	trinucleotide repeat containing 6B isoform 1	1206	Gln-rich.				gene silencing by RNA|regulation of translation	cytoplasmic mRNA processing body	nucleotide binding|RNA binding				0																		---	---	---	---
ST13	6767	broad.mit.edu	37	22	41231636	41231636	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:41231636C>T	uc003aze.2	-	7	649	c.506G>A	c.(505-507)CGA>CAA	p.R169Q	ST13_uc011aow.1_Missense_Mutation_p.R159Q	NM_003932	NP_003923	P50502	F10A1_HUMAN	heat shock 70kD protein binding protein	169	TPR 2.						protein binding, bridging				0																		---	---	---	---
DNAJB7	150353	broad.mit.edu	37	22	41257835	41257835	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:41257835A>G	uc003azj.2	-	1	296	c.164T>C	c.(163-165)GTA>GCA	p.V55A	XPNPEP3_uc011aox.1_Intron|XPNPEP3_uc003azh.2_Intron|XPNPEP3_uc003azi.2_Intron|XPNPEP3_uc011aoy.1_5'Flank|XPNPEP3_uc003azg.1_RNA|XPNPEP3_uc003azf.1_RNA|XPNPEP3_uc010gyh.1_5'Flank	NM_145174	NP_660157	Q7Z6W7	DNJB7_HUMAN	DnaJ (Hsp40) homolog, subfamily B, member 7	55	J.				protein folding		heat shock protein binding|unfolded protein binding			ovary(1)	1																		---	---	---	---
TOB2	10766	broad.mit.edu	37	22	41833069	41833069	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:41833069A>G	uc003azz.1	-	2	988	c.281T>C	c.(280-282)ATT>ACT	p.I94T		NM_016272	NP_057356	Q14106	TOB2_HUMAN	transducer of ERBB2, 2	94					female gamete generation|negative regulation of cell proliferation	cytoplasm|nucleus				ovary(1)	1																		---	---	---	---
MEI1	150365	broad.mit.edu	37	22	42128574	42128574	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:42128574C>T	uc003baz.1	+	11	1323	c.1298C>T	c.(1297-1299)GCT>GTT	p.A433V	WBP2NL_uc011ape.1_Intron|LOC339674_uc003bba.1_Intron|MEI1_uc003bay.3_Missense_Mutation_p.A433V|MEI1_uc011apd.1_RNA	NM_152513	NP_689726	Q5TIA1	MEI1_HUMAN	meiosis defective 1	433							binding			central_nervous_system(1)|skin(1)	2																		---	---	---	---
WBP2NL	164684	broad.mit.edu	37	22	42415422	42415422	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:42415422G>A	uc011ape.1	+	3	186	c.170G>A	c.(169-171)CGG>CAG	p.R57Q	WBP2NL_uc003bbt.2_Missense_Mutation_p.R57Q|WBP2NL_uc011apk.1_Intron|WBP2NL_uc003bbu.2_RNA|WBP2NL_uc003bbv.1_5'Flank	NM_152613	NP_689826	Q6ICG8	WBP2L_HUMAN	WBP2 N-terminal like	57	GRAM.				egg activation|male pronucleus assembly|meiosis	perinuclear theca	WW domain binding			ovary(2)	2																		---	---	---	---
A4GALT	53947	broad.mit.edu	37	22	43089639	43089639	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:43089639C>T	uc003bdb.2	-	3	580	c.319G>A	c.(319-321)GAA>AAA	p.E107K	A4GALT_uc010gzd.2_Missense_Mutation_p.E107K	NM_017436	NP_059132	Q9NPC4	A4GAT_HUMAN	alpha 1,4-galactosyltransferase	107	Lumenal (Potential).				glycosphingolipid biosynthetic process|plasma membrane organization	Golgi stack|integral to Golgi membrane|membrane fraction	lactosylceramide 4-alpha-galactosyltransferase activity			central_nervous_system(2)	2																		---	---	---	---
SAMM50	25813	broad.mit.edu	37	22	44385025	44385025	+	Silent	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:44385025C>T	uc003bej.2	+	13	1307	c.1110C>T	c.(1108-1110)GGC>GGT	p.G370G	SAMM50_uc011aqd.1_Silent_p.G160G|SAMM50_uc003bek.2_Silent_p.G175G	NM_015380	NP_056195	Q9Y512	SAM50_HUMAN	sorting and assembly machinery component 50	370				WAGGL -> LGRRW (in Ref. 1; AAD34046).	protein import into mitochondrial outer membrane	integral to membrane|integral to membrane of membrane fraction|mitochondrial sorting and assembly machinery complex	protein binding			skin(1)	1		all_neural(38;0.0966)|Ovarian(80;0.105)|Glioma(61;0.222)																---	---	---	---
KIAA1644	85352	broad.mit.edu	37	22	44681366	44681366	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:44681366T>C	uc003bet.2	-	4	674	c.541A>G	c.(541-543)ACA>GCA	p.T181A		NM_001099294	NP_001092764	Q3SXP7	K1644_HUMAN	hypothetical protein LOC85352 precursor	181	Cytoplasmic (Potential).					integral to membrane				ovary(1)	1		all_neural(38;0.0762)|Ovarian(80;0.105)|Glioma(61;0.222)																---	---	---	---
GTSE1	51512	broad.mit.edu	37	22	46722427	46722427	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:46722427G>A	uc011aqy.1	+	9	1812	c.1600G>A	c.(1600-1602)GCC>ACC	p.A534T	GTSE1_uc011aqz.1_Missense_Mutation_p.A381T|GTSE1_uc003bhl.1_Missense_Mutation_p.A159T|GTSE1_uc003bhm.1_Missense_Mutation_p.A159T|GTSE1_uc003bhn.2_5'Flank	NM_016426	NP_057510	Q9NYZ3	GTSE1_HUMAN	G-2 and S-phase expressed 1	515					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)														---	---	---	---
GRAMD4	23151	broad.mit.edu	37	22	47059987	47059987	+	Silent	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:47059987C>T	uc003bhx.2	+	7	729	c.690C>T	c.(688-690)TCC>TCT	p.S230S	GRAMD4_uc010had.2_Silent_p.S169S	NM_015124	NP_055939	Q6IC98	GRAM4_HUMAN	death-inducing-protein	230					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)														---	---	---	---
BRD1	23774	broad.mit.edu	37	22	50191595	50191595	+	Silent	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:50191595C>T	uc003biv.2	-	5	2443	c.1956G>A	c.(1954-1956)GCG>GCA	p.A652A	BRD1_uc011arf.1_Silent_p.A247A|BRD1_uc011arg.1_Silent_p.A701A|BRD1_uc011arh.1_Silent_p.A652A|BRD1_uc003biu.3_Silent_p.A652A	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)														---	---	---	---
CRELD2	79174	broad.mit.edu	37	22	50313884	50313884	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:50313884C>T	uc003bja.2	+	4	539	c.404C>T	c.(403-405)CCC>CTC	p.P135L	ALG12_uc003biy.2_5'Flank|CRELD2_uc003biz.3_Missense_Mutation_p.P135L|CRELD2_uc010haj.2_Missense_Mutation_p.P135L|CRELD2_uc010hal.2_Missense_Mutation_p.P135L|CRELD2_uc010hak.2_Missense_Mutation_p.P135L|CRELD2_uc010ham.2_Missense_Mutation_p.P135L	NM_024324	NP_077300	Q6UXH1	CREL2_HUMAN	cysteine-rich with EGF-like domains 2 isoform b	135						endoplasmic reticulum|extracellular region	calcium ion binding				0		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;0.198)|LUAD - Lung adenocarcinoma(64;0.247)														---	---	---	---
MAPK11	5600	broad.mit.edu	37	22	50705419	50705419	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:50705419G>A	uc003bkr.2	-	7	612	c.554C>T	c.(553-555)ACG>ATG	p.T185M	MAPK11_uc010hax.2_Missense_Mutation_p.T7M|MAPK11_uc011ars.1_RNA|MAPK11_uc010hay.1_RNA|MAPK11_uc011art.1_3'UTR|MAPK11_uc010haz.2_Missense_Mutation_p.T77M	NM_002751	NP_002742	Q15759	MK11_HUMAN	mitogen-activated protein kinase 11	185	Protein kinase.				activation of MAPK activity|innate immune response|mRNA metabolic process|muscle cell differentiation|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|nerve growth factor receptor signaling pathway|positive regulation of muscle cell differentiation|Ras protein signal transduction|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|MAP kinase activity|protein binding			lung(1)|breast(1)	2		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)														---	---	---	---
SBF1	6305	broad.mit.edu	37	22	50886824	50886824	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:50886824G>A	uc003blh.2	-	38	5396	c.5201C>T	c.(5200-5202)TCG>TTG	p.S1734L	SBF1_uc003ble.2_Missense_Mutation_p.S198L|SBF1_uc003blf.2_Missense_Mutation_p.S210L|SBF1_uc011arx.1_Missense_Mutation_p.S1372L	NM_002972	NP_002963	O95248	MTMR5_HUMAN	SET binding factor 1	1708					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)														---	---	---	---
CHKB	1120	broad.mit.edu	37	22	51020197	51020197	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:51020197C>T	uc003bms.2	-	3	646	c.428G>A	c.(427-429)CGG>CAG	p.R143Q	CHKB-CPT1B_uc003bmp.2_5'Flank|CHKB-CPT1B_uc003bmt.1_Intron|CHKB-CPT1B_uc003bmu.2_Missense_Mutation_p.R22Q|CHKB_uc003bmv.2_Missense_Mutation_p.R143Q|LOC100144603_uc003bmw.3_5'Flank	NM_005198	NP_005189	Q9Y259	CHKB_HUMAN	choline kinase beta	143					phosphatidylethanolamine biosynthetic process		ATP binding|choline kinase activity|ethanolamine kinase activity				0		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;4.04e-77)|OV - Ovarian serous cystadenocarcinoma(4;5.79e-74)|Epithelial(4;6.17e-70)|GBM - Glioblastoma multiforme(4;5.68e-08)|LUAD - Lung adenocarcinoma(64;0.0016)|Lung(4;0.00942)|BRCA - Breast invasive adenocarcinoma(115;0.205)	Choline(DB00122)													---	---	---	---
CSF2RA	1438	broad.mit.edu	37	X	1407540	1407540	+	Intron	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:1407540G>A	uc010nct.2	+						CSF2RA_uc011mhb.1_Intron|CSF2RA_uc004cpq.2_Intron|CSF2RA_uc004cpn.2_Intron|CSF2RA_uc004cpo.2_Intron|CSF2RA_uc010ncu.2_Intron|CSF2RA_uc011mhc.1_Intron|CSF2RA_uc004cpp.2_Intron|CSF2RA_uc010ncv.2_Intron|CSF2RA_uc004cpr.2_Intron	NM_001161529	NP_001155001			colony stimulating factor 2 receptor alpha chain							extracellular region|integral to plasma membrane	cytokine receptor activity			ovary(2)	2		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)													---	---	---	---
SFRS17A	8227	broad.mit.edu	37	X	1712587	1712587	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:1712587C>T	uc004cqa.2	+	2	428	c.232C>T	c.(232-234)CGC>TGC	p.R78C	SFRS17A_uc010ncx.1_Missense_Mutation_p.R78C|SFRS17A_uc004cqb.2_RNA|ASMT_uc004cqd.2_5'Flank	NM_005088	NP_005079	Q02040	AK17A_HUMAN	DNA segment on chromosome X and Y (unique) 155	78					B cell activation|mRNA processing|regulation of transcription, DNA-dependent|RNA splicing|signal transduction	nuclear speck|spliceosomal complex	nucleotide binding|protein binding|RNA binding				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)																---	---	---	---
NLGN4X	57502	broad.mit.edu	37	X	6069453	6069453	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:6069453C>T	uc010ndh.2	-	2	556	c.55G>A	c.(55-57)GTC>ATC	p.V19I	NLGN4X_uc004crp.2_Missense_Mutation_p.V19I|NLGN4X_uc004crq.2_Missense_Mutation_p.V19I|NLGN4X_uc010ndi.2_Missense_Mutation_p.V19I|NLGN4X_uc004crr.2_Missense_Mutation_p.V19I|NLGN4X_uc010ndj.2_Missense_Mutation_p.V19I	NM_181332	NP_851849	Q8N0W4	NLGNX_HUMAN	X-linked neuroligin 4 precursor	19					brainstem development|cell adhesion|cell-cell junction organization|cerebellum development|male courtship behavior|positive regulation of organ growth|regulation of excitatory postsynaptic membrane potential|social behavior|synapse assembly|territorial aggressive behavior|vocalization behavior	cell surface|dendrite|integral to plasma membrane|synapse	chloride ion binding|neurexin binding|protein homodimerization activity|receptor activity			skin(2)|large_intestine(1)|ovary(1)	4																		---	---	---	---
CA5B	11238	broad.mit.edu	37	X	15793407	15793407	+	Silent	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:15793407T>C	uc004cxe.2	+	6	711	c.594T>C	c.(592-594)GAT>GAC	p.D198D		NM_007220	NP_009151	Q9Y2D0	CAH5B_HUMAN	carbonic anhydrase VB, mitochondrial precursor	198					one-carbon metabolic process	mitochondrion	carbonate dehydratase activity|zinc ion binding				0	Hepatocellular(33;0.183)																	---	---	---	---
GRPR	2925	broad.mit.edu	37	X	16170757	16170757	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:16170757C>T	uc004cxj.2	+	3	1797	c.1144C>T	c.(1144-1146)CGG>TGG	p.R382W		NM_005314	NP_005305	P30550	GRPR_HUMAN	gastrin-releasing peptide receptor	382	Cytoplasmic (Potential).				cell proliferation	integral to plasma membrane	bombesin receptor activity			ovary(3)|lung(1)	4	Hepatocellular(33;0.183)																	---	---	---	---
RAI2	10742	broad.mit.edu	37	X	17819066	17819066	+	Silent	SNP	A	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:17819066A>T	uc004cyf.2	-	3	1635	c.1065T>A	c.(1063-1065)CCT>CCA	p.P355P	RAI2_uc004cyg.2_Silent_p.P355P|RAI2_uc010nfa.2_Silent_p.P355P|RAI2_uc004cyh.3_Silent_p.P355P|RAI2_uc011miy.1_Silent_p.P305P	NM_021785	NP_068557	Q9Y5P3	RAI2_HUMAN	retinoic acid induced 2	355					embryo development					ovary(1)|breast(1)	2	Hepatocellular(33;0.183)																	---	---	---	---
SCML2	10389	broad.mit.edu	37	X	18342013	18342013	+	Silent	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:18342013A>G	uc004cyl.2	-	5	520	c.363T>C	c.(361-363)TGT>TGC	p.C121C	SCML2_uc004cyk.3_RNA|SCML2_uc010nfd.1_Silent_p.C121C|SCML2_uc011miz.1_Silent_p.C55C	NM_006089	NP_006080	Q9UQR0	SCML2_HUMAN	sex comb on midleg-like 2	121	MBT 1.				anatomical structure morphogenesis	PcG protein complex	DNA binding|sequence-specific DNA binding transcription factor activity				0	Hepatocellular(33;0.183)																	---	---	---	---
CNKSR2	22866	broad.mit.edu	37	X	21534747	21534747	+	Nonsense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:21534747C>T	uc004czx.1	+	9	991	c.955C>T	c.(955-957)CAG>TAG	p.Q319*	CNKSR2_uc004czw.2_Nonsense_Mutation_p.Q319*|CNKSR2_uc011mjn.1_Intron|CNKSR2_uc011mjo.1_Nonsense_Mutation_p.Q319*	NM_014927	NP_055742	Q8WXI2	CNKR2_HUMAN	connector enhancer of kinase suppressor of Ras	319					regulation of signal transduction	cytoplasm|membrane	protein binding			large_intestine(1)|lung(1)	2																		---	---	---	---
MBTPS2	51360	broad.mit.edu	37	X	21896695	21896695	+	Silent	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:21896695T>C	uc004dae.2	+	9	1343	c.1146T>C	c.(1144-1146)AGT>AGC	p.S382S	MBTPS2_uc010nfr.2_5'UTR	NM_015884	NP_056968	O43462	MBTP2_HUMAN	membrane-bound transcription factor peptidase,	382	Poly-Ser.|Cys-rich.|Lumenal (Probable).				cholesterol metabolic process|proteolysis	Golgi membrane|integral to membrane	metal ion binding|metalloendopeptidase activity			ovary(1)	1																		---	---	---	---
EIF2S3	1968	broad.mit.edu	37	X	24082455	24082455	+	Intron	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:24082455A>G	uc004dbc.2	+							NM_001415	NP_001406			eukaryotic translation initiation factor 2,							cytosol	GTP binding|GTPase activity|protein binding|translation initiation factor activity			lung(1)	1																		---	---	---	---
MAGEB18	286514	broad.mit.edu	37	X	26157984	26157984	+	Silent	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:26157984C>T	uc004dbq.1	+	2	1069	c.882C>T	c.(880-882)ACC>ACT	p.T294T		NM_173699	NP_775970	Q96M61	MAGBI_HUMAN	melanoma antigen family B, 18	294	MAGE.						protein binding			central_nervous_system(1)	1																		---	---	---	---
DCAF8L1	139425	broad.mit.edu	37	X	27998732	27998732	+	Silent	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:27998732A>G	uc004dbx.1	-	1	835	c.720T>C	c.(718-720)ATT>ATC	p.I240I		NM_001017930	NP_001017930	A6NGE4	DC8L1_HUMAN	DDB1 and CUL4 associated factor 8-like 1	240	WD 2.									ovary(3)|skin(1)	4																		---	---	---	---
FAM47B	170062	broad.mit.edu	37	X	34961289	34961289	+	Missense_Mutation	SNP	G	A	A	rs146758510	byFrequency	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:34961289G>A	uc004ddi.1	+	1	359	c.341G>A	c.(340-342)CGG>CAG	p.R114Q		NM_152631	NP_689844	Q8NA70	FA47B_HUMAN	hypothetical protein LOC170062	114										ovary(3)|breast(1)	4																		---	---	---	---
FAM47C	442444	broad.mit.edu	37	X	37027731	37027731	+	Silent	SNP	G	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:37027731G>T	uc004ddl.1	+	1	1262	c.1248G>T	c.(1246-1248)TCG>TCT	p.S416S		NM_001013736	NP_001013758	Q5HY64	FA47C_HUMAN	hypothetical protein LOC442444	416										ovary(3)	3																		---	---	---	---
CYBB	1536	broad.mit.edu	37	X	37660564	37660564	+	Missense_Mutation	SNP	G	A	A	rs151043920		TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:37660564G>A	uc004ddr.2	+	8	921	c.860G>A	c.(859-861)CGG>CAG	p.R287Q	CYBB_uc011mke.1_RNA|CYBB_uc011mkf.1_Missense_Mutation_p.R255Q|CYBB_uc011mkg.1_Missense_Mutation_p.R20Q	NM_000397	NP_000388	P04839	CY24B_HUMAN	cytochrome b-245 beta polypeptide	287	Cytoplasmic (Potential).|FAD-binding FR-type.				electron transport chain|inflammatory response|innate immune response|respiratory burst|superoxide anion generation	NADPH oxidase complex	electron carrier activity|flavin adenine dinucleotide binding|heme binding|protein heterodimerization activity|superoxide-generating NADPH oxidase activity|voltage-gated ion channel activity			central_nervous_system(1)|skin(1)	2																		---	---	---	---
DDX3X	1654	broad.mit.edu	37	X	41206713	41206713	+	Intron	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:41206713A>G	uc004dfe.2	+						DDX3X_uc004dff.2_Intron|DDX3X_uc011mkq.1_Intron|DDX3X_uc011mkr.1_Intron|DDX3X_uc011mks.1_Intron|DDX3X_uc004dfg.2_Intron	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)			---	---	---	---
CASK	8573	broad.mit.edu	37	X	41495907	41495907	+	Missense_Mutation	SNP	T	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:41495907T>A	uc004dfl.3	-	9	885	c.839A>T	c.(838-840)GAT>GTT	p.D280V	CASK_uc004dfk.3_Missense_Mutation_p.D95V|CASK_uc004dfm.3_Missense_Mutation_p.D280V|CASK_uc004dfn.3_Missense_Mutation_p.D280V	NM_003688	NP_003679	O14936	CSKP_HUMAN	calcium/calmodulin-dependent serine protein	280					cell adhesion	actin cytoskeleton|cytoplasm|nucleus|plasma membrane	ATP binding|calmodulin binding|guanylate kinase activity|protein serine/threonine kinase activity			ovary(3)|lung(2)|stomach(1)	6																		---	---	---	---
GPR82	27197	broad.mit.edu	37	X	41586769	41586769	+	Silent	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:41586769C>T	uc004dfs.1	+	3	730	c.490C>T	c.(490-492)CTG>TTG	p.L164L	CASK_uc004dfl.3_Intron|CASK_uc004dfm.3_Intron|CASK_uc004dfn.3_Intron|GPR82_uc004dft.2_Silent_p.L164L|GPR82_uc004dfu.1_RNA	NM_080817	NP_543007	Q96P67	GPR82_HUMAN	G protein-coupled receptor 82	164	Helical; Name=4; (Potential).					integral to membrane|plasma membrane	G-protein coupled receptor activity			ovary(1)|pancreas(1)	2																		---	---	---	---
SLC9A7	84679	broad.mit.edu	37	X	46502829	46502829	+	Intron	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:46502829G>A	uc004dgu.1	-							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																		---	---	---	---
UBA1	7317	broad.mit.edu	37	X	47058234	47058234	+	Silent	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:47058234C>T	uc004dhj.3	+	2	184	c.33C>T	c.(31-33)CGC>CGT	p.R11R	UBA1_uc004dhk.3_Silent_p.R11R	NM_153280	NP_695012	P22314	UBA1_HUMAN	ubiquitin-activating enzyme E1	11					cell death|protein modification process		ATP binding|ligase activity|protein binding|small protein activating enzyme activity			ovary(1)	1																		---	---	---	---
WDR45	11152	broad.mit.edu	37	X	48933277	48933277	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:48933277G>A	uc004dmk.1	-	8	824	c.652C>T	c.(652-654)CGC>TGC	p.R218C	PRAF2_uc004dmh.2_5'Flank|PRAF2_uc004dmi.2_5'Flank|PRAF2_uc011mmt.1_Missense_Mutation_p.R116C|WDR45_uc004dmj.1_Missense_Mutation_p.R179C|WDR45_uc004dml.1_Missense_Mutation_p.R219C|WDR45_uc004dmm.1_Missense_Mutation_p.R183C|WDR45_uc010nim.1_Missense_Mutation_p.R218C|WDR45_uc004dmn.1_Missense_Mutation_p.R109C|WDR45_uc004dmo.1_Missense_Mutation_p.R241C|WDR45_uc004dmp.1_Missense_Mutation_p.R219C	NM_001029896	NP_001025067	Q9Y484	WIPI4_HUMAN	WD repeat domain 45 isoform 2	218	WD 2.				autophagy|response to starvation	organelle membrane	phosphatidylinositol-3,5-bisphosphate binding			ovary(1)	1																		---	---	---	---
MAGIX	79917	broad.mit.edu	37	X	49021359	49021359	+	Silent	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:49021359T>C	uc010nin.1	+	4	485	c.438T>C	c.(436-438)GCT>GCC	p.A146A	MAGIX_uc010nio.1_Intron|MAGIX_uc004dmt.2_Intron|MAGIX_uc004dmu.2_Silent_p.A87A|MAGIX_uc004dmw.2_Silent_p.A79A	NM_024859	NP_079135	Q9H6Y5	MAGIX_HUMAN	MAGI family member, X-linked isoform a	146	PDZ.										0																		---	---	---	---
Unknown	0	broad.mit.edu	37	X	51151391	51151391	+	3'UTR	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:51151391G>A	uc004dpj.2	+	1						NM_203407	NP_981952			hypothetical protein LOC340602																														---	---	---	---
KDM5C	8242	broad.mit.edu	37	X	53225970	53225970	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:53225970A>G	uc004drz.2	-	19	3412	c.2879T>C	c.(2878-2880)GTA>GCA	p.V960A	KDM5C_uc011moc.1_RNA|KDM5C_uc011mod.1_Missense_Mutation_p.V893A|KDM5C_uc004dsa.2_Missense_Mutation_p.V959A	NM_004187	NP_004178	P41229	KDM5C_HUMAN	jumonji, AT rich interactive domain 1C isoform	960					chromatin modification|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|protein binding|zinc ion binding			kidney(9)|ovary(5)|salivary_gland(1)|autonomic_ganglia(1)|haematopoietic_and_lymphoid_tissue(1)|oesophagus(1)	18								N|F|S		clear cell renal carcinoma								---	---	---	---
HUWE1	10075	broad.mit.edu	37	X	53565401	53565401	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:53565401C>T	uc004dsp.2	-	77	12295	c.11893G>A	c.(11893-11895)GTG>ATG	p.V3965M	HUWE1_uc004dsn.2_Missense_Mutation_p.V2773M|HUWE1_uc004dsq.1_Missense_Mutation_p.V265M	NM_031407	NP_113584	Q7Z6Z7	HUWE1_HUMAN	HECT, UBA and WWE domain containing 1	3965					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																		---	---	---	---
HUWE1	10075	broad.mit.edu	37	X	53571665	53571665	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:53571665G>A	uc004dsp.2	-	72	11509	c.11107C>T	c.(11107-11109)CGG>TGG	p.R3703W	HUWE1_uc004dsn.2_Missense_Mutation_p.R2511W|HUWE1_uc004dsq.1_Missense_Mutation_p.R18W	NM_031407	NP_113584	Q7Z6Z7	HUWE1_HUMAN	HECT, UBA and WWE domain containing 1	3703					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	54263702	54263702	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:54263702C>T	uc004dtd.1	-	20	4595	c.4156G>A	c.(4156-4158)GTG>ATG	p.V1386M	WNK3_uc004dtc.1_Missense_Mutation_p.V1433M	NM_001002838	NP_001002838	Q9BYP7	WNK3_HUMAN	WNK lysine deficient protein kinase 3 isoform 2	1386					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																		---	---	---	---
ARHGEF9	23229	broad.mit.edu	37	X	62898329	62898329	+	Nonsense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:62898329G>A	uc004dvl.2	-	5	1524	c.685C>T	c.(685-687)CAG>TAG	p.Q229*	ARHGEF9_uc004dvj.1_Nonsense_Mutation_p.Q118*|ARHGEF9_uc004dvk.1_Nonsense_Mutation_p.Q91*|ARHGEF9_uc011mos.1_Nonsense_Mutation_p.Q208*|ARHGEF9_uc004dvm.1_Nonsense_Mutation_p.Q208*|ARHGEF9_uc011mot.1_Nonsense_Mutation_p.Q176*|ARHGEF9_uc004dvn.2_Nonsense_Mutation_p.Q236*	NM_015185	NP_056000	O43307	ARHG9_HUMAN	Cdc42 guanine exchange factor 9	229	DH.				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																		---	---	---	---
ARR3	407	broad.mit.edu	37	X	69500430	69500430	+	Silent	SNP	C	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:69500430C>A	uc004dyb.2	+	14	1079	c.1011C>A	c.(1009-1011)GCC>GCA	p.A337A	ARR3_uc004dya.2_Silent_p.A337A|RAB41_uc004dyc.2_5'Flank|RAB41_uc010nkv.2_5'Flank	NM_004312	NP_004303	P36575	ARRC_HUMAN	arrestin 3, retinal (X-arrestin)	337					signal transduction|visual perception	cytoplasm|soluble fraction				large_intestine(2)|ovary(2)	4																		---	---	---	---
KIF4A	24137	broad.mit.edu	37	X	69550132	69550132	+	Missense_Mutation	SNP	A	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:69550132A>T	uc004dyg.2	+	9	1148	c.1021A>T	c.(1021-1023)ATT>TTT	p.I341F	KIF4A_uc010nkw.2_Missense_Mutation_p.I341F|KIF4A_uc004dyf.1_Missense_Mutation_p.I341F	NM_012310	NP_036442	O95239	KIF4A_HUMAN	kinesin family member 4	341	Kinesin-motor.				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	69749827	69749827	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:69749827A>G	uc004dyl.2	-	30	2750	c.2588T>C	c.(2587-2589)ATT>ACT	p.I863T	TEX11_uc004dyk.2_Missense_Mutation_p.I538T|TEX11_uc004dym.2_Missense_Mutation_p.I848T	NM_001003811	NP_001003811	Q8IYF3	TEX11_HUMAN	testis expressed sequence 11 isoform 1	863							protein binding			ovary(3)|breast(1)|skin(1)	5	Renal(35;0.156)																	---	---	---	---
TSIX	9383	broad.mit.edu	37	X	73045812	73045812	+	RNA	SNP	G	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:73045812G>C	uc004ebn.2	+	1		c.33773G>C			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	73066630	73066630	+	RNA	SNP	G	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:73066630G>T	uc004ebm.1	-	1		c.5959C>A				NR_001564				Homo sapiens cDNA: FLJ21545 fis, clone COL06195.												0																		---	---	---	---
XIST	7503	broad.mit.edu	37	X	73067776	73067776	+	RNA	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:73067776A>G	uc004ebm.1	-	1		c.4813T>C				NR_001564				Homo sapiens cDNA: FLJ21545 fis, clone COL06195.												0																		---	---	---	---
ATRX	546	broad.mit.edu	37	X	76938322	76938322	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:76938322T>C	uc004ecp.3	-	9	2658	c.2426A>G	c.(2425-2427)CAA>CGA	p.Q809R	ATRX_uc004ecq.3_Missense_Mutation_p.Q771R|ATRX_uc004eco.3_Missense_Mutation_p.Q594R|ATRX_uc004ecr.2_Missense_Mutation_p.Q741R|ATRX_uc010nlx.1_Missense_Mutation_p.Q780R|ATRX_uc010nly.1_Missense_Mutation_p.Q754R	NM_000489	NP_000480	P46100	ATRX_HUMAN	transcriptional regulator ATRX isoform 1	809					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						---	---	---	---
DRP2	1821	broad.mit.edu	37	X	100503162	100503162	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:100503162A>G	uc004egz.2	+	13	1706	c.1337A>G	c.(1336-1338)GAG>GGG	p.E446G	DRP2_uc011mrh.1_Missense_Mutation_p.E368G	NM_001939	NP_001930	Q13474	DRP2_HUMAN	dystrophin related protein 2	446					central nervous system development	cytoplasm|cytoskeleton	zinc ion binding			ovary(2)	2																		---	---	---	---
ZMAT1	84460	broad.mit.edu	37	X	101138591	101138591	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:101138591T>C	uc004eim.2	-	2	4793	c.1295A>G	c.(1294-1296)GAT>GGT	p.D432G	ZMAT1_uc011mrl.1_Missense_Mutation_p.D603G|ZMAT1_uc004ein.2_Missense_Mutation_p.D432G|ZMAT1_uc011mrm.1_Missense_Mutation_p.D432G	NM_032441	NP_115817	Q5H9K5	ZMAT1_HUMAN	zinc finger, matrin type 1 isoform 3	432						nucleus	zinc ion binding			ovary(1)	1																		---	---	---	---
ARMCX5	64860	broad.mit.edu	37	X	101857695	101857695	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:101857695C>A	uc004ejg.2	+	6	1507	c.626C>A	c.(625-627)CCC>CAC	p.P209H	ARMCX5_uc004ejh.2_Missense_Mutation_p.P209H	NM_022838	NP_073749	Q6P1M9	ARMX5_HUMAN	armadillo repeat containing, X-linked 5	209							binding			ovary(1)	1																		---	---	---	---
TCEAL3	85012	broad.mit.edu	37	X	102864333	102864333	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:102864333C>T	uc004ekq.2	+	3	603	c.341C>T	c.(340-342)ACG>ATG	p.T114M	TCEAL3_uc004ekr.2_Missense_Mutation_p.T114M	NM_001006933	NP_001006934	Q969E4	TCAL3_HUMAN	transcription elongation factor A (SII)-like 3	114					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus					0																		---	---	---	---
TEX13A	56157	broad.mit.edu	37	X	104464699	104464699	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:104464699C>T	uc004ema.2	-	2	495	c.383G>A	c.(382-384)CGG>CAG	p.R128Q	IL1RAPL2_uc004elz.1_Intron|TEX13A_uc004emb.2_Missense_Mutation_p.R128Q	NM_031274	NP_112564	Q9BXU3	TX13A_HUMAN	testis expressed sequence 13A	128						intracellular	zinc ion binding			ovary(2)	2																		---	---	---	---
IL1RAPL2	26280	broad.mit.edu	37	X	105011088	105011088	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:105011088A>G	uc004elz.1	+	11	2251	c.1495A>G	c.(1495-1497)AGT>GGT	p.S499G		NM_017416	NP_059112	Q9NP60	IRPL2_HUMAN	interleukin 1 receptor accessory protein-like 2	499	Cytoplasmic (Potential).|TIR.				central nervous system development|innate immune response	integral to membrane	interleukin-1, Type II, blocking receptor activity			breast(2)|ovary(1)	3																		---	---	---	---
COL4A6	1288	broad.mit.edu	37	X	107435743	107435743	+	Silent	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:107435743T>C	uc004enw.3	-	18	1246	c.1143A>G	c.(1141-1143)CTA>CTG	p.L381L	COL4A6_uc004env.3_Silent_p.L380L|COL4A6_uc011msn.1_Silent_p.L380L|COL4A6_uc010npk.2_Silent_p.L380L	NM_001847	NP_001838	Q14031	CO4A6_HUMAN	type IV alpha 6 collagen isoform A precursor	381	Triple-helical region.				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	108904820	108904820	+	Missense_Mutation	SNP	T	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:108904820T>A	uc004eoi.2	-	15	2265	c.1760A>T	c.(1759-1761)AAA>ATA	p.K587I	ACSL4_uc004eoj.2_Missense_Mutation_p.K546I|ACSL4_uc004eok.2_Missense_Mutation_p.K546I	NM_022977	NP_075266	O60488	ACSL4_HUMAN	acyl-CoA synthetase long-chain family member 4	587	Cytoplasmic (Potential).				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)													---	---	---	---
ACSL4	2182	broad.mit.edu	37	X	108911414	108911414	+	Silent	SNP	G	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:108911414G>T	uc004eoi.2	-	12	1859	c.1354C>A	c.(1354-1356)CGA>AGA	p.R452R	ACSL4_uc004eoj.2_Silent_p.R411R|ACSL4_uc004eok.2_Silent_p.R411R|ACSL4_uc010npp.1_Silent_p.R452R	NM_022977	NP_075266	O60488	ACSL4_HUMAN	acyl-CoA synthetase long-chain family member 4	452	Cytoplasmic (Potential).				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)													---	---	---	---
TRPC5	7224	broad.mit.edu	37	X	111025351	111025351	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:111025351C>T	uc004epl.1	-	8	2831	c.1912G>A	c.(1912-1914)GAG>AAG	p.E638K	TRPC5_uc004epm.1_Missense_Mutation_p.E638K	NM_012471	NP_036603	Q9UL62	TRPC5_HUMAN	transient receptor potential cation channel,	638	Cytoplasmic (Potential).				axon guidance	calcium channel complex|integral to plasma membrane	protein binding|store-operated calcium channel activity			urinary_tract(1)	1																		---	---	---	---
KLHL13	90293	broad.mit.edu	37	X	117032966	117032966	+	Missense_Mutation	SNP	A	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:117032966A>T	uc004eql.2	-	7	1935	c.1873T>A	c.(1873-1875)TCC>ACC	p.S625T	KLHL13_uc004eqk.2_Missense_Mutation_p.S574T|KLHL13_uc011mtn.1_Missense_Mutation_p.S465T|KLHL13_uc011mto.1_Missense_Mutation_p.S619T|KLHL13_uc011mtp.1_Missense_Mutation_p.S627T|KLHL13_uc004eqm.2_Missense_Mutation_p.S574T|KLHL13_uc011mtq.1_Missense_Mutation_p.S609T	NM_033495	NP_277030	Q9P2N7	KLH13_HUMAN	kelch-like 13	625	Kelch 6.				cytokinesis|mitosis|protein ubiquitination	Cul3-RING ubiquitin ligase complex				kidney(1)|skin(1)	2																		---	---	---	---
GRIA3	2892	broad.mit.edu	37	X	122537264	122537264	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:122537264C>T	uc004etq.3	+	10	1480	c.1187C>T	c.(1186-1188)GCT>GTT	p.A396V	GRIA3_uc004etr.3_Missense_Mutation_p.A396V|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_Missense_Mutation_p.A380V	NM_007325	NP_015564	P42263	GRIA3_HUMAN	glutamate receptor, ionotrophic, AMPA 3 isoform	396	Extracellular (Potential).				glutamate signaling pathway|synaptic transmission	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane	alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity			ovary(3)|central_nervous_system(1)|pancreas(1)	5					L-Glutamic Acid(DB00142)													---	---	---	---
ODZ1	10178	broad.mit.edu	37	X	123518351	123518351	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:123518351C>T	uc004euj.2	-	29	6473	c.6409G>A	c.(6409-6411)GAC>AAC	p.D2137N	ODZ1_uc011muj.1_Missense_Mutation_p.D2143N|ODZ1_uc010nqy.2_Missense_Mutation_p.D2144N	NM_014253	NP_055068	Q9UKZ4	TEN1_HUMAN	odz, odd Oz/ten-m homolog 1 isoform 3	2137	Extracellular (Potential).			MVICD -> HGNMC (in Ref. 1; AAF04723).	immune response|negative regulation of cell proliferation|nervous system development|signal transduction	extracellular region	heparin binding			ovary(11)|breast(4)|large_intestine(2)|skin(2)|pancreas(2)|upper_aerodigestive_tract(1)|lung(1)	23																		---	---	---	---
ODZ1	10178	broad.mit.edu	37	X	123519843	123519843	+	Silent	SNP	T	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:123519843T>G	uc004euj.2	-	28	5803	c.5739A>C	c.(5737-5739)TCA>TCC	p.S1913S	ODZ1_uc011muj.1_Silent_p.S1919S|ODZ1_uc010nqy.2_Silent_p.S1920S	NM_014253	NP_055068	Q9UKZ4	TEN1_HUMAN	odz, odd Oz/ten-m homolog 1 isoform 3	1913	Extracellular (Potential).|YD 9.				immune response|negative regulation of cell proliferation|nervous system development|signal transduction	extracellular region	heparin binding			ovary(11)|breast(4)|large_intestine(2)|skin(2)|pancreas(2)|upper_aerodigestive_tract(1)|lung(1)	23																		---	---	---	---
DCAF12L1	139170	broad.mit.edu	37	X	125686251	125686251	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:125686251C>T	uc004eul.2	-	1	592	c.341G>A	c.(340-342)GGC>GAC	p.G114D		NM_178470	NP_848565	Q5VU92	DC121_HUMAN	DDB1 and CUL4 associated factor 12-like 1	114										skin(3)|ovary(1)	4																		---	---	---	---
SMARCA1	6594	broad.mit.edu	37	X	128649683	128649683	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:128649683C>T	uc004eun.3	-	5	724	c.611G>A	c.(610-612)GGC>GAC	p.G204D	SMARCA1_uc004eup.3_Missense_Mutation_p.G204D|SMARCA1_uc011muk.1_Missense_Mutation_p.G204D|SMARCA1_uc011mul.1_Missense_Mutation_p.G204D	NM_003069	NP_003060	P28370	SMCA1_HUMAN	SWI/SNF-related matrix-associated	204	Helicase ATP-binding.				ATP-dependent chromatin remodeling|brain development|neuron differentiation|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	NURF complex	ATP binding|DNA binding|helicase activity|nucleosome binding|protein binding			ovary(3)|skin(1)	4																		---	---	---	---
UTP14A	10813	broad.mit.edu	37	X	129053226	129053226	+	Missense_Mutation	SNP	A	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:129053226A>T	uc004euz.2	+	7	641	c.613A>T	c.(613-615)ACC>TCC	p.T205S	UTP14A_uc011mup.1_Missense_Mutation_p.T153S|UTP14A_uc011muq.1_Missense_Mutation_p.T151S|UTP14A_uc004eva.1_5'Flank	NM_006649	NP_006640	Q9BVJ6	UT14A_HUMAN	UTP14, U3 small nucleolar ribonucleoprotein,	205					rRNA processing	nucleolus|small-subunit processome	protein binding			ovary(2)	2																		---	---	---	---
AIFM1	9131	broad.mit.edu	37	X	129271114	129271114	+	Silent	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:129271114T>C	uc004evg.2	-	10	1192	c.1014A>G	c.(1012-1014)GGA>GGG	p.G338G	AIFM1_uc011mur.1_5'UTR|AIFM1_uc011mus.1_3'UTR|AIFM1_uc004evh.2_Silent_p.G334G|AIFM1_uc004evi.2_Silent_p.G51G|AIFM1_uc004evk.2_RNA	NM_004208	NP_004199	O95831	AIFM1_HUMAN	programmed cell death 8 isoform 1	338	FAD-dependent oxidoreductase (By similarity).				activation of caspase activity|apoptosis in response to endoplasmic reticulum stress|cell redox homeostasis|DNA damage response, signal transduction resulting in induction of apoptosis|DNA fragmentation involved in apoptotic nuclear change	cytosol|mitochondrial inner membrane|mitochondrial intermembrane space|nucleus|perinuclear region of cytoplasm	DNA binding|electron carrier activity|flavin adenine dinucleotide binding|oxidoreductase activity|protein binding			ovary(4)|central_nervous_system(1)	5																		---	---	---	---
IGSF1	3547	broad.mit.edu	37	X	130408160	130408160	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:130408160T>C	uc004ewd.2	-	19	4010	c.3772A>G	c.(3772-3774)ACT>GCT	p.T1258A	IGSF1_uc004ewe.3_Missense_Mutation_p.T1252A|IGSF1_uc004ewf.2_Missense_Mutation_p.T1238A	NM_001555	NP_001546	Q8N6C5	IGSF1_HUMAN	immunoglobulin superfamily, member 1 isoform 1	1258	Extracellular (Potential).				regulation of transcription, DNA-dependent	extracellular region|integral to membrane	inhibin beta-A binding|inhibin beta-B binding			ovary(3)|lung(1)|central_nervous_system(1)	5																		---	---	---	---
MIR106A	406899	broad.mit.edu	37	X	133304280	133304280	+	RNA	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:133304280G>A	hsa-mir-106a|MI0000113	-			c.29G>A			MIR363_hsa-mir-363|MI0000764_5'Flank|MIR92A2_hsa-mir-92a-2|MI0000094_5'Flank|uc004exf.2_5'Flank|uc011mvi.1_5'Flank|MIR19B2_hsa-mir-19b-2|MI0000075_5'Flank|MIR20B_hsa-mir-20b|MI0001519_5'Flank|MIR18B_hsa-mir-18b|MI0001518_5'Flank|uc004exg.1_RNA																	0																		---	---	---	---
MIR424	494336	broad.mit.edu	37	X	133680689	133680689	+	RNA	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:133680689G>A	hsa-mir-424|MI0001446	-			c.53G>A			MGC16121_uc011mvm.1_5'Flank|MGC16121_uc004exm.2_5'Flank|MIR503_hsa-mir-503|MI0003188_5'Flank|uc011mvn.1_5'Flank|MGC16121_uc011mvo.1_RNA																	0																		---	---	---	---
FAM127A	8933	broad.mit.edu	37	X	134166426	134166426	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:134166426G>A	uc004eyd.2	+	1	94	c.13G>A	c.(13-15)GTG>ATG	p.V5M	uc004eye.1_RNA	NM_001078171	NP_001071639	A6ZKI3	F127A_HUMAN	family with sequence similarity 127, member A	5											0	Acute lymphoblastic leukemia(192;0.000127)																	---	---	---	---
SAGE1	55511	broad.mit.edu	37	X	134993981	134993981	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:134993981A>G	uc004ezh.2	+	18	2557	c.2390A>G	c.(2389-2391)GAC>GGC	p.D797G	SAGE1_uc010nry.1_Missense_Mutation_p.D766G|SAGE1_uc011mvv.1_Missense_Mutation_p.D421G	NM_018666	NP_061136	Q9NXZ1	SAGE1_HUMAN	sarcoma antigen 1	797										ovary(2)|skin(1)	3	Acute lymphoblastic leukemia(192;0.000127)																	---	---	---	---
GPR112	139378	broad.mit.edu	37	X	135405106	135405106	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:135405106C>A	uc004ezu.1	+	5	531	c.240C>A	c.(238-240)AAC>AAA	p.N80K	GPR112_uc010nsb.1_Intron	NM_153834	NP_722576	Q8IZF6	GP112_HUMAN	G-protein coupled receptor 112	80	Extracellular (Potential).				neuropeptide signaling pathway	integral to membrane|plasma membrane	G-protein coupled receptor activity			ovary(5)|large_intestine(2)|skin(2)|lung(1)|breast(1)|pancreas(1)	12	Acute lymphoblastic leukemia(192;0.000127)																	---	---	---	---
RBMX	27316	broad.mit.edu	37	X	135957302	135957302	+	Missense_Mutation	SNP	G	A	A	rs142954172	by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:135957302G>A	uc004fae.1	-	8	1018	c.808C>T	c.(808-810)CGT>TGT	p.R270C	RBMX_uc004fac.1_5'Flank|RBMX_uc011mwf.1_Silent_p.I161I|RBMX_uc004fad.1_Missense_Mutation_p.R270C|RBMX_uc011mwg.1_Missense_Mutation_p.R231C|RBMX_uc004faf.1_Missense_Mutation_p.R131C|RBMX_uc010nsf.1_Missense_Mutation_p.R231C|RBMX_uc004fag.1_Missense_Mutation_p.R142C	NM_002139	NP_002130	P38159	HNRPG_HUMAN	RNA binding motif protein, X-linked isoform 1	270						catalytic step 2 spliceosome|heterogeneous nuclear ribonucleoprotein complex|nucleoplasm	nucleotide binding|protein binding|RNA binding			ovary(1)	1	Acute lymphoblastic leukemia(192;0.000127)																	---	---	---	---
MAGEC3	139081	broad.mit.edu	37	X	140969366	140969366	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:140969366G>T	uc011mwp.1	+	4	693	c.693G>T	c.(691-693)GAG>GAT	p.E231D		NM_138702	NP_619647	Q8TD91	MAGC3_HUMAN	melanoma antigen family C, 3 isoform 1	231	MAGE 1.									skin(2)|central_nervous_system(1)	3	Acute lymphoblastic leukemia(192;6.56e-05)																	---	---	---	---
NSDHL	50814	broad.mit.edu	37	X	152014912	152014912	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:152014912G>A	uc004fgt.1	+	3	305	c.44G>A	c.(43-45)CGG>CAG	p.R15Q	NSDHL_uc004fgs.1_Missense_Mutation_p.R15Q	NM_001129765	NP_001123237	Q15738	NSDHL_HUMAN	NAD(P) dependent steroid dehydrogenase-like	15					cholesterol biosynthetic process	endoplasmic reticulum membrane|integral to membrane	3-beta-hydroxy-delta5-steroid dehydrogenase activity|binding|C-3 sterol dehydrogenase (C-4 sterol decarboxylase) activity|sterol-4-alpha-carboxylate 3-dehydrogenase (decarboxylating) activity				0	Acute lymphoblastic leukemia(192;6.56e-05)				NADH(DB00157)													---	---	---	---
NAA10	8260	broad.mit.edu	37	X	153195550	153195550	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:153195550G>T	uc004fjm.1	-	8	709	c.598C>A	c.(598-600)CTG>ATG	p.L200M	NAA10_uc004fjn.1_Missense_Mutation_p.L185M	NM_003491	NP_003482	P41227	NAA10_HUMAN	alpha-N-acetyltransferase 1A	200					DNA packaging|internal protein amino acid acetylation|N-terminal protein amino acid acetylation	cytoplasm|nucleus	peptide alpha-N-acetyltransferase activity|protein binding			ovary(1)	1																		---	---	---	---
HCFC1	3054	broad.mit.edu	37	X	153220705	153220705	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:153220705C>T	uc004fjp.2	-	17	3673	c.3145G>A	c.(3145-3147)GTC>ATC	p.V1049I		NM_005334	NP_005325	P51610	HCFC1_HUMAN	host cell factor 1	1049					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)																	---	---	---	---
GAB3	139716	broad.mit.edu	37	X	153941473	153941473	+	Intron	SNP	T	C	C			TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:153941473T>C	uc004fmj.1	-						GAB3_uc004fmk.1_Intron|GAB3_uc010nve.1_Intron|GAB3_uc004fml.1_Intron	NM_080612	NP_542179			Gab3 protein isoform 2											ovary(1)	1	all_cancers(53;8.15e-17)|all_epithelial(53;1.1e-10)|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)																	---	---	---	---
DKC1	1736	broad.mit.edu	37	X	154004579	154004579	+	Missense_Mutation	SNP	G	A	A	rs150319104	byFrequency;by1000genomes	TCGA-BR-4200-01A-01D-1126-08	TCGA-BR-4200-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:154004579G>A	uc004fmm.2	+	14	1666	c.1456G>A	c.(1456-1458)GGG>AGG	p.G486R	DKC1_uc010nvf.2_Missense_Mutation_p.G481R	NM_001363	NP_001354	O60832	DKC1_HUMAN	dyskerin isoform 1	486	Nuclear and nucleolar localization.				cell proliferation|pseudouridine synthesis|rRNA processing|telomere maintenance via telomerase	Cajal body|nucleolus|telomerase holoenzyme complex	protein binding|pseudouridine synthase activity|RNA binding|telomerase activity				0	all_cancers(53;8.15e-17)|all_epithelial(53;1.1e-10)|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)													Congenital_Dyskeratosis				---	---	---	---
